Evolving relationship of Nares Strait ice arches on sea ice along the Strait and the North Water, the Arctic's most productive polynya

Nares Strait, the waterway that separates northwest Greenland from Ellesmere Island, is a major pathway along which sea ice leaves the Arctic, including the planet's oldest and thickest sea ice that is experiencing an accelerated loss. Ice arches that develop during the winter at the Strait's northern or southern terminus can remain stable for months at a time during which the transport of sea ice ceases. The Arctic's most productive polynya, the North Water (NOW) or Pikialasorsuaq (West Greenlandic for 'great upwelling') forms at the Strait's southern end. There is evidence that a warming climate and the concomitant thinning of Arctic sea ice is weakening the arches and it has been proposed that this may impact the stability of NOW and the complex ecosystem that it sustains. Here we employ a categorization of recent winters with respect to the presence or absence of ice arches to explore their impact on sea ice along the Strait and over the NOW. We find that winters during which a southern ice arch is absent are associated with a reduced and thinner ice cover along the Strait with ice conditions over the NOW similar to that during winters with a southern arch. In winters, without a southern arch, there is also an acceleration of the winds along the Strait that contributes to the presence of reduced ice cover. Ocean color remote sensing data suggests that current levels of primary productivity over the NOW are independent of the presence or absence of an ice arch. The results suggest more research is needed to assess the stability of the NOW, with respect to reduced ice cover and primary productivity, in a future where ice arches cease to form along Nares Strait.

Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk

Objective: Obesity is a significant risk factor for adverse outcomes following coronavirus infection (COVID-19). However, BMI fails to capture differences in the body fat distribution, the critical driver of metabolic health. Conventional statistical methodologies lack functionality to investigate the causality between fat distribution and disease outcomes. Methods: We applied Bayesian network (BN) modelling to explore the mechanistic link between body fat deposition and hospitalisation risk in 459 participants with COVID-19 (395 non-hospitalised and 64 hospitalised). MRI-derived measures of visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), and liver fat were included. Conditional probability queries were performed to estimate the probability of hospitalisation after fixing the value of specific network variables. Results: The probability of hospitalisation was 18% higher in people living with obesity than those with normal weight, with elevated VAT being the primary determinant of obesity-related risk. Across all BMI categories, elevated VAT and liver fat (>10%) were associated with a 39% mean increase in the probability of hospitalisation. Among those with normal weight, reducing liver fat content from >10% to <5% reduced hospitalisation risk by 29%. Conclusion: Body fat distribution is a critical determinant of COVID-19 hospitalisation risk. BN modelling and probabilistic inferences assist our understanding of the mechanistic associations between imaging-derived phenotypes and COVID-19 hospitalisation risk.

Poor glycaemic control and ectopic fat deposition mediates the increased risk of non-alcoholic steatohepatitis in high-risk populations with type 2 diabetes: Insights from Bayesian-network modelling

BACKGROUND

An estimated 55.5% and 37.3% of people globally with type 2 diabetes (T2D) will have concomitant non-alcoholic fatty liver disease (NAFLD) and the more severe fibroinflammatory stage, non-alcoholic steatohepatitis (NASH). NAFLD and NASH prevalence is projected to increase exponentially over the next 20 years. Bayesian Networks (BNs) offer a powerful tool for modelling uncertainty and visualising complex systems to provide important mechanistic insight.

METHODS

We applied BN modelling and probabilistic reasoning to explore the probability of NASH in two extensively phenotyped clinical cohorts: 1) 211 participants with T2D pooled from the MODIFY study & UK Biobank (UKBB) online resource; and 2) 135 participants without T2D from the UKBB. MRI-derived measures of visceral (VAT), subcutaneous (SAT), skeletal muscle (SMI), liver fat (MRI-PDFF), liver fibroinflammatory change (liver cT1) and pancreatic fat (MRI-PDFF) were combined with plasma biomarkers for network construction. NASH was defined according to liver PDFF >5.6% and liver cT1 >800ms. Conditional probability queries were performed to estimate the probability of NASH after fixing the value of specific network variables.

