Measuring and Managing Healthcare Supply and Demand in Real-Time

Measuring the supply and demand for access to and wait-times for healthcare is key to managing healthcare services and allocating resources appropriately. Yet, few jurisdictions in distributed, socialized medicine settings have any way to do so. In this paper, we propose the requirements for a jurisdictional patient scheduling system that can measure key metrics, such as supply of and demand for regulated health care professional care, access to and wait times for care, real-time health system utilization and provide the data to compute patient journeys. The system is also capable of tracking new supply of providers and who does not have access to a primary care provider. Benefits, limitations and risks of the model are discussed.

A nose for trouble: ecotoxicological implications for climate change and disease in Saiga antelope (S. t. tatarica)

In recent decades, Saiga antelope (Saiga t. tatarica) mass die-offs have become more common. The mass die-off of 2015 in central Kazakhstan, recorded 140,000 individual deaths across multiple herds. Previously, research has shown atmospheric humidity, the bacterium Pasteurella multocida serotype B, and resultant haemorrhagic septicaemia, were the primary cause. However, other synergistic factors may have impacted this process. Here we use a multivariate compositional data analysis (CoDA) approach to assess what other factors may have been involved. We show a pollutant linkage mechanism where relative humidity and dewpoint temperature combine with environmental pollutants, potentially toxic elements (e.g., Hg, As), complex carbon compounds (e.g., Acetone, Toluene), and inorganic compounds (e.g., CHx, SO2) which affected the Saiga during the calving season (start and peak) and at the onset of the mass die-off. We suggest a mechanism for this process. Upon arrival at their carving grounds, the Saiga experienced a sudden precipitation event, a spike in temperatures, and resultant high humidity occurs. The infectious bacterium P. multocida serotype B then spreads. Further, environmental pollutants contained within steppe soils are released to the air, forming localised smog events, these synergistically combine, and mass die-off occurs.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

The impact of long haul travel on the sleep of elite athletes

In order to manage and implement strategies to alleviate the symptoms of jet lag it is essential to assess the impact of jet lag in athletes. The aim of this study was to assess the impact of long haul eastward travel on elite athletes' (n = 7 elite national track cyclists; male n = 3, and female n = 4) sleep. The athletes' sleep was monitored before, during and after travel using both actigraphy and self-report measures. Participants wore an activity monitor for 5 days prior to travel, during the long haul travel and 5 days upon arrival at their destination and completed a daily online sleep diary Actigraphy highlighted significant reductions in time in bed, total sleep time and sleep efficiency (%) due to long haul eastward travel, particularly in the 48 h after travel. Sleep diary data exhibited significant reductions in time in bed, total sleep time, sleep efficiency, sleep quality and a significant increase in fatigue going to bed as a result of long haul eastward travel. In order to facilitate the development of interventions to reduce the symptoms and severity of jet lag objective and subjective assessments of sleep should be coupled with assessments of chronotype and perceived sleep need.

1415 NOVEL APPROACHES TO POST DISCHARGE CARE. REMOTE HEALTHCARE MONITORING SYSTEMS FOLLOWING TRAUMATIC BRAIN INJURY IN OLDER ADULTS

Introduction

Major trauma including Traumatic Brain Injury (TBI) is an increasingly common cause of hospitalisation in older adults (OAs). We studied post-discharge recovery from TBI using a remote healthcare monitoring system that captures data on activity and sleep. We aim to assess the feasibility and acceptability of this technology to monitor recovery at home following a significant acute health event in OAs.

Methods

We installed Minder, a remote healthcare monitoring system, in recently discharged patients >60 years with moderate-severe TBI. We present descriptive analyses of post-discharge recovery for two males, corroborating data from Minder against verified activities and events. We recorded semi-structured interviews assessing acceptability. Both participants have similar household set-up, multimorbidity profiles and clinical frailty scores; however, one participant has prior cognitive impairment (PAT1), and one does not (PAT2).

Results

We present 10 weeks of sleep and activity data from Minder and feedback from interviews. Data observed from PAT1 revealed habitual patterns of activity and sleep. These remained stable, despite discrete clinical events. Conversely, PAT2's data revealed irregular sleep patterns that became increasingly fragmented. Activity was detected in multiple rooms throughout the house at night, consistent with carer reports of night-time wandering. Increased overnight activity coincided with multiple falls, prompting increased care provision. Initial feedback from interviews was the technology helped participants and those involved in their care feel supported.

Conclusions

As pressure on services mounts, novel approaches to post-discharge care are of increasing importance. Remote healthcare monitoring can provide high temporal resolution data offering ‘real world’ insights into the effects of significant health events in OAs. Our provisional results support our hypothesis that use of this technology is feasible and acceptable for frail, multimorbid participants and highlights the substantial potential of this technology to help clinicians improve community-based care and more effectively monitor interventions and chronic conditions.

P-414 Ultrastructural and functional defects in cilia of endometrial glands from women with reproductive failure

Study question

Do endometrial gland factors influence pregnancy success?

