Building Representation Learning Models for Antibody Comprehension

Antibodies are versatile proteins with both the capacity to bind a broad range of targets and a proven track record as some of the most successful therapeutics. However, the development of novel antibody therapeutics is a lengthy and costly process. It is challenging to predict the functional and biophysical properties of antibodies from their amino acid sequence alone, requiring numerous experiments for full characterization. Machine learning, specifically deep representation learning, has emerged as a family of methods that can complement wet lab approaches and accelerate the overall discovery and engineering process. Here, we review advances in antibody sequence representation learning, and how this has improved antibody structure prediction and facilitated antibody optimization. We discuss challenges in the development and implementation of such models, such as the lack of publicly available, well-curated antibody function data and highlight opportunities for improvement. These and future advances in machine learning for antibody sequences have the potential to increase the success rate in developing new therapeutics, resulting in broader access to transformative medicines and improved patient outcomes.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Deciphering the language of antibodies using self-supervised learning

An individual’s B cell receptor (BCR) repertoire encodes information about past immune responses and potential for future disease protection. Deciphering the information stored in BCR sequence datasets will transform our understanding of disease and enable discovery of novel diagnostics and antibody therapeutics. A key challenge of BCR sequence analysis is the prediction of BCR properties from their amino acid sequence alone. Here, we present an antibody-specific language model, Antibody-specific Bidirectional Encoder Representation from Transformers (AntiBERTa), which provides a contextualized representation of BCR sequences. Following pre-training, we show that AntiBERTa embeddings capture biologically relevant information, generalizable to a range of applications. As a case study, we fine-tune AntiBERTa to predict paratope positions from an antibody sequence, outperforming public tools across multiple metrics. To our knowledge, AntiBERTa is the deepest protein-family-specific language model, providing a rich representation of BCRs. AntiBERTa embeddings are primed for multiple downstream tasks and can improve our understanding of the language of antibodies.

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AntiBERTa is an antibody-specific transformer model for representation learning

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AntiBERTa embeddings capture aspects of antibody function

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Attention maps of AntiBERTa correspond to structural contacts and binding sites

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AntiBERTa can be fine-tuned for state-of-the-art paratope prediction

Understanding antibody function is critical for deciphering the biology of disease and for the discovery of novel therapeutic antibodies. The challenge is the vast diversity of antibody variants compared with the limited labeled data available. We overcome this challenge by using self-supervised learning to train a large antibody-specific language model, followed by transfer learning, to fine-tune the model for predicting information related to antibody function. We initially demonstrate the success of the model by providing leading results in antibody binding site prediction. The model is amenable to further fine-tuning for diverse applications to improve our understanding of antibody function.

Improved screening of fall risk using free-living based accelerometer data

Falls are one of the most costly population health issues. Screening of older adults for fall risks can allow for earlier interventions and ultimately lead to better outcomes and reduced public health spending. This work proposes a solution to limitations in existing fall screening techniques by utilizing a hip-based accelerometer worn in free-living conditions. The work proposes techniques to extract fall risk features from periods of free-living ambulatory activity. Analysis of the proposed techniques is conducted and compared with existing screening methods using Functional Tests and Lab-based Gait Analysis. 1705 Older Adults from Umea (Sweden) were assessed. Data consisted of 1 Week of hip worn accelerometer data, gait measurements and performance metrics for 3 functional tests. Retrospective and Prospective fall data were also recorded based on the incidence of falls occurring 12 months before and after the study commencing respectively. Machine learning based experiments show accelerometer based measures perform best when predicting falls. Prospective falls had a sensitivity and specificity of 0.61 and 0.66 respectively while retrospective falls had a sensitivity and specificity of 0.61 and 0.68 respectively.

POS1422 USE OF DISEASE MODIFYING ANTI-RHEUMATIC DRUGS AND RISK OF MULTIPLE MYELOMA IN PERSONS WITH RHEUMATOID ARTHRITIS

Background

Biologic therapies used in the management of rheumatoid arthritis (RA) target several cytokines that have been implicated in the pathogenesis of multiple myeloma (MM). Yet little is known about the association between use of biologic or targeted synthetic disease modifying anti-rheumatic drugs (b or tsDMARDs) in RA and the incidence of MM.

