309 Does Anaesthetic Type Effect Positive Excision Margin Rate for Non-Melanoma Skin Cancers?

Aim

Australia has the highest incidence of Non-melanoma skin cancers (NMSC) in the world estimated to be 2448/100,000 population with the state of Queensland carrying the highest burden. Surgical excision is the primary treatment and makes up a large proportion of general surgical lists in regional Queensland where they are typically removed using either local anaesthetic (LA) alone, local anaesthetic and sedation (LAS), or general anaesthesia (GA). There is little in the literature to suggest if anaesthetic type effects the rate of involved margins. The purpose of this study is to establish if anaesthetic type impacts the rate of positive excision margins in regional hospitals in Queensland.

Method

A retrospective audit was performed, incorporating a total of 194 squamous and basal cell carcinoma lesions excised between October 2019 and October 2020 at two hospitals in regional Australia. Data was recorded for the type of anaesthetic used and the histopathology of the lesions including type of lesion and microscopic margin involvement.

Results

Of the 194 excised lesions 39 of them had involved margins (20.1%). The rate of involved margins under LA, GA and LAS were found to be 19.79%, 18.52% and 22.73% respectively. When comparing these modalities with each other: LA vs GA, LAS vs GA and LA vs LAS no significant difference was found in involved margins for excision of NMSC with p-values (<0.05) of 1, 0.624 and 0.8225 respectively.

Conclusions

Modality of anaesthetic used for excision of NMSC does not affect the outcome of margin involvement.

310 Cost Savings Through Utilisation Of Procedural Clinics Over Operating Theatres for Skin Lesion Excisions

Aim

Skin lesion excisions make up a significant proportion of procedures performed by General Surgical teams. A large proportion are performed under local anaesthetic (LA) alone and are frequently performed in a main operating theatre (OT) but would be amenable to been performed in a minor procedures clinic (MPC) which could represent significant savings for excision of lesions in terms of money and better utilisation of OT. The purpose of this study is to evaluate the proportion of skin lesions currently excised under LA in OT that would be amenable to been performed in MPC and calculating the cost saving associated with this in terms of dollars and time in OT.

Method

A retrospective audit was performed of all skin lesion excised in OT at 2 regional hospitals in Queensland between October 2019 and October 2020. Data was recorded for the type of anaesthetic used, type of lesion excised and total time each patient spent in the OT. Cost per minute of both OT and MPC time were estimated using standard costs.

Results

A total of 229 patients had skin lesions excised in an OT in this period. Of these, 102 (44.5%) of them were excised under LA alone and used 4930 minutes of OT time. The dollar saving of performing these procedures in a MPC over OT is estimated to be $147,874.00 (approximately 71% less).

Conclusions

Utilising MPC over an OT for excision of skin lesions under LA represents a significant dollar cost saving and opportunity cost saving.

P–154 The role of the X Chromosome in early human embryo metabolism

Study question

What role does the X chromosome play in early embryo metabolism? Does X chromosome copy number contribute to sex differences in early embryonic metabolism?

Summary answer

Chromosome X contains several metabolism-related genes that are expressed prior to X-inactivation, suggesting that their dosage plays a role in sex-biased regulation of embryo metabolism.

What is known already

Published reports indicate that sex differences in preimplantation embryo metabolism exist across mammalian species, including humans. Two observations supporting this are that male embryos reach blastocyst stage earlier than their female counterparts, and that glucose uptake and processing is thought to be higher in female compared to male embryos. It has been hypothesized that these differences reflect the location of the metabolism gene G6PD, the rate limiting enzyme in the Pentose Phosphate Pathway, on Chromosome X.

Study design, size, duration

This study is a reanalysis of publicly available RNA-seq data, including 1176 single cells from 59 blastocysts (24 E5, 18 E6, 17 E7) published in one study (Petropoulos et al 2016).

Participants/materials, setting, methods

Cells were subjected to a digital karyotype inference algorithm and aneuploid samples were removed from the dataset. Sex differential gene expression analyses (DE) were then performed in euploid trophectoderm cells (TE; 233 XY from 16 embryos and 180 XX cells from 12 embryos). Cell numbers from ICM were too sparse to compare.

Main results and the role of chance

Analysis of XX and XY TE revealed 618 significantly differentially expressed genes (DEGs; 507 upregulated in XX cells, and 111 upregulated in XY cells). These genes are spread across autosomes and sex chromosomes. Interestingly, G6PD is not significantly more highly expressed in XX cells.

Gene Ontology (GO) analysis of the XX-biased DEGs revealed a transcriptional sex bias in metabolism-related GO categories, including “mitochondrial ATP synthesis coupled electron transport”, and “respiratory chain complex I”.

Gene-level assessment revealed that the drivers of these enrichments are spread across the genome, but 28/64 reside on Chromosome X (hypergeometric p-value = 5.984473e–27), including NDUFA1, NDUFB11, and COX7B (components of the electron transport chain), and SLC25A5 (an ATP/ADP transporter involved in maintaining mitochondrial membrane potential). This indicates a direct role for multiple X-linked genes in sex-biased regulation of embryo metabolism.

