tbuckley/cabot-search huggingface dataset:
Oncoscore, a Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes Can Differentiate Between CP-CML and BC-CML Associated Genes, and Between CP-CML Patients with Good and Bad Prognosis
Authors: Rocco Piazza, Luca Mologni, Daniele Ramazzotti, Roberta Spinelli, Alessandra Pirola, Luca De Sano, Pierangelo Ferrari, Vera Magistroni, Nitesh Sharma, Praveen Khandelwal, Carlo Gambacorti-Passerini
Journal: Blood (2016)
Improved long-term survival in patients with intermediate thickness primary melanoma managed by sentinel node biopsy
Authors: R. P. Scheri, L. Wanek, R. Essner, D. Morton
Journal: Journal of Clinical Oncology (2007)

8576 Background: Although improved disease-free survival (DFS) with sentinel node biopsy (SNB) for clinically localized melanoma was observed at the interim analysis from the first Multicenter Selective Lymphadenectomy Trial (MSLT-I) there was not yet an improvement in overall survival (OS). We hypothesize this was due to the few observed early deaths. To investigate this we simulated the MSLT-1 protocol using our institutional database. Methods: 3,800 patients undergoing wide excision with or without SNB were matched by primary stage/ulceration/site and patient demographics. Patients with positive sentinel nodes (SN) underwent immediate completion lymphadenectomy (CLND) whereas non-SNB patients managed by nodal observation underwent delayed CLND at nodal recurrence. Survival was determined by the Kaplan-Meier method. Significance was determined using log-rank and Cox regression analysis. Results: Among matched pairs of SNB and non-SNB patients with 1.2–3.5 mm primaries, projected 10-year OS was 76% with SNB versus 63% without SNB (p=0.0008). There was no corresponding statistically significant difference between all 2001 SNB patients and 1799 non-SNB patients, or within the thin primary and thicker primary groups. By multivariate analysis, only SN status (p&lt;0.0001), Breslow thickness (p&lt;0.0001) and ulceration (p=0.0001) were independently predictive of OS. Conclusions: Our long-term data suggest that performing SNB will improve OS in patients with intermediate thickness melanoma but not with thicker or thinner melanomas as compared to observation and delayed CLND. No significant financial relationships to disclose. [Table: see text]
Regression of hepatocellular adenomas and systemic inflammatory syndrome after cessation of estrogen therapy
Authors: Marie Sinclair, Anthony Schelleman, Daljean Sandhu, Peter W. Angus
Journal: Hepatology (2017)

We report a case of dramatic systemic inflammatory symptoms and biochemical signs of inflammation related to multiple hepatic adenomas that completely resolved after cessation of the oral contraceptive pill (OCP) and associated adenoma regression. This represents a case of dramatic symptoms that resolved after estrogen withdrawal alone. (H epatology 2017;66:989–991).
HIGH-SENSITIVITY TROPONIN-T, LEFT VENTRICULAR SIZE AND FUNCTION, AND LONG-TERM OUTCOMES IN CLINICALLY STABLE, APPARENTLY HEALTHY OLDER SUBJECTS
Authors: Manan Pareek, Deepak L. Bhatt, Muthiah Vaduganathan, Arman Qamar, Axel Diederichsen, Margrét Leósdóttir, Martin Magnusson, Peter M. Nilsson, Michael H. Olsen
Journal: Journal of the American College of Cardiology (2017)
IMPACT OF TARGET VESSEL ON LONG-TERM CARDIAC MORTALITY AFTER SUCCESSFUL PERCUTANEOUS CORONARY INTERVENTION FOR CHRONIC TOTAL OCCLUSION; JAPANESE MULTICENTER REGISTRY
Authors: Satoru Mitomo, Toru Naganuma, Kenichi Tsujita, Katsumasa Sato, Junei Obata, Tsuyoshi Kobayashi, Sunao Nakamura
Journal: Journal of the American College of Cardiology (2017)
Effect of metastasis associated in colon cancer-1 on lymphangiogenesis in human gastric cancer.
