bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3341: Rural and urban disparities in colonoscopy use persisted despite cost-sharing reduction among Medicare beneficiaries
Authors: Lee Min Jee , Jenkins Wiley , Boakye Eric Adjei , Ganai Sabha 
Published: August 2019

Abstract
Background: Due to passage of the Patient Protection and Affordable Care Act (ACA), Medicare began waiving Part B deductibles and eliminating coinsurance for all colonoscopies in 2011. As rural populations have significantly lower income than urban, there is hope the cost reduction would decrease rural screening disparities. We thus examined rural-urban colonoscopy use pre-/post-ACA implementation.
Methods: We used Behavioral Risk Factor Surveillance System data (2008-2016) to examine colonoscopy utilization for two years pre-ACA (2008 and 2010) and three years post-ACA (2012, 2014, and 2016) with stratification by rural/urban residence. Multivariate logistic regression was used to examine the differences in screening likelihood across rural and urban groups, while controlling for other factors such as age, sex, marital status, race/ethnicity, household income, educational attainment, gastroenterologist availability, exercise, smoking, and years.
Results: Of the 302,941 eligible Medicare beneficiaries, 203,426 (67.2%) received a colonoscopy. Colonoscopy receipt increased from 62.8% pre-ACA to 70.2% post-ACA years (p&lt;.001). Across rural-urban areas, we found a significant increase in the receipt of colonoscopy from pre- to post-ACA (p&lt;.001). The receipt of colonoscopy was higher among urban residents (69.2%) compared to rural residents (63.5%, p&lt;.001). After adjusting for covariates, urban residents were more likely to receive colonoscopy both pre-ACA (OR=1.11, 95% CI: 1.06-1.15) and post-ACA (OR=1.11, 95% CI: 1.06-1.16).
Conclusions: Despite cost-sharing reduction of Medicare coverage for colonoscopy, rural and urban differences in colonoscopy use persisted over time among Medicare beneficiaries. Although the receipt of colonoscopy increased over time, the gap between rural and urban populations has remained.
Colonoscopy Use Before and After Implementation of The ACAPreACAPost ACARuality%OR95%CI%OR95%CIRural59.4166.61Urban64.91.111.061.1572.11.111.061.16
Citation Format: Min Jee Lee, Wiley Jenkins, Eric Adjei Boakye, Sabha Ganai. Rural and urban disparities in colonoscopy use persisted despite cost-sharing reduction among Medicare beneficiaries [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3341.
Abstract 3344: Effect of anticoagulation on the cancer stage at time of diagnosis of endometroid adenocarcinoma in a cohort of postmenopausal patients
Authors: Shukr Ghadear , Pham Tra , Buekers Thomas 
Published: August 2019