Metabolic genes that are not sex-biased are distributed across the genome, with no significant enrichment on Chromosome X (76/266, hypergeometric p-value=0.607). Together, these data indicate that GO metabolic term X enrichment is a feature of sex-biased expression and not due to an accumulation of metabolism-related genes on the X.

Limitations, reasons for caution

This analysis draws on publicly available data, and thus we are unable to perform orthogonal validation of karyotype calls. Additionally, while the initial dataset is large, the quality-filtered dataset (euploid XX and XY TE) is small, and single cell data is infamously variable. Further data collection is required.

Wider implications of the findings: Our analysis of sex-biased gene expression in early human embryos suggests a more important role for the X chromosome in modulating sex biases in early embryo metabolism than previously recognized. This study provides insight into the mechanisms underlying the development of metabolic sex differences throughout the lifespan.

Trial registration number

NA

POS0303 PREVENTION OF CHRONIC DISEASES DUE TO INFLAMMATION IN INFLAMMATORY ARTHRITIS: RESULTS OF A DELPHI PROCESS TO SELECT CARE RECOMMENDATIONS FOR AN ELECTRONIC MEDICAL RECORD (EMR) INTERVENTION

Background:

Inflammatory arthritis (IA) predisposes patients to several chronic conditions including cardiovascular diseases (CVD), diabetes (DM), osteoporosis (OP) and infections, likely due to systemic effects of inflammation. Studies have found that patients with IA often receive suboptimal care for screening and managing these conditions.

Objectives:

This is the first phase of a study which will develop and pilot test automated EMR reminders for family physicians. The reminders will prompt family physicians to screen for and address risk factors for these conditions. We conducted a Delphi process to select care recommendations to be addressed by the EMR reminders.

Methods:

We conducted a review of current BC, Canadian and international guidelines for screening and addressing risk factors for CVD, DM, OP and infection. A list of 22 care recommendations, including their level of evidence and risks/benefits of implementation, was reviewed by a panel of six family physicians, three rheumatologists and three IA patients, in a three-round online modified Delphi process. Panelists rated each care recommendation, using 9-point scales, on 1) their clinical importance, 2) their likelihood of improving outcomes, and 3) implementation feasibility. Results were discussed in an online forum. Panelists then rated slightly revised care recommendations, modified based on feedback from the discussion. Care recommendations were retained if the median rating was ≥7 with no disagreement as defined by the RAND/UCLA Method handbook.

Results:

A list of 15 care recommendations was selected by the Delphi process for EMR integration, including recommendations that address CVD risk assessment (1), hypertension screening (1), DM screening (2), fracture risk assessment (1), BMD testing (1), osteoporosis prevention (1) and treatment (1) with bisphosphonates, preventing infections through immunization (2), minimizing steroids (1) and hepatitis screening (1), screening for hydroxychloroquine retinal toxicity (1), and counselling for lifestyle modifications (2). We excluded 7 recommendations which addressed lipid testing (1), BMD testing in steroid users (1), immunizations (2), weight management (1), and DMARD laboratory test monitoring (2). Recommendations were excluded on the basis of importance (1) or feasibility (6).

Conclusion:

The results of the Delphi process will inform the development of reminders, integrated in EMRs, that will support family physicians in their efforts to engage IA patients in addressing risk factors for chronic diseases related to inflammation. We hope to improve the prevention of these diseases, which represent an important cause of morbidity and mortality for people with inflammatory arthritis.

Acknowledgements:

Iman Sheriff’s work on this project was funded by the CRA summer studentship programme. Dr. Lacaille is supported by the Mary Pack Chair in Arthritis Research from UBC and The Arthritis Society of Canada. Thank you to all who participated in the Delphi survey.

Disclosure of Interests:

None declared

Prevalence of antibiotic resistance and virulence genes in the biofilms from an aquifer recharged with stormwater

An improved understanding of the diversity and composition of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with stormwater is essential to comprehend potential human health risks from water reuse. A high-throughput functional gene array was used to study the prevalence of ARGs and VGs in aquifer biofilms (n = 27) taken from three boreholes over three months. Bacterial genera annotated as opportunistic pathogens such as Aeromonas, Burkholderia, Pseudomonas, Shewanella, and Vibrio were ubiquitous and abundant in all biofilms. Bacteria from clinically relevant genera, Campylobacter, Enterobacter, Klebsiella, Mycobacterium, Mycoplasma, and Salmonella were detected in biofilms. The mean travel time of stormwater from the injection well to P1 and P3 boreholes was 260 and 360 days respectively. The presence of ARGs and VGs in the biofilms from these boreholes suggest a high spatial movement of ARGs and VGs in the aquifer. The ARGs with the highest abundance were small multidrug resistance efflux pumps (SMR) and multidrug efflux (Mex) followed by β-lactamase C genes. β- lactamase C encoding genes were primarily detected in Enterobacteriaceae, Pseudomonadaceae, Bacillaceae, and Rhodobacteraceae families. The VGs encoding siderophores, including aerobactin (iro and iuc genes), followed by pilin, hemolysin, and type III secretion were ubiquitous. Canonical correspondence analysis suggested that Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), turbidity, and Fe concentration has a significant impact on the microbial community structure of bacteria carrying ARGs and VGs. Post abstraction treatment of groundwater may be prudent to improve water security and reduce potential health risks.