Authors: Li Sun, Lin Wang, Wenjun Liao, Hui Huang, Jiangman Duan, Huanrong Ma, Yulin Liao, Wangjun Liao
Journal: Journal of Clinical Oncology (2014)

4042 Background: Metastasis-associated in colon cancer-1 (MACC1), a new oncogene predominantly expressed in several solid tumors including gastric cancer (GC), is associated with cancer lymph node positivity. Nodal dissemination of GC critically determines clinical outcome of affected patients. Therefore, we conducted the study to investigate whether MACC1 influences GC lymphatic metastasis and to explore the potential underlying mechanism. Methods: Immunohistochemistry analysis was performed in 190 GC tissues with MACC1, LVYE-1 to find out the relationship between MACC1 and lymph node metastasis as well as lymphangiogenensis. MTT, Transwell migration and 3D-culture assay were conducted to evaluate the effects of MACC1 on the proliferation, migration and capillary-like structure capacity of human lymphatic endothelial cells (HLECs) after co-cultured with MACC1 supernatant. Besides, vascular endothelial growth factor-C (VEGF-C)/VEGF-D expression in GC cells were detected by qRT-PCR, Western blot and ELISA. Results: Presence of MACC1 was correlated with lymph node metastasis (p<0.01) and lymphangiogenesis (p<0.001); meanwhile, absence of MACC1 expression contributed to a better prognosis for GC patients (p<0.001). Additionally, in vitro studies demonstrated that MACC1 upregulated HLECs’ capacity of tube-like formation through enhancing cell proliferation and migration. MACC1 also promoted both lymphangiogenesis and lymphatic invasion in nude mice transplantation assay. Moreover, MACC1 significantly increased the expression of VEGF-C/VEGF-D in GC cells and transplanted tumors both in protein and gene level, which was subsequently suppressed by inhibitor of hepatocyte growth factor (HGF)/c-Met signaling axis. Conclusions: All these data suggested a critical role for MACC1 in lymphatic dissemination of gastric cancer, providing evidence that MACC1 upregulated VEGF-C/VEGF-D expression to promote lymphangiogensis partially via HGF/c-Met pathway.
Erratum to: A benchmark for RNA-seq quantification pipelines
Authors: Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Journal: Genome biology (2016)
Targetable genetic alterations screen by broad, hybrid capture-based next generation sequencing in driver-negative advanced malignant tumor facilitated personalized therapy.
Authors: Xiaochun Zhang, Helei Hou, Weizheng Mao, Shengli Yuan, Wei Chen, Mei Sun, Suihan Wu, Lei Zhao, Hong Sun, Zhongxin Zhang, Xinglin Zhang, Yan Zhang, Weili Jia, Zhenkui Pan, Weihua Sun, Pingping Dai, Xi Chen, Dezhen Peng, Yi Xin
Journal: Journal of Clinical Oncology (2015)

e22066 Background: There were few effective regimens in treating advanced malignant tumor, especially for those which previous routine genetic assay had not yielded a targetable alteration. In this study, a broad, hybrid capture-based next generation sequencing (NGS) assay was used to identify additionally targetable genetic alterations from cancer tissue. Consequently, approved molecular target drugs or available agents on clinical trials could be selected for these driver-negative patients. Methods: 114 cases of advanced tumor (19 lung cancers, 46 breast cancers, 21 gastric cancers, and 28 colorectal cancers) were tested. The 114 tumor biopsies were all previously tested “negative” of specific alterations by multiple non-NGS methods (including EGFR, k-ras mutation, and ALK rearrangement in lung cancer, HER2 gene copy number amplification in breast or gastric cancer, RAS and RAF mutation in colorectal cancer). 7708 exons of 508 tumor related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was 460×. Results: The targetable genetic alterations were detected in 13 of 19 (68.4%) lung cancers and 16 of 28 (57.1%) colorectal cancers. It’s worth noting that these alterations were only found in 18 of 46 (39.1%) breast cancers and as low as 6 of 21(28.6%) gastric cancers. More specifically, the common actionable alterations were in PTEN (n = 8), EGFR (n = 7), PIK3CA (n = 6), HER2 (n = 5), BRCA1/2 (n = 4), andFBXW7 (n = 4). Partial patients had received targeted therapy including TKI inhibitor, mTOR inhibitor and anti-HER2 agents. Conclusions: 46.5 % (53/114) of driver-negative advanced malignant tumor harbored at least one actionable genetic alteration identified by NGS testing. The detected genetic alterations frequency in lung cancer and colorectal cancer was much higher than that of breast cancer and gastric cancer. These findings suggest that high throughput NGS testing in cancer tissue might help identify available targeted drugs especially for the driver-negative advanced malignances.
SARC006: Phase II trial of chemotherapy in sporadic and neurofibromatosis type 1 (NF1)-associated high-grade malignant peripheral nerve sheath tumors (MPNSTs).
