A circumpolar parasite: Evidence of a cryptic undescribed species of sucking louse, Linognathus sp., collected from Arctic foxes, Vulpes lagopus, in Nunavut (Canada) and Svalbard (Norway)

The North has experienced unprecedented rates of warming over the past few decades, impacting the survival and development of insects and the pathogens that they carry. Since 2019, Arctic foxes from Canada (Nunavut) have been observed with fur loss inconsistent with natural shedding of fur. Adult lice were collected from Arctic foxes from Nunavut (n = 1) and Svalbard (n = 2; Norway) and were identified as sucking lice (suborder Anoplura). Using conventional PCR targeting the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), lice from Canada and Svalbard were 100% similar (8 pooled samples from Nunavut and 3 pooled samples from Svalbard), indicating that there is potential gene flow between ectoparasites on Scandinavian and North American Arctic fox populations. The cox1 sequences of Arctic fox lice and dog sucking lice (Linognathus setosus) had significant differences (87% identity), suggesting that foxes may harbour a cryptic species that has not previously been recognised. Conventional PCR targeting the gltA gene for Bartonella bacteria amplified DNA from an unknown gammaproteobacteria from two pooled louse samples collected from Svalbard foxes. The amplified sequences were 100% identical to each other but were only 78% like Proteus mirabilis reported in GenBank (CP053614), suggesting that lice on Arctic foxes may carry unique microorganisms that have yet to be described.

Radiographers' organisational commitment and occupational stress: First Covid-19 wave

INTRODUCTION

Radiographers, like many health professionals, are in a high-risk group for succumbing to workplace demands beyond their ability to cope, particularly in the context of the COVID-19 pandemic resulting in occupational stress. Occupational stress has been linked to poor organisational commitment. Therefore, the purpose of this research was to evaluate radiographers' organisational commitment and occupational stress after the first wave of the COVID-19 pandemic.

METHODS

A mixed method approach entailed data collected from purposively sampled Australian radiographers working during the first COVID-19 wave. The quantitative phase used an online commitment questionnaire, and 21 semi-structured individual virtual interviews were conducted in the qualitative phase. Data interpretation and analysis used statistical and thematic approaches.

RESULTS

The quantitative data revealed a higher level of continuance than affective and normative commitment. Whereas the qualitative findings showed participants high levels of affective commitment to their occupation and, together with leadership support, working collectively towards a positive outcome.

CONCLUSION

Despite the variety of occupational stressors that arose during the COVID-19 crisis, Australian radiographers enjoy a high level of occupational and organisational commitment.

IMPLICATIONS FOR PRACTICE

Radiographers' organisational commitment represents their emotional and psychological attachment to their workplace, and radiographers experiencing occupational stress represent high levels of psychosomatic distress and burnout. Therefore, considering radiographers' organisational commitment and occupational stress is essential in the delivery of services, quality of patient care and radiographers well-being.

Impact evaluation of the TAMANI project to improve maternal and child health in Tanzania

BACKGROUND

The Tabora Maternal and Newborn Health Initiative project was a multicomponent intervention to improve maternal and newborn health in the Tabora region of Tanzania. Components included training healthcare providers and community health workers, infrastructure upgrades, and improvements to health management. This study aimed to examine the impact of trainings on four key outcomes: skilled birth attendance, antenatal care, respectful maternity care and patient-provider communication.

METHODS

Trainings were delivered sequentially at four time points between 2018 and 2019 in eight districts (two districts at a time). Cross-sectional surveys were administered to a random sample of households in all districts at baseline and after each training wave. Due to practical necessities, the original stepped wedge cluster randomised design of the evaluation was altered mid-programme. Therefore, a difference-in-differences for multiple groups in multiple periods was adopted to compare outcomes in treated districts to not yet treated districts. Risk differences were estimated for the overall average treatment effect on the treated and group/time dynamic effects.

RESULTS

Respondents reported 3895 deliveries over the course of the study. The intervention was associated with a 12.9 percentage point increase in skilled birth attendance (95% CI 0.4 to 25.4), which began to increase 4 months after the end of training in each district. There was little evidence of impact on antenatal care visits, respectful treatment during delivery and patient-provider communication.

CONCLUSION

Interventions to train local healthcare workers in basic and comprehensive emergency obstetric and newborn care increased skilled birth attendance but had limited impact on other pregnancy-related outcomes.

Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations

BACKGROUND

Although wild ungulate populations are heavily monitored throughout Europe, we understand little of how parasites affect population dynamics, and there is no systematic, long-term monitoring of parasite diversity and parasite loads. Such monitoring is in part hampered by a lack of time- and cost-effective assay methodologies with high sensitivity and good taxonomic resolution. DNA metabarcoding has been successfully used to characterize the parasitic nemabiome with high taxonomic resolution in a variety of wild and domestic hosts. However, in order to implement this technique in large-scale, potentially non-invasive monitoring of gastrointestinal parasitic nematodes (GIN), protocol optimization is required to maximize biodiversity detection, whilst maintaining time- and cost-effectiveness.