Objectives

Our objective was to estimate the association between b/tsDMARD use and the risk of MM among persons with RA using Veterans Health Administration (VHA) data. We hypothesized that b-/tsDMARD use is associated with a lower incidence of MM compared with conventional synthetic DMARDs (csDMARDs).

Methods

In this retrospective cohort study, we identified patients >18 years of age diagnosed with RA in any United States VHA facility from 1/1/2002 and 12/31/2018. All patients met the following inclusion criteria: 1) two or more International Classification of Diseases Version 9 or 10 (ICD9 or ICD10) codes for RA at least 7 days apart but no more than 365 days apart 2) a prescription for a csDMARD within 90 days of the first RA diagnosis 3) one inpatient or outpatient visit 30 days to 2 years preceding first RA diagnosis (indicating a regular user of VHA). Medication data was derived from the outpatient prescription fills, bar coded medication administration (BCMA), and intravenous (IV) data domains. The csDMARDs included in these analyses were: methotrexate, sulfasalazine, leflunomide, and hydroxychloroquine. The bDMARDs included were tumor necrosis factor inhibitors (TNFi) and non-TNFi biologics such as tocilizumab, rituximab, abatacept, and biosimilars; tsDMARD was tofacitinib. Patients with MM before the diagnosis of RA were excluded. Incident MM was determined by 1 or more ICD9/10 code or ICD-oncology codes. Multivariable Cox proportional hazards model were performed to estimate the hazard ratio for developing MM among those during and following the use of a b-/tsDMARD relative to b-/tsDMARD-naïve persons adjusting for age, gender, race, and ethnicity.

Results

27,540 veterans with RA met study eligibility criteria, of whom 8,322 (30%) had taken a b-/tsDMARD. Over the study period there were 77 incident MM over a total of 192,000 person years. There were 55 events in users of csDMARDs, an incidence rate (IR) of 0.40 (95% CI 0.30-0.52) per 1000 person-years and 22 in persons currently or formerly using b-/tsDMARDs (IR 0.41, 0.25-0.61 per 1000 person years). The unadjusted hazard ratio for MM following bDMARD use relative to csDMARD only use was 1.04 (0.63, 1.73), which increased to 1.28 (0.76, 2.16) after adjusting for demographic characteristics (Table 1).

Table 1.

Multivariable Cox proportional hazards model for association between use of disease modifying anti-rheumatic drugs and incident multiple myeloma.

Clinical characteristicHazards ratio (95% CI)csDMARDReferenceb-/tsDMARD use1.28 (0.76-2.16)Age*1.04 (1.02-1.07)Female0.58 (0.20-1.62)RaceReferenceWhite2.11 (1.15-3.86)Black0.70 (0.10-5.08)OtherHispanic Ethnicity0.71 (0.17-2.92)

Abbreviations: b-/tsDMARD- biologic or targeted synthetic disease modifying anti-rheumatic drug; CI: confidence interval

*Hazards ratio reflects risk per every 1-year increase in age

Model adjusted for age, gender, race, and ethnicity

Conclusion

In this nationwide VA study, we did not observe an association between bDMARD use and the incidence of MM. Of note, the median interval from initiation of a bDMARD to the end of follow-up was approximately 5.8 years, which does not allow for an examination of a possible longer term influence.

Disclosure of Interests

None declared

POS1434 USE OF BIOLOGIC OR TARGETED SYNTHETIC DISEASE MODIFYING ANTI-RHEUMATIC DRUGS AND THE RISK OF LYMPHOMA IN RHEUMATOID ARTHRITIS

Background

Epidemiologic studies suggest that disease duration and degree of inflammatory activity of rheumatoid arthritis (RA) contribute to lymphoma development (1). Whether the decrease in inflammatory burden seen with use of biologic or targeted synthetic disease modifying anti-rheumatic drugs (bDMARDs or tsDMARDs) translates into a lower risk of lymphoma in RA needs to be studied.

Objectives

The objective of our study was to examine the effect of administration of b/tsDMARDS on the incidence of lymphoma relative to conventional synthetic DMARDs (csDMARDs) in an inception cohort of Veterans with RA.

