Abstract PD8-04: Neoadjuvant chemotherapy for breast cancer: Nodal downstaging is highly correlated with pathological complete response

Background: Neoadjuvant chemotherapy (NAC) is employed in patients with larger tumors to attempt to downstage locally advanced cancers to allow breast conservation and to assess in vivo tumor response. The Multi-Institutional Neoadjuvant Therapy MammaPrint Project I (MINT) study asked a secondary question of whether complete nodal downstaging could also be achieved with NAC.

Methods: This analysis included 147 eligible invasive breast cancer patients with high tumor burdens, classified as cT2-4N0-3M0 (T2 greater than 3.5cm if N0). Patients who had a positive core biopsy and/or fine needle aspiration (FNA) on an axillary node prior to starting NAC were included in this analysis. Those who had a surgical sentinel lymph node biopsy were not included. Nodal involvement was established following neoadjuvant treatment by axillary lymph node dissection (ALND).

Results: This population was 54% postmenopausal, average age 53 yrs (range 25 to 80 yrs). Tumor characteristics were 91% invasive ductal carcinoma; 65% T2, 29% T3, 6% T4; 87% LN1, 13% LN2-3; 3% low grade, 38% intermediate grade, 59% high grade; 65% ER-positive, 49% PR-positive, and 28% HER2-positive by immunohistochemistry; 84% High Risk (HR) and 16% Low Risk (LR) by MammaPrint (MP). After NAC, 45% (66/147) of these LN-positive patients were down-staged to ypN0 and also achieved a complete pathological response in the primary tumor. The potential for down-staging was inversely-related to tumor burden, where 47% (60/128) of N1, 35% (6/17) of N2, and 0% (0/2) of N3 patients were down-staged to ypN0. There were 3 patients who were down-staged (2 N2 to N1, and 1 N3 to N2), but not to ypN0. At surgery, 34% (44/128) of patients had no change, and 19% (24/129) progressed in LN staging.

Pre vs Post NAC Nodal StagePre NAC Nodal StageypN0ypN1ypN2ypN3TotalcN16044222128cN2626317cN3  112Total6646296147

Conclusions: We confirmed that upon achieving a complete response of the primary tumor that there was also a pathologic complete response in the LN. About 53% of patients had no change or progression of LN involvement following NAC.

Citation Format: Blumencranz P, Habibi M, Treece T, Blumencranz L, Yoder E, Audeh W, Carter E, McNaughton L, Roussos J, Shivers S, Acs G, Cox C, MINT Investigators Group. Neoadjuvant chemotherapy for breast cancer: Nodal downstaging is highly correlated with pathological complete response [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 PD8-04.

Abstract P5-15-08: Economic Impact of MammaPrint (70-gene signature) in a clinical high risk population: A 10yr Markov model, 6,000-patient retrospective analysis of US claim data

Background: MINDACT provided evidence that MammaPrint (MP) can identify patients (pts) with early-stage breast cancer (ESBC) who can safely forego adjuvant chemotherapy (CT). As a result, 46% of clinicopathologically high-risk pts were spared from unnecessary CT toxicities. This study investigates direct and indirect costs for pts and payers during ESBC treatment regimens. The study objective was to quantify average cost of care and savings in a clinical high-risk group where the value of CT is unclear, and MP demonstrates economic and clinical impact. Methods: Risk assessment was based on 6,000 MP tests performed on BCBS members (2016-17). CT claims were retrospectively analyzed utilizing a Blue Cross Blue Shield (BCBS) member database (January-December 2016). Case data was restricted to HR+HER2- ESBC and filtered by authorization for the MP test. All CT claims were including, but not limited to standard of care (SOC) systemic drugs such as cyclophosphamide, docetaxel, paclitaxel and doxorubicin. HCPCS codes were utilized to filter member CT claims. Exclusion criteria: <3 SOC CT claims and previous history of BC. A hybrid decision tree-Markov model was used to estimate cost effectiveness of MP compared to modified Adjuvant Online (mAOL) from a US healthcare payer perspective over a 10yr timeframe. Overall, distant metastasis free survival, and test-utility scores were collected from MINDACT for HR+HER2- pts, and costs derived from the BCBS registry and literature (2016 US dollars). Two scenarios were modelled (1) all women classified as high-risk received CT plus endocrine therapy (ET) while low-risk pts received ET; (2) MP guided treatment was modelled based on the IMPACT study (91% MP Low Risk pts received ET and 83% MP High Risk pts received CT). Outcome measures were quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs). Results: The majority, 3,540 (59.0%) pts were Low Risk or could safely forgo CT; 2,460 (41.0%) were High Risk. The primary driver for cost differences was whether all services were performed in a physician office ($4.6M) or an outpatient setting ($2M). Including provider settings (inpatient, outpatient, emergency), SOC CT regimens and related services the final average amount authorized was $39,675 per patient. In the first scenario, MP guided treatment was associated with a 0.06 QALY gain (0.05 in scenario 2) compared to mAOL. For cost savings and QALY gain MP was dominant over mAOL in both scenarios. Budget impact analysis estimated cost savings of 88.2- 96.6 million dollars based on BCBS registry data. Given the new cases of BC that are expected to be diagnosed in women in the U.S. annually, pts covered in this population by BCBS (˜30%) and MP eligible cohort (˜36K pts), projected cost savings are estimated at 529.2-644.3 million dollars per annum for the health insurer. Conclusions: CT was associated with significant annual costs from both patient and payer perspectives. As demonstrated in MINDACT, less treatment for some pts is optimal without risk to safety or survival. These findings suggest that MP is cost effective and provides substantial value by sparing pts from toxicities, both therapeutic and financial.