METHODS

Faecal samples were collected from a wild moose population and GIN communities were characterized and quantified using both parasitological techniques (egg and larva counting) and DNA metabarcoding of the ITS2 region of rDNA. Three different isolation methods were compared that differed in the volume of starting material and cell lysis method.

RESULTS

Similar nematode faunas were recovered from all samples using both parasitological and metabarcoding methods, and the approaches were largely congruent. However, metabarcoding assays showed better taxonomic resolution and slightly higher sensitivity than egg and larvae counts. The metabarcoding was not strictly quantitative, but the proportion of target nematode sequences recovered was correlated with the parasitologically determined parasite load. Species detection rates in the metabarcoding assays were maximized using a DNA isolation method that included mechanical cell disruption and maximized the starting material volume.

CONCLUSIONS

DNA metabarcoding is a promising technique for the non-invasive, large-scale monitoring of parasitic GINs in wild ungulate populations, owing to its high taxonomic resolution, increased assay sensitivity, and time- and cost-effectiveness. Although metabarcoding is not a strictly quantitative method, it may nonetheless be possible to create a management- and conservation-relevant index for the host parasite load from this data. To optimize the detection rates and time- and cost-effectiveness of metabarcoding assays, we recommend choosing a DNA isolation method that involves mechanical cell disruption and maximizes the starting material volume.

Age and the anaesthetist: considerations for the individual anaesthetist and workforce planning: Guidelines about the ageing anaesthetic workforce from the Association of Anaesthetists: Guidelines for the ageing anaesthetic workforce from the Association of Anaesthetists

There is clear evidence of a growing workforce gap and this is compounded by demographic data that show the current workforce is ageing. Within the current workforce, more doctors are taking voluntary early retirement and the loss of these experienced clinicians from departments can have wide-ranging effects. Older doctors are at risk of age-related health problems (e.g. sight, musculoskeletal, menopause) and are more susceptible to the effects of fatigue, which may increase the risk of error and or complaint. The purpose of this working party and advocacy campaign was to address concerns over the number of consultants retiring at the earliest opportunity and whether a different approach could extend the working career of consultant anaesthetists and SAS doctors. This could be viewed as 'pacing your career'. The earlier this is considered in a clinician's career the greater the potential mitigation on individuals.

Bariatric surgery reverses ventricular repolarisation heterogeneity in obesity: mechanistic insights into fat-related arrhythmic risk

Background

Obesity is a growing global health problem that confers higher risks of atrial arrhythmias and sudden cardiac death. Despite this, the proarrhythmic substrate in obesity and its reversibility with weight loss has not been studied in-depth.

Purpose

To characterise the proarrhythmic substrate in obese patients, and its reversibility with bariatric surgery, using electrocardiographic imaging (ECGi).

Methods

ECGi was performed in 16 obese patients pre-bariatric surgery (PreSurg; mean age 43±12 years, 13 female) and 16 age- and sex-matched non-obese (lean) individuals (42±11 years). 12 of the 16 obese patients also underwent ECGi after bariatric surgery (PostSurg). Over 2000 atrial and ventricular epicardial electrograms were computed using high density body surface mapping (256-lead ECG) and heart-torso geometries from cardiac magnetic resonance imaging, by solving the inverse problem of electrocardiography. Local atrial and ventricular epicardial activation times (AT) were calculated as the steepest downslope of their respective activation complexes, and local ventricular repolarisation times (RT) as the steepest upslope of the T-wave. Atrial activation gradients (ATG) and ventricular repolarisation gradients (RTG) were calculated as the maximum difference within 10 mm radius divided by the corresponding distance.

Results

Body mass index was greater in PreSurg vs lean (46.7±5.5 vs 22.8±2.6 kg/m2, p<0.0001) and decreased with surgery (PostSurg 36.8±6.5 kg/m2, p<0.0001). Epicardial adipose tissue (EAT) was greater in PreSurg vs lean (83±56 vs 28±13 ml, p<0.0001) and decreased post-surgery (PostSurg 69±45 ml, p=0.0010). Total atrial AT was prolonged in PreSurg vs lean (62±15 vs 46±12 ms, p=0.0028), which persisted post-surgery (PostSurg 67±15 ms, p=0.86). Atrial ATG were also greater in PreSurg vs lean (26±11 vs 14±8 ms, p=0.0007) and did not change with weight loss (PostSurg 25±12, p=0.44). Ventricular RTG were greater in PreSurg vs lean (26±11 vs 15±7 ms/mm, p=0.0024) and decreased with weight loss (PostSurg 19±8, p=0.0009). Ventricular RTG were similar between PostSurg and lean (p=0.20). EAT from lean and PreSurg individuals correlated with atrial ATG (r=0.36, p=0.044) and ventricular RTG (r=0.54, p=0.0014). Ventricular AT were similar between lean (31±6 ms), PreSurg (34±5 ms) and PostSurg (35±9 ms); all p>0.05.