Parathyroid hormone independently predicts fracture, vascular events, and death in patients with stage 3 and 4 chronic kidney disease

Doctors do not know whether treatment of high parathyroid hormone levels is linked to better outcomes in their patients with kidney disease. In this study, lower parathyroid hormone levels at baseline were linked to lower risk of fracture, vascular events, and death in people with kidney disease.

PURPOSE

Chronic kidney disease (CKD) affects ~ 20% of older adults, and secondary hyperparathyroidism (HPT) is a common condition in these patients. To what degree HPT predicts fractures, vascular events, and mortality in pre-dialysis CKD patients is debated. In stage 3 and 4 CKD patients, we assessed relationships between baseline serum PTH levels and subsequent 10-year probabilities of clinical fractures, vascular events, and death.

METHODS

We used Marshfield Clinic Health System electronic health records to analyze data from adult CKD patients receiving care between 1985 and 2013, and whose PTH was measured using a second-generation assay. Covariates included PTH, age, gender, tobacco use, vascular disease, diabetes, hypertension, hyperlipidemia, obesity, GFR, and use of osteoporosis medications.

RESULTS

Five thousand one hundred eight subjects had a mean age of 68 ± 17 years, 48% were men, and mean follow-up was 23 ± 10 years. Fractures, vascular events, and death occurred in 18%, 71%, and 56% of the cohort, respectively. In univariate and multivariate models, PTH was an independent predictor of fracture, vascular events, and death. The hazards of fracture, vascular events and death were minimized at a baseline PTH of 0, 69, and 58 pg/mL, respectively.

CONCLUSIONS

We found that among individuals with stage 3 and 4 CKD, PTH was an independent predictor of fractures, vascular events, and death. Additional epidemiologic studies are needed to confirm these findings. If a target PTH range can be confirmed, then randomized placebo-controlled trials will be needed to confirm that treating HPT reduces the risk of fracture, vascular events, and death.

Abstract OT3-03-01: Open-label, single-arm study evaluating the antitumor activity and safety of niraparib as neoadjuvant treatment in patients with localized, HER2-negative, BRCA-mutant breast cancer

Background: Neoadjuvant chemotherapy is administered to patients with operable breast cancer to downstage the tumor to allow for less extensive surgery and to provide prognostic information about drug efficacy and risk of disease recurrence. Patients who achieve a pathological complete response (pCR) following neoadjuvant treatment have a more favorable outcome than patients with residual invasive disease. Single-agent poly(ADP-ribose) polymerase (PARP) inhibitors have clinical efficacy in BRCA-mutated breast cancer. Niraparib, a potent and selective PARP1/2 inhibitor, is approved for maintenance treatment of patients with recurrent ovarian cancer and has demonstrated strong antitumor activity in in vivo studies with BRCA1-mutant breast cancer. The objective of this study is to evaluate the antitumor activity of single-agent niraparib in the neoadjuvant treatment of patients with localized, human epidermal growth factor receptor 2 (HER2)-negative, BRCAmut breast cancer.

Trial Design: This is an open-label, single-arm pilot study with a target enrollment of 20 evaluable patients. Eligible patients are those ≥18 years old with histologically-confirmed HER2-negative localized breast cancer and either a BRCA1 or BRCA2 mutation (germline or somatic) and no prior anti-cancer therapies for the current malignancy. Patients will receive 200 mg of oral niraparib once daily for 2 months, after which they may either proceed directly to surgery or receive chemotherapy at the discretion of the physician. The primary endpoint is tumor response rate based on the change in tumor volume as measured by breast MRI after 2 months of treatment with niraparib; a response is defined as ≥30% reduction of tumor volume from baseline. Secondary endpoints include pCR rate, tumor response rate based on the change in tumor volume as measured by breast ultrasound, and safety and tolerability. Data will be summarized in a descriptive nature by frequency distributions (number and percentage of patients) for categorical variables and by the mean, median, and standard deviation for continuous variables. Tumor response rate will be tabulated together with its 95% binomial exact confidence interval.

Funding: TESARO, Inc., Waltham, MA, USA sponsored the study.