Methods

We identified patients >18 years of age diagnosed with RA in any US Veterans Affairs (VA) facility from 1/1/2002 and 12/31/2018 using the VA Corporate Data Warehouse (CDW). To be included, each patient was required to meet the following criteria: 2+ RA diagnostic codes at least 7 days apart but no more than 365 days apart; 2) a prescription for a csDMARD within 90 days of the first RA diagnosis; and 3) an inpatient or outpatient visit 30 days to 2 years preceding first RA diagnosis (indicating they are a regular user of the VA). The csDMARDs included in these analyses were: methotrexate, sulfasalazine, leflunomide, and hydroxychloroquine. The bDMARDs included were tumor necrosis factor inhibitors (TNFi) and non-TNFi biologics such as tocilizumab, rituximab, abatacept, and biosimilars; tsDMARD was tofacitinib. Patients with prevalent lymphoma were excluded. Lymphoma diagnoses were identified using International Classification of Diseases Version 9, 10 and Oncology (ICD9, ICD10, ICDO) codes.

We used marginal structural models as described by Hernan et al (2) and time-varying Cox models to control for confounding by indication while evaluating this association. We adjusted for baseline demographics (age, sex, race, ethnicity, year of cohort entry, rheumatology visits), and time-varying CRP and time-varying Rheumatoid Disease Comorbidity Index (RDCI) (3) to control for confounding.

Results

27,421 Veterans with RA met our eligibility criteria. Most of the Veterans (56%) were in the age range 61-80 years old; 89% male, 76% White, 14% African American. 8,225 (30%) patients were treated with a b-/tsDMARD. The crude incidence rates were 1.71 (95% CI 1.5-1.94) per 1000 person-years for those only on csDMARDs and 1.78 (95% CI 1.44-2.18) for patients during or following use of a b/tsDMARDs. After adjustment with both time-fixed and time-varying covariates using marginal structural models, the incidence of lymphoma was not different between patients who did and did not use a b/tsDMARD (hazard ratio=1.06, 95% CI= 0.82-1.37) (Table 1).

Table 1.

Estimates of Effect of bDMARD or tsDMARD use on Lymphoma relative to use of csDMARDs

Marginal Structural Models; adjusted for:@Demographics1.04(0.80, 1.34)#Demographics + CRP1.06(0.82, 1.37)

* per 1000 person-years

@Demographics = age, gender, race, ethnicity, rheumatology visits, and year of cohort entry

#Adjusts for CRP, baseline rheumatology visits (yes/no) and RDCI.

CRP = C-Reactive Protein, RDCI = Rhematic Disease Comorbidity Index, CI = Confidence Interval, b/tsDMARD = biologic or targeted synthetic DMARD, csDMARD = conventional synthetic DMARD

Conclusion

In this large study using the nationwide VA data, we did not observe an association between the use of b/ts DMARDs and an increased risk of lymphoma.

References

[1]Baecklund E, Iliadou A, Askling J, Ekbom A, Backlin C, Granath F, et al. Association of chronic inflammation, not its treatment, with increased lymphoma risk in rheumatoid arthritis. Arthritis Rheum. 2006;54(3):692-701.

[2]Robins JM, Hernan MA, Brumback B. Marginal structural models and causal inference in epidemiology. Epidemiology. 2000;11(5):550-60.

[3]England BR, Sayles H, Mikuls TR, Johnson DS, Michaud K. Validation of the rheumatic disease comorbidity index. Arthritis care & research. 2015;67(6):865-72.

Disclosure of Interests

None declared

Mechanistic diversity in MHC class I antigen recognition

Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.

Effect of dietary supplementation of Bacillus subtilis DSM29784 on hen performance, egg quality indices, and apparent retention of dietary components in laying hens from 19 to 48 weeks of age