Conclusion

Steep ventricular repolarisation gradients and prolonged atrial activation contribute to the proarrhythmic substrate in obesity. Ventricular repolarisation gradients correlate with epicardial adiposity and both regress post-bariatric surgery. By contrast, atrial activation remains prolonged after weight loss. These results provide mechanistic insights into obesity-related arrhythmic risks and their reversibility with weight loss following bariatric surgery.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): British Heart FoundationNational Institute for Health Research (NIHR) Imperial Biomedical Research Centre (BRC).

Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes

BACKGROUND

Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility.

PATIENTS AND METHODS

We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer.

ELIGIBILITY CRITERIA

female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD.

RESULTS

159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10^-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10^-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM.

CONCLUSIONS

This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.

Setting the international research agenda for sarcoma together with patients and carers: first results of the Sarcoma Patient EuroNet (SPAEN) priority setting partnership

Background

Research in sarcomas has historically been the domain of scientists and clinicians attempting to understand the disease to develop effective treatments. This traditional approach of placing scientific rigor before the patient’s reality is changing. This evolution is reflected in the growth of patient-centered organizations and patient advocacy groups that seek to meaningfully integrate patients into the research process. The aims of this study are to identify the unanswered questions regarding sarcomas (including gastrointestinal stromal tumors and desmoid fibromatosis) from patient, carer, and clinical perspectives and examine how patients and carers want to be involved in sarcoma research.

Methods

The Patient-Powered Research Network of Sarcoma Patients EuroNet set up a Priority Setting Partnership (PSP) in collaboration with stakeholders from the sarcoma research field. This PSP is largely based on the James Lind Alliance methodology.

Results

In total, 264 sarcoma patients (73%) and carers (27%) from all over the world participated in the online survey and covered the full spectrum of sarcomas. The topics mentioned were labeled in accordance with the Common Scientific Outline of the International Cancer Research Partnership and lists for potential research topics, advocacy topics, and requests for information were constructed. With regard to patient and carer involvement, 64% were very willing to be actively involved and mainly in the following areas: sharing perspectives, discussing patient-clinician interactions, and attending research meetings.

Conclusions

The first results of this sarcoma PSP identified important research questions, but also important topics for patient advocacy groups and further improvement of information materials. Sarcoma patients and carers have a strong wish to be involved in multiple aspects of sarcoma research. The next phase will identify the top 10 research priorities per tumor type. These priorities will provide guidance for research that will achieve greatest value and impact.

•

The results from this international sarcoma Priority Setting Partnership (PSP) identified important research questions.

•

This PSP also identified important topics for patient advocacy and requests for information.

•

Sarcoma patients and carers have a strong wish to be involved in multiple aspects of sarcoma research.

•

The next phase of this PSP will aim to prioritize the research questions per tumor type.

Bariatric surgery reduces ventricular repolarisation gradients in obese patients - results from an electrocardiographic imaging study

Funding Acknowledgements

Type of funding sources: Public Institution(s). Main funding source(s): National Institute for Health Research (NIHR) British Heart Foundation

Background

Obesity confers higher risks of atrial arrhythmias and is associated with abnormal ventricular repolarisation. Despite this, the proarrhythmic substrate in obesity and its reversibility with weight loss has not been studied in-depth.

Purpose

To characterise the proarrhythmic substrate in obese patients, and its reversibility with bariatric surgery, using electrocardiographic imaging (ECGi).

Methods

ECGi was performed in 8 obese patients before (PreOb) and after (PostOb) bariatric surgery (mean age 39+/-11years, 7 female), and in 8 age- and sex-matched non-obese controls (NOb) (40+/-11 years). ECGi recordings were made at rest, on exercise, and during recovery from exercise. For ECGi analysis, &gt;2000 atrial and ventricular epicardial electrograms were calculated from body surface potential recordings from 256 sites and information from cardiac magnetic resonance imaging, by solving the inverse problem. Local atrial and ventricular epicardial activation times (AT) were calculated as the steepest downslope of their respective activation complexes, and local ventricular repolarisation times (RT) as the steepest upslope of the T-wave. Atrial activation gradients (ATG) and ventricular repolarisation gradients (RTG) were calculated as the maximum difference within 10mm radius divided by the corresponding Euclidean distance.