RESULTS

In the T2D cohort we observed a stepwise increase in the probability of NASH with each obesity classification (normal weight: 13%, overweight: 23%, obese: 36%, severe obesity: 62%). In the T2D and non-T2D cohorts, elevated (vs. normal) VAT conferred a 20% and 1% increase in the probability of NASH, respectively, while elevated SAT caused a 7% increase in NASH risk within the T2D cohort only. In those with T2D, reducing HbA1c from the 'high' to 'low' value reduced the probability of NASH by 22%.

CONCLUSION

Using BNs and probabilistic reasoning to study the probability of NASH, we highlighted the relative contribution of obesity, ectopic fat (VAT and liver) and glycaemic status to increased NASH risk, namely in people with T2D. Such modelling can provide insights into the efficacy and magnitude of public health and pharmacological interventions to reduce the societal burden of NASH.

258 Are Electronic Algorithmic Referral Systems the Future of Triage? Evaluating the Use of The Oxford Acute Referrals System (OARS) For Plastic Surgery

Introduction

A traditional referral involves transfer of information over a telephone call and is typically documented in an unstructured format on paper notes, producing poor continuity of referrals between shifts, increasing the risk of error, and compromising patient safety. The Oxford Acute Referrals System (OARS) is an electronic platform that keeps a complete record of referrals, whilst providing the referring clinician with step-by-step specialist advice according to inbuilt BSSH guidelines. This audit demonstrates our experience of its’ use in a tertiary centre Plastics department.

Method

One week of referrals in 2019, prior to the implementation of OARS, were compared with the equivalent week in 2020 once OARS was established. Data was collected retrospectively using electronic patient records.

Results

In one week in 2019, 120 cases were reviewed in the emergency clinic compared with 155 OARS referrals for the equivalent week in 2020. Following OARS implementation, 69% of referred cases did not footfall in the emergency clinic. 46% were managed locally with specialist advice from Plastic Surgery. 10% were brought directly into a theatre list, of which 7% were subsequently treated conservatively. A Plastic surgery consultant reviewing OARS referrals taken by juniors, changed the decision of how or where to manage the patient in 6% of cases.

Conclusions

OARS is an effective triage system that has considerably reduced footfall in the emergency clinic, whilst simultaneously expediting patient care down the correct treatment pathway. Its use led to safe management of patients remotely, which has important implications during a pandemic.

An exploratory study to investigate animal health and reproductive wastage among Australian meat goat producers

The Australian goat meat industry has grown significantly in the last decade, with the value of exports nearly tripling. However, because carcase weight has remained constant over this time, the drivers of industry growth are price and supply. Animal health and reproduction are key factors contributing to supply and productivity, yet limitations to production management are poorly understood, hampering advice for effective intervention. This exploratory study aims to provide insights into the animal health and reproductive management practices and perceptions among meat goat producers in Australia. To achieve this aim, 20 producers, located in New South Wales, Queensland, Western Australia and Victoria, operating under different production systems were interviewed. The results of this study suggest that animal health management could be improved and that producers perceive a lack of relevant and species-specific information available to help them make informed decisions. Reproductive management and records varied greatly across producers interviewed. Kid loss was identified as an issue, with a 28% estimated average (6%-47% range) of losses from kidding until weaning. Producers identified predation, doe nutrition and mismothering as the biggest contributors to kid loss, with the majority of losses occurring within a week of birth. All producers believed management could minimise kid loss. This study highlights the importance of improving reproductive rates among goat enterprises and provides new information on the current practices within the Australian meat goat industry. This may assist the development of appropriate strategies for improving health and reproductive management and delivery of advice to producers.

Sexual risk and HIV testing disconnect in men who have sex with men (MSM) recruited to an online HIV self-testing trial

OBJECTIVES

We report the frequency of previous HIV testing at baseline in men who have sex with men (MSM) who enrolled in an HIV self-testing (HIVST) randomized controlled trial [an HIV self-testing public health intervention (SELPHI)].