Summary answer

Increased proportion of cilia defects during the window of implantation in endometrial glands from women with reproductive failure compared to controls

What is known already

Endometrial glands are important for embryo implantation and successful pregnancy. There is an unmet clinical need to relate endometrial gland structure to function, identify markers for reproductive failure and targets for therapeutic interventions. Ciliated epithelial cells in the endometrium are a distinct cell type with a particular cell transcriptomic signature. Cilia defects have been reported in endometrial glands from women with reproductive failure however, a quantitative study of cilia defects in endometrial glands is yet to be established.

Study design, size, duration

An observational study comparing women with subfertility, recurrent pregnancy loss and controls

Participants/materials, setting, methods

Endometrial samples were collected during the implantation period from fertile controls (n = 10), women with subfertility (n = 11) and women with recurrent pregnancy loss (n = 15). Ciliated cells in endometrial glands were imaged by transmission electron microscopy and the proportion of cilia defects were quantified and compared between study groups. Endometrial glands were isolated from endometrial biopsies and the cilia beat frequency of ciliated cells was quantified by high-speed video analysis.

Main results and the role of chance

Our study reports a significant increase in the proportion of cilia ultrastructural defects in endometrial glands from women with subfertility versus fertile controls (P < 0.05). Cilia defects included microtubule disarrangement, transposition and loss of cilia inner dynein arm motor proteins. Ciliated cells in endometrial glands from women with recurrent pregnancy loss demonstrated a higher proportion of defects compared to fertile controls but this did not reach statistical significance (P = 0.07). A significant decrease in cilia beat frequency was reported in ciliated cells of endometrial glands from women with subfertility compared to fertile controls (P < 0.05).

Limitations, reasons for caution

This is an observational study with a relatively small sample size however, the participants in the study and control groups were matched for age, BMI and menstrual cycle characteristics.

Wider implications of the findings

This study quantified ultrastructural and functional differences of ciliated cells in endometrial glands from women with reproductive failure. Endometrial glands with perturbed cilia structure and function may be non-conductive to successful pregnancy. Differences in endometrial gland cilia could be used to identify a perturbed endometrium and develop targeted therapies.

Trial registration number

not applicable

Association of Race and Other Social Determinants of Health With HIV Pre-Exposure Prophylaxis Use: A County-Level Analysis Using the PrEP-to-Need Ratio

Research is limited on the effect of racism and social determinants of health on HIV pre-exposure prophylaxis (PrEP) use. This study used the PrEP-to-Need Ratio (PNR), which measures PrEP prescriptions divided by HIV diagnoses in the county, to evaluate sufficient PrEP use. AIDSVu datasets were compared to county-level social determinants of health. Standardized regression coefficients (β) were compared to identify strongest associations with PNR. Overall, factors including percent African American and percent uninsured had negative correlations with PNR, whereas median household income and severe housing cost burden had positive associations. Stratifying for population size, percent African American, percent uninsured, and severe housing cost burden were significant for low population areas, whereas median household income, percent in poverty, percent uninsured, and percent African American were significant for large populations. To reduce PrEP disparities, public health must develop strategies to reach those most in need, especially historically disadvantaged communities.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

254 OPTIMISING COMMUNICATION WITH FAMILIES OF PATIENTS ON ACUTE STROKE AND GERIATRIC MEDICINE WARDS IN A LARGE TERTIARY HOSPITAL

Background

Good communication with patients and families is important for older adults admitted to acute stroke or geriatric medicine wards, particularly with COVID19-related restricted visiting. These patients often have communication difficulties including aphasia, delirium, cognitive or hearing impairment, limiting their own communication with relatives. Using the Plan, Do, Study, Act (PDSA) approach we undertook a quality improvement project to optimise communication with families of patients on above wards in a large tertiary hospital.

Methods

PDSA cycle 1: Staff were surveyed to identify satisfaction level with communication and ways to optimise communication. Inpatients on study wards were identified, we recorded demographic and clinical details and prevalence of communication difficulties. We created a designated folder with individual ‘communication sheets’ in conjunction with ward doctors and the nurse manager. PDSA cycle 2: We performed a rapid interval audit of the communication folder use. ‘Outlier’ patients were excluded as their teams did not receive education about folder use.

Results

PDSA cycle 1: A total of 90 inpatients on three wards were included, mean age 78y (SD ±14.4y), 47% were male. Three-quarters (73%) had a communication difficulty noted, reported by nursing staff. Two patients were intubated and six had stroke-related aphasia. Half of surveyed staff reported communication with families was suboptimal. Most (86%) suggested a centrally-located communication logbook would be helpful. PDSA cycle 2: Over two weeks, communication sheets were reviewed for all included patients. Median frequency of calls to families was 4 days (range 0–14). Most (79%) had the name of the primary contact clearly documented. Many (52%) included no contact number. Only 9% had secondary contact information documented.

Conclusion

Communication with families of patients on acute stroke and geriatric medicine wards was suboptimal. Over a short interval this improved with regular phone calls using specific centrally-located communication folders. Further optimisation of their use is needed.

