The influence of oyster reefs and surrounding sediments on nitrogen removal - An in-situ study along the East coast of Australia

Oyster reefs play a crucial role in the removal of nitrogen (N) from aquatic systems by facilitating nutrient regeneration and denitrification, both in their tissues and shells and surrounding sediments. However, we still have a limited understanding about the contribution of each component of the reefs (e.g. oysters vs sediments) to N processes, and whether rates are dependent on site-specific characteristics. To address these knowledge gaps, we conducted an experiment across six oyster reefs along 1080 km of the Eastern Australian coast with different sediment characteristics. By using in-situ clear and dark incubation chambers, we assessed how benthic metabolism, nutrient and dinitrogen gas (N2) fluxes varied among the following treatments: 'oysters', 'sediments', and 'sediments + oysters' that were used to represent components of the whole reef habitat (i.e. reef matrix vs surrounding sediments vs the interaction among them, respectively), and sites. We found that during dark conditions and at siltier sites, N2 effluxes from oysters can be up to 23 times higher than sediments, while N2 effluxes from chambers with both sediments and oysters were similar to sediment treatments, and lower than oyster treatments. These results can be explained by sediment processes including nutrient assimilation by benthic microalgae and/or lower nutrient diffusion into interstitial space. Additionally, oyster treatments showed an uptake of nitrate (NO3-) that was likely converted into N2, whereas sediment treatments showed an overall release of NO3-. In dark conditions, ammonium (NH4+) fluxes remained consistent across treatments and sites, indicating that any exports from oyster excretion (in those treatments including oysters) were either counterbalanced by or comparable to exports from sediments. This study provides evidence that the crucial contribution of oyster reefs to N removal is dependent on interactions between reef components and environmental factors.

Every child, every day, back to play: the PICUstars protocol - implementation of a nurse-led PICU liberation program

BACKGROUND

As admissions to paediatric intensive care units (PICU) rise and mortality rates decline, the focus is shifting from survival to quality of survivorship. There is paucity of internationally accepted guidelines to manage complications like over-sedation, delirium, and immobility in the paediatric setting. These have a strong adverse impact on PICU recovery including healthcare costs and long-term functional disability. The A2F bundle (ABCDEF), or ICU Liberation, was developed to operationalise the multiple evidence-based guidelines addressing ICU-related complications and has been shown to improve clinical outcomes and health-care related costs in adult studies. However, there is little data on the effect of ICU Liberation bundle implementation in PICU.

METHODS

PICU-STARS will be a single centre before-and-after after trial and implementation study. It is designed to evaluate if the multidimensional, nurse-led ICU Liberation model of care can be applied to the PICU and if it is successful in minimising PICU-related problems in a mixed quaternary PICU. In a prospective baseline measurement, the present practises of care in the PICU will be assessed in order to inform the adaptation and implementation of the PICU Liberation bundle. To assess feasibility, implementation outcomes, and intervention effectiveness, the implementation team will use the Consolidated Framework for Implementation Research (CIFR) and process assessment (mixed methods). The implementation process will be evaluated over time, with focus groups, interviews, questionnaires, and observations used to provide formative feedback. Over time, the barriers and enablers for successful implementation will be analysed, with recommendations based on "lessons learned." All outcomes will be reported using standard descriptive statistics and analytical techniques, with appropriate allowance for patient differentials in severity and relevant characteristics.

DISCUSSION

The results will inform the fine-tune of the Liberation bundle adaptation and implementation process. The expected primary output is a detailed adaptation and implementation guideline, including clinical resources (and investment) required, to adopt PICU-STARS in other children's hospitals.

PATIENT AND PUBLIC INVOLVEMENT STATEMENT

The authors thank the PICU education and Liberation Implementation team, and our patients and families for their inspiration and valuable comments on protocol drafts. Results will be made available to critical care survivors, their caregivers, relevant societies, and other researchers.