METHODS

Criteria for enrolment were age ≥ 16 years, being a man (including trans men) who ever had anal intercourse (AI) with a man, not being known to be HIV positive and having consented to national HIV database linkage. Using online survey baseline data (2017-2018), we assessed associations with never having tested for HIV and not testing in the previous 6 months, among men who reported at least two recent condomless AI (CAI) partners.

RESULTS

A total of 10 111 men were randomized; the median age was 33 years [interquartile range (IQR) 26-44 years], 89% were white, 20% were born outside the UK, 0.8% were trans men, 47% were degree educated, and 8% and 4% had ever used and were currently using pre-exposure prophylaxis (PrEP), respectively. In the previous 3 months, 89% reported AI and 72% reported CAI with at least one male partner. Overall, 17%, 33%, 54%, and 72% had tested for HIV in the last 3 months, 6 months, 12 months and 2 years, respectively; 13% had tested more than 2 years ago and 15% had never tested. Among 3972 men reporting at least two recent CAI partners, only 22% had tested in the previous 3 months. Region of residence and education level were independently associated with recent HIV testing. Among current PrEP users, 15% had not tested in the previous 6 months.

CONCLUSIONS

Most men in SELPHI, particularly those reporting at least two CAI partners and current PrEP users, were not testing in line with current UK recommendations. The results of the trial will inform whether online promotion of HIVST addresses ongoing testing barriers.

Approaches to training multiclass semantic image segmentation of damage in concrete

This paper addresses the problem of creating a large quantity of high-quality training segmentation masks from scanning electron microscopy (SEM) images. The images are acquired from concrete samples that exhibit progressive amounts of degradation resulting from alkali-silica reaction (ASR), a leading cause of deterioration, cracking and loss of capacity in much of the nation's infrastructure. The target damage classes in concrete SEM images are defined as paste damage, aggregate damage, air voids and no damage. We approached the SEM segmentation problem by applying convolutional neural network (CNN)-based methods to predict the damage classes due to ASR for each image pixel. The challenges in using the CNN-based methods lie in preparing large numbers of high-quality training labelled images while having limited human resources. To address these challenges, we designed damage- and context-assisted approaches to lower the requirements on human resources. We then evaluated the accuracy of CNN-based segmentation methods using the datasets prepared with these two approaches. LAY DESCRIPTION: This work is about automated segmentation of Scanning Electron Microscopy (SEM) images taken from core and prism samples of concrete. The segmentation must detect several damage classes in each image in order to understand properties of concrete-made structures over time. The segmentation problem is approached with an artificial network (AI) based model. The training data for the AI model are created using damage- and context-assisted approaches to lower the requirements on human resources. The access to all training data and to a web-based validation system for scoring segmented images is available at https://isg.nist.gov/deepzoomweb/data/concreteScoring.

Growing Old in the Emergency Department

The research team were concerned that older patients requiring emergency admission seemed to wait longer for a hospital bed, and as such were disproportionately affected by Emergency Department overcrowding. To investigate this theory and explore any changes over time, a ten year dataset (2005-2014 inclusive) was extracted from the information systems at Beaumont Hospital, Dublin. This research examines the changing age profile of ED patients, identifies the relationship between age and the total time spent in the Emergency Department (Patient Experience Time (PET)), and examines the public belief that EDs are busiest in winter when reports of overcrowding and elderly patients waiting on trolleys get most media attention. The results highlight that the ED is busy all year round (but for different seasonal reasons) and point to an overdue need to plan for the current and future healthcare of older patients within and beyond acute hospitals.

Attributable mortality of hospital-acquired bloodstream infections in Ireland

AIM

To estimate the attributable mortality of hospital-acquired bloodstream infections (HA-BSI) in Ireland.

METHODS

A retrospective case-cohort study was conducted, based on notifications from Irish microbiology laboratories and administrative patient records from six Irish hospitals from January 2007 to December 2013. Probabilistic linkage was used to link 1252 cases of bloodstream infection from a cohort of 343,189 hospitalized patients. Independent predictors of mortality were determined using a multi-variable logistic regression model, and included: patient age, emergency or re-admission to hospital, length of stay in an intensive care unit, number of procedures, number of diagnoses, major diagnostic category and presence of HA-BSI.