The aim of the current study was to evaluate egg production, quality, and apparent retention (AR) of components in response to a multi-dose application of a single strain Bacillus subtilis (SSB; DSM29784) in a corn-soybean meal basal diet fed to hens (19 to 48 wk of age). The treatments consisted of a basal diet with either no probiotic (control, CON), 1.1E+08 (low, LSSB), 2.2E+08 (medium, MSSB) or 1.1E+09 (high, HSSB) CFU/kg of diet. A total of 336, 19-wk old Shaver White layers were used at a stocking density of 7 and 6 hens/replicate-cage in layer I (week-19 to 28) and layer II (week-29 to 48) phases, respectively. Evaluated variables included feed intake (FI), body weight (BW), feed conversion ratio (FCR), egg production, weight, mass, and egg quality (shell thickness, shell breaking strength, albumen height (AH), and Haugh unit (HU)). Excreta was collected at the end of week-28 for AR of components and apparent metabolizable energy (AME). Supplementation of SSB increased (P = 0.008) FI during peak egg-lay (week-24) and BW increased linearly (P = 0.019) in early layer II (week-32). In layer I, LSSB compared with CON increased EM (g/egg) by 3.3% (P = 0.049). In layer II, SSB inclusion tended to improve FCR (linear, P = 0.094; g FI: g EM). Although shell breaking strength was lowest at week-20 with HSSB (4.518 vs. 4.889 kgf for HSSB vs. CON; P = 0.045), AH and HU were improved at higher dose of SSB, in both phases (P ≤ 0.005). Apparent retention of dry matter, AME, and minerals were improved (P < 0.0001) in a dose response. Hence, while the low dose of B. subtilis DSM29784 improved hen performance and maintained egg quality in both phases, a higher dose of SSB improved the interior protein quality of eggs (AH and HU).

Growth performance, apparent retention of components, and excreta dry matter content in Shaver White pullets (5 to 16 week of age) in response to dietary supplementation of graded levels of a single strain Bacillus subtilis probiotic

Administered in adequate amounts, probiotics can be an alternative to antibiotic growth promoters in poultry production. This study evaluated dose response of a single strain of Bacillus subtilis (SSB, DSM29784) on growth performance, apparent retention (AR) of components, and excreta DM content in pullets. A basal corn-soybean meal diet was formulated to meet the specifications for grower (week 5 to 10) and developer (week 11 to 16) phases. In each phase, SSB was added to the basal diet to create 4 test diets: 0 (control, CON), 1.1E+08 (low; LSSB), 2.2E+08 (medium; MSSB), or 1.1E+09 (high; HSSB) CFU of SSB/kg of feed. All diets had TiO2 (0.5%) as a digestibility marker. A total of 720 day-old Shaver White chicks were placed in 48 cages (15 pullets per cage) and reared on a commercial antibiotic free diet for a 4-wk period. At the beginning of week 5, treatments were allocated based on cage BW (n = 12). Birds had free access to feed and water throughout. The BW, BW uniformity, feed intake (FI) and FCR were obtained weekly. Excreta was collected at the end of each phase for AR of DM, organic matter, CP, neutral detergent fiber, minerals, and AME, as well as excreta DM content. In response to SSB inclusion, BW improved in a linear (P < 0.005) and quadratic (P < 0.0001) manner in grower. FI decreased in a linear and quadratic pattern (P < 0.05, week 8 to 10) in grower, and linearly (P < 0.05) across the developer phase. Overall FCR improved in linear and quadratic pattern (P < 0.01) in the grower phase. In both the phases, AME improved in a quadratic pattern (P < 0.05). Inclusion of SSB had a linear reduction (P < 0.0001) in excreta moisture content in the grower phase. In summary, these results demonstrate that B. subtilis probiotic improved performance through enhanced nutrient utilization and reduced excreta moisture content indicating improved pullet gut health.

Growth performance and gastrointestinal responses in heavy Tom turkeys fed antibiotic free corn-soybean meal diets supplemented with multiple doses of a single strain Bacillus subtilis probiotic (DSM29784)1

Growth performance and gastrointestinal (GIT) responses to a single-strain of Bacillus subtilis (SSB) were investigated using 960 Hybrid Converter Toms. A total of 4 iso-caloric and iso-nitrogenous corn-soybean meal-based diets were allocated to 12 replicate cages/pens and fed (ad libitum) in a four-phase feeding program (starter; days 0 to 28, grower-1; days 29 to 56, grower-2; days 57 to 84, and finisher; days 85 to 126). The diets had either 0 (control), 1E+08 (low), 2E+08 (mid) or 1E+09 (high) cfu B. subtilis/kg. Feed intake (FI) and BW were recorded by phase. Excreta samples were collected towards the end of starter and grower-1 phases for apparent retention (AR) of components by marker method and litter moisture, respectively. Selected birds were necropsied on days 28 and 56 for GIT weight and samples for jejunal histomorphology and ceca digesta short chain fatty acids (SCFA). Supplemental SSB had linear and non-linear (P < 0.05) response on BW gain (BWG). Specifically, relative to the control, birds fed low SSB had higher BWG in starter and grower-1 phases whereas bird fed mid and high SSB had lower BWG in grower-2 and birds fed low and mid SSB had higher BWG in finisher phase. Consequently, birds fed low and mid SSB doses were heavier (P < 0.05) than control fed birds at the end of trial. The FCR response to SSB was linear and non-linear (P < 0.05) with birds fed low SSB showing lower FCR than control fed birds in starter, grower-1 and finisher phases. Supplemental SSB had linear and non-linear (P < 0.05) effects on AR of components (DM, ash, crude protein, crude fat, neutral detergent fiber, and gross energy), litter moisture, GIT weight, jejunal histomorphology, and SCFA. Relative to control, birds fed high SSB showed higher AR of components, villi height, day 56 ceca digesta total SCFA concentration, and lower litter moisture. In conclusions, under condition of the current study, growth performance was optimized by low to mid SSB. Improved nutrient retention and indices of gut health suggested higher SSB doses may optimize growth performance under challenging farm conditions.

