tbuckley/cabot-search huggingface dataset:
Objective measures of performance status in cancer: A pilot Alliance study.
Authors: William Allen Wood, Xianming Tan, Natalie Sophia Grover, Angela M. Stover, Arun Kannappan, Philip M Carr, Robert Burkes, Thomas C. Shea, Andrew S. Artz, Steven Michael Devine, Jennifer A. Ligibel, Antonia Vickery Bennett, Ethan M. Basch
Journal: Journal of Clinical Oncology (2018)

284 Background: Clinician-assessed performance status (cPS) is prognostic in oncology. However, cPS may be limited by subconscious bias, and is confined to clinic visits. A more objective PS measure derived from cardiorespiratory fitness (VO2peak) and/or sensor-derived biometrics (activity (A), heart rate (HR), and activity/HR combinations (A/HR)) could better inform treatment selection, trial design, safety monitoring, and outcomes assessment. A multi-site study was conducted to examine the feasibility and utility of VO2peak and sensor-derived biometrics as complements to cPS and patient-reported PS (pPS). Methods: We enrolled 45 patients receiving chemotherapy at 4 institutions in 3 cohorts (solid tumor, hematologic malignancy, bone marrow transplant) to assess the feasibility and usefulness of VO2peak and sensor-derived biometrics. Patients underwent VO2peak prior to a cycle of treatment, wore a sensor for 4 weeks, and self-reported PS, physical function (PF), mental health (MH), and instrumental activities of daily living (IADLs). Sensor-derived variables included A, HR, and A/HR. Spearman’s rank correlations described bivariate relationships. Results: 70% of participants underwent VO2peak testing. 81% provided ≥ 2 weeks of sensor data. At baseline, VO2peak was moderately to strongly correlated with pPS and A/HR (r = 0.44-0.66, p &lt; 0.05). pPS, but not cPS, was correlated with MH, PF, and IADLs (r = 0.58-0.69, p &lt; 0.05). During treatment, pPS, PF, and IADLs were moderately to strongly correlated with A/HR (r &gt; 0.4, p &lt; 0.05). Conclusions: VO2peak testing and biometric sensor deployment were feasible within a multi-institutional setting of cancer patients receiving chemotherapy. Sensor-derived A/HR variables were correlated with underlying fitness, as well as patient-reported functioning throughout treatment. A/HR variables are candidates for further development and validation as digital biomarkers of performance status in cancer patients. Support: UG1CA189823; Clinicaltrials.gov Id: NCT02786628
Informing Physicians of Fatal Overdose Curbs Opioid Prescribing
Authors: Anita Slomski
Journal: JAMA (2018)

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Abstract 20695: Junctional Ectopic Tachycardia in Recent Surgical Era : Clinical Epidemiology, Risk Factors & Outcomes
Authors: Sabikha Alam, Austin Kane, Kevin O Maher, Peter Fischbach, Shriprasad R Deshpande
Journal: Circulation (2016)

Background: JET is common after congenital heart surgeries & has been associated with high mortality (up to 14%). We aim to report JET incidence, risk factors & outcomes in the current era. Methods...
Implementation of a patient experience–focused review at the time of radiation therapy simulation.
Authors: John M. Robertson, Elizabeth Rutka, Hong Ye
Journal: Journal of Clinical Oncology (2018)