Heavy metal (PTE) ecotoxicology, data review: Traditional vs. a compositional approach

Potentially Toxic Elements (PTEs) otherwise known as heavy metals are ubiquitous in soils and can have a range of negative health and environmental impacts. In terrestrial systems understanding how PTEs move in the environment is made challenging by the complex interactions within soil and the wider environment and the compositional nature of PTEs. PTEs are compositional because data of individual PTEs within in a sample are ratios which may be under a sum constraint, where individual components sum up to a whole. In this study three different scenarios were considered, one using the centred log ratio transformation (clr) a compositional transformation, the more "traditional" log10 transformation (log10) and untransformed data acting as a comparison (unt) were applied to four different datasets. Three were the Liver, Muscle and Kidney tissue of Eurasian Badgers (Meles meles) and the fourth was soil and data were extracted from a regional geospatial survey. Cluster analysis demonstrated that the clr and log10 transformation were able to resolve compositional trends at the point of the individual sample, whilst unt could not and did not meet the preconditions for the next phase of analysis. At the level of compositional trends between PTEs complex heatmaps demonstrated that clr was able to isolate PTE relationships and highlight commonalities between different datasets, whilst log10 could not. In the final phase, principal component analysis (PCA) of the clr transformation showed similarities between the signals in the soft tissues and the disparities they had with soil, whilst the log10 transformation was unable to achieve this. Overall, the clr transformation was shown to perform more consistently under a variety of analytical scenarios and the compositional approach will provide more realistic interpretations about PTEs in both soil and animal soft tissue than the log10 or unt conditions.

Potentially toxic element accumulation in badgers (Meles meles): a compositional approach

Potentially Toxic Elements (PTEs) in Badgers (Meles meles), otherwise known as heavy metals, are unique amongst environmental pollutants occurring, both naturally and anthropogenically. PTEs have a broad range of negative health and environmental effects, therefore identifying their sources and pathways through the environment is imperative for public health policy. This is difficult in terrestrial systems due to the compositional nature of soil geochemistry. In this study, a compositional statistical approach was used to identify how PTEs accumulate in a terrestrial carnivorous mammal, Eurasian Badgers (Meles meles). Compositional principal component analysis (PCA) was used on geochemical data from the Tellus survey, the soil baseline and badger tissue data to map geo-spatial patterns of PTEs and show accumulative trends measured in time. Mapping PCs identified distinct regions of PTE presence in soil and PTE accumulation in badger tissues in Northern Ireland. PTEs were most elevated in liver, kidney and then muscle tissues. Liver and kidney showed the most distinct geo-spatial patterns of accumulation and muscle was the most depleted. PC1 and 2 for each type were modelled using generalised additive mixed models (GAMM) to identify trends through time. PC1 for the liver and muscle were associated with rainfall and ∂N15 in the liver, showing a link to diet and a bioaccumulation pathway, whilst PC2 for both tissues was associated with mean temperature, showing a link to seasonal activity and a bioaccessibility pathway. However, in kidney tissue these trends are reversed and PC1 was associated with bioaccessibility and PC2 with bioaccumulation. Combined these techniques can elucidate both geo-spatial trends in PTEs and the mechanisms by which they move in environment and in future may be an effective tool for assessing PTE bioavailability in environmental health surveys.

Human placental villi contain stromal macrovesicles associated with networks of stellate cells

Placental function is essential for fetal development and establishing the foundations for lifelong health. The placental villous stroma is a connective tissue layer that supports the fetal capillaries and villous trophoblast. All the nutrients that cross the placenta must also cross the stroma, and yet little is known about this region. This study uses high‐resolution three‐dimensional imaging to explore the structural complexity of this region within the placental villi. Serial block‐face scanning electron microscopy and confocal microscopy were used to image the placental villous stroma in three‐dimensions. Transmission electron microscopy (TEM) was used to generate high resolution two‐dimensional images. Stereological approaches were used to quantify volumes of stromal constituents. Three‐dimensional imaging identified stromal extracellular vesicles, which constituted 3.9% of the villous stromal volume. These stromal extracellular vesicles were ovoid in shape, had a median length of 2750 nm (range 350–7730 nm) and TEM imaging confirmed that they were bounded by a lipid bilayer. Fifty‐nine per cent of extracellular vesicles were in contact with a fibroblast‐like stellate cell and these vesicles were significantly larger than those where no contact was observed. These stellate cells formed local networks with adherent junctions observed at contact points. This study demonstrates that the villous stroma contains extracellular macrovesicles which are considerably larger than any previously described in tissue or plasma. The size and abundance of these macrovesicles in the villous stroma highlight the diversity of extracellular vesicle biology and their roles within connective tissues.

The Success and Evolution of a Urological "Boot Camp" for Newly Appointed UK Urology Registrars: Incorporating Simulation, Nontechnical Skills and Assessment

BACKGROUND

Urological training has dramatically changed in recent years. Training durations are shorter and a drive toward consultant led care has reduced trainees experience. Within the UK, approximately 50 registrars annually embark on a 5-year Urology training programme, with variable levels of basic urological experience.