RESULTS

Attributable mortality was calculated from the crude mortality of case subjects after adjusting for other predictors of mortality, and was found to be 15.3% (95% confidence interval 14.8-15.8%). The study was further stratified according to the causative organism, including: Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus and Streptococcus pneumoniae, and, where available, their antimicrobial resistance patterns. The highest attributable mortality among these organisms was reported for E. faecium at 18.1% and the lowest attributable mortality was reported for E. coli at 13.6%. A significantly higher attributable mortality was found for antimicrobial resistance patterns of some organisms, most notably for meticillin-resistant S. aureus at 19.5%, vs meticillin-susceptible S. aureus at 13.3%.

CONCLUSIONS

HA-BSI is an important cause of mortality, and attributable mortality differs significantly among causative organisms and antimicrobial resistance patterns.

Klebsiella pneumoniae bloodstream infection, antimicrobial resistance and consumption trends in Ireland: 2008 to 2013

This study aimed to describe the epidemiology and antimicrobial resistance trends of Klebsiella pneumoniae bloodstream infection (BSI) in Ireland, in conjunction with national antimicrobial consumption data, during the period 2008 to 2013. A retrospective cohort study of K. pneumoniae BSI cases was conducted, based on notifications from Irish microbiology laboratories to the Health Protection Surveillance Centre (HPSC). In total, 1942 K. pneumoniae BSI cases were identified over 6 years, with 310 reported in 2008 and 326 reported in 2013. From 2008 to 2013, the proportion of isolates resistant to co-amoxiclav (24 % versus 29 %), piperacillin-tazobactam (11 % versus 27 %), third generation cephalosporins (3GC) (11 % versus 21 %), fluoroquinolones (13 % versus 21 %) and gentamicin (11 % versus 17 %) increased overall, concurrent with increasing national rates of antimicrobial consumption in Ireland (acute hospitals: 35.87 versus 39.77 defined daily doses (DDD) per 100 bed days used (BDU); and community: 6.38 versus 7.85 DDD per 1000 inhabitants per day (DID)). Enhanced data on the patient's admission route was available for 735 (38 %) cases. Overall, 51 % (n = 378) were categorised as 'acquired in the reporting hospital'. The all-cause mortality was 20 %, with 115 deaths, 101 (88 %) of whom died within 30 days of blood culture sampling date. K. pneumoniae is the second most common cause of Gram-negative BSI in Ireland, with most cases healthcare-associated and an all-cause mortality of 20 % reported in this study. Annual increases in resistance to different antimicrobial classes and in a multi-drug resistant phenotype have been observed, concurrent with increasing national broad spectrum antimicrobial consumption. These trends portend a risk to patient outcomes and highlight the urgency for individual prescribers to evaluate their antimicrobial prescribing habits in hospitals, long-term care and community settings.

Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore

The hyperactivity of the cyclic dependent kinase 5 (CDK5) induced by the activator protein p25 has been linked to a number of pathologies of the brain. The CDK5-p25 complex has thus emerged as a major therapeutic target for Alzheimer's disease (AD) and other neurodegenerative conditions. Experiments have shown that the peptide p5 reduces the CDK5-p25 activity without affecting the endogenous CDK5-p35 activity, whereas the peptide TFP5, obtained from p5, elicits similar inhibition, crosses the blood-brain barrier, and exhibits behavioral rescue of AD mice models with no toxic side effects. The molecular basis of the kinase inhibition is not currently known, and is here investigated by computer simulations. It is shown that p5 binds the kinase at the same CDK5/p25 and CDK5/p35 interfaces, and is thus a non-selective competitor of both activators, in agreement with available experimental data in vitro. Binding of p5 is enthalpically driven with an affinity estimated in the low µM range. A quantitative description of the binding site and pharmacophore is presented, and options are discussed to increase the binding affinity and selectivity in the design of drug-like compounds against AD.