TRIAL REGISTRATION

ACTRN, ACTRN382863 . Registered 19/10/2021 - Retrospectively registered.

STUDY STATUS

recruiting.

Analysis of misses in imaging of head and neck pathology by attending neuroradiologists at a single tertiary academic medical centre

AIM

To analyse errors in head and neck (H&N) pathology made by attending neuroradiologists at a single tertiary-care centre.

MATERIALS AND METHODS

A neuroradiology quality assurance (QA) database of radiological errors was searched for attending physician errors in H&N pathology from 2014-2020. Data were limited to computed tomography (CT) and magnetic resonance imaging (MRI) reports. Data were collected on missed pathologies and study types. Misses were grouped into three categories: central neck (thyroid gland, aerodigestive tract), lateral neck (salivary glands, lymph nodes, soft tissues), and face/orbits (orbits, sinuses, masticator space).

RESULTS

During the study period, a total of 283,248 CT and MRI neuroradiology examinations were interpreted (all indications). Seventy-four H&N misses were identified comprising 85.1% perceptual and 14.9% interpretive errors. The distribution of errors was face/orbits (37.8%), central neck (36.5%), and lateral neck (25.7%). Clinically significant errors were found most commonly in the aerodigestive tract (21%), orbits (17.7%), masticator space, and parotid glands (14.5% each). The majority (67.6%) of the misses were detected on examinations that were not performed for a primary H&N indication; MRI brain was the most common examination (27%). Clearly malignant or potentially malignant masses accounted for 48.6% of all misses.

CONCLUSION

The majority of H&N misses were perceptual and were detected on examinations not performed for a H&N indication. Clearly malignant or potentially malignant masses represented half of all misses.

A weight-of-evidence approach for identifying potential sources of untreated sewage inputs into a complex urbanized catchment

The Hawkesbury-Nepean River (HNR) is the largest catchment in the Sydney region and is undergoing unprecedented population growth. The HNR system receives a mix of anthropogenic inputs such as treated sewage, stormwater and agricultural runoff. Combined, these can diminish the ecological system health and pose potential concerns to human health. Of particular concern are inputs of untreated sewage, that can occur due to a range of different reasons including illegal point source discharges, failure of the sewerage network, and overloading of wastewater treatment plants during storm events. Here, we present findings of an intensive assessment across the HNR catchment where we used a weight-of-evidence (WOE) approach to identify untreated sewage contamination in surface waters against the background of treated effluent and diffuse inputs during post high flow conditions. Total nitrogen and phosphorus concentrations were used to assess treated effluent and diffuse inputs, and microbial analysis, including both culture-based traditional methods for E. coli and enterococci and qPCR analysis of Bacteroides and Lachnospiraceae, were used to assess raw sewage contamination. Despite a background of diffuse inputs from recent high flow events and the influence of treated wastewater, we found no gradient of faecal contamination along the HNR system or its tributaries. We observed two sites with evidence of untreated sewage contamination, where the human markers Bacteroides and Lachnospiraceae qPCR copy numbers were high. The biological and chemical approaches suggested these latter two hotspots originate from an industrial runoff source and possibly from a dry weather sewage leak. Our findings demonstrate the potential of a WOE approach in the assessment of human faecal signal in an urban river that can also pinpoint small sources of contamination as a strategy that can reshape the way monitoring is performed and the chemical end-points chosen to provide pertinent information on the potential risks to aquatic system health.

Randomized controlled trial of topical corticosteroid and home-based narrowband ultraviolet B for active and limited vitiligo: results of the HI-Light Vitiligo Trial

BACKGROUND

Evidence for the effectiveness of vitiligo treatments is limited.

OBJECTIVES

To determine the effectiveness of (i) handheld narrowband UVB (NB-UVB) and (ii) a combination of potent topical corticosteroid (TCS) and NB-UVB, compared with TCS alone, for localized vitiligo.