OBJECTIVE

To describe a simulation programme aimed at delivering the knowledge and skills necessary to safely and effectively start working as a registrar in Urology by intensive training with a 1:1 faculty to delegate ratio.

DESIGN, SETTING, AND PARTICIPANTS

Our course content mirrors the UK training syllabus for junior Urology registrars. We delivered 8 modules over a 4-day programme with a fifth day of assessments. Delegates level of urological knowledge, operative competency and confidence pre-, immediately post-training and at 3-months postcourse were assessed. Objective delegate and faculty feedback was also collected. Technical skills modules include; inguinoscrotal surgery, ureteroscopy, transurethral resection, urodynamics, and Botox administration as well as basic reconstructive and laparoscopic operative skills. "Nontechnical" skills included simulated ward round, out-patient, and emergency scenarios.

RESULTS

Feedback from delegates and faculty members has been overwhelmingly positive. We have used this feedback to tailor the content of the course for following years. An increased knowledge level (based on mean examination scores [precourse 55.5%, postcourse 70.1%]) and operative competency was observed in all skills assessed (transurethral resection of the prostate, transurethral resection of bladder tumor, Ureteroscopy, laparoscopic skills, and instrument assembly). Operative confidence was increased immediately and at 3-months postcourse.

CONCLUSIONS

Our "boot camp" course provides a realistic introduction and foundation to begin Urological practice. Being delivered at the beginning of the training scheme, prior to intensive patient exposure, registrars are in an optimum position to develop their newly acquired knowledge and skills to enhance training and intends to improve patient safety and satisfaction.

Optimal remediation design and simulation of groundwater flow coupled to contaminant transport using genetic algorithm and radial point collocation method (RPCM)

The simulation-optimisation models of groundwater and contaminant transport can be a powerful tool in the management of groundwater resources and remediation design. In this study, using Multiquadratic Radial Basis Function (MRBF) a coupled groundwater flow and reactive transport of contaminant and oxidant was developed in the framework of the Meshfree method. The parameter analysis has determined the optimum shape parameter (0.97), and the results of the model were compared with a physical sandbox model which were in good agreement. The genetic algorithm approach was used to find the optimum design of the remediation using permanganate as an oxidant. To find the optimum design we considered two objectives and two constraints. The results revealed that the breakthrough of contaminant to the downstream area of interest and the concentration of the contaminant in this area is reduced significantly with optimisation.

Current ESWL practice and outcomes in the UK: A multicentre snapshot

Objectives:

The objective of this article is to investigate the current clinical practice and outcomes of extracorporeal shock wave lithotripsy (SWL) in the United Kingdom.

Patients and methods:

Patient demographics, stone characteristics and SWL protocols were collected prospectively for 30 consecutive new patient referrals at each of seven contributing UK institutions performing SWL. Final outcomes in terms of stone-free rates (SFRs), and complications were recorded.

Results:

Completed demographic data were available for 204 patients. Treatment protocols varied between centres. Mean patient age was 51 years. Over 70% of stones treated measured between 5 and 10 mm, and one-third were in the ureter, with two-thirds in the kidney, where the majority (31% overall) were in the lower pole. The overall cumulative SFR was 50.3% (range 33–70% between centres). SWL was notably more effective for ureteric stones (SFR 59.3% overall) than for renal calculi (SFR 45.6% overall). Complications were noted in six patients.

Conclusion:

This study provides a valuable snapshot of real-life clinical practice and demonstrates considerable variability in the application of SWL in the UK. The results support existing data which suggest that SWL is a safe and well tolerated treatment modality; however, overall SFRs were low.

EuPathDB: the eukaryotic pathogen genomics database resource

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions.

Neuroendocrine tumours of the small bowel: interpretation of raised circulating chromogranin A, urinary 5 hydroxy indole acetic acid and circulating neurokinin A

BACKGROUND

Neuroendocrine tumours (NETs) of the small bowel are difficult to diagnose as symptoms are non-specific and more often found in common gastrointestinal diseases. Chromogranin A (CGA), urinary 5 hydroxy indole acetic acid (U-5HIAA) and Neurokinin A (NKA) are used as laboratory diagnostic tests but results may be misleading or confusing.

AIM

To clarify the relevance of NET biomarkers for diagnosis of small bowel NETs.

DESIGN

A review of laboratory test results.

METHODS

We reviewed 500 consecutive raised plasma CGA, U-5HIAA and plasma NKA, results from patients in N Ireland. The diagnosis of NET was confirmed by the Northern Ireland Cancer Registry.