Citation Format: Han H, Hamilton E, Irie H, Isakoff S, Jelovac D, Liem A, Liu MC, Milillo A, Nangia J, Page D, Reeves J, Santa-Maria C, Duncan M, Graham JR, Chen J, Dezube BJ, Spring L. Open-label, single-arm study evaluating the antitumor activity and safety of niraparib as neoadjuvant treatment in patients with localized, HER2-negative, BRCA-mutant breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT3-03-01.

The Patient Reported Outcomes, Burdens and Experiences (PROBE) Project: development and evaluation of a questionnaire assessing patient reported outcomes in people with haemophilia

Background

The interest of health care agencies, private payers and policy makers for patient-reported outcomes (PRO) is continuously increasing. There is a substantial need to improve capacity to collect and interpret relevant PRO data to support implementation of patient-centered research and optimal care in haemophilia. The Patient Reported Outcomes, Burdens and Experiences (PROBE) Project aims to develop a patient-led research network, to develop a standardized questionnaire to gather patient-reported outcomes and to perform a feasibility study of implementing the PROBE questionnaire.

Methods

A pilot questionnaire was developed using focus group methodology. Content and face validity were assessed by a pool of persons living with haemophilia (PWH) and content experts through interactive workshops. The PROBE questionnaire was translated with the forward-backward approach. PROBE recruited national haemophilia patient non-governmental organizations (NGOs) to administer the questionnaire to people with and without haemophilia. PROBE measured the time to complete the questionnaire and gathered feedback on its content and clarity; staff time and cost required to implement the questionnaire were also collected.

Results

The PROBE questionnaire is comprised of four major sections (demographic data, general health problems, haemophilia-related health problems and health-related quality of life using EQ-5D-5L and EQ-VAS). Seventeen NGOs participated in the pilot study of the PROBE Project, recruiting 656 participants. Of these, 71% completed the questionnaire within 15 min, and all participants completed within 30 min. The median total staff and volunteer time required for the NGOs to carry out the study within their country was 9 h (range 2 to 40 h). NGO costs ranged from $22.00 to $543.00 USD per country, with printing and postage being the most commonly reported expenditures.

Conclusions

The PROBE questionnaire assesses patient-important reported outcomes in PWH and control participants, with a demonstrated short completion time. PROBE proved the feasibility to engage diverse patient communities in the structured generation of real-world outcome research at all stages.

Trial registration

Trial registration: NCT02439710.

Electronic supplementary material

The online version of this article (10.1186/s40814-018-0253-0) contains supplementary material, which is available to authorized users.

Abstract P5-05-02: A laboratory/machine learning based comparative genetics model accurately predicts breast cancer in a human cohort

Inherited genetic variants are estimated to account for 30-35% of overall breast cancer risk. A few rare, highly penetrant, genetic determinants of risk in humans have been well defined. However, the actions of many common weakly penetrant breast cancer risk loci remain uncharacterized. Additionally, it is well established that endocrine factors in general, and estrogens in particular, influence breast cancer etiology. We are using the ACI rat model of 17β-estradiol (E2)-induced mammary cancer to parse the contributions of individual genetic risk variants to breast cancer susceptibility in a physiologically relevant context. ACI females develop mammary carcinomas at an incidence approaching 100% when exposed to physiological levels of E2, and these carcinomas share many features with luminal-type breast cancers in humans. In contrast, Brown Norway (BN) rats are highly resistant to E2-induced mammary cancer. Linkage analyses of progeny from intercrosses between susceptible ACI and resistant BN rats led to the identification of multiple quantitative trait loci for E2-induced mammary cancer. One such locus, Estrogen-induced mammary cancer 4 (Emca4), is the focus of the current investigation. We generated a series of novel congenic rat strains which carry BN alleles at distinct regions of interest across the Emca4 locus, introgressed onto the ACI genetic background. Characterization of mammary cancer phenotypes in the congenic strains facilitated fine resolution mapping of the Emca4 locus. These studies revealed that Emca4 is a complex locus harboring at least four interacting genetic determinants of risk, designated Emca4.1 – Emca4.4, and is orthologous to the 8q24.21 breast cancer risk locus in humans. To assess the relevance of the rat genetic data to human populations, novel machine learning methods were employed to generate risk prediction models using data from a human cohort. Genotype data for 76 SNPs located in the regions of the human genome orthologous to Emca4.1 – 4.4 were obtained from the Cancer Genetics Markers of Susceptibility case control population. Models generated from this data set were optimized with novel algorithms to identify a subset of 16 variants that significantly influenced the risk models. The best model distinguished breast cancer cases from controls with a remarkably high degree of accuracy for a model based on genotype (AUC = 0.6, P < 10-11 relative to random guessing). It is worth noting that the predictive power of this model arose from interactions between human SNPs. Our data show that Emca4 is a complex locus containing multiple interacting determinants of risk; variants in the orthologous 8q24.21 breast cancer risk locus in human interact to influence breast cancer risk as predicted by the rat model; and accounting for interactions between variants achieves a predictive power beyond what is observed with individual SNPs. We have demonstrated, for the first time, the ability to develop a multi-component genetic model in rats and test it in a human population. This illustrates the power of the rat model to elucidate the complex mechanisms through which common, weakly penetrant variants influence breast cancer risk in humans.

Citation Format: Dennison KL, Chack A, Escanilla NS, Page D, Shull JD. A laboratory/machine learning based comparative genetics model accurately predicts breast cancer in a human cohort [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-05-02.

Abstract OT1-01-05: Phase 1b/2 study of intratumoral Ad-RTS-hIL-12 + veledimex in patients with chemotherapy-responsive locally advanced or metastatic breast cancer

Background: Immune-based strategies involving T-cell activation have recently shown significant activity in multiple tumor types. The presence of immune elements in breast cancers has prognostic and predictive impact. Thus, strategies that optimize the interplay between a breast cancer and the effected individual's immune system may be therapeutic. Interleukin-12 (IL-12), a pro-inflammatory cytokine, reverses immune escape mechanisms induced by myeloid derived suppressor and dendritic cells which, in turn, improves the function of activated CD8+ T cells and promotes tumor stroma collapse. Because tumor neoantigens may be generated in response to chemotherapy, IL12-mediated immune modulation may be optimal in patients with chemotherapy-sensitive metastatic breast cancer. Ad-RTS-hIL-12 (Ad) is a novel gene therapy candidate expressing IL-12 under the control of an orally-administered activator ligand, veledimex (V) through the proprietary RheoSwitch Therapeutic System® (RTS).

Trial Design: Open-label, phase 1b/2, single-arm, single-center study of Ad+V in women with stable or responsive disease after ≥ 12-weeks of 1st or 2nd-line chemotherapy. Eligible patients will be placed on chemotherapy-holiday and enter the immunotherapy phase, consisting of a single cycle of Ad administered intratumorally (Day 1), along with V (80 mg QDx7). HER2-directed antibody therapy may be continued during the immunotherapy phase for women with HER2- disease.

Key Eligibility Criteria: Women ≥18 years with histologically-confirmed locally advanced or metastatic breast cancer of any subtype who have achieved a partial response (PR) or stable disease (SD) to 1st or 2nd-line chemotherapy are eligible. Exclusion criteria include use of immunosuppressive drugs, compromised immune function, autoimmune disorder, or brain metastases.

Specific Aims: To evaluate the safety and tolerability of Ad+V immunotherapy in eligible women. Secondary endpoints include 12 week overall response rate, 12 week disease control rate and the impact of treatment on exploratory immune biomarkers.

Statistical Methods: Safety and efficacy will be evaluated separately for HER2-/HER2+ patients. Tumor response will be evaluated by RECIST v1.1 at 6 and 12 weeks. To ensure safety, stopping rules defined by grade 3/4 adverse events and12-week progression rate were adopted.

Target Accrual: Up to 40 patients, including up to 8 patients (20%) with HER2+ disease.

Summary: Ad+V is a novel gene therapy which controls local expression of IL-12 and may induce tumor stroma collapse and stimulation of an anti-cancer T cell immune response. The ability to regulate the production of IL-12 by modulating V dosing may result in an improved therapeutic index in combination with standard of care. The data from this study will directly inform future studies.

Study Contact (Clinical Trials.gov: NCT02423902).

Citation Format: McArthur HL, Page D, Proverbs-Singh T, Solomon S, Hudis C, Norton L, Patil S, Barrett JA, Lebel F. Phase 1b/2 study of intratumoral Ad-RTS-hIL-12 + veledimex in patients with chemotherapy-responsive locally advanced or metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT1-01-05.

Pathogen Decay during Managed Aquifer Recharge at Four Sites with Different Geochemical Characteristics and Recharge Water Sources

Recycling of stormwater water and treated effluent via managed aquifer recharge (MAR) has often been hampered because of perceptions of low microbiological quality of recovered water and associated health risks. The goal of this study was to assess the removal of selected pathogens in four large-scale MAR schemes and to determine the influence of aquifer characteristics, geochemistry, and type of recharge water on the pathogen survival times. Bacterial pathogens tested in this study had the shortest one log removal time (, <3 d), followed by oocysts (, <120 d), with enteric viruses having the biggest variability in removal times (, 18 to >200 d). Human adenovirus and rotavirus were relatively persistent under anaerobic conditions (, >200 d). Human adenovirus survived longer than all the other enteric virus tested in the study and hence could be used as a conservative indicator for virus removal in groundwater during MAR. The results suggest that site-specific subsurface conditions such as groundwater chemistry can have considerable influence on the decay rates of enteric pathogens and that viruses are likely to be the critical pathogens from a public health perspective.

A PheWAS approach in studying HLA-DRB1*1501

HLA-DRB1 codes for a major histocompatibility complex class II cell surface receptor. Genetic variants in and around this gene have been linked to numerous autoimmune diseases. Most notably, an association between HLA-DRB1*1501 haplotype and multiple sclerosis (MS) has been defined. Utilizing electronic health records and 4235 individuals within Marshfield Clinic's Personalized Medicine Research Project, a reverse genetic screen coined phenome-wide association study (PheWAS) tested association of rs3135388 genotype (tagging HLA-DRB1*1501) with 4841 phenotypes. As expected, HLA-DRB1*1501 was associated with MS (International Classification of Disease version 9-CM (ICD9) 340, P=0.023), whereas the strongest association was with alcohol-induced cirrhosis of the liver (ICD9 571.2, P=0.00011). HLA-DRB1*1501 also demonstrated association with erythematous conditions (ICD9 695, P=0.0054) and benign neoplasms of the respiratory and intrathoracic organs (ICD9 212, P=0.042), replicating previous findings. This study not only builds on the feasibility/utility of the PheWAS approach, represents the first external validation of a PheWAS, but may also demonstrate the complex etiologies associated with the HLA-DRB1*1501 loci.

Microbiological risks of recycling urban stormwater via aquifers

With the release of the Australian Guidelines for Water Recycling: Managed Aquifer Recharge (MAR), aquifers are now being included as a treatment barrier when assessing risk of recycled water systems. A MAR research site recharging urban stormwater in a confined aquifer was used in conjunction with a Quantitative Microbial Risk Assessment to assess the microbial pathogen risk in the recovered water for different end uses. The assessment involved undertaking a detailed assessment of the treatment steps and exposure controls, including the aquifer, to achieve the microbial health-based targets.

Integrating machine learning and physician knowledge to improve the accuracy of breast biopsy

In this work we show that combining physician rules and machine learned rules may improve the performance of a classifier that predicts whether a breast cancer is missed on percutaneous, image-guided breast core needle biopsy (subsequently referred to as "breast core biopsy"). Specifically, we show how advice in the form of logical rules, derived by a sub-specialty, i.e. fellowship trained breast radiologists (subsequently referred to as "our physicians") can guide the search in an inductive logic programming system, and improve the performance of a learned classifier. Our dataset of 890 consecutive benign breast core biopsy results along with corresponding mammographic findings contains 94 cases that were deemed non-definitive by a multidisciplinary panel of physicians, from which 15 were upgraded to malignant disease at surgery. Our goal is to predict upgrade prospectively and avoid surgery in women who do not have breast cancer. Our results, some of which trended toward significance, show evidence that inductive logic programming may produce better results for this task than traditional propositional algorithms with default parameters. Moreover, we show that adding knowledge from our physicians into the learning process may improve the performance of the learned classifier trained only on data.

Protective proteins are differentially expressed in tomato genotypes differing for their tolerance to low-temperature storage

When stored at low temperature, tomato fruits exhibit chilling injury symptoms, such as rubbery texture and irregular ripening. To identify proteins related to chilling tolerance, we compared two tomato near isogenic lines differing for their texture phenotype at harvest in a fruit-storage trial including two temperatures (4 and 20 degrees C) along several days of conservation. Fruit evolution was followed by assessing fruit color, ethylene emission and texture parameters. The most contrasted samples were submitted to proteomic analysis including two-dimensional electrophoresis and mass spectrometry of protein spots to identify the proteins, whose expression varied according to the genotype or the storage conditions. Unexpectedly, the most firm genotype at harvest was the most sensitive to cold storage. The other genotype exhibited a delay in fruit firmness loss leading to the texture differences observed after 20 days of 4 degrees C storage. The proteome analysis of these contrasted fruits identified 85 proteins whose quantities varied with temperature or genotype. As expected, cold storage decreased the expression of proteins related to maturation process, such as acidic invertase, possibly controlled post-translational regulation of polygalacturonase and up-regulated proteins related to freezing tolerance. However, the study point out proteins involved in the differential resistance to chilling conditions of the two lines. This includes specific isoforms among the large family of small heat shocked proteins, and a set of proteins involved in the defense against of the reticulum endoplasmic stress.

Managed aquifer recharge: rediscovering nature as a leading edge technology

Use of Managed Aquifer Recharge (MAR) has rapidly increased in Australia, USA, and Europe in recent years as an efficient means of recycling stormwater or treated sewage effluent for non-potable and indirect potable reuse in urban and rural areas. Yet aquifers have been relied on knowingly for water storage and unwittingly for water treatment for millennia. Hence if 'leading edge' is defined as 'the foremost part of a trend; a vanguard', it would be misleading to claim managed aquifer recharge as a leading edge technology. However it has taken a significant investment in scientific research in recent years to demonstrate the effectiveness of aquifers as sustainable treatment systems to enable managed aquifer recharge to be recognised along side engineered treatment systems in water recycling. It is a 'cross-over' technology that is applicable to water and wastewater treatment and makes use of passive low energy processes to spectacularly reduce the energy requirements for water supply. It is robust within limits, has low cost, is suitable from village to city scale supplies, and offers as yet almost untapped opportunities for producing safe drinking water supplies where they do not yet exist. It will have an increasingly valued role in securing water supplies to sustain cities affected by climate change and population growth. However it is not a universal panacea and relies on the presence of suitable aquifers and sources of water together with effective governance to ensure human health and environment protection and water resources planning and management. This paper describes managed aquifer recharge, illustrates its use in Australia, outlining economics, guidelines and policies, and presents some of the knowledge about aquifer treatment processes that are revealing the latent value of aquifers as urban water infrastructure and provide a driver to improving our understanding of urban hydrogeology.

Pathogen inactivation during passage of stormwater through a constructed reedbed and aquifer transfer, storage and recovery

A study was undertaken to determine the potential inactivation rates of selected enteric microorganisms in captured urban stormwater within a constructed reedbed and in tertiary carbonated aquifer during an Aquifer Storage, Transfer and Recovery (ASTR) scheme. The study was undertaken in-situ in the constructed reedbed and aquifer using diffusion chambers. The results showed that all tested bacteria had one log(10) reduction time of less than 6 and 2.5 days respectively in constructed reedbeds and aquifer, which suggests that presence of enteric bacteria in the recovered water is unlikely. However, adenovirus and Cryptosporidium oocysts showed lower inactivation rates with one log(10) reduction times of more than 33 days in the constructed reedbeds. This means that the constructed reedbed with a mean residence time 10 days cannot be relied upon as an efficient treatment barrier for virus and protozoa. Storage of stormwater in aquifer with brackish water resulted in slow inactivation of enteric viruses over the 35 day incubation period with adenovirus and rotavirus showing slowest inactivation times (extrapolated T(90) of >100 days). Cryptosporidium oocysts showed similar inactivation rate in the constructed reedbed and aquifer.

Characterising aquifer treatment for pathogens in managed aquifer recharge

In this study the value of subsurface treatment of urban stormwater during Aquifer Storage Transfer Recovery (ASTR) is characterised using quantitative microbial risk assessment (QMRA) methodology. The ASTR project utilizes a multi-barrier treatment train to treat urban stormwater but to date the role of the aquifer has not been quantified. In this study it was estimated that the aquifer barrier provided 1.4, 2.6, >6.0 log(10) removals for rotavirus, Cryptosporidium and Campylobacter respectively based on pathogen diffusion chamber results. The aquifer treatment barrier was found to vary in importance vis-à-vis the pre-treatment via a constructed wetland and potential post-treatment options of UV-disinfection and chlorination for the reference pathogens. The risk assessment demonstrated that the human health risk associated with potable reuse of stormwater can be mitigated (disability adjusted life years, DALYs <1 × 10(-6)) if the aquifer is integrated with suitable post treatment options into a treatment train to attenuate pathogens and protect human health.

Estimation of the warfarin dose with clinical and pharmacogenetic data

BACKGROUND

Genetic variability among patients plays an important role in determining the dose of warfarin that should be used when oral anticoagulation is initiated, but practical methods of using genetic information have not been evaluated in a diverse and large population. We developed and used an algorithm for estimating the appropriate warfarin dose that is based on both clinical and genetic data from a broad population base.

METHODS

Clinical and genetic data from 4043 patients were used to create a dose algorithm that was based on clinical variables only and an algorithm in which genetic information was added to the clinical variables. In a validation cohort of 1009 subjects, we evaluated the potential clinical value of each algorithm by calculating the percentage of patients whose predicted dose of warfarin was within 20% of the actual stable therapeutic dose; we also evaluated other clinically relevant indicators.

RESULTS

In the validation cohort, the pharmacogenetic algorithm accurately identified larger proportions of patients who required 21 mg of warfarin or less per week and of those who required 49 mg or more per week to achieve the target international normalized ratio than did the clinical algorithm (49.4% vs. 33.3%, P<0.001, among patients requiring < or = 21 mg per week; and 24.8% vs. 7.2%, P<0.001, among those requiring > or = 49 mg per week).

CONCLUSIONS

The use of a pharmacogenetic algorithm for estimating the appropriate initial dose of warfarin produces recommendations that are significantly closer to the required stable therapeutic dose than those derived from a clinical algorithm or a fixed-dose approach. The greatest benefits were observed in the 46.2% of the population that required 21 mg or less of warfarin per week or 49 mg or more per week for therapeutic anticoagulation.

Tomato fruit ascorbic acid content is linked with monodehydroascorbate reductase activity and tolerance to chilling stress

Quantitative trait loci (QTL) mapping is a step towards the identification of factors regulating traits such as fruit ascorbic acid content. A previously identified QTL controlling variations in tomato fruit ascorbic acid has been fine mapped and reveals that the QTL has a polygenic and epistatic architecture. A monodehydroascorbate reductase (MDHAR) allele is a candidate for a proportion of the increase in fruit ascorbic acid content. The MDHAR enzyme is active in different stages of fruit ripening, shows increased activity in the introgression lines containing the wild-type (Solanum pennellii) allele, and responds to chilling injury in tomato along with the reduced/oxidized ascorbate ratio. Low temperature storage of different tomato introgression lines with all or part of the QTL for ascorbic acid and with or without the wild MDHAR allele shows that enzyme activity explains 84% of the variation in the reduced ascorbic acid levels of tomato fruit following storage at 4 degrees C, compared with 38% at harvest under non-stress conditions. A role is indicated for MDHAR in the maintenance of ascorbate levels in fruit under stress conditions. Furthermore, an increased fruit MDHAR activity and a lower oxidation level of the fruit ascorbate pool are correlated with decreased loss of firmness because of chilling injury.

A critical evaluation of combined engineered and aquifer treatment systems in water recycling

Australian experience at five research sites where stormwater and reclaimed water have been stored in aquifers prior to reuse, have yielded valuable information about water treatment processes in anaerobic and aerobic aquifers. One of these sites is the stormwater to potable water ASTR project at the City of Salisbury, a demonstration project within the broader EC project 'RECLAIM WATER'. A framework for characterising the effectiveness of such treatment for selected organic chemicals, natural organic matter, and pathogens is being developed for inclusion in new Australian Guidelines for Management of Aquifer Recharge. The combination of pre-treatments (including passive systems such as reed beds) and aquifer treatment effectiveness in relation to source waters and intended uses of recovered water will be described. Advantages and disadvantages of various types of pre-treatments in relation to effectiveness and sustainability of managed aquifer recharge will be discussed taking account of aquifer characteristics. These observations will be consolidated into a draft set of principles to assist in selection of engineered treatments compatible with passive treatment in aquifers.

Use of the embedded peritoneal dialysis catheter: Experience and results from a North American Center

Since 2000, the Ottawa Hospital Home Dialysis Program has used a variation on the embedded peritoneal dialysis catheter technique described by Moncrief et al. In this paper, we describe our approach to placement of peritoneal access and report our experience with 304 embedded catheters placed between January 2000 and December 2003. We review the advantages and disadvantages of this technique and describe factors that have been important to the success of our program.

Impact of restricting fluoroquinolone prescription on bacterial resistance in an intensive care unit

The purpose of this study was to assess the effect of reducing prescription of fluoroquinolones in an intensive care unit (ICU) upon bacterial resistance, particularly as regards Pseudomonas aeruginosa. For six months between January 2001 and June 2001, administration of fluoroquinolones was kept to a minimum. A bacteriological screening of patients was performed to assess the incidence of fluoroquinolone-resistant bacteria. There was a 75.8% restriction in prescriptions of fluoroquinolones. There was no significant change in bacterial ecology between the periods preceding (12 months) and following (12 months) restriction. There was a significant recovery of sensitivity of P. aeruginosa to ciprofloxacin (P<or=0.01), with a decrease in resistant strains from 71.3% in the pre-restriction period to 52.4% in the post-restriction period. Regarding clinical data, no significant differences were noted between the pre-restriction and the post-restriction periods, except for the number of cases of ventilator-associated pneumonia with P. aeruginosa resistant to ciprofloxacin. This study demonstrated the possibility of introducing rotation of antibiotics in an ICU.

Implications for practice: challenges for healthcare leaders in fostering patient safety

Although various government and regulatory organisations have identified practices that may enhance patient safety, there is little empirical or theoretical research to inform the decisions of healthcare leaders seeking to create patient safety programmes within their hospitals and clinics. In order to understand the challenges facing hospital and health system executives, we describe the experience of the Executive Session on Patient Safety. The executives identified five major problems in leading patient safety: 1) how should executives structure their organisations to deliver safe care? 2) how should executives monitor and measure their organisation's safety performance? 3) how should executives spread and sustain patient safety innovation? 4) how should executives manage the relationship with the external environment? and 5) how should executives manage their own behaviour in order to lead for safety? The organisational infrastructure needed for safer care is being developed by practitioners out in the field as a matter of necessity. Strengthening the scientific basis for organisational leadership in patient safety is a vital but neglected area of study.

Implications for practice: challenges for healthcare leaders in fostering patient safety

Although various government and regulatory organisations have identified practices that may enhance patient safety, there is little empirical or theoretical research to inform the decisions of healthcare leaders seeking to create patient safety programmes within their hospitals and clinics. In order to understand the challenges facing hospital and health system executives, we describe the experience of the Executive Session on Patient Safety. The executives identified five major problems in leading patient safety: 1) how should executives structure their organisations to deliver safe care? 2) how should executives monitor and measure their organisation's safety performance? 3) how should executives spread and sustain patient safety innovation? 4) how should executives manage the relationship with the external environment? and 5) how should executives manage their own behaviour in order to lead for safety? The organisational infrastructure needed for safer care is being developed by practitioners out in the field as a matter of necessity. Strengthening the scientific basis for organisational leadership in patient safety is a vital but neglected area of study.