Results

BMI was greater in PreOb vs NOb (46.6+/-4.8 vs 23.8+/-2.6kg/m2, p&lt;0.0001) and decreased with surgery (PostOb 35.3+/-4.2kg/m2, p&lt;0.0001). Total atrial AT was prolonged in PreOb vs NOb (68+/-12 vs 45+/-10ms, p=0.016) and did not change post-surgery (PreOb vs PostOb: 68+/-12 vs 67+/-16ms, p=0.81). Atrial ATG were also greater in PreOb vs NOb: max 254+/-111 vs 106+/-58ms, p=0.035; mean 24+/-6 vs 12+/-6ms, p=0.0087) and did not change with weight loss (PreOb vs PostOb: max 254+/-111 vs 222+/-69ms/mm, p=0.61; mean 24+/-6 vs 21+/-7ms/mm, p=0.52). Ventricular RTG were greater in PreOb vs NOb (max: 287+/-73 vs 131+/-89ms/mm, p=0.012; mean: 33+/-10 vs 17+/-9ms/mm, p=0.0052). Ventricular RTG decreased with weight loss (PreOb vs PostOb: max 287+/-73 vs 151+/-54ms/mm, p=0.0070; mean: 33+/-10 vs 21+/-8ms/mm, p=0.018), and were similar between PostOb and NOb (max, p=0.81; mean p=0.58). Ventricular AT and RT were non-different in NOb, PreOb and PostOb.

Conclusion

Obesity is associated with pro-arrhythmic electrophysiological remodelling, including steeper ventricular repolarisation gradients and slower atrial activation. At 6 months post-bariatric surgery, there was a reduction in ventricular repolarisation gradients though atrial conduction abnormalities persisted. These findings provide a mechanistic insight into obesity-related arrhythmic risks and its potential reversibility with weight loss surgery.

The impacts of vertical off-centring, tube voltage, and phantom size on computed tomography numbers: An experimental study

INTRODUCTION

This experimental study explored the effect of vertical off-centring on computed tomography (CT) numbers in combination with various tube voltages and phantom sizes for two CT units.

METHODS

CIRS Model 062 Electron Density and system performance phantoms were imaged on Siemens Emotion 16-slice CT and GEMINI-GXL scanners, respectively. Uniformity and accuracy were evaluated as a function of vertical off-centring (20, 40, 60, and 80 mm above the gantry isocentre) using different water phantom sizes (18, 20, and 30 cm) and tube voltages (80, 90, 110, 120, 130 and 140 kVp).

RESULTS

Vertical off-centring and phantom size accounted for 92% of the recorded variance and the resultant change in CT numbers. The uniformity test recorded maximum changes of 14 and 27.2 HU for peripheral ROIs across the X- and Y-axes for an 80 mm phantom shift above the gantry isocentre on the GEMINI GXL and Siemens scanners, respectively. The absolute CT number differences between the superior and inferior ROIs were 13.7 HU for the 30 cm phantom and 4.8 HU for the 20 cm phantom for 80 mm vertical off-centring. The largest differences were observed at lower tube voltages.

CONCLUSIONS

It is essential to highlight the significance of CT number variation in clinical decision-making. Phantom off-centring affected the uniformity of these numbers, which were further impacted by the ROI position in this experimental study. CT number variation was more evident in peripheral phantom areas, lower tube voltages and larger phantom sizes.

IMPLICATIONS FOR PRACTICE

CT number is observed to be a variable under certain common conditions. This significantly impacts several applications where clinical decisions depend on CT number accuracy for tissue lesion characterisation.

COVID-19 vaccination intent among London healthcare workers

Background

The 10-month timeline from conception to regulatory approval of the Pfizer–BioNTech vaccine against SARS-CoV-2 is unprecedented in modern medicine. However, the climate of the pandemic has also seen anti-vaccination sentiments flourish.

Aims

To determine the intent to accept COVID-19 vaccination among healthcare workers at a London Hospital Trust and examine variation in uptake between demographic groups.

Methods

We conducted a cross-sectional survey open to staff working at the trust. Staff rated on a five-point scale the likelihood of them accepting COVID-19 vaccination.

Results

We received 514 responses, representing 16% of the workforce. About 59% of staff intended to seek vaccination, 24% to reject and 17% were unsure. There was significantly reduced intended uptake in females, younger age groups, healthcare assistants, nurses, staff of black ethnic backgrounds and those who rejected influenza vaccination. Safety was the dominant concern.

Conclusions

Our study finds COVID-19 vaccinate hesitancy is prevalent among healthcare workers at a London Hospital Trust. It is particularly concerning that hesitancy was highest amongst groups most exposed to COVID-19 and most at risk of severe disease. Reasons behind disparities in uptake must be addressed to protect staff and prevent deepening inequalities within the healthcare workforce.