211 Background: Anxiety impairs information retention and may lower patient satisfaction. Because anxiety is highest at the time of radiation therapy (RT) simulation, we added a personal patient experience (PX) review of the treatment process focusing on resolution of any outstanding concerns and measured for a benefit using patient satisfaction scores. Methods: A single PX trained Senior Radiation Therapist met patients at simulation and reviewed multiple factors from registration to any outstanding medical issues, with the goal of addressing and resolving all questions. A CMS-approved patient satisfaction tool was recorded during this time to assess for any benefit of this PX review. The tool asks 17 questions in 5 domains (Registration, Facility, Your Treatment, Personal Issues, and Overall Assessment) and calculates an Overall Facility Rating. Tools received between the date of simulation and the date of follow-up were considered an on-treatment evaluation and were used for assessment. Scores were compared with a Mann-Whitney U test. There were no other formal departmental patient satisfaction efforts during this time. Results: Between 2/16 and 6/18 a total of 1369 patients (median 65 yrs; 64% women; 38% breast cancer; 82% curative) were met at simulation by our Senior Therapist spending a median of 23 minutes per patient (range 0 – 117). We received 732 patient satisfaction surveys (median 67 yrs; 61% women; 40% breast cancer; 90% curative) including 98 on-treatment respondents, 69 of whom had the PX review and reported significantly better scores for 10 of the 17 questions and 4 of the 5 domains (Registration p = 0.04, Facility p = 0.03, Personal Issues p = 0.02, Overall Assessment p = 0.002). The PX review was significantly better for the calculated Overall Facility Rating (p = 0.04). Conclusions: The PX review at simulation was associated with significantly higher patient satisfaction scores in 4 of 5 domains, including areas not specifically addressed during the interview (e.g. cleanliness). Improvements of this amount are typically associated with very large improvements in percentile rankings. This intervention was extremely successful but durability of this benefit into the follow up period was not assessed.
Survival gains in multiple myeloma from 2003 to 2014.
Authors: Rafael Fonseca, Anupam B. Jena, Desi Peneva, Zoe Clancy
Journal: Journal of Clinical Oncology (2018)

98 Background: Survival probabilities for patients with multiple myeloma have increased considerably over the past several decades, and a conservative estimate of 5-year survival today is approximately 50%, perhaps higher with optimal treatment. Treatment options for multiple myeloma have grown significantly beginning in 2003 with the approval of bortezomib, followed by approvals for lenalidomide and thalidomide in 2006. The second wave of novel agent approvals began in 2012 with carfilzomib, followed by pomalidomide in 2013. The aim of this study was to estimate the survival gains associated with multiple myeloma therapies after the introduction of novel therapies beginning in 2003 in the United States. Methods: We estimated survival gains for multiple myeloma patients diagnosed in the 5-year period from 2010-2014—who had access to newer therapies like lenalidomide, bortezomib, pomalidomide, and carfilzomib—compared with patients diagnosed in the 5 years prior to the approval of bortezomib (1998–2002). We used data from the Surveillance, Epidemiology, and End Results (SEER) Program cancer registry and a generalized gamma regression survival model. The sample from SEER included patients aged &gt; 18 years who had a diagnosis of multiple myeloma between 1983 and 2014. Results: Of 88,462 patients identified in the full sample, 14,446 patients were diagnosed in 1998–2002 and 25,948 patients were diagnosed in 2010–2014. Overall survival was 51% longer ( P&lt; 0.001) in multiple myeloma patients diagnosed in 2010–2014 than in patients diagnosed in 1998–2002. Patients diagnosed in 2010–2014 had median and mean survival of 1.32 and 2.27 years longer, respectively, than patients diagnosed in 1998–2002. Conclusions: Patients diagnosed with multiple myeloma during 2010–2014 had significant improvement in survival relative to patients diagnosed in 1998–2002. This study found continued improvement in survival in multiple myeloma patients in the most recent 5-years of survival data available, demonstrating the considerable progress made since the wave of multiple myeloma innovation began in 2003.
Differences in comprehension of somatic genomic profiling between younger and older adults with advanced genitourinary cancer.
Authors: Cristiane Decat Bergerot, Paulo Gustavo Bergerot, Joann Hsu, Nazli Dizman, Stacy W. Gray, Sumanta K. Pal
Journal: Journal of Clinical Oncology (2018)

228 Background: Genomic profiling (GP) plays an important role in the care of patients diagnosed with advanced cancer, and has been used to guide clinical decision making. As age has been associated with low health literacy, we sought to determine comprehension of the goals and objectives of GP between younger (age &lt; 65) and older (age ≥65) with genitourinary cancers. Methods: Eligible patients had agreed to receive somatic GP as a part of routine clinical care through a CLIA-certified commercially available platform. Participating physicians conducted a standardized dialogue with patients pertaining to the rationale for and clinical utility of somatic GP. Patients then received an in-person survey lasting approximately 10-15 min and assessing a broad range of perceptions related to GP. Results: Among 47 patients, 62% were characterized as older adults. Diagnoses encountered included kidney (43%), prostate (32%), and bladder (25%). Only older adults perceived any shortcomings in the description of GP. These shortcomings related to the clarity of the descriptions of genomic data, as well as the accuracy, detail and compassion with which this information was conveyed. Older adults demonstrated a very strong reliance on physician input in their decision to obtain somatic GP - 42% of older adults suggested that trust in their physician was among the top three reasons for which they opted to do genomic testing, in contrast to just 10% of younger patients (P = 0.04). Both older and younger patients demonstrated frequent misconceptions pertaining to the role of GP. For example, the majority of younger (78%) and older (52%) patients suggested the test was being performed for prognostic purposes. Both groups also frequently held the notion that somatic testing could identify hereditary cancer-related disorders (younger: 78% vs older: 66%). Conclusions: Detailed surveys of patients with genitourinary cancers reveal varied comprehension of somatic GP between younger and older patients. Interventions to enhance understanding of the principles of GP may be helpful in facilitating shared decision-making, particularly among older patients.
Development and validation of an endoscopic images‐based deep learning model for detection with nasopharyngeal malignancies
Authors: Chaofeng Li, Bingzhong Jing, Liangru Ke, Bin Li, Weixiong Xia, Caisheng He, Chaonan Qian, Chong Zhao, Haiqiang Mai, Mingyuan Chen, Kajia Cao, Haoyuan Mo, Ling Guo, Qiuyan Chen, Linquan Tang, Wenze Qiu, Yahui Yu, Hu Liang, Xinjun Huang, Guoying Liu, Wangzhong Li, Lin Wang, Rui Sun, Xiong Zou, Shanshan Guo, Peiyu Huang, Donghua Luo, Fang Qiu, Yishan Wu, Yijun Hua, Kuiyuan Liu, Shuhui Lv, Jingjing Miao, Yanqun Xiang, Ying Sun, Xiang Guo, Xing Lv
Journal: Cancer Communications (2018)

Due to the occult anatomic location of the nasopharynx and frequent presence of adenoid hyperplasia, the positive rate for malignancy identification during biopsy is low, thus leading to delayed or missed diagnosis for nasopharyngeal malignancies upon initial attempt. Here, we aimed to develop an artificial intelligence tool to detect nasopharyngeal malignancies under endoscopic examination based on deep learning.An endoscopic images-based nasopharyngeal malignancy detection model (eNPM-DM) consisting of a fully convolutional network based on the inception architecture was developed and fine-tuned using separate training and validation sets for both classification and segmentation. Briefly, a total of 28,966 qualified images were collected. Among these images, 27,536 biopsy-proven images from 7951 individuals obtained from January 1st, 2008, to December 31st, 2016, were split into the training, validation and test sets at a ratio of 7:1:2 using simple randomization. Additionally, 1430 images obtained from January 1st, 2017, to March 31st, 2017, were used as a prospective test set to compare the performance of the established model against oncologist evaluation. The dice similarity coefficient (DSC) was used to evaluate the efficiency of eNPM-DM in automatic segmentation of malignant area from the background of nasopharyngeal endoscopic images, by comparing automatic segmentation with manual segmentation performed by the experts.All images were histopathologically confirmed, and included 5713 (19.7%) normal control, 19,107 (66.0%) nasopharyngeal carcinoma (NPC), 335 (1.2%) NPC and 3811 (13.2%) benign diseases. The eNPM-DM attained an overall accuracy of 88.7% (95% confidence interval (CI) 87.8%-89.5%) in detecting malignancies in the test set. In the prospective comparison phase, eNPM-DM outperformed the experts: the overall accuracy was 88.0% (95% CI 86.1%-89.6%) vs. 80.5% (95% CI 77.0%-84.0%). The eNPM-DM required less time (40 s vs. 110.0 ± 5.8 min) and exhibited encouraging performance in automatic segmentation of nasopharyngeal malignant area from the background, with an average DSC of 0.78 ± 0.24 and 0.75 ± 0.26 in the test and prospective test sets, respectively.The eNPM-DM outperformed oncologist evaluation in diagnostic classification of nasopharyngeal mass into benign versus malignant, and realized automatic segmentation of malignant area from the background of nasopharyngeal endoscopic images.
Placental formation in early pregnancy: how is the centre of the placenta made?
Authors: Anna L Boss, Lawrence W Chamley, Joanna L James
Journal: Human Reproduction Update (2018)

Correct development of the placenta is critical to establishing pregnancy and inadequate placentation leads to implantation failure and miscarriage, as well as later gestation pregnancy disorders. Much attention has been focused on the placental trophoblasts and it is clear that the trophoblast lineages arise from the trophectoderm of the blastocyst. In contrast, the cells of the placental mesenchyme are thought to arise from the inner cell mass, but the details of this process are limited. Due to ethical constraints and the inaccessibility of very early implantation tissues, our knowledge of early placentation has been largely based on historical histological sections. More recently, stem cell technologies have begun to shed important new light on the origins of the placental mesenchymal lineages. This review aims to amalgamate the older and more modern literature regarding the origins of the non-trophoblast lineages of the human placenta. We highlight ways in which rapidly developing stem cell technologies may shed new light on these crucial peri-implantation events. Relevant articles were identified using the PubMed database and Google Scholar search engines. A pearl growing method was used to expand the scope of papers relevant to the cell differentiation events of non-trophoblast placental lineages. At the start of pregnancy, cells of the extraembyronic mesoderm migrate to underlie the primitive trophoblast layers forming the first placental villi. The mesenchymal cells in the villus core most likely originate from the hypoblast of the embryo, but whether cells from the epiblast also contribute is yet to be determined. This is important because, following the formation of the villus core, vasculogenesis and haematopoiesis take place in the nascent placenta before it is connected to the embryonic circulation, making it likely that haematopoietic foci, placental macrophages, endothelial cells and vascular smooth muscle cells all arise in the placenta de novo. Evidence from the stem cell field indicates that these cells could directly differentiate from the extraembryonic mesoderm. However, the lineage hierarchy involved in cell fate decisions has not been well-established. Mesodermal progenitors capable of differentiating into both vascular and haematopoietic lineages can be derived from human embryonic stem cells, but the identification of such stem cells in the placenta is lacking. Future work profiling rare progenitor populations in early placentae will aid our understanding of early placentation. Understanding the origins of the cell lineages of the normal placenta will help us understand why so many pregnancies fail and address mechanisms that may salvage some of these losses.
Use of myelosuppressive chemotherapy and colony-stimulating factor (CSF) prophylaxis: A longitudinal assessment of practices participating in the Centers for Medicare and Medicaid Services (CMS) oncology care model (OCM).
Authors: Derek Weycker, Ahuva Hanau, Alex Lonshteyn, Christopher Kim, Prasad L. Gawade, Charles Bowers
Journal: Journal of Clinical Oncology (2018)