Cow-calf reproductive, genetic, and nutritional management to improve the sustainability of whole beef production systems

Optimizing efficiency in the cow-calf sector is an important step toward improving beef sustainability. The objective of the study was to use a model to identify the relative roles of reproductive, genetic, and nutritional management in minimizing beef production systems' environmental impact in an economically viable, socially acceptable manner. An economic and environmental diet optimizer was used to identify ideal nutritional management of beef production systems varying in genetic and reproductive technology use. Eight management scenarios were compared to a least cost baseline: average U.S. production practices (CON), CON with variable nutritional management (NUT), twinning cattle (TWN), early weaning (EW), sire selection by EPD using either on-farm bulls (EPD-B) or AI (EPD-AI), decreasing the calving window (CW), or selecting bulls by EPD and reducing the calving window (EPD-CW). Diets to minimize land use, water use, and/or greenhouse gas (GHG) emissions were optimized under each scenario. Increases in diet cost attributable to reducing environmental impact were constrained to less than stakeholder willingness to pay for improved efficiency and reduced environmental impact. Baseline land use, water use, and GHG emissions were 188 m, 712 L, and 21.9 kg/kg HCW beef. The NUT scenario, which assessed opportunities to improve sustainability by altering nutritional management alone, resulted in a simultaneous 1.5% reduction in land use, water use, and GHG emissions. The CW scenario improved calf uniformity and simultaneously decreased land use, water use, and GHG emissions by 3.2%. Twinning resulted in a 9.2% reduction in the 3 environmental impact metrics. The EW scenario allowed for an 8.5% reduction in the 3 metrics. The EPD-AI scenario resulted in an 11.1% reduction, which was comparable to the 11.3% reduction achieved by EPD-B in the 3 metrics. Improving genetic selection by using AI or by purchasing on-farm bulls based on their superior EPD demonstrated clear opportunity to improve sustainability. When genetic and reproductive technologies were adopted, up to a 12.4% reduction in environmental impact was achievable. Given the modeling assumptions used in this study, optimizing nutritional management while concurrently improving genetic and reproductive efficiency may be promising avenues to improve productivity and sustainability of U.S. beef systems.

Background intensity correction for terabyte-sized time-lapse images

Several computational challenges associated with large-scale background image correction of terabyte-sized fluorescent images are discussed and analysed in this paper. Dark current, flat-field and background correction models are applied over a mosaic of hundreds of spatially overlapping fields of view (FOVs) taken over the course of several days, during which the background diminishes as cell colonies grow. The motivation of our work comes from the need to quantify the dynamics of OCT-4 gene expression via a fluorescent reporter in human stem cell colonies. Our approach to background correction is formulated as an optimization problem over two image partitioning schemes and four analytical correction models. The optimization objective function is evaluated in terms of (1) the minimum root mean square (RMS) error remaining after image correction, (2) the maximum signal-to-noise ratio (SNR) reached after downsampling and (3) the minimum execution time. Based on the analyses with measured dark current noise and flat-field images, the most optimal GFP background correction is obtained by using a data partition based on forming a set of submosaic images with a polynomial surface background model. The resulting image after correction is characterized by an RMS of about 8, and an SNR value of a 4 × 4 downsampling above 5 by Rose criterion. The new technique generates an image with half RMS value and double SNR value when compared to an approach that assumes constant background throughout the mosaic. We show that the background noise in terabyte-sized fluorescent image mosaics can be corrected computationally with the optimized triplet (data partition, model, SNR driven downsampling) such that the total RMS value from background noise does not exceed the magnitude of the measured dark current noise. In this case, the dark current noise serves as a benchmark for the lowest noise level that an imaging system can achieve. In comparison to previous work, the past fluorescent image background correction methods have been designed for single FOV and have not been applied to terabyte-sized images with large mosaic FOVs, low SNR and diminishing access to background information over time as cell colonies span entirely multiple FOVs. The code is available as open-source from the following link https://isg.nist.gov/.