Hypoxia inducible factor-1a drives metabolic adaptation of natural killer cells during pathogen infection

Natural killer (NK) cells provide an early response to pathogen infection, limiting host morbidity and lethality. This response requires NK cells to adapt due to the energy demands of activation and biosynthesis. We found that NK cells upregulate the metabolic adaptor hypoxia inducible factor-1a (HIF-1a) during murine cytomegalovirus (MCMV) infection in vivo. Specific deletion of HIF-1a in NK cells impaired their ability to reduce viral load and protect against morbidity. While HIF-1a-deficient NK cells had no defects in effector functions, their numbers were significantly reduced during early responses and there was blunted expansion of Ly49H+ NK cells. However, NK cell proliferation per se was not impaired during in vivo infection and in vitro cytokine stimulation. Instead, we found that the absence of HIF-1a impaired glucose metabolism and up-regulated the pro-apoptotic protein Bim during cytokine stimulation in vitro. Furthermore, during MCMV infection in vivo HIF1a-deficient NK cells upregulated Bim and had increased caspase activity. Thus, HIF-1a normally drives glucose metabolism and represses Bim expression during pathogen infection to sustain NK cell numbers for an optimal response.

Vitamin D deficiency predicts latent TB reactivation independent of preventive therapy: a longitudinal study

BACKGROUND: Vitamin D deficiency is associated with progression of latent tuberculosis (TB) infection to active disease. The impact of preventive therapy on this association is unknown.METHOD: Serum 25-hydroxyvitamin D (25(OH)D) levels were retrospectively linked to adults diagnosed with latent TB between April 2010 and January 2019 in a hospital in London, UK. Individuals in the cohort who progressed to active TB were identified by matching to a national notification register. A logistic regression model was used to examine baseline vitamin D deficiency and use of preventive therapy with subsequent incidence of TB disease.RESULTS: Of 1509 latently infected individuals with 3902 patient-years of follow-up, 687 (45.5%) were identified as vitamin D deficient and 691 (45.8%) individuals had a LTBI regimen prescribed. There were 29 (1.9%) instances of TB reactivation. On multivariate analysis, profound (<25 nmol/L) vitamin D deficiency (aHR 5.68, 95%CI 2.18-14.82; P = 0.0003) and the absence of preventive therapy (aHR 3.84, 95%CI 1.46-10.08; P = 0.006) were associated with progression to active TB disease. There was no evidence that preventive therapy modified the association between vitamin D status and TB reactivation.CONCLUSION: Our results show an independent association between vitamin D deficiency and progression from latent TB infection to active disease.

Norwich COVID-19 testing initiative pilot: evaluating the feasibility of asymptomatic testing on a university campus

Background

There is a high prevalence of COVID-19 in university-age students, who are returning to campuses. There is little evidence regarding the feasibility of universal, asymptomatic testing to help control outbreaks in this population. This study aimed to pilot mass COVID-19 testing on a university research park, to assess the feasibility and acceptability of scaling up testing to all staff and students.

Methods

This was a cross-sectional feasibility study on a university research park in the East of England. All staff and students (5625) were eligible to participate. All participants were offered four PCR swabs, which they self-administered over two weeks. Outcome measures included uptake, drop-out rate, positivity rates, participant acceptability measures, laboratory processing measures, data collection and management measures.

Results

798 (76%) of 1053 who registered provided at least one swab; 687 (86%) provided all four; 792 (99%) of 798 who submitted at least one swab had all negative results and 6 participants had one inconclusive result. There were no positive results. 458 (57%) of 798 participants responded to a post-testing survey, demonstrating a mean acceptability score of 4.51/5, with five being the most positive.

Conclusions

Repeated self-testing for COVID-19 using PCR is feasible and acceptable to a university population.

Vision and Orientation and Mobility Consultation for Children with Severe Multiple Disabilities

Vision consultants who work with professionals and parents of children with severe multiple impairments perform a professional role that is changing and challenging. Educational planning is unique, since many children with different levels of disabilities must be served in a variety of individual settings. This article discusses the role of orientation and mobility specialists and teacher-consultants for children who have visual impairments and severe multiple disabilities. Examples of programming contributions of both types of vision consultant are given.

Novel chyme reinfusion device for gastrointestinal fistulas and stomas: feasibility study

Background

High-output enterostomies and enteroatmospheric fistulas are common causes of intestinal failure, and may necessitate parenteral nutrition and prolonged hospital stay. Reinfusing lost chyme into the distal gut is known to be beneficial, but implementation has been limited because manual reinfusion is unpleasant and labour-intensive, and no devices are available. A new device is presented for reinfusing chyme easily and efficiently, with first-in-human data.