Large-area electrode design for vertical electrical impedance scanning of concrete bridge decks

Vertical electrical impedance (VEI) testing is a method that was developed specifically for quantifying the level of protection against chloride ingress in concrete bridge decks. A significant operational difficulty associated with VEI testing has been establishing the required rebar tap as a ground reference. As described in this work, the use of a large-area electrode (LAE) can potentially remove the need for a rebar tap and therefore significantly simplify and accelerate the VEI testing process. The specific objective of the research was to develop both theoretical and practical guidance for the design of an LAE for VEI testing. To investigate several variables that can affect the accuracy of VEI measurements obtained using an LAE connection, including various combinations of deck cover and water resistivity values, electrode separation distance, counter electrode (CE) effective area, and area ratio between the LAE and the CE, an analytical model (AM) and a finite-element model (FEM) were developed and validated with laboratory and field experiments. From the results of the AM and FEM simulations and the results of the laboratory and field experiments, LAE design considerations were developed for each of these variables that should allow proper implementation of a VEI measurement system using an LAE connection.

Bronchiectasis in the Kimberley region of Western Australia

OBJECTIVE

To review the work-up and inpatient management of non-cystic fibrosis bronchiectasis exacerbations against best practice guidelines in the Kimberley, a remote region of Western Australia, with the ultimate goal of improving treatment in the region.^ DESIGN: Retrospective cohort study and audit of remote adult bronchiectasis hospital admissions between 2011 and 2016.

SETTING

Remote hospital inpatients.

PARTICIPANTS

Thirty-two patients and 110 hospital admissions were included. Patients were ≥15 years old, had computed tomography confirmed bronchiectasis and at least one hospital admission for acute respiratory illness prior to January 2011.

MAIN OUTCOMES MEASURED

The 5-year mortality and compliance to a Lung Foundation position statement on non-cystic fibrosis bronchiectasis which suggests investigating for an underlying cause at diagnosis and during exacerbations prolonged antibiotics (10-14 days) and prolonged hospital admissions (≥7 days) are required.

RESULTS

The overall 5-year mortality was 21.8%, with the median age at death of 37 years (interquartile range, 27-63). The median duration of hospital admission was shorter than the recommended 3 days (interquartile range, 2-5) with 11 of 100 (11%) patients admitted for ≥7 days. The median duration of antibiotics was also shorter than the recommended 7 days (interquartile range, 4-10), with 31 of the 98 (32%) patients prescribed ≥10 days and 6 of the 98 (6%) prescribed ≥14 days of therapy.

CONCLUSION

We found under-treatment and under-investigation of non-cystic fibrosis bronchiectasis in the Kimberley region. Five-year mortality was high, consistent with other rural Australian Indigenous cohorts.§ Following this audit, a strategy to improve awareness, as well as update and promote regional guidelines has been developed.

Who receives contraception counseling when starting new lupus medications? The potential roles of race, ethnicity, disease activity, and quality of communication

OBJECTIVE

Family planning discussions are an important aspect of medical care for women with systemic lupus erythematosus (SLE) as active disease is a risk factor for poor pregnancy outcomes, and the medications used for treatment can be harmful to the fetus when used during conception and pregnancy. Our objective was to examine the impact of patient perception of quality and type of communication on receiving contraception counseling.

METHODS

Data were derived from patients enrolled in the University of California, San Francisco Lupus Outcomes Study. Individuals participate in a yearly structured telephone interview that includes assessment of contraception counseling when starting new medications, and measures of communication and decision making. Logistic regression was performed to identify predictors of not receiving contraception counseling.