RESULTS

In 500 specimens recording raised CGA, 52.2% were from patients with NETs, 13.6% being small bowel tumours, 5.4% of specimens from patients with auto-immune atrophic gastritis and 15.4% from patients taking proton pump inhibitors. In 500 specimens with raised U-5HIAA, 87.8% were from patients with NETs, 68.2% being small bowel tumours. Lung NETs contributed 12.2% and NETs from other sites, 7.4%. Of 500 specimens with raised NKA (reference range (RR) > 20 ng/L), 72.6% were from patients with small bowel NETs and 6% specimens from patients with other NETs. In 20% of specimens NKA concentrations were 21-23 ng/L, within limits of assay precision.

CONCLUSION

CGA remains the best general circulating marker for NETs although only half of raised test results are due to an NET. U-5HIAA is an excellent marker for small bowel and lung NETs with 80% of high test results confirming these diagnoses. NKA is the most specific biomarker for small bowel NETs.

New St. Jude Medical Portico™ transcatheter aortic valve: features and early results

Patients with symptomatic aortic valve disease who are inoperable or have high surgery-related risks may be treated with transcatheter aortic valve implantation devices. With this method increasingly applied, device innovations are aimed at achieving improved procedural results and therapeutic outcome. This paper describes the innovations implemented in the St. Jude Medical Portico™ system for transcatheter aortic valve implantation, the application of this system and initial clinical experience.

Epigenetic regulation of the innate immune response to LPS in bovine peripheral blood mononuclear cells (PBMC)

Epigenetic regulation of gene expression could help explain variation in responses to infection and differences in disease susceptibility in cattle. The aim of this study was to examine epigenetic mechanisms in the regulation of LPS-induced innate immune gene expression in peripheral blood mononuclear cells (PBMCs) from five healthy calves. Firstly, epigenetic enzyme gene expression (histone deacetylase (HDAC) and DNA methyltransferase (DNMT)) was measured after LPS stimulation. Secondly, the effect of the histone deacetylase inhibitor Trichostatin A (TSA) on histone H3 acetylation and on innate immune gene expression was also measured. Results showed differential expression of HDAC6, HDAC7 and DNMT3A genes in response to LPS in cells from all animals, while TSA significantly inhibited pro-inflammatory cytokine (TNF, IL2 and IFNG) expression (P<0.05), presumably by histone acetylation. These results suggest an important role for the HDAC family of enzymes in the regulation of bovine innate immune gene expression.

EuPathDB: the eukaryotic pathogen database

EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNA-seq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010.

A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen

Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.

Targeted prostate cancer screening in men with mutations in BRCA1 and BRCA2 detects aggressive prostate cancer: preliminary analysis of the results of the IMPACT study

OBJECTIVE

To evaluate the role of targeted prostate cancer screening in men with BRCA1 or BRCA2 mutations, an international study, IMPACT (Identification of Men with a genetic predisposition to ProstAte Cancer: Targeted screening in BRCA1/2 mutation carriers and controls), was established. This is the first multicentre screening study targeted at men with a known genetic predisposition to prostate cancer. A preliminary analysis of the data is reported.

PATIENTS AND METHODS

Men aged 40-69 years from families with BRCA1 or BRCA2 mutations were offered annual prostate specific antigen (PSA) testing, and those with PSA > 3 ng/mL, were offered a prostate biopsy. Controls were men age-matched (± 5 years) who were negative for the familial mutation.

RESULTS

In total, 300 men were recruited (205 mutation carriers; 89 BRCA1, 116 BRCA2 and 95 controls) over 33 months. At the baseline screen (year 1), 7.0% (21/300) underwent a prostate biopsy. Prostate cancer was diagnosed in ten individuals, a prevalence of 3.3%. The positive predictive value of PSA screening in this cohort was 47·6% (10/21). One prostate cancer was diagnosed at year 2. Of the 11 prostate cancers diagnosed, nine were in mutation carriers, two in controls, and eight were clinically significant.

CONCLUSIONS

The present study shows that the positive predictive value of PSA screening in BRCA mutation carriers is high and that screening detects clinically significant prostate cancer. These results support the rationale for continued screening in such men.

Prostate cancer in male BRCA1 and BRCA2 mutation carriers has a more aggressive phenotype

There is a high and rising prevalence of prostate cancer (PRCA) within the male population of the United Kingdom. Although the relative risk of PRCA is higher in male BRCA2 and BRCA1 mutation carriers, the histological characteristics of this malignancy in these groups have not been clearly defined. We present the histopathological findings in the first UK series of BRCA1 and BRCA2 mutation carriers with PRCA. The archived histopathological tissue sections of 20 BRCA1/2 mutation carriers with PRCA were collected from histopathology laboratories in England, Ireland and Scotland. The cases were matched to a control group by age, stage and serum PSA level of PRCA cases diagnosed in the general population. Following histopathological evaluation and re-grading according to current conventional criteria, Gleason scores of PRCA developed by BRCA1/2 mutation carriers were identified to be significantly higher (Gleason scores 8, 9 or 10, P=0.012) than those in the control group. Since BRCA1/2 mutation carrier status is associated with more aggressive disease, it is a prognostic factor for PRCA outcome. Targeting screening to this population may detect disease at an earlier clinical stage which may therefore be beneficial.