Abstract
Objectives: We sought to determine whether postmenopausal women on chronic anticoagulation were diagnosed with endometrial cancer at an earlier stage.
Methods: A retrospective case-control study of women at a tertiary care medical center with a diagnosis of Endometrioid Adenocarcinoma on chronic anticoagulation at time of diagnosis in comparison with patients not on anticoagulation was performed. Patients with personal history of cancer, including breast cancer, non-postmenopausal bleeding, and non-Endometrioid Adenocarcinoma histopathology were excluded. Anticoagulation was defined as use of Enoxaparin, Warfarin, Apixaban, Rivaroxaban or Clopidogrel. Indications for anticoagulation included atrial fibrillation, deep vein thrombosis/pulmonary embolism, or stroke. The primary outcome was Endometrioid Cancer stage (I, II, III/IV and X). The secondary outcomes were duration of bleeding to presentation and presentation to diagnosis. Statistical analysis was performed using Wilcoxan-Rank Sum Test and Cochran-Armitage Trend Test.
Results: 25 postmenopausal patients met the inclusion criteria for being treated in the last 10 years. 100 controls not on anticoagulation (non-AC) were identified for a 4:1 comparison to obtain a 2-sided alpha level of 0.05. Results were divided into 3 groups: 1) All patients, 2) Non-white patients, 3) White patients. Subjects were controlled for age (P&lt;0.001) and BMI (P&lt;0.049). The results indicated that non-AC patients were more likely to be diagnosed at Stage 1 when compared to the AC patients in all 3 categories. The trend was not statistically significant for the non-white patients (p=0.133), but was statistically significant in the overall population (p&lt;0.001) and White patients (p&lt;0.001). No statistical significance was detected for duration from bleeding to presentation and presentation to diagnosis between the AC and non-AC groups. However, median days from bleeding to presentation are considerably larger for the non-AC than AC (Group 1: 42 vs 14 days, Group 2: 75 vs 33 days Group 3: 30 vs 14 days, respectively).
Conclusion: Non-anticoagulated patients had an earlier cancer stage at diagnosis. Although anticoagulated patients may present earlier, they have advanced cancer stage. These findings should prompt immediate evaluation of patients on chronic anticoagulation to optimize oncologic management and prognosis.
Citation Format: Ghadear Shukr, Tra Pham, Thomas Buekers. Effect of anticoagulation on the cancer stage at time of diagnosis of endometroid adenocarcinoma in a cohort of postmenopausal patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3344.
Abstract 3353: Four vs six cycles of docetaxel and cyclophosphamide (TC) in early stage triple-negative breast cancer
Authors: Basu Aparna , Mohammed Hadi A. , Mahmood Sharmeen , Dabak Vrushali , Loutfi Randa 
Published: August 2019

Abstract
Background: ABC trials established the use of non-anthracycline containing regimen, docetaxel and cyclophosphamide (TC) in the adjuvant setting in early stage breast cancer. In clinical practice, TC is commonly used in Stage I Triple-Negative Breast Cancer (TNBC). However, no specific recommendations exist in literature, regarding the number of cycles that can be used. i.e. TC4 vs TC6. Our aim, was to determine if TC4 is non-inferior to TC6 when used as adjuvant therapy in early stage TNBC.
Methods: We retrospectively reviewed 77 patients who were diagnosed with early stage TNBC between 2007 to 2017, at our institution who had received either TC4 or TC6 as adjuvant therapy. The number of cycles the patients received were based on provider preference. The two groups (TC4, TC6) were compared in regard to stage of cancer at diagnosis based on AJCC 7thedition, grade of adverse events, recurrence and death from breast cancer recurrence.
Results: Out of 77 patients, based on T stage, 25 (32.5%) were T1b, 38(49.4%) were T1c, 13(16.9%) were T2 and 1(1.3%) was T3. All patients were node negative. 53(68.8%) received TC4 and 24(31.2%) received TC6. Regarding side effects, adverse of any grade were seen in 42(79.2%) patients who received TC4 and 23(95.8%) in patients who received TC6(p=0.091). Adverse events which were grade 3 or higher were seen in 7(15.9%) in TC4 group and 3(13%) in the TC6 group (p=1.000). Recurrence in the TC4 group was seen in 4 patients (7.5%) and 3(12.5%) patient in the TC6 group (p=0.259). Death due to breast cancer recurrence was seen in 1 patient (1.9%) in the TC4 group and 1(4.1%) patient in the TC6 group.
Conclusions: In this limited series, TC4 appears to be equally effective to TC6, with fewer adverse events of any grade. However, a longer follow up and a larger patient base is required to be studied for a more definitive conclusion.
Citation Format: Aparna Basu, Hadi A. Mohammed, Sharmeen Mahmood, Vrushali Dabak, Randa Loutfi. Four vs six cycles of docetaxel and cyclophosphamide (TC) in early stage triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3353.
Abstract 3354: Patterns of care for patients with non-operable T1-4 N+ M0 non-small cell lung cancer in the US and outcomes with radiation or chemotherapy monotherapies
Authors: Kim Ellen , Daly Megan E. , Westover Kenneth , Murphy James , Mitin Timur 
Published: August 2019