Authors: Brigitte C. Widemann, Denise K. Reinke, Lee J. Helman, Joseph A. Ludwig, Scott Schuetze, Arthur P. Staddon, Mohammed M. Milhem, Daniel A Rushing, Christopher L. Moertel, Stewart Goldman, Michael B. Livingston, Lars M. Wagner, Eve T. Rodler, Eva Dombi, Arie Perry, Christina M. Annunziata, Lauren Long, David Viskochil, Seth M. Steinberg, Laurence H. Baker
Journal: Journal of Clinical Oncology (2013)

10522 Background: MPNSTs occur in 10% of the NF1 population, and retrospective, pooled analyses have reported worse chemotherapy response for NF1 (9-18%) compared to sporadic MPNSTs (39-55%). Methods: We prospectively evaluated the objective response (OR) rate, [complete responses (CR) and partial responses (PR) WHO criteria] of children and adults with high-grade, unresectable or metastatic chemotherapy naive NF1 associated versus sporadic MPNST after 2 cycles of ifosfamide and doxorubicin (IA) followed by 2 cycles of ifosfamide and etoposide (IE) as primary endpoint. This was followed by surgery and/or radiation for local control and up to 2 more cycles of IA and IE each. Pathology was centrally confirmed. A Simon optimal two-stage design was used with a target response rate of 40% and 17 patients per stratum in the first stage. With 4+/17 ORs, enrollment was to be expanded to 37 patients per stratum, and 11+/37 ORs would be potentially consistent with a 40% OR rate. Results: Both initial stages met criteria for enrollment expansion with 4/17 PRs in NF1 and 4/12 PRs in sporadic MPNSTs, but only 1 additional PR was observed in the expanded NF1 stratum. Of the 9 PRs, 5 were first observed after 2 cycles IA, and additional 4 after 2 cycles IE. Enrollment was slower than expected and the trial was closed before full accrual. Conclusions: While the primary trial objective was not reached due to slow enrollment, with only 5/29 ORs in the NF1 stratum the desired OR rate of 11+/37 would have unlikely been met even if accrual had been completed. We observed a lower OR rate in NF1 compared to sporadic MPNSTs similar to retrospective literature reports. However, our trial was not powered to detect a difference in response rates between the two strata. In addition to PRs after both IA and IE, disease stabilization was achieved in most patients. Novel strategies including the evaluation of targeted agents in combination with chemotherapy should be considered. Clinical trial information: NCT00304083. [Table: see text]
5-Azacytidine in 82 Low/Intermediate-1 IPSS Risk Myelodysplastic Syndromes: Results from the Italian Patient Named Program
Authors: Pellegrino Musto, Luca Maurillo, Alessandra Spagnoli, Antonella Gozzini, Flavia Rivellini, Caterina Tatarelli, Monia Lunghi, Carla Fili, Enrico Orciuolo, Lucia Ciuffreda, Ernesto Vigna, Paola Della Cioppa, Anna Candoni, Dario Ferrero, Salvatore Palmieri, Giuseppe Palumbo, Nicola Di Renzo, Esther Oliva, Grazia Sanpaolo, Domenico Pastore, Anna Tonso, Alberto Santagostino, Stefano Rocco, Oreste Villani, Fiorella D’Auria, Alfonso Maria D’Arco, Gianluca Gaidano, Sara Galimberti, Domenico Russo, Adriano Venditti, Maria Antonietta Aloe-Spiriti, Giuseppe Leone, Valeria Santini
Journal: Blood (2008)
The NCI Community Cancer Centers Program (NCCCP): A model for reducing cancer health care disparities.