RESULTS

Of the 68 women included in this analysis, one-third did not receive contraception counseling when starting new medications. Older age, white race, depressive symptoms, and higher SLE disease activity were independently associated with not receiving contraception counseling. Participants who did not receive contraception counseling rated their physicians lower in shared decision-making (SDM) communication.

CONCLUSIONS

This study demonstrates a gap in family planning counseling among women with SLE starting new medications. Future studies to address these potential areas of intervention, including education about the need for contraception through menopause, and mechanisms to engage in SDM surrounding contraception are needed to improve quality of care for women with lupus.

Evaluation of a commercially available organic acid product on body weight loss, carcass yield, and meat quality during preslaughter feed withdrawal in broiler chickens: a poultry welfare and economic perspective

The effect of a commercial organic acid (OA) product on BW loss (BWL) during feed withdrawal and transportation, carcass yield, and meat quality was evaluated in broiler chickens. Two experiments were conducted in Brazil. Commercial houses were paired as control groups receiving regular water and treated groups receiving OA in the water. Treated birds had a reduction in BWL of 37 g in experiment 1 and 32.2 g in experiment 2. In experiment 2, no differences were observed in carcass yield between groups. Estimation of the cost benefit suggested a 1:16 ratio by using the OA. In experiment 3, conducted in Mexico, significant differences on water consumption, BWL, and meat quality characteristics were observed in chickens that were treated with the OA (P < 0.05). These data suggest this OA product may improve animal welfare and economic concerns in the poultry industry by reducing BWL and improving meat quality attributes.

Abstract P4-16-04: Amrubicin as second- or third-line treatment for patients with HER2-negative metastatic breast cancer (MBC): Final results from a phase II trial of the Sarah Cannon Research Institute (SCRI)

Background: Anthracyclines are among the most effective agents in the treatment of breast cancer; however, dose-dependent cumulative cardiotoxicity limits their use. Amrubicin is a synthetic anthracycline topoisomerase II inhibitor demonstrating potent antitumor effects coupled with little potential for cardiotoxicity. We report the final results from a phase I/II trial of amrubicin as second- or third-line therapy for HER2-negative MBC.

Methods: Eligible patients (pts) included women with measurable HER2-negative MBC who had received 1 or 2 prior chemotherapy regimens for MBC. Previous anthracyclines were permitted if ≥ 6 months prior to study entry. Normal LVEF was required. Amrubicin 110 mg/m2 IV (dose established from phase I portion) was administered every 3 weeks until disease progression or intolerable toxicity; growth factor use was permitted. Disease evaluations were performed every 6 weeks and LVEF assessments every 12 weeks. Progression-free survival (PFS) was the primary endpoint; a median PFS ≥ 4.5 months would merit further evaluation of amrubicin in MBC. Toxicity, overall survival, and overall response rate (ORR) were secondary endpoints.

Results: Between 1/2010 and 3/2012, 78 pts were enrolled, and 66 pts are included in this analysis (ph I: 3 pts; ph II 63 pts). Baseline characteristics included: median age 59 years; hepatic metastases in 50%; ≥ 3 sites of metastatic disease in 32%. Triple-negative histology was noted in 27%; prior adjuvant chemotherapy in 50%; prior anthracyclines in 32%; and 2 prior cytotoxic regimens for MBC in 35%. Median treatment duration was 18 weeks (6 cycles), range 1- 24 cycles. The ORR was 21% in evaluable pts (2 CR, 10 PR); 5 of these 12 pts had prior anthracyclines. 14% were not evaluable. The clinical benefit rate (CBR) was 42% (CBR = CR+PR+SD≥ 4 months); 35% of these responders received ≥12 cycles of amrubicin. Median PFS for all pts was 4.0 months (95% CI 2.5- 5.8 months) and did not significantly differ by line of therapy administered (4.0 months as 2nd line vs 4.7 as 3rd line therapy). 36% of pts were free of progression at 6 months. Neutropenia was the most common grade 3/4 toxicity present in 42% and accompanied by fever in 7%. No grade 3/4 non-hematologic toxicity occurred in &gt; 5% pts. One pt previously treated with anthracyclines experienced a transient 20% LVEF decline to 44% at cycle 4. This recovered to baseline within 2 weeks and pt continued to receive 2 additional cycles of amrubicin before experiencing PD. No other grade 3/4 cardiac events were noted. In 3 pts, amrubicin was discontinued due to toxicity (G4 neutropenia, G2 thrombocytopenia, G2 nausea/vomiting/vertigo).