Delivery of cancer genetics services: The Royal Marsden telephone clinic model

We have conducted a telelink telephone-led cancer genetic counselling model at The Royal Marsden NHS Foundation Trust. The study commenced in March 2004 and evaluation of the clinic was conducted over 17 months from March 2005 to the end of July 2006. A total of 612 patients had telephone consultations during this time, 228 of whom were referred from primary care with a median of 30 patients counselled per month (range of 19-63, depending on staff availability with average of two staff per clinic). Waiting times were measured for General Practitioner referrals and all 228 were counselled within the national target-stipulated 13 weeks (median 6 weeks, range 1-12). An additional 132 patients who were sent appointment letters after receipt of their family history questionnaires did not attend their appointments (18% of all potential referrals) and required recontacting by letter. After telephone counselling, 42% of patients were able to be discharged from the telephone clinic without a subsequent face-to-face appointment, thereby saving resources. The telephone clinic also had a short set-up time with flexibility on timing and day of administration, which would be an advantage in centres where outreach clinic facilities are scarce. The telelink telephone counselling model is highly efficient in triaging high risk individuals for face-to-face counselling as per the Kenilworth model, in effecting concentration of resources and in providing a flexible individual-centred approach to cancer genetic counselling delivery.

Microbial analysis of soil and groundwater from a gasworks site and comparison with a sequenced biological reactive barrier remediation process

AIMS

To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater.

METHODS AND RESULTS

Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal.

CONCLUSION

The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

The Conserved CPH Domains of Cul7 and PARC Are Protein-Protein Interaction Modules That Bind the Tetramerization Domain of p53

Cul7 is a member of the Cullin Ring Ligase (CRL) family and is required for normal mouse development and cellular proliferation. Recently, a region of Cul7 that is highly conserved in the p53-associated, Parkin-like cytoplasmic protein PARC, was shown to bind p53 directly. Here we identify the CPH domains (conserved domain within Cul7, PARC, and HERC2 proteins) of both Cul7 and PARC as p53 interaction domains using size exclusion chromatography and NMR spectroscopy. We present the first structure of the evolutionarily conserved CPH domain and provide novel insight into the Cul7-p53 interaction. The NMR structure of the Cul7-CPH domain reveals a fold similar to peptide interaction modules such as the SH3, Tudor, and KOW domains. The p53 interaction surface of both Cul7 and PARC CPH domains was mapped to a conserved surface distinct from the analogous peptide-binding regions of SH3, KOW, and Tudor domains, suggesting a novel mode of interaction. The CPH domain interaction surface of p53 resides in the tetramerization domain and is formed by residues contributed by at least two subunits.

AIDIT and IMPACT: building research collaborations in targeted prostate cancer screening

AIDIT (Advancing International Co-operation and Developing Infrastructure for Targeted Screening of Prostate Cancer in Men with Genetic Predisposition) is a project funded by the Sixth Framework Programme of the European Community which is endeavouring to facilitate co-operation between European countries in the field of cancer research. The project also aims to raise awareness of familial prostate cancer among health professionals and the public within the associated candidate countries (ACCs) and new member states of the European Union (EU). AIDIT will focus on linking clinical and research teams in the ACCs and new member states with the IMPACT Consortium (Identification of Men with a genetic predisposition to ProstAte Cancer: Targeted screening in BRCA1/2 mutation carriers and controls), an international team investigating screening and diagnosis for men with a genetic risk of prostate cancer predisposition genes BRCA1 or BRCA2). Cancer research has been targeted as a high priority for the European Community; however, research is most successful when centralised and well coordinated, avoiding the duplication and fragmentation associated with smaller, isolated studies. AIDIT will consolidate the current IMPACT consortium and allow research partners from across the world to benefit from shared knowledge and experience. To date, the AIDIT team has established a website to facilitate communication between project collaborators (www.impact-study.co.uk), has been represented at several international meetings and has facilitated a conference for the IMPACT study to bring together international research teams, clinicians and policy makers.

The global atmospheric environment for the next generation

Air quality, ecosystem exposure to nitrogen deposition, and climate change are intimately coupled problems: we assess changes in the global atmospheric environment between 2000 and 2030 using 26 state-of-the-art global atmospheric chemistry models and three different emissions scenarios. The first (CLE) scenario reflects implementation of current air quality legislation around the world, while the second (MFR) represents a more optimistic case in which all currently feasible technologies are applied to achieve maximum emission reductions. We contrast these scenarios with the more pessimistic IPCC SRES A2 scenario. Ensemble simulations for the year 2000 are consistent among models and show a reasonable agreement with surface ozone, wet deposition, and NO2 satellite observations. Large parts of the world are currently exposed to high ozone concentrations and high deposition of nitrogen to ecosystems. By 2030, global surface ozone is calculated to increase globally by 1.5 +/- 1.2 ppb (CLE) and 4.3 +/- 2.2 ppb (A2), using the ensemble mean model results and associated +/-1 sigma standard deviations. Only the progressive MFR scenario will reduce ozone, by -2.3 +/- 1.1 ppb. Climate change is expected to modify surface ozone by -0.8 +/- 0.6 ppb, with larger decreases over sea than over land. Radiative forcing by ozone increases by 63 +/- 15 and 155 +/- 37 mW m(-2) for CLE and A2, respectively, and decreases by -45 +/- 15 mW m(-2) for MFR. We compute that at present 10.1% of the global natural terrestrial ecosystems are exposed to nitrogen deposition above a critical load of 1 g N m(-2) yr(-1). These percentages increase by 2030 to 15.8% (CLE), 10.5% (MFR), and 25% (A2). This study shows the importance of enforcing current worldwide air quality legislation and the major benefits of going further. Nonattainment of these air quality policy objectives, such as expressed by the SRES-A2 scenario, would further degrade the global atmospheric environment.