Authors: Donna M. O'Brien, Mary Anne Bright, Steven B. Clauser, Mary Fennell, Jay K. Harness, Deborah D. Hood, Maureen Johnson, Nora C. Katurakes, Worta McCaskill-Stevens, Jane Zapka, Brenda A. Adjei, Kathleen M. Castro, Eileen P. Dimond, Diane C. St. Germain, Sanya Springfield
Journal: Journal of Clinical Oncology (2012)

6086 Background: In 2007, NCI launched the NCCCP, a public-private partnership with 16 community hospital cancer centers in 14 states, to explore methods to improve patient access to advanced cancer care in the community. With 40% of its NCI funding directed to reduce disparities across the cancer continuum, the NCCCP aims to: 1) Enhance access to care; 2) Improve quality of care; and 3) Increase clinical trials accrual. This approach supports priorities in the 2009 ASCO Policy Statement: Disparities in Cancer Care. Methods: A disparities workplan was developed to support the three aims. NCI and the sites worked as a learning collaborative to develop strategies and metrics for: race and ethnicity data tracking; near real-time reporting of adherence to Commission on Cancer (CoC) treatment quality measures; community outreach and patient navigation to increase cancer screening; and improved clinical trial underserved accrual. The tools and resources supporting these efforts will be discussed. ( http://ncccp.cancer.gov/About/Progress.htm ). Results: Evaluation of the 3 year pilot shows improvement for underserved populations: Concordance with CoC treatment quality measures for radiation therapy for breast conserving surgery among Medicaid patients improved from 59.5 percent to 84.8 percent (p&lt;.05). Increased community screening events (from 992 to 1,585) and community partnerships focused on underserved populations (from 78 to 195). Increased accrual to NCI trials (minority accrual from 82 to 151 and elderly from 200 to 641). Conclusions: To be effective in reducing healthcare disparities, a multi-level approach is needed. This includes having: organizations which demonstrate a strong community-oriented mission; commitment by hospital management; engagement of private practice physicians; targeted training of staff; use of standardized data collection and metrics; involvement of strategic partners with aligned goals at the national and local level; support by relevant NCI experts; and sharing best practices across a learning collaborative. The NCCCP disparities model was used in a variety of community settings targeting different underserved populations and has demonstrated effect in care in the respective communities.
Early results of a phase I study of weekly topotecan (T) in combination with weekly platinum compounds
Authors: L. A. White, N. N. Sjak-Shie, C. Kimminau, A. M. Schmidt, A. O. Greco, J. R. Eckardt
Journal: Journal of Clinical Oncology (2004)

2128 Background: Topotecan is synergistic in combination with platinum compounds. Unfortunately, the combination has demonstrated significant toxicities when administered on a q 3-wk schedule. Therefore, we initiated a phase I study of weekly topotecan in combination with the 3 commercially available platinum compounds to try to decrease toxicity and maintain activity. Methods: Patients were treated with platinum compounds given at a fixed dose of either: cisplatin (C) 30mg/m2/wk, carboplatin (Cb) AUC 2/wk or oxaliplatin (OX) 40 mg/m2/wk on D 1, 8, and 15 of a 28 day cycle. The starting dose of topotecan was 2.5 mg/m2/wk for 3 of 4 wks with dose escalation in increments of 0.5 mg/m2. Results: To date, 16 pts have been entered. Patient eligibility criteria were typical for a phase I study in patients with refractory solid tumors, sex (11F/5M), Median age of 63 yrs (range 40 – 79). Patients have been treated as follows: T/C = 6 pts in dose level (DL)1, 1 in DL 2. T/OX = 7 pts in DL 1, 1 in DL 2. T/Cb = 1 pt in DL 1. Toxicity on the 1st DL of T/C include 3 pts. with gr 3 neutropenia, 2 pts with gr 3 thrombocytopenia, 1 pt with gr 3 anemia, 1 pt with gr 3 infection. One pt in DL 1 had a gr 2 thrombocytopenia requiring dose delay for 2 weeks and a dose reduction. Therefore the DL 1 cohort was expanded to 6 pts. Two patients in the 1st DL had a delay to start the 2nd cycle. One patient has been enrolled at the 2nd DL and it is too early to evaluate. T/OX toxicity on DL 1: 1 pt with gr 3 anemia and gr 4 fatigue (DLT) requiring hospitalization, and dose delay, 1 pt with gr 3 thrombocytopenia, 1 pt with gr 3 infection. One patient has been enrolled at the 2nd DL and it is too early to evaluate. T/Cb toxicity on DL 1: 1 pt with gr 3 neutropenia and anemia but no DLT in the 1st cycle. Responses on T/C include: 1 pt with ovarian had a CR after 4 cycles, 1 pt with CUP had a PR after 4 cycles. Responses on T/OX include: 1 pt with small cell carcinoma of the abdomen has maintained a PR after 8 cycles. Conclusions: Platinum compounds when given with topotecan and administered weekly appear to have activity in a variety of tumor types. The safety profile appears to be acceptable. Enrollment will continue until the MTD is identified for each topotecan doublet. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Aventis Aventis GlaxoSmithKline