Conclusions: Amrubicin was active and well tolerated in the second- or third-line MBC setting with manageable toxicity. The ORR of 21% and median PFS of 4 months are comparable to other single agents in this setting. The observed CBR of 42%, and the fact that nearly 1/3 of these responders received ≥12 cycles of amrubicin with no cardiotoxicity, suggests that future evaluations of amrubicin in breast cancer are warranted.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-16-04.

Close cooperation between science, management and industry benefits sustainable exploitation of the Falkland Islands squid fisheries

The Falkland Islands fishing industry is unique, as 60-80% of its annual catch consists of two squid species, Illex argentinus and Doryteuthis gahi. Short annual life cycles make both species susceptible to intra-annual environmental changes, resulting in large biomass fluctuations that must be addressed in management of the stocks. In the D. gahi fishery, short chains of communication between science, management and industry allow effective cooperation in the interest of long-term sustainable exploitation. The industry is responsive to short-notice requests for in-season information about the fishery. Management takes into account both scientific advice and industry recommendations, through ongoing consultations before and during the fishing seasons. As a result of this cooperation, D. gahi is one of the best managed squid fisheries in the world with local fishing companies being amongst the largest and most profitable enterprises in the Falklands economy. The I. argentinus fishery has the same potential, but a further level of cooperative management is needed as this squid is a straddling stock between several countries and the high seas. Development of a regional fisheries management organization in the South Atlantic Ocean is required to control multilateral exploitation and ensure long-term sustainability of I. argentinus stocks.

Abstract P5-17-05: Sorafenib plus Ixabepilone as First-Line Treatment for Patients with HER2-Negative Metastatic Breast Cancer: Preliminary Results of the Phase II Trial of the Sarah Cannon Research Institute

Background: Sorafenib (S) is an oral multi-kinase inhibitor with effects on tumor proliferation and angiogenesis, targeting VEGFR1 and VEGFR2. It has modest activity as a single agent in breast cancer. In combination with capecitabine, S demonstrated a significant improvement of 2.3 months in progression free survival (PFS) in patients (pts) with metastatic breast cancer (MBC) and added benefit when combined with paclitaxel. Ixabepilone (Ixa) is a semi-synthetic analog of epothilone B with excellent single agent activity in MBC. The phase I portion of this trial identified the MTD of the Ixa and S combination. We now report the initial results of the phase II trial with this novel combination.

Methods: Eligibility criteria included: HER2-negative MBC previously untreated with chemotherapy; measurable disease; ECOG PS 0–2; normal LVEF; and adequate bone marrow and organ function. Prior hormonal therapy for MBC was permitted. Pts received Ixa 32mg/m2 IV on day 1 of each 21-day cycle and S 400mg PO BID. Following a minimum of 4 cycles of the combination, responding pts could discontinue Ixa and remain on study treatment with S monotherapy. Granulocyte-stimulating growth factors were permitted after cycle one. Tumor assessments were performed every 9 weeks. Pts continued study treatment until disease progression or unacceptable toxicity. The primary endpoint of this trial was PFS; the addition of S to Ixa was hypothesized to improve PFS from 4.2 month to 6.2 months in this patient population. The total enrollment goal is 85 pts, and the trial is currently open to accrual.

Results: Between 5/2010 and 4/2012, 76 pts have been enrolled, and 57 pts (56 females, 1 male) are included in this analysis. Baseline characteristics included: median age 58; 61% were ER and/or PR positive; 39% were triple-negative; 39% received neoadjuvant therapy. Anthracycline exposure was noted in 34 pts and prior taxane exposure in 39 pts. 29 pts received prior hormonal therapy, 7 of these for MBC. Sites of metastatic disease included lymph nodes 42%, lung 35%, liver 30%, bone 30%, and 23% other. 19 pts (33%) had 3 or more sites of metastatic disease. Median treatment duration was 3 cycles (9 weeks), range 1–11+ cycles with 9 pts discontinuing Ixa after a median of 6 cycles and continuing on S monotherapy. 12 pts (21%) had objective responses (1 CR, 11 PR); 3 of the 22 (14%) triple-negative patients had responses (1 CR, 2 PR). An additional 24 patients (42%) had stable disease at first reevaluation. Neutropenia was the most common grade 3/4 toxicity (26%) with growth factor use reported in 35%. Grade 3/4 non-hematologic toxicity occurring in &gt; 5% of patients consisted of: rash (12%), fatigue (11%), hypersensitivity reaction (7%, Ixa= 3 pts and S= 1 pt), and neuropathy (7%). Discontinuation due to adverse events occurred in 11%.