Citation Format: Blumencranz LE, Høst-Ragab A, Retèl VP, Garlich H, Hwang C, Neijenhuis S, Habibi M, Audeh W. Economic Impact of MammaPrint (70-gene signature) in a clinical high risk population: A 10yr Markov model, 6,000-patient retrospective analysis of US claim data [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 P5-15-08.

Development of a helicon ion source: Simulations and preliminary experiments

In the present context, the extraction system of a helicon ion source has been simulated and constructed. Results of the ion source commissioning at up to 20 kV are presented as well as simulations of an ion beam extraction system. Argon current of more than 200 μA at up to 20 kV is extracted and is characterized with a Faraday cup and beam profile monitoring grid. By changing different ion source parameters such as RF power, extraction voltage, and working pressure, an ion beam with current distribution exhibiting a central core has been detected. Jump transition of ion beam current emerges at the RF power near to 700 W, which reveals that the helicon mode excitation has reached this power. Furthermore, measuring the emission line intensity of Ar ii at 434.8 nm is the other way we have used for demonstrating the mode transition from inductively coupled plasma to helicon. Due to asymmetrical longitudinal power absorption of a half-helix helicon antenna, it is used for the ion source development. The modeling of the plasma part of the ion source has been carried out using a code, HELIC. Simulations are carried out by taking into account a Gaussian radial plasma density profile and for plasma densities in range of 10¹⁸-10¹⁹ m^-3. Power absorption spectrum and the excited helicon mode number are obtained. Longitudinal RF power absorption for two different antenna positions is compared. Our results indicate that positioning the antenna near to the plasma electrode is desirable for the ion beam extraction. The simulation of the extraction system was performed with the ion optical code IBSimu, making it the first helicon ion source extraction designed with the code. Ion beam emittance and Twiss parameters of the ellipse emittance are calculated at different iterations and mesh sizes, and the best values of the mesh size and iteration number have been obtained for the calculations. The simulated ion beam extraction system has been evaluated using optimized parameters such as the gap distance between electrodes, electrodes aperture, and extraction voltage. The gap distance, ground electrode aperture, and extraction voltage have been changed between 3 and 9 mm, 2-6.5 mm, and 10-35 kV in the simulations, respectively.

Crumpling-based soft metamaterials: the effects of sheet pore size and porosity

Crumpled-based materials are relatively easy to fabricate and show robust mechanical properties for practical applications, including meta-biomaterials design aimed for improved tissue regeneration. For such requests, however, the structure needs to be porous. We introduce a crumpled holey thin sheet as a robust bio-metamaterial and measure the mechanical response of a crumpled holey thin Mylar sheet as a function of the hole size and hole area fraction. We also study the formation of patterns of crease lines and ridges. The area fraction largely dominated the crumpling mechanism. We also show, the crumpling exponents slightly increases with increasing the hole area fraction and the total perimeter of the holes. Finally, hole edges were found to limit and guide the propagation of crease lines and ridges.