Methods

The device comprises a compact centrifugal pump that fits inside a standard stoma appliance. The pump is connected to an intestinal feeding tube inserted into the distal intestinal limb. The pump is activated across the appliance by magnetic coupling to a hand-held driver unit, effecting intermittent bolus reinfusion while avoiding effluent contact. Safety, technical and clinical factors were evaluated.

Results

Following microbiological safety testing, the device was evaluated in ten patients (median duration of installation 39·5 days; total 740 days). Indications included remediation of high-output losses (8 patients), dependency on parenteral nutrition (5), and gut rehabilitation before surgery (10). Reinfusion was well tolerated with use of regular boluses of approximately 200 ml, and no device-related serious adverse events occurred. Clinical benefits included resumption of oral diet, cessation of parenteral nutrition (4 of 5 patients), correction of electrolytes and liver enzymes, and hospital discharge (6 of 10). Of seven patients with intestinal continuity restored, one experienced postoperative ileus.

Conclusion

A novel chyme reinfusion device was developed and found to be safe, demonstrating potential benefits in remediating high-output losses, improving fluid and electrolyte balance, weaning off parenteral nutrition and improving surgical recovery. Pivotal trials and regulatory approvals are now in process.

Exaggeration of PFS by blinded, independent, central review (BICR)

BACKGROUND

Recent published studies have shown meaningful discrepancies between local investigator and blinded, independent, central review (BICR) assessed median progression-free survival (PFS). When the local review but not BICR shows progression, generally, no further assessments are carried out and patients are censored in the BICR analysis, leading to violation of the statistical assumptions of independence between censoring and outcome used in survival analysis methods.

METHODS

We carried out a simulation study to assess methodological reasons behind these discrepancies and corroborated our findings in a case study of three BRCA-mutated ovarian cancer trials. We briefly outline possible methodological solutions that may lead to improved estimation of the BICR medians.

RESULTS

The Kaplan-Meier (KM) curve for the BICR PFS can often be exaggerated. The degree of bias is largest when there is reasonably strong correlation between BICR and local PFS, especially when PFS is long compared with assessment frequency. This can result in an exaggeration of the medians and their difference; however, the hazard ratio (HR) is much less susceptible to bias. Our simulation shows that when the true BICR median PFS was 19 months, and patients assessed every 12 weeks, the estimated KM curves were materially biased whenever the correlation between BICR and local PFS was 0.4 or greater. This was corroborated by case studies where, in the active arm, the BICR median PFS was between 6 and 11 months greater than the local median PFS. Further research is required to find improved methods for estimating BICR survival curves.

CONCLUSIONS

In general, when there is a difference between local and BICR medians, the true BICR KM curve is likely to be exaggerated and its true median will probably lie somewhere between the observed local and BICR medians. Presentation of data should always include both BICR and local results whenever a BICR is carried out.

Routine germline BRCA1 and BRCA2 testing in patients with ovarian carcinoma: analysis of the Scottish real-life experience

OBJECTIVE

To determine the rates of germline BRCA1 and BRCA2 mutations in Scottish patients with ovarian cancer, before and after a change in testing policy.

DESIGN

Retrospective cohort study.

SETTING

Four cancer/genetics centres in Scotland.

POPULATION

Patients with ovarian cancer undergoing germline BRCA1 and BRCA2 (gBRCA1/2) sequencing before 2013 (under the 'old criteria', with selection based solely on family history), after 2013 (under the 'new criteria', with sequencing offered to newly presenting patients with non-mucinous ovarian cancer), and in the 'prevalent population' (who presented before 2013, but were not eligible for sequencing under the old criteria but were sequenced under the new criteria).

METHODS

Clinicopathological and sequence data were collected before and for 18 months after this change in selection criteria.

MAIN OUTCOME MEASURES

Frequency of germline BRCA1, BRCA2, RAD51C, and RAD51D mutations.

RESULTS

Of 599 patients sequenced, 205, 236, and 158 were in the 'old criteria', 'new criteria', and 'prevalent' populations, respectively. The frequency of gBRCA1/2 mutations was 30.7, 13.1, and 12.7%, respectively. The annual rate of gBRCA1/2 mutation detection was 4.2 before and 20.7 after the policy change. A total of 48% (15/31) 'new criteria' patients with gBRCA1/2 mutations had a Manchester score of <15 and would not have been offered sequencing based on family history criteria. In addition, 20 patients with gBRCA1/2 were identified in the prevalent population. The prevalence of gBRCA1/2 mutations in patients aged >70 years was 8.2%.

CONCLUSIONS

Sequencing all patients with non-mucinous ovarian cancer gives a much higher annual gBRCA1/2 mutation detection rate, with the frequency of positive tests still exceeding the 10% threshold upon which many family history-based models operate.

TWEETABLE ABSTRACT

BRCA sequencing all non-mucinous cancer patients increases mutation detection five fold.