METHODS

A pragmatic, three-arm, placebo-controlled randomized controlled trial (9-month treatment, 12-month follow-up). Adults and children, recruited from secondary care and the community, aged ≥ 5 years and with active vitiligo affecting < 10% of skin, were randomized 1 : 1 : 1 to receive TCS (mometasone furoate 0·1% ointment + dummy NB-UVB), NB-UVB (NB-UVB + placebo TCS) or a combination (TCS + NB-UVB). TCS was applied once daily on alternating weeks; NB-UVB was administered on alternate days in escalating doses, adjusted for erythema. The primary outcome was treatment success at 9 months at a target patch assessed using the participant-reported Vitiligo Noticeability Scale, with multiple imputation for missing data. The trial was registered with number ISRCTN17160087 on 8 January 2015.

RESULTS

In total 517 participants were randomized to TCS (n = 173), NB-UVB (n = 169) and combination (n = 175). Primary outcome data were available for 370 (72%) participants. The proportions with target patch treatment success were 17% (TCS), 22% (NB-UVB) and 27% (combination). Combination treatment was superior to TCS: adjusted between-group difference 10·9% (95% confidence interval 1·0%-20·9%; P = 0·032; number needed to treat = 10). NB-UVB alone was not superior to TCS: adjusted between-group difference 5·2% (95% CI - 4·4% to 14·9%; P = 0·29; number needed to treat = 19). Participants using interventions with ≥ 75% expected adherence were more likely to achieve treatment success, but the effects were lost once treatment stopped. Localized grade 3 or 4 erythema was reported in 62 (12%) participants (including three with dummy light). Skin thinning was reported in 13 (2·5%) participants (including one with placebo ointment).

CONCLUSIONS

Combination treatment with home-based handheld NB-UVB plus TCS is likely to be superior to TCS alone for treatment of localized vitiligo. Combination treatment was relatively safe and well tolerated but was successful in only around one-quarter of participants.

An economic evaluation of the randomized controlled trial of topical corticosteroid and home-based narrowband ultraviolet B for active and limited vitiligo (the HI-Light Vitiligo Trial)

BACKGROUND

Economic evidence for vitiligo treatments is absent.

OBJECTIVES

To determine the cost-effectiveness of (i) handheld narrowband ultraviolet B (NB-UVB) and (ii) a combination of topical corticosteroid (TCS) and NB-UVB compared with TCS alone for localized vitiligo.

METHODS

Cost-effectiveness analysis alongside a pragmatic, three-arm, placebo-controlled randomized controlled trial with 9 months' treatment. In total 517 adults and children (aged ≥ 5 years) with active vitiligo affecting < 10% of skin were recruited from secondary care and the community and were randomized 1: 1: 1 to receive TCS, NB-UVB or both. Cost per successful treatment (measured on the Vitiligo Noticeability Scale) was estimated. Secondary cost-utility analyses measured quality-adjusted life-years using the EuroQol 5 Dimensions 5 Levels for those aged ≥ 11 years and the Child Health Utility 9D for those aged 5 to < 18 years. The trial was registered with number ISRCTN17160087 on 8 January 2015.

RESULTS

The mean ± SD cost per participant was £775 ± 83·7 for NB-UVB, £813 ± 111.4 for combination treatment and £600 ± 96·2 for TCS. In analyses adjusted for age and target patch location, the incremental difference in cost for combination treatment compared with TCS was £211 (95% confidence interval 188-235), corresponding to a risk difference of 10·9% (number needed to treat = 9). The incremental cost was £1932 per successful treatment. The incremental difference in cost for NB-UVB compared with TCS was £173 (95% confidence interval 151-196), with a risk difference of 5·2% (number needed to treat = 19). The incremental cost was £3336 per successful treatment.

CONCLUSIONS

Combination treatment, compared with TCS alone, has a lower incremental cost per additional successful treatment than NB-UVB only. Combination treatment would be considered cost-effective if decision makers are willing to pay £1932 per additional treatment success.

Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)

Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment.

Convolutional Neural Network-Based Automated Segmentation of the Spinal Cord and Contusion Injury: Deep Learning Biomarker Correlates of Motor Impairment in Acute Spinal Cord Injury

BACKGROUND AND PURPOSE

Our aim was to use 2D convolutional neural networks for automatic segmentation of the spinal cord and traumatic contusion injury from axial T2-weighted MR imaging in a cohort of patients with acute spinal cord injury.

MATERIALS AND METHODS

Forty-seven patients who underwent 3T MR imaging within 24 hours of spinal cord injury were included. We developed an image-analysis pipeline integrating 2D convolutional neural networks for whole spinal cord and intramedullary spinal cord lesion segmentation. Linear mixed modeling was used to compare test segmentation results between our spinal cord injury convolutional neural network (Brain and Spinal Cord Injury Center segmentation) and current state-of-the-art methods. Volumes of segmented lesions were then used in a linear regression analysis to determine associations with motor scores.

RESULTS

Compared with manual labeling, the average test set Dice coefficient for the Brain and Spinal Cord Injury Center segmentation model was 0.93 for spinal cord segmentation versus 0.80 for PropSeg and 0.90 for DeepSeg (both components of the Spinal Cord Toolbox). Linear mixed modeling showed a significant difference between Brain and Spinal Cord Injury Center segmentation compared with PropSeg (P < .001) and DeepSeg (P < .05). Brain and Spinal Cord Injury Center segmentation showed significantly better adaptability to damaged areas compared with PropSeg (P < .001) and DeepSeg (P < .02). The contusion injury volumes based on automated segmentation were significantly associated with motor scores at admission (P = .002) and discharge (P = .009).

CONCLUSIONS

Brain and Spinal Cord Injury Center segmentation of the spinal cord compares favorably with available segmentation tools in a population with acute spinal cord injury. Volumes of injury derived from automated lesion segmentation with Brain and Spinal Cord Injury Center segmentation correlate with measures of motor impairment in the acute phase. Targeted convolutional neural network training in acute spinal cord injury enhances algorithm performance for this patient population and provides clinically relevant metrics of cord injury.

Congenital bilateral anterior nasal atresia in 16 half-sibling Holstein-Friesian calves

CASE REPORT

Cases of bilateral anterior nasal atresia, sometimes referred to as arhinia or partial arhinia, are extremely rare in cattle and have only been reported as single events. This report describes the birth of 16 Holstein Friesian calves over a 3-month period, all affected with bilateral atresia of the nares and anterior nasal cavity, with 2 calves having additional severe deviation of the nasomaxillary bones and nasal septum. One affected calf was born with an anatomically normal twin. Parentage testing demonstrated that a single Holstein Friesian bull sired all cases tested.

CONCLUSION

This is the first report of multiple cases of bilateral anterior nasal atresia in cattle with evidence that demonstrates a heritable condition.

Unravelling complexity in seagrass systems for management: Australia as a microcosm

Environmental decision-making applies transdisciplinary knowledge to deliver optimal outcomes. Here we synthesise various aspects of seagrass ecology to aid environmental decision-making, management and policy. Managers often mediate conflicting values and opinions held by different stakeholders. Critical to this role is understanding the drivers for change, effects of management actions and societal benefits. We use the diversity of seagrass habitats in Australia to demonstrate that knowledge from numerous fields is required to understand seagrass condition and resilience. Managers are often time poor and need access to synthesised assessments, commonly referred to as narratives. However, there is no single narrative for management of seagrass habitats in Australia, due to the diversity of seagrass meadows and dominant pressures. To assist the manager, we developed a classification structure based on attributes of seagrass life history, habitat and meadow form. Seagrass communities are formed from species whose life history strategies can be described as colonising, opportunistic or persistent. They occupy habitats defined by the range and variability of their abiotic environment. This results in seagrass meadows that are either transitory or enduring. Transitory meadows may come and go and able to re-establish from complete loss through sexual reproduction. Enduring meadows may fluctuate in biomass but maintain a presence by resisting pressures across multiple scales. This contrast reflects the interaction between the spatial and temporal aspects of species life history and habitat variability. Most management and monitoring strategies in place today favour enduring seagrasses. We adopt a functional classification of seagrass habitats based on modes of resilience to inform management for all seagrass communities. These concepts have world-wide relevance as the Australian case-studies have many analogues throughout the world. Additionally, the approach used to classify primary scientific knowledge into synthesised categories to aid management has value for many other disciplines interfacing with environmental decision-making.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5-20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