Abstract
Background Standard management of unresectable N+ M0 non-small cell lung cancer (NSCLC) is concurrent chemoradiation (CRT). However, some patients may receive only radiation therapy (RTmono) or chemotherapy (CTmono) as monotherapies. The primary aim of this study was to investigate the patterns of care in the US and analyze the outcomes achieved with monotherapies.
Methods Patients in the National Cancer Database (NCDB) diagnosed in 2004-2013 with N+ M0 NSCLC who did not undergo surgery and received monotherapy with either high dose radiation alone (RTmono) or chemotherapy alone (CTmono) were studied. Patient characteristics and overall survival (OS) were compared with descriptive statistics (chi-square, Kruskal-Wallis, logistic regression), Kaplan-Meier and stratified Cox models, and restricted mean survival times (RMST); all used alpha of 0.05.
Findings 74,867 patients received CRT (10,915, 15%), CTmono alone (34,978, 47%), RTmono (2,396, 3%), or no treatment (26,578, 36%). In a multivariable model, RTmono was associated with non-Medicare insurance, academic or research facility, Western geography, lower T and N stages, and older age. CTmono had better RMST compared to RTmono: at 3 years, average survival was 17.9 vs 16.1 months (difference 1.8, 95% CI 1.3-2.3); at 5 years, average survival was 21.6 vs 18.7 months (difference 2.9, 95% CI 2.2-3.6). In stratified Cox models, improved survival was associated with female gender, White race, private insurance, metropolitan location, lower Charlson comorbidity score, lower T and N stage, smaller tumor, younger age, and later year of diagnosis.
Interpretation Despite the established benefits of CRT, only 15% of non-operable N+ M0 NSCLC US patients received definitive CRT. Future clinical studies should focus on patients not receiving concurrent CRT, as outcomes with monotherapies (RTmono or CTmono) are suboptimal.
Note: This abstract was not presented at the meeting.
Citation Format: Ellen Kim, Megan E. Daly, Kenneth Westover, James Murphy, Timur Mitin. Patterns of care for patients with non-operable T1-4 N+ M0 non-small cell lung cancer in the US and outcomes with radiation or chemotherapy monotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3354.
Abstract 3357: The fibrolamellar registry: A model for the study of rare diseases
Authors: Desmond Michelle , Latone Julie , Lett Siobhan , Migler Rachael D. , Simon Elana P. , Simon Sanford M. 
Published: August 2019

Abstract
Advances in genomics and proteomics have enabled more precise characterizations of tumors with the consequence that many cancers are being segregated into smaller categories. With this larger number of categories, more cancers are being categorized as rare. The downside to such categorizations is that the reduced numbers of patients in each category makes it difficult to gather enough information about each cancer. We are a group of patients and caregivers who have joined together to form a repository for patient-shared data and reports in an IRB-approved, non-profit medical registry for the rare and usually lethal childhood liver cancer, fibrolamellar hepatocellular carcinoma (FLC). Since the Fibrolamellar Registry is patient-run and patient-owned, we have the trust of the patient community that the records will not be sold for profit. This has enabled us, in our first two years, to gather detailed medical records, scans and tests from over 140 patients. With input from scientists and clinicians who study FLC, we have written 600 questions of specific interest to this disease. Most of our patients have also opted to allow these medical records to be shared with a tissue FLC repository that already has samples from 110 patients. We have initiated two different collaborations with the clinical-research community to explore the records and our patients have been answering additional questions when pertinent to a particular study. Our ability to gather so many records for what is a rare cancer comes from our ability to involve patients from across institutions and across the globe. We are working with other patient groups and we feel that the Fibrolamellar Registry could be a model for gathering and organizing data for many rare diseases.
Citation Format: Michelle Desmond, Julie Latone, Siobhan Lett, Rachael D. Migler, Elana P. Simon, Sanford M. Simon. The fibrolamellar registry: A model for the study of rare diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3357.
Abstract 3368: Prevalence and significance of drug-drug interactions among patients with lung cancer
Authors: Rashdan Sawsan , Yang Hui , Le Tri , Hsieh David , Alvarez Carlos A. , Gerber David 
Published: August 2019