Aligning product development and user perspectives: social-behavioural dimensions of multipurpose prevention technologies

Multipurpose prevention technologies provide a compelling response to the multiple and reinforcing sexual and reproductive health risks faced by women globally. To ensure that this potential is realised, product-specific characteristics and their social-behavioural correlates must be considered early in the product development process. This paper provides an overview of the key user-related social and behavioural dimensions of three broad categories of multipurpose prevention technologies: 1) sustained release vaginal rings, 2) pericoital vaginal products, and 3) co-formulated or co-administered injectables. The authors build upon the broad parameters of Target Product Profiles for such products, aligning them with user perspective considerations.

The Living with Dysarthria group for post-stroke dysarthria: the participant voice

BACKGROUND

The Living with Dysarthria group programme, devised for people with post-stroke dysarthia and family members, was piloted twice. Feedback from those who experience an intervention contributes to the evaluation of speech and language therapy programmes, giving the participant view of the intervention's value and guiding further developments.

RESEARCH QUESTION

What feedback do participants in the Living with Dysarthria programme provide, informing on its perceived usefulness and guiding its future development?

METHODS & PROCEDURES

Nine people with chronic dysarthria following stroke and four family members who completed the Living with Dysarthria programme all contributed to Focus Group (FG) discussion, transcribed and thematically analysed, and completed an Anonymous Questionnaire Evaluation (AQE), comprising closed statements and open questions. An anonymous descriptive adjective selection task (ADAST) was also used.

OUTCOMES & RESULTS

The varied forms of feedback provided complementary information. Thematic analysis of FG data and AQE open question responses were configured around programme benefits, programme structure and content, and programme practicalities. Benefits associated with participation included learning and insight, being supported by peers and professionals, and improved speech and confidence. These are consistent with the main programme elements of education, support and speech practice. All activities were seen as relevant and positively received. Flexibility, recognition of and catering to individual needs were valued characteristics. The community location was approved by all. Most participants thought the format of eight weekly sessions of 2 h was appropriate. Responses to AQE closed statements provided almost unanimous confirmation of the very positive feedback conveyed in FG discussions. The main response to suggested improvements in AQEs was that the number of sessions should be increased. Feedback indicated that for a few individuals there was negative reaction to some facts about stroke, home practice tasks were difficult to complete, the person with dysarthria/family member pair may not be the optimum combination for paired practice activities and pre-programme information should be extended. The ADAST showed that the programme was enjoyable, interesting, stimulating and useful.

CONCLUSIONS & IMPLICATIONS

Participant feedback indicates that group therapy, with family member participation, is a valid form of management for chronic post-stroke dysarthria. Education, peer and professional support, and speech practice are confirmed as relevant programme components. Consistent majority opinions were communicated in different situations and via varied mediums. Some individuals expressed views relevant to their own needs, and these responses also inform future implementation of the Living with Dysarthria programme.

More Outcomes than Trials: A Call for Consistent Data Collection across Stroke Rehabilitation Trials

Stroke survivors experience complex combinations of impairments, activity limitations, and participation restrictions. The essential components of stroke rehabilitation remain elusive. Determining efficacy in randomized controlled trials (RCTs) is challenging; there is no commonly agreed primary outcome measure for rehabilitation trials. Clinical guidelines depend on proof of efficacy in RCTs and meta-analyses. However, diverse trial aims, differing methods, inconsistent data collection, and use of multiple assessment tools hinder comparability across trials. Consistent data collection in acute stroke trials has facilitated meta-analyses to inform trial design and clinical practice. With few exceptions, inconsistent data collection has hindered similar progress in stroke rehabilitation research. There is an urgent need for the routine collection of a core dataset of common variables in rehabilitation trials. The European Stroke Organisation Outcomes Working Group, the National Institutes of Neurological Disorders and Stroke Common Data Elements project, and the Collaborative Stroke Audit and Research project have called for consistency in data collection in stroke trials. Standardizing data collection can decrease study start up times, facilitate data sharing, and inform clinical guidelines. Although achieving consensus on which outcome measures to use in stroke rehabilitation trials is a considerable task, perhaps a feasible starting point is to achieve consistency in the collection of data on demography, stroke severity, and stroke onset to inclusion times. Longer term goals could include the development of a consensus process to establish the core dataset. This should be endorsed by researchers, funders, and journal editors in order to facilitate sustainable change.

Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells

We present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are physically in contact with each other. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting, tracking and lineage modelling in cell biology. The segmentation method presented in this paper consists of (1) background reconstruction to obtain noise-free foreground pixels and (2) incorporation of biological insight about dividing and nondividing cells into the segmentation process to achieve reliable separation of foreground pixels defined as pixels associated with individual cells. The segmentation results for a time-lapse image stack were compared against 238 manually segmented images (8219 cells) provided by experts, which we consider as reference data. We chose two metrics to measure the accuracy of segmentation: the 'Adjusted Rand Index' which compares similarities at a pixel level between masks resulting from manual and automated segmentation, and the 'Number of Cells per Field' (NCF) which compares the number of cells identified in the field by manual versus automated analysis. Our results show that the automated segmentation compared to manual segmentation has an average adjusted rand index of 0.96 (1 being a perfect match), with a standard deviation of 0.03, and an average difference of the two numbers of cells per field equal to 5.39% with a standard deviation of 4.6%.

A computer-aided algorithm to quantitatively predict lymph node status on MRI in rectal cancer

OBJECTIVE

The aim of this study was to demonstrate the principle of supporting radiologists by using a computer algorithm to quantitatively analyse MRI morphological features used by radiologists to predict the presence or absence of metastatic disease in local lymph nodes in rectal cancer.

METHODS

A computer algorithm was developed to extract and quantify the following morphological features from MR images: chemical shift artefact; relative mean signal intensity; signal heterogeneity; and nodal size (volume or maximum diameter). Computed predictions on nodal involvement were generated using quantified features in isolation or in combinations. Accuracies of the predictions were assessed against a set of 43 lymph nodes, determined by radiologists as benign (20 nodes) or malignant (23 nodes).

RESULTS

Predictions using combinations of quantified features were more accurate than predictions using individual features (0.67-0.86 vs 0.58-0.77, respectively). The algorithm was more accurate when three-dimensional images were used (0.58-0.86) than when only middle image slices (two-dimensional) were used (0.47-0.72). Maximum node diameter was more accurate than node volume in representing the nodal size feature; combinations including maximum node diameter gave accuracies up to 0.91.

CONCLUSION

We have developed a computer algorithm that can support radiologists by quantitatively analysing morphological features of lymph nodes on MRI in the context of rectal cancer nodal staging. We have shown that this algorithm can combine these quantitative indices to generate computed predictions of nodal status which closely match radiological assessment. This study provides support for the feasibility of computer-assisted reading in nodal staging, but requires further refinement and validation with larger data sets.

Role of penile biopsy in the diagnosis of penile dermatoses

The aim of this study was to review the utility of penile biopsy in genitourinary (GU) medicine clinics, its acceptability and the range of penile dermatoses diagnosed histologically. A retrospective case-notes review of 401 cases attending a dedicated penile dermatoses clinic from 1 June 2001 to 30 November 2007 was carried out. In 115/401 (28.7%) of cases a biopsy was invoked to resolve ambiguities of diagnosis. In 60/401 (15%) of those cases differential diagnosis was resolved, in 26/401 (6.5%) clinically suspected diagnoses were confirmed and in 22/401 (5.5%) clinically unsuspected diagnoses were identified. In 7/401 (1.7%) of cases the biopsy was also the treatment. Targeted penile biopsy has an important role in the diagnosis of penile dermatoses, particularly where there is clinical uncertainty. As a diagnostic tool in GU medicine departments it should be readily available even if not for routine use. There were indications that circumcision may reduce the incidence of penile dermatoses. There was also some indication of a possible ethnic factor in the relative incidences of penile lichen sclerosus and lichen planus in biopsied patients.