Improving medication adherence in rheumatoid arthritis (RA): a pilot study

The aim of this exploratory pilot study was to adapt a psychological intervention to improve adherence to medication for patients with rheumatoid arthritis (RA). The approach draws on cognitive behavioural therapy (CBT) techniques, including motivational interviewing . The current study aimed to (i) adapt the intervention for patients with RA, (ii) assess its effectiveness in improving adherence to medication and (iii) evaluate patients' experience of the intervention. Participants were randomly allocated to either the 'intervention group' (N  =  10), receiving up to six weekly sessions of 'Compliance Therapy', or to the 'wait-list control' group (N  =  8), who received standard care. Data was collected pre intervention (baseline), post intervention and at six weeks post intervention (follow-up). Eighteen female participants with a mean age of 48.78 years (SD 15.12) took part in the study. Comparisons across the two time points for each group found that only those in the 'intervention' group demonstrated significant improvement in mean scores on adherence measures. Between-group comparisons were not significant. The pilot study suggests that an intervention based on CBT may improve adherence in patients with RA, but further research is required.

The effects of different component response requirements in multiple and concurrent schedules

Six pigeons were trained on multiple and concurrent schedules. The reinforcement rates were varied systematically (a) when lever pressing was required in one component and key pecking in the successive component; (b) when lever pressing was required in both multiple components; (c) when key pecking was required in both multiple components; and (d) when key pecking was required on one schedule and lever pressing was required on the concurrently-available schedule. Only the absolute level of responding was changed by different response requirements. Analyzed by the generalized matching law, performance under different response requirements resulted in a bias toward key pecking, and the measured response bias was the same in multiple and concurrent schedule arrangements. The bias in time measures obtained from concurrent schedule performance was reliably smaller than the obtained response biases. The sensitivity to reinforcement-rate changes was ordered: concurrent key-lever; multiple key-key; multiple lever-key; and, the least sensitive, multiple lever-lever. The results confirm that requirements of different topographical responses can be handled by the generalized matching law mainly in the bias parameter, but problems for this type of analysis may be caused by the changing sensitivity to reinforcement in multiple schedule performance as response requirements are changed.

Phylogeographic structure of brown trout Salmo trutta in Britain and Ireland: glacial refugia, postglacial colonization and origins of sympatric populations

The phylogeographical structure of brown trout Salmo trutta in Britain and Ireland was studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of four mitochondrial DNA segments (16S/ND1, ND5/6, COXIII/ND5 and ND5/12S). Analysis of 3636 individuals from 83 sites-morphotypes revealed a total of 25 haplotypes. These haplotypes were nested in seven two-step clades. Although there was a clear geographical patterning to the occurrence of derived clades, admixture among ancestral clades was extensive throughout the studied area. A relevant feature of the data was that some populations contained mixtures of highly divergent clades. This type II phylogeographic pattern is uncommon in nature. Clade intermixing is likely to have taken place during earlier interglacials as well as since the Last Glacial Maximum. The anadromous life history of many S. trutta populations has probably also contributed to clade mixing. Based on the data presented here and published data, postglacial colonization of Britain and Ireland most likely involved S. trutta from at least five potential glacial refuges. Probable locations for such refugia were: south of England-western France, east of the Baltic Sea, western Ireland, Celtic Sea and North Sea. Ferox S. trutta, as defined by their longevity, late maturation and piscivory, exhibited a strong association with a particular clade indicating that they share a common ancestor. Current evidence indicates that the Lough Melvin gillaroo S. trutta and sonaghen S. trutta sympatric types diverged prior to colonization of Lough Melvin and, although limited gene flow has occurred since secondary contact, they have remained largely reproductively isolated due to inlet and outlet river spawning segregation. Gillaroo S. trutta may reflect descendents of a previously more widespread lineage that has declined due to habitat alterations particularly affecting outlet rivers. The mosaic-like distribution of mtDNA lineages means that conservation prioritization in Britain and Ireland should be based on the biological characteristics of local populations rather than solely on evolutionary lineages.