Correction to: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

In our recent article [1], it has come to our attention that the sample labels are not consistent between Table 1, the data labels deposited in the Sequence Read Archive, and Additional file 1: Table S2. We are therefore providing an updated Additional file 1: Table S2 so identical samples now have the same label.

Creating a framework for the prioritization of biosecurity risks to the New Zealand dairy industry

The New Zealand dairy sector relies on robust biosecurity measures to control and mitigate a wide range of threats to the industry. To optimize the prioritization of organisms and manage the risk they pose to the sector in a transparent and credible way, the Dairy Biosecurity Risk Evaluation Framework (D-BRiEF) was developed. This comprehensive framework was specifically designed for decision support, using a standardized approach to address the full spectrum of biosecurity threats to the sector, including exotic and endemic animal disease organisms, pest plants and insects. D-BRiEF is underpinned by three main processes, namely (i) hazard identification; (ii) multicriteria risk assessment; and (iii) communication for risk management. Expert knowledge and empirical data, including associated uncertainty, are harnessed in a standardized format. Results feed into a probability-impact model that was developed in close collaboration with dairy sector economists to provide overall comparative 10-year quantitative economic impact estimates for each assessed risk organism. A description of the overarching framework, which applies to diverse organism groups, is presented with detailed methodology on both endemic and exotic animal disease risk organisms. Examples of visual outputs are included, although actual ranking results are not reported due to industry confidentiality. D-BRiEF can provide a decision advantage to DairyNZ biosecurity risk managers and sector stakeholders by creating a transparent process that can be interrogated and updated at multiple levels to fully understand the layers of risk posed by different organisms.

A global view of structure-function relationships in the tautomerase superfamily

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure-function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase-like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

Kinetic and structural characterization of a cis-3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily

A Pseudomonas sp. UW4 protein (UniProt K9NIA5) of unknown function was identified as similar to 4-oxalocrotonate tautomerase (4-OT)-like and cis-3-chloroacrylic acid dehalogenase (cis-CaaD)-like subgroups of the tautomerase superfamily (TSF). This protein lacks only Tyr-103 of the amino acids critical for cis-CaaD activity (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114). As it may represent an important variant of these enzymes, its kinetic and structural properties have been determined. The protein shows tautomerase activity with phenylenolpyruvate, but lacks native 4-OT activity and dehalogenase activity with the isomers of 3-chloroacrylic acid. It shows mostly low-level hydratase activity at pH 7.0, converting 2-oxo-3-pentynoate to acetopyruvate, consistent with cis-CaaD-like behavior. At pH 9.0, this compound results primarily in covalent modification of Pro-1, which is consistent with 4-OT-like behavior. These observations could reflect a pK_a for Pro-1 that is closer to that of cis-CaaD (∼9.2) than to 4-OT (∼6.4). A structure of the native enzyme, at 2.6 Å resolution, highlights differences at the active site from those of 4-OT and cis-CaaD that add to our understanding of how contemporary TSF reactions and mechanisms may have diverged from a common 4-OT-like ancestor.

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Background

Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections.

Results

We found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11. We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11-high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling.

Conclusions

Respiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1140-8) contains supplementary material, which is available to authorized users.

Evaluating Functional Annotations of Enzymes Using the Gene Ontology

The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.

Nurses in Action: A Response to Cultural Care Challenges in a Pediatric Acute Care Setting

Culturally congruent care is satisfying, meaningful, fits with people's daily lives, and promotes their health and wellbeing. A group of staff nurses identified specific clinical challenges they faced in providing such care for Hispanic and underserved Caucasian children and families in the pediatric medical-surgical unit of an urban regional children's hospital in the southeastern U.S. To address these challenges, an academic-practice partnership was formed between a group of nurse managers and staff nurses at the children's hospital and nursing faculty and graduate students at a local, research-intensive public university. Using the culture care theory, the partners collaborated on a research study to discover knowledge that would help the nursing staff resolve the identified clinical challenges. Twelve families and 12 healthcare providers participated. Data analysis revealed five care factors that participants identified as most valuable: family, faith, communication, care integration, and meeting basic needs. These themes were used to formulate nursing actions that, when applied in daily practice, could facilitate the provision of culturally congruent care for these children and their families. The knowledge generated by this study also has implications for healthcare organizations, nursing educators, and academic-practice partnerships that seek to ensure the delivery of equitable care for all patients.

A multi-perspective service evaluation exploring tuberculosis contact screening attendance among adults at a North London hospital

BACKGROUND

Non-attendance at TB contact screening clinics has been highlighted as a common phenomenon across a number of sites during recruitment to the PREDICT TB Study. This has obvious implications for the safety of patients, their communities and for NHS resources. The objective of this study was to explore why adults who have been in contact with TB do, and do not, attend their screening appointment, thereby allowing identification of interventions to reduce non-attendance.

METHODS

A multi-method approach was taken using 15 questionnaires with adults who attended for screening, 15 telephone questionnaires with adults who did not attend and in-depth interviews with 8 TB nurses. Interviews were coded to trace emerging descriptive themes, then refined through an iterative process of interpretation and recoding.

RESULTS

Findings from the questionnaires and interviews were categorized into three principle themes following analysis: awareness, hospital factors and leadership. These themes deconstruct the complex phenomena of patients' lack of attendance at this TB contact screening service.

CONCLUSION

Recommendations related to issues of leadership, outreach services, flexibility of clinic timing and awareness amongst both the local community and GPs were made.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Changing clinical patterns and increasing prevalence in CADASIL

OBJECTIVES

CADASIL is a monogenic small vessel vasculopathy causing recurrent stroke. Early descriptions suggested dementia and disability were common from the 5th decade but there is evidence of marked phenotypic variability. We investigated the prevalence and clinical features of CADASIL in the west of Scotland.

METHODS

We undertook a retrospective review of clinical records of patients with confirmed CADASIL identified through a specialist clinic. Patients were divided to examine the effect of date of diagnosis on clinical outcomes and the characteristics at different ages. The location of pedigree members was used to estimate prevalence.

RESULTS

Twenty-one different CADASIL-causing NOTCH3 mutations were identified in 49 pedigrees (61% in exon 4). Disease prevalence in Glasgow was 4.6/100,000 adults. Mutation prevalence was estimated at 10.7/100,000 population. Median age at first stroke in women (57 years) was higher than previous estimates, and stroke age in men was higher in patients diagnosed more recently (pre 2006 46 years, post 2006 56 years, P=0.034). In patients over 58 years of age, 13/34 (38%) were living independently and 17/28 (61%) were mobile without aids when last seen.

CONCLUSIONS

CADASIL prevalence is at least 4.6 per 100,000 adults. Median age of first stroke may be older than previously thought. Clinicians should consider CADASIL in the differential diagnosis even in older patients with stroke.

The differential production cross section of the [Formula: see text](1020) meson in [Formula: see text] = 7 TeV [Formula: see text] collisions measured with the ATLAS detector

A measurement is presented of the [Formula: see text] production cross section at [Formula: see text] = 7 TeV using [Formula: see text] collision data corresponding to an integrated luminosity of 383 [Formula: see text], collected with the ATLAS experiment at the LHC. Selection of [Formula: see text](1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section is measured as a function of the transverse momentum, [Formula: see text], and rapidity, [Formula: see text], of the [Formula: see text](1020) meson in the fiducial region 500 [Formula: see text] 1200 MeV, [Formula: see text] 0.8, kaon [Formula: see text] 230 MeV and kaon momentum [Formula: see text] 800 MeV. The integrated [Formula: see text]-meson production cross section in this fiducial range is measured to be [Formula: see text] = 570 [Formula: see text] 8 (stat) [Formula: see text] 66 (syst) [Formula: see text] 20 (lumi) [Formula: see text].

A gene expression study of normal and damaged cartilage in anteromedial gonarthrosis, a phenotype of osteoarthritis

OBJECTIVE

To identify osteoarthritis (OA) relevant genes and pathways in damaged and undamaged cartilage isolated from the knees of patients with anteromedial gonarthrosis (AMG) - a specific form of knee OA.

DESIGN

Cartilage was obtained from nine patients undergoing unicompartmental knee replacement (UKR) for AMG. AMG provides a spatial representation of OA progression; showing a reproducible and histologically validated pattern of cartilage destruction such that damaged and undamaged cartilage from within the same knee can be consistently isolated and examined. Gene expression was analysed by microarray and validated using real-time PCR.

RESULTS

Damaged and undamaged cartilage showed distinct gene expression profiles. 754 genes showed significant up- or down-regulation (non-False discovery rate (FDR) P < 0.05) with enrichment for genes involved in cell signalling, Extracellular Matrix (ECM) and inflammatory response. A number of genes previously unreported in OA showed strongly altered expression including RARRES3, ADAMTSL2 and DUSP10. Confirmation of genes previously identified as modulated in OA was also obtained e.g., SFRP3, MMP3 and IGF1.

CONCLUSIONS

This is the first study to examine a common and consistent phenotype of OA to allow direct comparison of damaged and undamaged cartilage from within the same joint compartment. We have identified specific gene expression profiles in damaged and undamaged cartilage and have determined relevant genes and pathways in OA progression. Importantly this work also highlights the necessity for phenotypic and microanatomical characterization of cartilage in future studies of OA pathogenesis and therapeutic development.