Combination of H120 and 1/96 avian infectious bronchitis virus vaccine strains protect chickens against challenge with IS/1494/06 (variant 2)-like infectious bronchitis virus

Avian infectious bronchitis (IB) is a worldwide chicken disease, caused by avian infectious bronchitis virus (IBV) which infects all commercial poultry lines. The present study was done to evaluate protection caused by two different serotype vaccines (Massachusetts and 793/B) in order to evaluate protection against challenge with IS/1494/06-like virus (variant 2-like virus), which is prevalent in the Middle East. SPF chickens were divided into four groups (n = 20). First and second group as negative control group and non-vaccinated-challenged group received no vaccine. Groups 3 and 4 received H120-H120 and H120-1/96 IBV vaccine strains at the 1st and 14th day, respectively. Twenty one days after last vaccination, non-vaccinated-challenged group and vaccinated group were challenged using variant 2-like IBV. Serum samples were collected before challenge to measure humoral immune response of chickens. Five days after challenge, the tissue samples from the trachea, lungs and kidneys were taken to evaluate cilliary activity, viral load (quantitative real-time RT-PCR), and histopathological evaluation. Clinical sign scores were also recorded after challenge. Overall, the results showed a protective efficacy of the used vaccination program. Best cross protection (69.2%) was obtained in the H120-1/96 vaccinated group. Virus replication of the challenged virus in H120-1/96 group compared with H120-H120 group showed a significant reduction of viral load in trachea (1.5×103 compared to 503) and kidneys. Clinical sign scores of the challenged groups showed significant effect of the vaccination program to reduce clinical signs. The trachea pathological scores and histopathological findings in the lungs and kidneys also confirmed better protective efficacy of vaccinated groups. In conclusion, using combination of heterologous IBV vaccine serotypes (Massachusetts and 793/B) would be a better strategy to control variant 2-like viruses, but more evaluation is needed using other circulating isolates to find the best combination of vaccines.

Deep learning with word embeddings improves biomedical named entity recognition

MOTIVATION

Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult.

RESULTS

We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall.

AVAILABILITY AND IMPLEMENTATION

The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/ .

CONTACT

habibima@informatik.hu-berlin.de.

Aqueous extract from Orthosiphon stamineus leaves prevents bladder and kidney infection in mice

BACKGROUND

Extracts from the leaves of Orthosiphon stamineus are used in phytotherapy for treatment of uncomplicated urinary tract infections.

PURPOSES

Evaluation of an aqueous extract against infection with uropathogenic Escherichia coli in vivo; investigation of underlying microbiological mechanisms.

STUDY DESIGN

In vivo studies in mice and in vitro investigations on cytotoxicity, antiadhesive potential, influence on bacterial gene expression and quorum sensing.

METHODS

Extract OWE was prepared by hot water extraction. For in vivo studies BALB/c mice were used in an UPEC infection model. The effect of OWE on bacterial load in bladder/kidney tissue was monitored in pre- and posttreatment. Cytotoxicity of OWE against different UPEC strains, T24 bladder/A498 kidney cells, gene expression analysis, monitoring of phenotypic motility and quorum sensing was investigated by standard methods of microbiology.

RESULTS

OWE was quantified (UHPLC) according to the content of rosmarinic acid, cichoric acid, caffeic acid. Three- and 5-day treatment of animals with OWE (750mg/kg) after transurethral infection with UPEC CFT073 reduced the bacterial load in bladder and kidney, similar to norfloxacin. Four- and 7-day pretreatment of mice prior to the infection with UPEC NU14 reduced bacterial bladder colonization. In vitro investigations indicated that OWE (≤2mg/ml) has no cytotoxic or proliferation-inhibiting activity against different UPEC strains as well as against T24 bladder and A498 kidney cells. OWE exerts a dose dependent antiadhesive activity against UPEC strains NU14 and UTI89. OWE reduced gene expression of fimH, but evoked increase of the expression of motility/fitness gene fliC. Increase of bacterial motility on gene level was confirmed by a changed bacterial phenotype by an increased bacterial motility in soft agar assay. OWE inhibited in a concentration-dependent manner bacterial quorum sensing.

CONCLUSION

OWE is assessed as a strong antiadhesive plant extract for which the traditional use in phytotherapy for UTI might be justified.

Comparison of anterior segment parameter values obtained with Scheimpflug-Placido topographer, optical low coherence reflectometry and noncontact specular microscopy in morbid obesity

OBJECTIVE

To investigate the measurement of anterior segment parameters using Sirius Scheimpflug-Placido topographer, Lenstar optical low coherence reflectometry (OLCR), and noncontact specular microscopy (SM) in morbidly obese and nonobese subjects.

PATIENTS AND METHODS

Twenty-eight morbidly obese subjects (BMI ≥ 40; Group 1) and 28 age- sex-matched healthy nonobese subjects (BMI 18.50-24.99; Group 2) were included in this study. Anterior segment parameters were measured by Scheimpflug-Placido topographer and OLCR. Corneal endothelial cell parameters were measured by non-contact SM. The group data were analyzed using the Mann-Whitney U test and Student's t-test. Bland-Altman plots were used to assess agreement among the instruments, and 95% limits of agreement (LoA) for each comparison were calculated.