A Novel Tumour-Based Test To Identify Breast Cancer Due to BRCA1 and BRCA2 Mutations

Background: Family history and young onset are the usual indicators of an underlying genetic predisposition to breast cancer development. BRCA1 associated breast tumours are more likely to be ER negative and express “basal” markers, however most patients with ER negative/ basal marker positive breast cancers (especially young onset) do not have inherited BRCA1 mutations. BRCA1 and BRCA2 gene carriers may have novel treatment options available and may need to consider future cancer prevention strategies. Genetic counselling and germline mutation analysis remains a relatively expensive option that is not appropriate for most breast cancer patients.Aim: To design a sensitive and specific pathology based predictor that would improve identification of BRCA1 and 2 gene carriers.Method: We assembled a training panel of breast cancer tumour blocks from 67 BRCA1, 71 BRCA2 associated and 105 sporadic young onset cases (≤ 40 years at diagnosis). All gene carriers were diagnosed before 50 years and were matched to sporadic cases for ER status. Tissue micro arrays (TMAs) were assembled and subjected to immunohistochemical analysis with a panel of 18 antibodies. DNA was extracted from micro dissected tumour tissue and matched patient lymphocytes and subjected to high resolution tiling path microarray-based Comparative Genomic Hybridisation (aCGH). Using robust statistical approaches, regions significantly differentially lost, gained or amplified in BRCA1, BRCA2 and controls were identified. Probes for chromogenic in situ hybridisation (CISH) for amplified regions were generated.Results: Two differentially amplified clones in BRCA1 cases designated P1 at 3q25.31 and P2 at 3q25.2 and one in BRCA2 cases, P3 at 20q13.13, were identified and amplifications validated in the training set using CISH. Logistic regression analysis of the panel comprising CISH and IHC markers was used to develop the best predictor. The best predictor for BRCA1 gene carriers was a combination of P1, ER and HER2. This combination outperformed all combinations of immunohistochemical markers, including ER and basal markers; the Positive Predictive Value (PPV) was 87.5% and NPV 92% giving a Receiver Operator Characteristic (ROC) curve with an AUC of 0.92 (CI 0.88-0.97). The BRCA2 signature panel is currently being evaluated. These BRCA1 and BRCA2 predictor panels are being validated in a new set of TMAs comprising 223 tumours from the POSH study1.Conclusion: This tumour based predictor for BRCA1 and BRCA2 carriers may prove useful to identify gene carriers at low a priori chance of having a mutation, to direct BRCA1/2 targeted treatment approaches and to identify familial non BRCA1/2 cases that may be suitable for new gene discovery studies.1. Eccles D et al. BMC Cancer 2007; 7(1):160.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5032.

Myoglobin polymorphism in the pollan (Osteichthyes: Coregoninae)

Three electrophoretically separable phenotypes of heart and lateral line muscle myoglobin were found in the Irish pollan (Coregonus pollan). This polymorphism appears to be under the control of two co-dominant alleles. The allele frequencies were found to be virtually identical in samples from two lakes which have probably been isolated since the close of the last Ice Age. A significant excess of heterozygotes was found in samples from both lakes. This myoglobin polymorphism appears to be balanced, maintained due to heterozygote superiority.