RISK STRATIFICATION WITH THE TIMI RISK SCORE FOR SECONDARY PREVENTION AMONG PATIENTS WITH DIABETES AND ELEVATED CARDIOVASCULAR RISK
Authors: Brian Bergmark, Deepak Bhatt, Erin Bohula, David Morrow, Philippe Steg, Ofri Mosenzon, Itamar Raz, Eugene Braunwald, Benjamin Scirica
Journal: Journal of the American College of Cardiology (2017)
PREDICTIVE FACTORS FOR RAPID AORTIC GROWTH FOLLOWING ACUTE TYPE A AORTIC DISSECTION PATIENTS: A STUDY FROM THE INTERNATIONAL REGISTRY OF ACUTE AORTIC DISSECTION
Authors: Milan Patel, Thoralf Sundt, Truls Myrmel, Edward Chen, Alan Braverman, Arturo Evangelista, Thomas Gleason, Udo Sechtem, Reed Pyeritz, Eduardo Bossone, Toru Suzuki, Daniel Montgomery, Christoph Nienaber, Eric Isselbacher, Santi Trimarchi, Kim Eagle
Journal: Journal of the American College of Cardiology (2017)
AMONG OLDER HEART FAILURE (HF) PATIENTS WITH IN-HOSPITAL ACUTE KIDNEY INJURY (AKI), AN IMPROVEMENT IN KIDNEY FUNCTION IS ASSOCIATED WITH A HIGHER RISK OF POST-DISCHARGE MORTALITY BUT NOT READMISSION
Authors: Phillip Hong Lam, Daniel Dooley, Poonam Bhyan, Paul W. Sanders, Gregg Fonarow, Wen-Chih Wu, Prakash Deedwania, Javed Butler, Charity Morgan, Sumanth Prabhu, Ravindra Mehta, Marc Blackman, Ross Fletcher, Wilbert Aronow, Anupam Agarwal, Stefan Anker, Richard Allman, Ali Ahmed
Journal: Journal of the American College of Cardiology (2017)
PATTERNS OF RED BLOOD CELL TRANSFUSION AND ASSOCIATED OUTCOMES IN PATIENTS UNDERGOING TAVR: INSIGHTS FOR THE STS/ACC TVT REGISTRY
Authors: Matthew William Sherwood, Katelyn Xiang, Roland Matsouaka, Sreekanth Vemulapalli, Amit Vora, Eric Peterson, Sunil Rao
Journal: Journal of the American College of Cardiology (2017)
Incidence of chemotherapy-induced nausea and vomiting after highly and moderately emetogenic chemotherapy in the era of NK-1 receptor antagonists. Perception versus reality
Authors: M. Majem, E. Moreno, J. Perez, N. Calvo, A. Feliu, I. Gich, A. Tibau, M. A. Mangues, A. Barnadas
Journal: Journal of Clinical Oncology (2009)

e20636 Background: Physicians and nurses had underestimated the incidence of chemotherapy-induced nausea and vomiting (CINV) after both high emetogenic chemotherapy (HEC) and moderately emetogenic chemotherapy (MEC) (Grumberg, Cancer 2004;100:2261–8; Erazo Valle, Curr Med Res Opin 2006;22:2403–10). We have assessed if physicians and nurses’ perception of CNIV in their own practices after the introduction of Aprepitant was closer to reality. Methods: A prospective, observational unicenter study of adult patients receiving their first chemotherapy cycle was performed. Medical oncologists and oncology nurses also estimated the incidence of acute (Day 1) and delayed (Days 2–5) CINV after first administration of HEC and MEC. Eligible patients completed a 6-day diary including emetic episodes, nausea assessment, and antiemetic medication use. Observed incidence rates of acute and delayed CINV were compared with physician/nurse predictions. Results: Twenty-nine physicians and nurses and 95 patients (86.3% receiving HEC and 13.7%MEC) were recruited. Acute nausea and emesis were observed in 14.3% and 2.4% respectively of HEC patients receiving Aprepitant, and delayed nausea and emesis were observed in 14.3% and 7.1% of these patients, respectively. Physicians and nurses accurately predicted the incidence of acute and delayed CINV after HEC patients receiving Aprepitant. Acute nausea and emesis were observed in 22.2% and 0% respectively of MEC patients and delayed nausea and emesis in 33.3% and 22.2% of MEC patients, respectively. All physicians and nurses underestimated the incidence of acute nausea and delayed nausea and emesis after MEC by 15, 28 and 18 percentage points, respectively. Conclusions: The addition of aprepitant in the prevention of CINV after HEC allows a better control of CINV that is perceived accurately by physicians and nurses. By contrary, physicians and nurses continue markedly underestimating the incidence of CINV after MEC. CINV still remain important targets for improved therapeutic intervention and physicians and nurses must be aware about the real incidence of CNIV. No significant financial relationships to disclose.