Change the scope of practice of paramedics? An EMS/public health policy perspective

OBJECTIVE

To analyze the potential for expanding the scope of practice of paramedics from public health, health planning, and health policy perspectives, utilizing data covering more than 42,000 emergency patients.

METHODS

The authors conducted a retrospective study of 42,918 patients seen in two Baltimore emergency departments over a six-month period, 5,259 of whom were transported by emergency ambulance. The authors constructed epidemiologic profiles of in-hospital and prehospital patients, and merged ambulance data with discharge diagnoses.

RESULTS

The 42,918 patients had a total of 2,118 different discharge diagnoses. The ten most frequent diagnoses of ambulance-transported patients were convulsions, injuries, asthma, congestive heart failure, chest pain, syncope and collapse, otitis media, abdominal pain, cardiac arrest, and respiratory abnormality. The ten most frequent diagnoses for all ED patients were otitis media, asthma, finger and nonspecific injuries, upper respiratory infections, chest pain, bronchitis, pharyngitis, gastroenteritis, nonspecific viral infections, and urinary tract infections. Infections accounted for 31.6% of the top 50% of diagnoses by volume, followed by injuries (24%) and cardiovascular cases (16.5%). However, 26.9% of ED patients received an assessment and diagnosis of general symptoms (no procedure).

CONCLUSIONS

The high number of diagnoses and the frequency of infections as a primary complaint in this patient sample reconfirm the primacy of the physician in prioritizing patients and assigning treatment pathways. The authors suggest a methodology that may allow properly trained medics to alter some of their role as physician extenders, but suggest that system planners must first ensure that any changes not reduce the public health benefits that each EMS system already provides.

A medically wise approach to expanding the role of paramedics as physician extenders

The authors examined a portion of the complex issue of the scope of practice of paramedics in light of the epidemiologic profile of emergency patients seen at two Baltimore hospitals. They suggest that the same approach could and should be used to help decide on the scope of work of prehospital personnel in any jurisdiction. The findings lead the authors to urge caution toward any potential changes to the work done by medics, because of the enormous breadth of presenting patient conditions. The authors suggest that the epidemiologic profile witnessed in Baltimore would require increased direct physician input on patient destination decisions for all medics who would be working under an expanded scope of functions, and the paper suggests a mechanism for accomplishing this goal. Finally, while there may be compelling economic reasons to change what medics do in the field, this article cautions health care managers to design changes, based on solid evidence, that will have a positive public health impact, and then work to evaluate the character of the impact after changes are implemented.

Health care and its costs for children with perinatally acquired HIV infection

OBJECTIVE

To describe survival patterns, use of health services and related costs for Australian children with perinatally acquired human immunodeficiency virus (HIV) infection.

METHODOLOGY

A retrospective cross-sectional survey was made of 20 children with HIV infection (91% of those diagnosed) and 13 children with maternal antibodies who subsequently seroreverted, treated at 10 medical centres. Details of disease progression and use of health services were obtained from hospital medical records. Monthly costs for three phases of infection were estimated by linking service usage rates with estimates of the unit cost of each service. The average lifetime cost was estimated by combining monthly costs and phase duration estimates from the literature.

RESULTS

Patterns of disease progression were similar to those reported internationally, with a median survival of 8 years. Use of health services increased with severity of illness. Mean monthly costs were $120 per month (1992 Australian dollars) for children with maternal antibodies who subsequently seroreverted, $320 per month for children with HIV infection but no acquired immunodeficiency syndrome (AIDS)-defining illness, and $1830 per month for children with AIDS. The present value of total lifetime cost for a child with HIV infection was $48174, 46% of which was for treatment of AIDS.

DISCUSSION

The mean lifetime cost for a perinatally infected child was just over half that for a man with HIV in Australia. Health service usage and costs were lower for Australian than American children with HIV.

Reverse transcriptase mutations in sequential HIV-1 isolates in a patient with AIDS

Sequential human immunodeficiency virus type 1 (HIV-1) isolates were obtained over a 29-month period from a person before, during, and after AZT therapy. DNA sequence analysis of polymerase chain-amplified reverse-transcriptase gene showed a gradual accumulation of mutations to peak resistance (IC50 2.13 microM AZT) in association with mutations at codons 44, 210, and 369, as well as at 41, 67, 70, and 215. Eight months after cessation of AZT therapy, when an HIV-1 isolate from the patient was again sensitive to AZT, these mutations had all returned to the pretherapy sequence.