TWIST1 and PITX2 expression in bone marrow of women with clinical stage II/III breast cancer identifies patients at risk for the development of early metastatic disease

Abstract #108

Background: The presence of disseminated tumor cells (DTCs) in bone marrow of women with newly diagnosed breast cancer has been associated with increased risk of recurrent disease development. We have previously described a 67-gene signature associated with the presence of DTCs using gene array analysis after immunomagnetic enrichment of these cells and found that the expression of one of the 67-genes in bone marrow of breast cancer patients, TWIST1, correlated with the development of early recurrent disease. We have now tested the remaining genes in the 67-gene signature for correlation with the development of recurrent disease. Our goal is to identify genes associated with DTCs with high metastatic potential for early detection and intervention.&#x2028; Methods: Expression of each of the 67 genes was analyzed using qRT-PCR in a breast cancer cell lines (MCF7, SKBR3, MDA/MB 231) diluted into normal human bone marrow at varying concentrations. Levels of expression in the breast cancer cells and in human bone marrow were quantitated. Genes with high expression in breast cancer cell lines and no observed expression in normal human bone marrow were further tested by qRT-PCR for expression in a validation set of bone marrows comprised of 50 specimens collected from 30 patients with clinical stage II/III breast cancer prior to any treatment. Thirteen of these patients developed recurrent disease within 16 months.&#x2028; Results: Within the 67 gene signature, 5 genes were identified that were highly expressed in breast cancer cell lines and had no detectable expression in normal human bone marrow. Expression of the 5 genes as well as keratin 19 were examined in the validation set of bone marrows. PITX2 was expressed in the bone marrow of 5 of the 13 patients who recurred within one year. Only expression of TWIST1 and PITX2 were found to correlate with the time to development of early recurrent disease (p &lt;0.0001 and 0.0002 respectively).&#x2028; Conclusion: We have found that the expression of TWIST1 and PITX2 in the bone marrow of breast cancer patients prior to any treatment identifies patients at risk of early distant disease recurrence. These genes are not expressed in normal human bone marrow. Both are transcription factors involved in the embryonic development and appear to be expressed by DTCs with high metastatic potential. Expression of TWIST1 and PITX2 may prove to be excellent markers for identifying women at high risk for distant relapse and lead to new targets for chemotherapeutic intervention.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 108.

Identification of complex shapes using a self organizing neural system

We present a multilayer hierarchical neural system for automatic classification of complex contour patterns. The system consists of a neocognitron-like network structure combined with self-organizing maps to automatically determine feature classes. We present results showing that multilayer hierarchical networks are able to tolerate pattern distortion considerably better than standard neural network implementations.

A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.

Anal and dry sex in commercial sex work, and relation to risk for sexually transmitted infections and HIV in Meru, Kenya

OBJECTIVE

To examine the practices of anal intercourse and dry sex within a cohort of female sex workers (FSWs) in Kenya, focusing on the prevalence and perceived risk of the practices, demographic and behavioural correlates, and association with sexually transmitted infections (STI).

METHODS

A survey was conducted among FSWs in Meru, Kenya, with 147 participants randomly sampled from an existing cohort of self identified FSWs.

RESULTS

40.8% of participants reported ever practising anal intercourse and 36.1% reported ever practising dry sex. Although the majority of women surveyed believed anal intercourse and dry sex to be high risk practices for HIV infection compared with vaginal sex, about one third of women reported never or rarely using condoms during anal intercourse, and about 20% never or rarely using condoms during dry sex. Reported consistent condom use was lower with both of these practices than with penile-vaginal intercourse. Anal intercourse was associated with experience of recent forced sexual intercourse, while dry sex was not. Anal intercourse was almost always initiated by clients, whereas dry sex was likely to be initiated by the women themselves. Sex workers reported charging higher fees for both practices than for vaginal intercourse. Both practices were associated with reported symptoms and diagnoses of STI.

CONCLUSIONS

Both anal intercourse and dry sex were common in this sample, and although perceived as high risk practices, were not adequately protected with condom use. Education and other interventions regarding these high risk sexual behaviours need to be translated into safer practices, particularly consistent condom use, even in the face of financial vulnerability.

Quality of health care and its effects in the utilisation of maternal and child health services in Kenya

OBJECTIVE

To assess the quality of care provided by the Kisumu Municipal health facilities, with special reference to Maternal and Child health services (MCH).

DESIGN

A descriptive cross-sectional survey.

SETTING

Kisumu Municipal Health facilities.

SUBJECTS

Four hundred and eighty two mothers were interviewed in a household survey.

RESULTS

A total of 482 mothers were interviewed in the household survey. Out of these, only 40.4%, 53.7% and 45.7% had respectively used Municipal facilities for antenatal services (ANC), immunisation and treatment of their children the last time they required such a service. This translates to by-pass rates for Municipal health facilities of 59.5%, 46.3% and 54.3% respectively for the three services. By-pass was higher for the more central urban catchment areas than the more peripheral ones, a finding that was associated with the socio-economic status of the respondents and the relative location of the municipal facilities vis-a-vis competing facilities, mainly the District and Provincial hospitals. The main reasons cited for by-pass were poor care (21%), lack of drugs and supplies (17%) and lack of/poor laboratory services (12%). From the facility audit, most of the clinics had a reasonable capacity to offer basic health care with only three scoring less than 50% in the scale used. The worst areas were in availability of drugs, equipment and management issues. There was a strong relationship between the perceived quality of care and utilisation of MCH services as well as by-pass. The capacity of the facilities to offer care was however not associated with utilisation of MCH services or by-pass.

CONCLUSION

There is under-utilisation of Municipal health facilities for MCH services. This is related to the perceived poor quality of care in the facilities. Perception of quality is influenced by a person's socio-economic status especially education.

Neurobehavioral effects of treatment for opiate withdrawal

A partially randomised, controlled trial was performed to test the hypothesis that opiate exposed infants treated with diluted tincture of opium (DTO) and phenobarbital would have better neurobehavioral scores than infants treated with DTO alone. Compared with those treated with DTO alone (n = 15), infants treated with DTO and phenobarbital (n = 17) were more interactive, had smoother movements, were easier to handle, and less stressed. Dual treatment results in improved neurobehavioral organisation during the first three weeks of life, which may indicate a more rapid recovery from opiate withdrawal.

Sexual patterning and condom use among a group of HIV vulnerable men in Thika, Kenya

BACKGROUND/AIM

A composite sample of 37 peer educators and 215 members of self help groups of male informal sector workers in Thika, Kenya, targeting HIV/AIDS prevention, were interviewed about their sexual behaviour, using a customised template, as part of a broader survey on gender attitudes and peer pressure.

METHOD

Details on each sexual partner reported by each man over a 12 month recall period included type of partner, months during which sexual relations took place, and condom use.

RESULTS

The men reported 471 sexual partners over the recall period, with a range of 0-16 partners, and an average of just under two partners. 8% of men had had no sexual partner, half were monogamous, and 3% had multiple partners with whom they used condoms exclusively, leaving 39% at varying degrees of risk. Condom use increased significantly with reduced intimacy of partner. 16% of men reported having at least one liaison with a female sex worker and two thirds of such liaisons were exclusively protected by condom use. Younger, single men had significantly more partners, but were more likely to use condoms. Duration of membership in self help groups was strongly associated with exclusive use of condoms with casual or FSW partners. Recorded attitudes corresponded somewhat with practice, but the data showed large gaps between the two, and low levels of gender sensitivity.

CONCLUSION

There is some evidence that group membership has resulted in increased condom use and partner reduction, but there are doubts as to the extent to which the "ABC" strategy can be successful in stemming the HIV/AIDS epidemic. It may be necessary for interventions to target contextual issues, particularly gender relations, if the approach is to be more successful.