12 Background: The CMS OCM is a 5-year program (7/2016 – 6/2021) focused on improving oncology care by incentivizing practices via financial and performance accountability. Little is known about practices participating in the OCM and whether patterns of care have changed over time. Methods: We used a retrospective cohort with structured elements from national electronic health record dataset provided by Flatiron Health (1/2012-12/2017). Data were de-identified to prevent patient and provider re-identification. Study population included adults with breast, colorectal, lung, or ovarian cancer or non-Hodgkin lymphoma who received chemotherapy with intermediate/high-risk for febrile neutropenia (FN). Patient characteristics, treatment, and supportive care within OCM and non-OCM practices were evaluated overall and by calendar year. Results: Study population included 42,699 patients at 53 OCM practices, and 25,613 patients at 149 non-OCM practices. OCM practices were larger (mean: 806 vs. 172 patients); age (mean: 62 vs. 62 years), cancer type (breast cancer: 53% vs. 52%), chemotherapy (high FN-risk: 49% vs. 48%), and other characteristics were comparable between patients in OCM and non-OCM practices. Use of high (vs. intermediate) FN-risk chemotherapy in 2012, 2015, and 2017 was 48%, 50%, and 48% in OCM practices and 50%, 50%, and 48% in non-OCM practices. CSF prophylaxis use, while higher in OCM practices, decreased over time in both subgroups (OCM: 70% in 2012 to 65% in 2017; non-OCM: 63% in 2012 to 58% in 2017). Use of pegfilgrastim (vs. short-acting CSFs) was &gt; 94% across years in OCM and non-OCM practices. Use of the on-body injector (vs. prefilled syringe) increased from 26% of pegfilgrastim use in 2015 to 73% in 2017 in OCM practices and from 16% to 63% in non-OCM practices. Conclusions: Although OCM practices are larger and more commonly use CSF prophylaxis than non-OCM practices, trends in use of high FN-risk chemotherapy and declining prophylactic support appear to be similar between subgroups. Additional research is needed to evaluate whether such changes impacted health outcomes.
Family History Associates With Increased Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases
Authors: N. Jewel Samadder, John F. Valentine, Stephen Guthery, Harminder Singh, Charles N. Bernstein, Jonathan A. Leighton, Yuan Wan, Jathine Wong, Kenneth Boucher, Lisa Pappas, Kerry Rowe, Randall W. Burt, Karen Curtin, Ken R. Smith
Journal: Clinical Gastroenterology and Hepatology (2018)
Synergistic Interaction of <i>HOXB13</i> and <i>CIP2A</i> Predisposes to Aggressive Prostate Cancer
Authors: Csilla Sipeky, Ping Gao, Qin Zhang, Liang Wang, Otto Ettala, Kirsi M. Talala, Teuvo L.J. Tammela, Anssi Auvinen, Fredrik Wiklund, Gong-Hong Wei, Johanna Schleutker
Journal: Clinical Cancer Research (2018)

Abstract Purpose: Distinguishing aggressive prostate cancer from indolent disease improves personalized treatment. Although only few genetic variants are known to predispose to aggressive prostate cancer, synergistic interactions of HOXB13 G84E high-risk prostate cancer susceptibility mutation with other genetic loci remain unknown. The purpose of this study was to examine the interplay of HOXB13 rs138213197 (G84E) and CIP2A rs2278911 (R229Q) germline variants on prostate cancer risk. Experimental Design: Genotyping was done in Finnish discovery cohort (n = 2,738) and validated in Swedish (n = 3,132) and independent Finnish (n = 1,155) prostate cancer cohorts. Expression pattern analysis was followed by functional studies in prostate cancer cell models. Results: Interplay of HOXB13 (G84E) and CIP2A (R229Q) variants results in highest observed inherited prostate cancer risk (OR, 21.1; P = 0.000024). In addition, this synergism indicates a significant association of HOXB13 T and CIP2A T dual carriers with elevated risk for high Gleason score (OR, 2.3; P = 0.025) and worse prostate cancer–specific life expectancy (HR, 3.9; P = 0.048), and it is linked with high PSA at diagnosis (OR, 3.30; P = 0.028). Furthermore, combined high expression of HOXB13-CIP2A correlates with earlier biochemical recurrence. Finally, functional experiments showed that ectopic expression of variants stimulates prostate cancer cell growth and migration. In addition, we observed strong chromatin binding of HOXB13 at CIP2A locus and revealed that HOXB13 functionally promotes CIP2A transcription. The study is limited to retrospective Nordic cohorts. Conclusions: Simultaneous presence of HOXB13 T and CIP2A T alleles confers for high prostate cancer risk and aggressiveness of disease, earlier biochemical relapse, and lower disease-specific life expectancy. HOXB13 protein binds to CIP2A gene and functionally promotes CIP2A transcription.