Abstract
IMPORTANCE: Significant drug-drug interactions may exclude patients from clinical trials and complicate routine clinical care. Prevalence and significance of drug-drug interaction (DDI) among cancer populations is unknown.
OBJECTIVE: To determine the rate of all potential drug interactions as well as the rate of major DDIs among individuals newly diagnosed with lung cancer in a national cohort.
DESIGN, SETTING, AND PARTICIPANTS: We performed a retrospective cross-sectional study of adult patients in the United States Veterans’ Affairs (VA) medical system diagnosed with lung cancer between 2003 and 2016. Data were obtained from the VA Corporate Data Warehouse. Lists and categorization of potential DDIs were obtained from the Flockhart table provided by Indiana University School of Medicine. A list of commonly prohibited medications that are associated with major DDI, was determined after 11 clinical trials protocols of tyrosine kinase inhibitors in lung cancer treatment were reviewed.
MAIN OUTCOMES AND MEASURES: The primary endpoint was the prevalence of exposure to all potential DDI during the three months leading up to and including the date of lung cancer diagnosis. The secondary endpoint was the prevalence of exposure to major DDIs (prohibited medications).
RESULTS: Overall, 280 068 patients were included in the study. Mean age was 70 years, 98% were male, and 72% were white. Overall, 55.9% of patients were prescribed medications associated with potential DDI, and 5.1% of patients were prescribed medications with major DDIs that would be prohibited in
certain clinical trials. Among the 20 most commonly prescribed drugs associated with potential DDI, only two (gemfibrozil and phenytoin) were associated with major DDI.
CONCLUSIONS AND RELEVANCE: Medications with potential DDI are commonly prescribed to patients with lung cancer. However, only about 5% of patients are prescribed medications with major DDIs that would be prohibited in certain clinical trials. Further studies to determine the true clinical risk of all potential DDIs are warranted.
Note: This abstract was not presented at the meeting.
Citation Format: Sawsan Rashdan, Hui Yang, Tri Le, David Hsieh, Carlos A. Alvarez, David Gerber. Prevalence and significance of drug-drug interactions among patients with lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3368.
Abstract 3374: Assessing the impact of neoantigen load on checkpoint blockade efficacy
Authors: Kosaloglu-Yalcin Zeynep , Frentzen Angela , Premlal Ashmitaa Logandha Ramamoorthy , Greenbaum Jason , Sette Alessandro , Peters Bjoern 
Published: August 2019

Abstract
Mutations acquired during oncogenesis can result in so-called neoantigens, i.e. mutation-bearing peptides that have the potential to be bound by HLA molecules and recognized by T cells. Neoantigens were suggested to be crucial for the outcome of immune checkpoint therapies and accordingly, the neoantigen load of a tumor is often being used to predict therapy outcome. Current approaches utilize HLA binding predictions to rank peptides, assuming that neoepitopes are ranked towards the top. The neoantigen load of a given tumor is then usually defined as the number of peptides binding above a certain threshold. Using this approach some reports found a very strong correlation of neoantigen load and response to checkpoint blockade therapy while others found a better correlation when mutational load was used instead. However, comparing results between studies is hard because they used different tools and thresholds to identify mutations, and applied different criteria to prioritize their set of mutated peptides. We sought to overcome this lack of uniformity in re-analyzing data from several published checkpoint blockade therapy studies to consistently define the mutational burden and neoantigen load, and correlate them with therapy outcomes
We obtained sequencing data from checkpoint blockade studies deposited in NCBI dbGaP and run all datasets through our in-house mapping and variant calling pipelines. Neoepitope candidates were predicted and scored using our previously published pipeline. We applied different scoring schemes to define the neoantigen load which were based on HLA binding predictions with varying thresholds and different metrics used (i.e. predicted IC50 vs. percentile rank). We found that the exact definition of neoantigen load has a major impact on how well this metric performs in predicting checkpoint blockade therapy outcome. Furthermore, we implemented a likelihood score which is based on data of known immunogenic neoantigens and describes the likelihood of a predicted neoantigen to be immunogenic. Based on our preliminary analysis to date, we found that the cumulative likelihood score of a patient is a good predictor of checkpoint blockade therapy outcome, outperforming tumor mutational burden and predicted neoantigen load in several cohorts.
Citation Format: Zeynep Kosaloglu-Yalcin, Angela Frentzen, Ashmitaa Logandha Ramamoorthy Premlal, Jason Greenbaum, Alessandro Sette, Bjoern Peters. Assessing the impact of neoantigen load on checkpoint blockade efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3374.
Abstract 3375: leveraging protein dynamics to identify mutational hotspot communities in cancer driver genes
Authors: Kumar Sushant , Clarke Declan , Gerstein Mark 
Published: August 2019

Abstract
Large-scale exome sequencing of tumor genomes has enabled the identification of cancer driver genes using recurrence analysis and clustering-based approaches. Some of these methods also employ 3D protein structural data to identify missense mutational hotspots in many cancer-associated genes. However, in determining such mutational clusters in protein structures, a majority of these approaches overlook the role of protein dynamics. In this work, we present a novel framework to identify cancer driver genes using a more sensitive search of mutational hotspot communities on protein structures by incorporating models of protein dynamics. We applied our method to the TCGA pan-cancer atlas missense mutation catalog to identify cancer genes with hotspot mutational clusters within their associated PDB structures. Overall, our analysis predicts one or more mutational hotspot within the resolved structures of known as well as novel cancer driver genes. Ontological enrichment analysis implicates the roles of genes with predicted hotspots in vital biological processes, including cell differentiation, cell proliferation, signal transduction, kinase activity, and nucleotide binding. Furthermore, a comparison between our approach with previous 3D structure-based cancer hotspot detection methods suggests that the including protein dynamics significantly improves the identification of additional putative driver genes. In summary, our proposed framework predicts novel cancer driver genes and provides mechanistic insight into cancer progression through the lens mutational hotspots.
Citation Format: Sushant Kumar, Declan Clarke, Mark Gerstein. leveraging protein dynamics to identify mutational hotspot communities in cancer driver genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3375.
Abstract 3384: Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection
Authors: Pritykin Yuri , Leslie Christina 
Published: August 2019

Abstract
Recent studies in mouse models of cancer and chronic viral infection applied genomic assays to profile various states of impaired T cell function and demonstrated that T cell dysfunction is epigenetically imprinted. However, comprehensive characterization of T cell dysfunction across models based on their epigenetic and transcriptional profiles is lacking. We reanalyzed a large collection of recently published chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data sets. After batch effect correction, we observed that epigenetic profiles of dysfunctional tumor-infiltrating T cells and exhausted T cells in chronic viral infection were surprisingly extremely similar. Furthermore, we observed that temporal progression towards dysfunction in chronic infection resembles that in tumorigenesis, and found that T cells committed to becoming dysfunctional early after activation. Motif analysis using generalized linear modeling allowed us to find candidate transcription factors associated with development of dysfunction in both immune settings. This analysis provides a better systematic understanding of cell-intrinsic mechanisms driving different functional states of CD8 T cells and demonstrates the power of systems biology approaches in cancer immunology.
Citation Format: Yuri Pritykin, Christina Leslie. Genome-wide epigenetic and transcriptional comparison of CD8 T cell functional states between mouse models of cancer and chronic viral infection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3384.