Australia's contribution to tropical health: past and present

Australian research workers have made important contributions to tropical medicine and tropical public health. Recognised high points of international significance (for example, Joseph Bancroft and filariasis, 1876; Thomas Bancroft and dengue fever, 1906; Burnet and Australian X disease, 1934; Derrick and Q fever, 1937; and Fairley and malaria, 1947) must be seen in the context of much detailed work of national relevance by institutions and individuals. The directions of Australian research can be related to several major themes: the large extent of Australia that is tropical or subtropical; interactions with neighbouring countries, especially Papua New Guinea; and concern for the health of Australian Aborigines.

Hepatitis viruses and protection against infection in children

Molecular biology techniques are now a vital part of hepatitis virology, with a central role in studies of diagnosis, epidemiology, virology, pathogenesis, and natural history of infection. Cloning of the genome of hepatitis E virus has allowed its tentative classification as a calici- or related virus, and is the first step toward the development of a vaccine. Long-term implications of hepatitis C for groups such as children with hemophilia, thalassemia, and even leukemia can be better understood by comparison of virus load measured by molecular amplification of the plasma viral RNA with the serologic and clinical status of the respective cohorts of children. A new vaccine for hepatitis A has been licensed in several European countries, and recent experience with severe hepatitis in infants after unexpected transmission of hepatitis B from anti-hepatitis B e positive mothers reemphasizes the value of universal hepatitis B immunization programs. Mother-to-infant transmission of hepatitis C virus has now been well documented, but there are still insufficient data on the dynamics of this, particularly in the absence of passive immunoprophylaxis or a vaccine, to permit recommendations regarding the management of individual pregnancies or deliveries. There is especially too little information to suggest whether breast feeding may be an important mechanism for transmission.

The effect of treatment with zidovudine with or without acyclovir on HIV p24 antigenaemia in patients with AIDS or AIDS-related complex

OBJECTIVE

To evaluate changes in serum HIV p24-antigen levels in a subset of patients who participated in a European/Australian double-blind, placebo-controlled trial evaluating the efficacy of zidovudine (250 mg every 6 h) alone or in combination with acyclovir (800 mg every 6 h) in patients with AIDS, AIDS-related complex (ARC) or Kaposi's sarcoma (KS).

DESIGN

Double-blind, placebo-controlled randomized clinical trial of less than or equal to 6 months' therapy.

SETTING

Samples were obtained from patients attending teaching hospital outpatient clinics in seven European countries and Australia.

SUBJECTS

One hundred and ninety-seven HIV-infected patients (60 with AIDS and 137 with ARC or KS).

MAIN OUTCOME MEASURES

Serum HIV p24-antigen levels measured using the Abbott HIV solid-phase enzyme immunoassay.

RESULTS

Of 76 ARC/KS patients who were initially HIV p24-antigen-positive, one out of 25 randomized to placebo, eight out of 23 to zidovudine and 11 out of 28 to the zidovudine/acyclovir combination became antigen-negative. The proportion of patients who became antigen-negative was significantly higher in both the zidovudine group (P = 0.016) and the zidovudine/acyclovir group (P = 0.004), compared with the placebo group. There were no statistical differences between the zidovudine and the zidovudine/acyclovir groups. During the trial p24-antigen levels in the zidovudine-treated patients reached their minimum after 4-8 weeks of therapy, and tended to increase gradually thereafter. Disease progression occurred irrespective of whether p24-antigen levels declined during therapy. No association between p24-antigen responses to therapy and baseline disease stage, Karnofsky score or baseline CD4 cell count was detectable.

CONCLUSION

Acyclovir does not potentiate the effect of zidovudine on p24-antigen levels. Change in antigen level in response to antiviral therapy needs further investigation before it is used as a surrogate marker for clinical efficacy of antiviral therapy.

Clinical effects and in vitro studies of trifluorothymidine combined with interferon-alpha for treatment of drug-resistant and -sensitive herpes simplex virus infections

Three AIDS patients with severe cutaneous herpes simplex virus (HSV) infection refractory to therapy with acyclovir and foscarnet (2 patients) were treated with a topical preparation of trifluorothymidine (TFT) and interferon-alpha. Complete healing of lesions occurred in 1 patient; a second had significant regression of the infected area. In the third, the lesion was stabilized twice after application of the preparation and reduced in size after a subsequent treatment. In vitro studies confirmed that isolates from these patients were acyclovir- or acyclovir/foscarnet-resistant. In addition, they revealed strong synergy between TFT and interferon-alpha for these isolates and for strains with wild-type drug sensitivity profiles. Topical TFT/interferon-alpha may be of benefit in the therapy of mucocutaneous HSV infections, especially when they are resistant to treatment with systemic antiviral agents.