Initial assessment of a model relating intratumoral genetic heterogeneity to radiological morphology

Tumour heterogeneity has major implications for tumour development and response to therapy. Tumour heterogeneity results from mutations in the genes responsible for mismatch repair or maintenance of chromosomal stability. Cells with different genetic properties may grow at different rates and exhibit different resistance to therapeutic interventions. To date, there exists no approach to non-invasively assess tumour heterogeneity. Here we present a biologically inspired model of tumour growth, which relates intratumoral genetic heterogeneity to gross morphology visible on radiological images. The model represents the development of a tumour as a set of expanding spheres, each sphere representing a distinct clonal centre, with the sprouting of new spheres corresponding to new clonal centres. Each clonal centre may possess different characteristics relating to genetic composition, growth rate and response to treatment. We present a clinical example for which the model accurately tracks tumour growth and shows the correspondence to genetic variation (as determined by array comparative genomic hybridisation). One clinical implication of our work is that the assessment of heterogeneous tumours using Response Evaluation Criteria In Solid Tumours (RECIST) or volume measurements may not accurately reflect tumour growth, stability or the response to treatment. We believe that this is the first model linking the macro-scale appearance of tumours to their genetic composition. We anticipate that our model will provide a more informative way to assess the response of heterogeneous tumours to treatment, which is of increasing importance with the development of novel targeted anti-cancer treatments.

Giving away the grog: an ethnography of Aboriginal drinkers who quit without help

The paper presents preliminary findings from a qualitative study of Australian Aboriginal men who have stopped drinking without the assistance of residential treatment, counselling or other programs. Main reasons advanced by interviewees for ceasing drinking were one or more of: medical condition and/or doctor's warning; family factors; trauma from accidents; conversion to Christianity. The author concludes that employment both helps and hinders abstention from drinking, and that social ties often pose major difficulties for those trying to give up drinking. The paper also discusses the importance of Aboriginal beliefs regarding personal autonomy.

Expanding knowledge among Aboriginal service providers on treatment options for excessive alcohol use

Approaches to the prevention of alcohol problems among Aboriginal people in Australia have tended to emphasize primary and tertiary prevention, while neglecting secondary prevention or early intervention. In contrast, members of the wider Australian community can now access a variety of early interventions through general practice, in hospital settings and through drug and alcohol treatment agencies. As part of a survey of the use of brief interventions, 178 agencies throughout Australia were interviewed, and findings are presented from the 29 agencies in this sample which provided services primarily for Aboriginal people. Approximately half offered a variety of approaches including brief interventions, with goals of moderation; the other half were entirely abstinence-orientated. These findings are discussed in the context of expanding the options that might be offered by Aboriginal-run agencies.

iGenomicViewer, a Gynecologic Oncology Group software library for the creation of highly customizable, portable, interactive, and linked visualizations of high throughput genomic data

e16544

Background: An R software library was created with the goal of creating customizable, platform independent, and portable visualization tools for the annotation, dissemination and interrogation of high dimensioned genomic data. Methods: A set of R functions were created to extend the functionality of the sendplot R library. The functions were applied to BAC aCGH data generated for several GOG studies. Results: The iGenomicViewer function calls created and populated a directory structure which was then ported to a password protected server for interrogation by research team members. The linked html and image output allows users to examine genome wide plots of aberration frequencies and p-values and then drill down to visualizations of regions of interest. Users can interrogate a panel of plots which includes: 1) a heat map of the aCGH data for with tool-tip display of sample and assay specific data (e.g., assay values, sample IDs, and hyperlinks to UCSC browser and sample specific images); 2) a set of interactive annotation tracks which display location of cancer, disease and DNA repair genes; and 3) a plot which displays -log10 p-values and/or aberration frequencies for the BAC assays depicted in the heatmap. For the smallest regions of interest, the panel of plots contains a tiled heatmap which depicts the overlap and gaps in BAC coverage and their alignment with the gene locations represented in the adjacent annotation track. Conclusions: The iGenomicViewer library provides open source software for creation of customizable visualization tools for collaborative research projects involving high dimensioned genomic data.

No significant financial relationships to disclose.