RESULTS

In group 1, the mean CCT by Scheimpflug-Placido topographer, OLCR, and noncontact SM were 549.44±30.10 µm, 544.15±31.48 µm, and 541.59±29.87 µm respectively. In group 2, the mean CCT by Scheimpflug-Placido topographer, OLCR, and noncontact SM were 531.0±22.09 µm, 523.15±21.39 µm, and 521.12±21.70 µm respectively. Mean CCT values obtained by the three methods were significantly higher in the morbidly obese than the nonobese subjects. In both groups, mean CCT was significantly higher when measured by Scheimpflug-Placido topographer than by OLCR and noncontact SM, and mean AD and ACD were significantly higher when measured by Scheimpflug-Placido topographer than OLCR. No significant differences were found between mean corneal curvature and corneal astigmatism when measured by Scheimpflug-Placido topographer and OLCR.

CONCLUSIONS

The mean CCT of the morbidly obese subjects were significantly higher than the nonobese subjects when measured by all three methods. The CCT values obtained by Scheimpflug-Placido topographer were significantly higher than those by OLCR and SM.

Effect of dietary fish oil with or without vitamin E supplementation on fresh and cryopreserved ovine sperm

This study was carried out to determine whether dietary fish oil (FO) with or without vitamin E (VE) supplementation would have a beneficial effect on characteristics of fresh and cryopreserved ovine sperm. Sixteen rams were allotted to four groups and fed one of the four diets: control diet (CON; without FO and VE supplementation), VE diet supplying 200 IU VE/day.ram, FO diet containing 2.5% (dry matter basis) FO, and OVE diet containing FO and VE. Semen samples were collected at Weeks 7, 9 and 11 for evaluation of seminal quality. Frozen samples from Weeks 9 and 11 were subjected to computer-assisted semen analysis (CASA). Seminal volume, percentage of sperm with normal morphology and intact acrosome and seminal concentration of malondialdehyde were increased in FO rams (P < 0.05). In VE rams, semen volume and percentage of morphologically normal sperm were higher compared with CON rams; however, in OVE rams these attributes were not different from those in CON rams. Other traits in fresh semen were not affected by the diet. Fish oil alone negatively affected the sperm viability, but not motility, of the frozen–thawed semen; however, simultaneous supplementation with FO and VE resulted in increased percentage of morphologically normal sperm, motility, and viability. The percentages of CASA type A (showing rapid progressive motility) and type B (showing medium progressive motility) sperm were higher in OVE compared with other groups. Vitamin E supplementation decreased the beat-cross frequency values compared with other groups. Other CASA parameters were not affected by the diets. In conclusion, dietary FO and VE in the breeding season of ram, generally, do not cause significant changes in fresh sperm quality but, for cryopreservation of sperm, supplementation of the diet with an antioxidant such as VE may be beneficial when polyunsaturated fatty acids are added to the diet.

Nesfatin-1 hormone levels in morbidly obese patients after laparoscopic sleeve gastrectomy

OBJECTIVE

To investigate changes in body mass index (BMI) and nesfatin-1 levels in patients with morbid obesity who had undergone laparoscopic sleeve gastrectomy (LSG).

PATIENTS AND METHODS

Blood samples were collected from, and the BMI calculated of 30 morbidly obese patients pre-surgery and at 3 and 6 months post-surgery. Nesfatin-1 hormone levels were measured using enzyme-linked immunosorbent assay (ELISA). Descriptive statistical analysis of the data was performed using Kruskal-Wallis variance analysis, one-way ANOVA, and the Bonferroni-Dunn test. The correlations between continuous variables not displaying normal distribution and those displaying normal distributions were analyzed using the Spearman correlation test and the Pearson correlation test, respectively.

RESULTS

The mean age of the 30 patients was 41.23 ± 10.37 years. The mean BMI values (kg/m2) were 49.30 ± 7.92, 39,48 ± 7.32, and 34.39 ± 7.56 presurgery, three months post-surgery, and six months post-surgery, respectively (p < 0.001). Mean nesfatin-1 levels (ng/ml) were 22.80 ± 14.16, 60.23 ± 52.92, and 96.99 ± 40.20 presurgery, three months post-surgery, and six months post-surgery, respectively (p < 0.001). The postoperative months 3 and 6 BMI values were significantly lower than the preoperative BMI value and the postoperative month 6 BMI value was significantly lower than the postoperative month 3 BMI value (p < 0.001). The postoperative months 3 and 6 nesfatin-1 levels were significantly higher than the preoperative nesfatin-1 levels. A negative correlation was found between age and preoperative nesfatin-1 values (p = 0.001, r = -0.0557).

CONCLUSIONS

Observation of significant increases in nesfatin-1 hormone levels in morbidly obese patients who had undergone LSG indicate that nesfatin-1 has important anorexigenic effects post-surgery and may be an important component of future obesity treatments.

Recognizing chemicals in patents: a comparative analysis

Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data. Here, we evaluate the two state-of-the-art chemical NER tools, tmChem and ChemSpot, on four different annotated patent corpora, two of which consist of full texts. We study the overall performance of the tools, compare their results at the instance level, report on high-recall and high-precision ensembles, and perform cross-corpus and intra-corpus evaluations. Our findings indicate that full patents are considerably harder to analyze than patent abstracts and clearly confirm the common wisdom that using the same text genre (patent vs. scientific) and text type (abstract vs. full text) for training and testing is a pre-requisite for achieving high quality text mining results.

Does diazinon-sprayed market melon alter cholinesterase activity in healthy consumers? A randomized control trial

OBJECTIVE

Food contributes in measurable body burden of the widely used organophosphate pesticides. We designed a randomized controlled open label trial in Mashhad University Hospital in Iran, to study the possible alterations in cholinesterase activity resulting from consuming market melon known to be exposed to diazinon.

PATIENTS AND METHODS

Fifty-three young healthy volunteers were recruited. Participants were randomized to consume 250 g per day of organic (N = 22) vs. market melon (N = 31) during fifteen days. The primary outcome was the variation of red blood-cell (RBC) cholinesterase activity between day 15 (after) and day 0 (prior the intervention). The secondary outcome was a variation of the plasma cholinesterase activity between both dates.

RESULTS

Baseline RBC [5.21 ± 0.93 vs. 5.53 ± 0.99 IU/mL, mean ± SD] and plasma cholinesterase activities [54.0 ± 8.1 vs. 57.4 ± 8.6%] did not significantly differ between organic and market melon-exposed participants, respectively. RBC [5.86 ± 1.27 vs. 5.11 ± 1.2 IU/mL] and plasma cholinesterase activities [58.7 ± 10.0 vs. 50.5 ± 13.0%] significantly increased in organic melon-exposed vs. market melon-exposed participants (p = 0.002 and p = 0.001, respectively).

CONCLUSIONS

RBC and plasma cholinesterase activities significantly improved after eating organic instead of market melon during fifteen days. However, the consequences on the health of the observed cholinesterase alterations attributed to diazinon dietary intake remain to be determined.

The retinal nerve fiber layer, choroidal thickness, and central macular thickness in morbid obesity: an evaluation using spectral-domain optical coherence tomography

OBJECTIVE

To assess the effect of morbid obesity on retinal nerve fiber layer (RNFL) thickness, central macular thickness (CMT), retinal ganglion cell (RGC), choroidal thickness (CT), central corneal thickness (CCT), and intraocular pressure (IOP).

PATIENTS AND METHODS

Sixty-seven patients defined as having morbid or class III obesity (BMI ≥ 40; Group 1) scheduled to undergo sleeve gastrectomy surgery and 29 nonobese patients (BMI 18.50-24.99; Group 2) underwent complete ophthalmic examination for measurement of IOP, CT, RNFL thickness, CMT, RGC, and CCT. RNFL thickness, CMT, and RGC were measured using spectral-domain optical coherence tomography (SD-OCT). CT measurement was performed using the enhanced depth imaging technique of the SD-OCT. The group data were analyzed and compared using the Mann-Whitney U test and Student's t-test. The relationship between the clinical ocular variables and obesity was analyzed using the Spearman's rank correlation test.

RESULTS

The mean IOP and CCT of Group 1 were found to be significantly higher (p < 0.001) and the mean RNFL, RGC, and CT significantly lower (p < 0.05) than those of Group 2. While Group 2 was found to have a slightly larger cup-to-disc ratio and Group 1 to have a thinner CMT, the differences between Groups 1 and 2 regarding these variables were not found to be statistically significant (p = 0.322 and p = 0.072, respectively). The results of Spearmen correlation analysis indicated the existence of a moderately positive correlation between IOP and BMI (p < 0.001; r = 0.5-0.6).

CONCLUSIONS

We have demonstrated by SD-OCT that morbid obesity may have a significant influence on RNFL, RGC, and CT. Morbid obesity may induce inflammatory, hormonal, and metabolic changes.