Conclusion: The combination of Ixa and full dose S was well tolerated with no new observed toxicities. Adverse events were manageable and consisted primarily of G3/4 neutropenia and rash. Study is ongoing and updated results will be presented.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-17-05.

Prevalence of ketoacidosis at diagnosis of childhood onset Type 1 diabetes in Wales from 1991 to 2009 and effect of a publicity campaign

AIMS

To determine the proportion of cases of childhood Type 1 diabetes that present with ketoacidosis and any temporal trend. To assess the impact of a publicity campaign promoting earlier diagnosis.

METHODS

We used an all-Wales register of incident cases with data on 2046 children from 1991 to 2009. The proportion with ketoacidosis at diagnosis was compared with the Yorkshire Childhood Diabetes Register. On World Diabetes Day posters were sent to every pharmacy, school and general practitioner surgery across Wales and radio interviews given. A questionnaire survey was conducted in Gwent to assess penetrance of the campaign.

RESULTS

Annually, in 1991-2009 the proportion presenting with ketoacidosis varied between 20% and 33% (mean 25%) with no change over time. Similar proportions occurred in Yorkshire. Ketoacidosis was more common before age 5 years (37% of cases) than at age 5-9 years (20%) or 10-14 years (23%) (P < 0.001). From November 2006-2007 30% of cases presented with ketoacidosis and from November 2007-2008 25% cases presented with ketoacidosis. After the campaign (November 2008-2009) 26% presented with ketoacidosis (P = 0.72). The information had reached a low proportion of families. General practitioners referred immediately cases that presented to them.

CONCLUSIONS

Over 20 years in Wales there has been no change in the proportion of children with Type 1 diabetes initially presenting with ketoacidosis. This presentation occurs in a higher proportion of new cases aged under 5 years. Publicity to increase awareness did not reduce the proportion with ketoacidosis at diagnosis in Wales. We need to get the educational message through to parents to reduce ketoacidosis at presentation.

P3-14-29: Neoadjuvant Sunitinib Administered with Weekly Paclitaxel/Carboplatin in Patients with Locally Advanced Triple-Negative Breast Cancer: A Sarah Cannon Research Institute Phase I/II Trial

Background: Angiogenesis plays a substantial role in breast cancer development as well as in triple negative breast cancer (TNBC). Sunitinib is an inhibitor of the tyrosine kinase receptors for VEGF, platelet-derived growth factor (PDGF), KIT, RET, and fms-like tyrosine kinase receptor-3 (FLT3). As monotherapy in heavily pretreated breast cancer patients (pts), sunitinib demonstrated a response rate of 15% in TNBC (11% of all pts) with stable disease or better in 16% of all pts. The combination of paclitaxel and carboplatin is ideally suited for further exploration as neoadjuvant chemotherapy for TNBC, based on the established preclinical and clinical sensitivity of TNBC to these cytotoxic agents. This open label, phase I/II trial was designed to evaluate the combination of sunitinib plus paclitaxel and carboplatin as neoadjuvant treatment for locally advanced breast cancer. The primary objective for the phase I portion was to determine the maximum tolerated dose (MTD); these results are presented. Methods: Women with histologically confirmed invasive triple-negative adenocarcinoma of the breast, (defined as &lt;10% staining by IHC for ER/PR; IHC 0–1+ or FISH negative for HER2), with no evidence of metastatic disease and normal LVEF were eligible. All pts received sunitinib (days 1–28), paclitaxel (days 1, 8, 15), and carboplatin (day 1) in 28-day treatment cycles x6. Following 6 cycles, pts had definitive surgery. After ≥2 weeks and evidence of adequate wound healing, maintenance sunitinib 25mg PO daily was initiated to complete a total of 52 weeks. Three dose levels were evaluated as shown in the table below: