tbuckley/cabot-search huggingface dataset:
Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015
Authors: Laure Fonteneau, Nathalie Jourdan Da Silva, Laetitia Fabre, Philip Ashton, Mia Torpdahl, Luise Müller, Brahim Bouchrif, Abdellah El Boulani, Eleni Valkanou, Wesley Mattheus, Ingrid Friesema, Silvia Herrera Leon, Carmen Varela Martínez, Joël Mossong, Ettore Severi, Kathie Grant, François-Xavier Weill, Céline M Gossner, Sophie Bertrand, Tim Dallman, Simon Le Hello
Journal: Eurosurveillance (2017)

Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case–case study involving French patients with salmonellosis who travelled to Morocco that year. A univariate conditional logistic regression was performed to quantify associations. The microbiological study included a whole genome sequencing (WGS) analysis of clinical and non-human isolates of S . Chester of varied place and year of isolation. A total of 162 cases, mostly from France, followed by Belgium, the Netherlands, Spain, Denmark and Sweden were reported, including 86 (53%) women. The median age per country ranged from 3 to 38 years. Cases of S . Chester were more likely to have eaten in a restaurant and visited the coast of Morocco. The results of WGS showed five multilocus sequence types (ST), with 96 of 153 isolates analysed clustering into a tight group that corresponded to a novel ST, ST1954. Of these 96 isolates, 46 (48%) were derived from food or patients returning from Morocco and carried two types of plasmids containing either qnrS1 or qnrB19 genes. This European-wide outbreak associated with travel to Morocco was likely a multi-source outbreak with several food vehicles contaminated by multidrug-resistant S . Chester strains.
Primary adrenocortical tumors: EGFR, c-Kit and Her-2/neu receptor staining patterns
Authors: V. Samnotra, V. A. Memoli, M. S. Ernstoff, C. P. G. Tretter, J. A. Heaney, M. Korc, T. J. Farell, P. Simmons
Journal: Journal of Clinical Oncology (2005)

4770 Background: Primary neoplasms of the adrenal cortex are extremely rare malignancies, estimated to represent 0.05–0.2% of all cancers diagnosed in the United States annually. These cancers carry an extremely poor prognosis and are resistant to systemic chemotherapy. Because of the extreme rarity of these tumors few studies have been published addressing the molecular biology of these tumors. Methods: We evaluated all confirmed cases of primary adrenocortical cancers (n = 7) and primary adrenal adenomas (n = 11) collected over the past three decades at Dartmouth-Hitchcock Medical Center for the following molecular markers: c-Kit tyrosine kinase receptor using polyclonal rabbit anti-human CD117 antibody (Dako), the Her-2/neu receptor using monoclonal mouse anti-human antibody (BioGenex) and EGF (epidermal growth factor) receptor using mouse monoclonal anti-human antibody (Dako). All of these molecular targets are the sites of action of modern drugs: Imatinib (Gleevec) targets c-Kit, trastuzumab (Herceptin) targets her-2/neu and gefitinib (Iressa) acts on EGFR. Results: No specimen stained 3+ or 2+ positive (clinically positive) for Her-2/neu. 1 carcinoma stained for c-kit the other 17 specimens did not. 12 of 18 specimens stained positive for EGFR (3/7 carcinomas and 10/11 adenomas). Conclusions: Primary adrenocortical carcinomas and adenomas do not significantly express c-Kit or Her -2/neu in our patient population. EGFR is expressed in a large percentage of carcinomas and a larger percentage of adenomas. Further studies are warranted to determine the extent of EGFR expression in carcinomas and adenomas. However EGFR may be a worthwhile target for clinical therapies for metastatic adrenocortical carcinoma. This project was supported by a grant from Astra-Zeneca. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration AstraZeneca
The radiation oncology EMR as a quality and outcomes-based informatics platform: A multicenter pilot study.
Authors: Jason Mark Pawlowski, Tammy Wotring, Andrew S. Kennedy
Journal: Journal of Clinical Oncology (2016)

168 Background: Radiation oncology specific oncology information systems (OIS) are highly specialized and capture large amounts of rich data related to patient care. There is great potential to expand the utility of these systems from data collection and point-of-care documentation to platforms for radiation oncology informatics. To this end, we have begun an effort to consolidate and standardize the OIS within a large network of radiation oncology clinics. We report initial findings from a multi-center OIS standardization pilot involving five clinics. Methods: Five radiation oncology clinics were converted from a paper-based medical record to an electronic medical record (EMR) on a single instance of the OIS. Clinician-led workgroups developed best-practice EMR workflows to ensure high-quality data were input into the OIS. Database configuration, clinical workflows, and documentation were standardized to enable consortium-wide reporting and dashboarding. Results: Standardization for the five radiation oncology centers was completed in September 2014. Clinical and operational dashboards were generated including dashboards to study radiation toxicity, treatment modality utilization, time studies for each task from referral to treatment, SRS/SBRT utilization, follow-up rates, and referral patterns. Consortium-wide analysis revealed substantive differences in operational and clinical practices. For example: IMRT utilization for prostate cancer patients treated with external beam radiotherapy ranged from 83% to 100% amongst facilities; the time required to contour target volumes on 80% of patients ranged from 2 to 10 days amongst physicians; and follow-up rates ranged from 50% to 83% amongst physicians. Conclusions: Standardization and consolidation of the radiation oncology OIS significantly increased reporting capabilities to include measures based on quality, safety, and patient outcomes. Disparate practices amongst radiation oncology clinics were observed and best practices discovered. OIS consolidation and standardization was essential to develop a consortium-wide understanding of clinical and operational quality.
Long-Term Maintenance with Lenalidomide Improves Progression Free Survival In Myeloma Patients with High-Risk Cytogenetics: An IFM Study
Authors: Hervé Avet-Loiseau, Denis Caillot, Gerald Marit, Valerie Lauwers-Cances, Murielle Roussel, Thierry Facon, Cyrille Hulin, Thierry Lamy, Brigitte Pegourie, Herve Maisonneuve, Laurent Garderet, Philippe Moreau, Anne-Marie Stoppa, Mamoun Dib, Jerome Jaubert, Philippe Casassus, Claire Mathiot, Jean-Luc Harousseau, Philippe Moreau, Michel Attal
Journal: Blood (2010)
Changes in health-related quality of life (HRQL) after bladder cancer (BC) diagnosis (DX): A longitudinal population-based study.
Authors: Chunkit Fung, Chintan Pandya, Elizabeth A. Guancial, Shri Noel, Katia Noyes, Deepak M. Sahasrabudhe, Edward M. Messing, Emelian Scosyrev, Supriya Gupta Mohile
Journal: Journal of Clinical Oncology (2014)

317 Background: Few studies have examined longitudinal changes in HRQL among BC patients. To our knowledge, this is the largest prospective population-based study to quantify HRQL changes from before to after BC DX and to compare their HRQL with a non-cancer cohort. Methods: Our sample included 179 BC patients (≥ age 65) and 376,986 non-cancer subjects within the SEER-Medicare Health Outcomes Survey database (1998-2007). We assessed HRQL as measured by physical (PCS) and mental (MCS) component summary scores of the veterans RAND 12-item health survey. An analysis of covariance model was used to estimate changes in HRQL scores for patients after BC DX relative to control subjects with adjustment for baseline HRQL scores and covariates. Results: 84.4% (N=151) of BC patients had non-muscle invasive BC (NMIBC) and 15.6% (N=28) had muscle invasive BC (MIBC). 49.2% and 39.1% of BC patients had ≥2 comorbid conditions and ≥1 activities of daily living (ADL) deficit, respectively. Compared to the control subjects, more BC patients were men (67.0% vs 38.5%; P&lt;0.01), current or former smokers (58.7% vs 37.3%; P&lt;0.01), and had income ≥ $50,000(15.1% vs 8.8%; P=0.02). Other baseline demographic and socioeconomic characteristics were similar (P&gt;0.05). After DX, BC patients reported a significant decline in PCS (1.9; 95% CI 0.1, 3.7) score compared to non-cancer controls whereas the decrease in MCS score (1.4; 95% CI -0.1, 3.0) was not statistically significant. For those with NMIBC, HRQL was not significantly different than that of the non-cancer cohort (P&gt;0.05) after DX. However, the PCS and MCS scores of MIBC patients decreased by 5.3 (95% CI 0.9, 9.8) and 3.8 points (95% CI -0.1, 7.7) after DX, respectively. Older age at BC DX, lower educational and income levels, smoking history, and higher numbers of comorbid conditions and ADL deficits were significantly associated with inferior PCS and MCS scores after BC DX (P&lt;0.01). Conclusions: Treatment-related side effects and/or symptoms due to BC adversely affect HRQL of BC patients, especially in those with MIBC, and should be consistently assessed by health care providers. Future research that examines interventions to improve HRQL is critical to improve BC care.
Survival Patterns among Chronic Lymphocytic Leukemia and Other Lymphoma Patients with Family History of Lymphoma.
Authors: Lesley A. Anderson, Ruth M. Pfeiffer, Joshua S. Rapkin, Gloria Gridley, Lene Mellemkjaer, Kari Hemminki, Magnus Bjorkholm, Lynn R. Goldin, Neil E. Caporaso, Ola Langren
Journal: Blood (2007)
Characterization of the mTOR pathway in renal cell carcinoma and its use in predicting patient selection for agents targeting this pathway
Authors: R. A. Figlin, D. Seligson, H. Wu, G. Thomas, J. T. Leppert, T. O’Toole, G. Dukart, J. Gibbons, A. S. Belldegrun, A. J. Pantuck
Journal: Journal of Clinical Oncology (2005)

4539 Background: The Target of Rapamycin (mTOR) pathway is upregulated in many human cancers, through activation of downstream targets such as AKT and HIF. Pre-clinical data suggests that agents targeting this pathway may be more effective in PTEN null tumors. Studies of agents targeting the mTOR pathway in RCC have shown frequent disease stabilization but relatively few objective responses. The aim of this study was to characterize the mTOR pathway in RCC by immunohistochemistry (IHC), and to determine its utility in selecting patients for agents targeting the mTOR pathway. Methods: An RCC tissue microarray containing specimens for 417 patients was subjected to IHC with antibodies against PTEN, pAKT, pS6, p27, and HIF1 alpha. The original tumors were staged according to the 1997 TNM, graded according to Fuhrman, and histologically subtyped according to the recommendations of the UICC. IHC expression was analyzed according to tumor type, stage, and grade. Pearson correlation analyses were used to determine the relationships between markers. Results: Loss of PTEN was increased in all RCC compared to normal, with the greatest loss occurring in Clear Cell Tumors (24.8%) and tumors having sarcomatoid features (34.4%). pAKT staining frequency was greatest in Collecting Duct (88.9%) followed by Clear Cell (57.5%), suggesting pathways of AKT activation other than PTEN loss. S6 kinase was highly expressed by sarcomatoid (61.1%) and Clear Cell tumors (40.8%) and was expressed more in high grade (73% vs. 31%) and high stage (50% vs 30%) tumors. Expression of HIF1 was highest in Clear Cell, but at only 25% positivity. PTEN expression was correlated with pAKT (p=0.028) and HIF expression (p<0.0001). Conclusions: IHC analysis suggest that not all RCC tumor types are equally amenable to treatment strategies targeting the mTOR pathway, but that a majority of patients have at least one component of the mTOR pathway impacted. Furthermore, the results suggest the mTOR pathway is more significantly altered in high grade tumors and tumors with poor prognostic features. Further evaluation is needed to assess the relationship of IHC results and clinical response, which could result in better patient selection. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Wyeth
The prognostic impact of circulating tumor cells in patients with small cell lung cancer.
Authors: T. Naito, F. Tanaka, K. Yoneda, T. Takahashi, H. Murakami, Y. Nakamura, A. Tsuya, M. Endo, H. Kenmotsu, K. Kaira, T. Shukuya, A. Ono, H. Akamatsu, S. Miura, M. Kimura, N. Yamamoto
Journal: Journal of Clinical Oncology (2011)

10617 Background: There has been an increasing interest in the circulating tumor cells (CTC) in various solid tumors for predicting clinical outcomes. The aim of this study is to evaluate the relationship between CTC-count and prognosis in patients with small cell lung cancer (SCLC). Methods: A total of 51 patients with newly diagnosed SCLC who had received chemotherapy were prospectively enrolled (27 with limited disease and 24 with extensive disease). Blood samples were drawn at baseline, after chemotherapy, and at the time of relapse. CTCs were isolated using the CellSearch System (Veridex LLC). Results: CTCs at baseline were detected in 40 patients, 78.4% (95% CI, 65.4-87.5), and the median CTC-count was 4 (0-5,648) per 7.5ml. The patients with CTC-count of <9 (favorable group) lived longer than those with CTC-count of >=9 (unfavorable group) when measured at baseline, after treatment, and at the time of relapse; adjusted hazard ratio (95% CI) were 8.9 (2.5-43.1), 4.7 (1.1-19.1), and 8.1 (2.0-47.3), respectively. Patients whose CTC-count remained favorable after chemotherapy showed better survival than those converted from unfavorable to favorable (hazard ratio, 8.1 [1.9-42.0]) or those remained unfavorable after treatment (hazard ratio, 12.3 [2.3-78.3]). Conclusions: CTCs were highly detectable in SCLC and a higher CTC-count was strongly associated with shorter survival from any point of blood draw. Remaining favorable CTC-count or conversion from unfavorable to favorable CTC-count might indicate better prognosis than remaining unfavorable CTC-count after chemotherapy.
PD-L1 expression in primary clear cell renal cell carcinomas (ccRCCs) and their metastases.
Authors: Marcella Callea, Elizabeth M Genega, Mamta Gupta, André P Fay, Jiaxi Song, Ingrid Carvo, Rupal Satish Bhatt, David F. McDermott, Michael B. Atkins, Toni K. Choueiri, Gordon J Freeman, Sabina Signoretti
Journal: Journal of Clinical Oncology (2014)

467 Background: Clinical trials evaluating anti-PD-1 and anti-PD-L1 antibodies (Abs) in ccRCC have shown promising efficacy in a subset of patients. Preliminary studies have demonstrated that tumor PD-L1 expression increases the likelihood of benefit with anti-PD-1 Ab, but fails to identify all responders. One potential explanation for these results is that predictive biomarkers are usually evaluated in the primary tumors, which are more readily available; however, biomarker expression in nephrectomy samples may not accurately reflect expression in the metastases that are being targeted by therapy. In this study, we compared PD-L1 expression in a series of ccRCCs and their metastases. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue blocks from 34 primary ccRCCs and corresponding metastases were retrieved. Multiple areas of the primary tumors, including areas of predominant and highest Fuhrman nuclear grade (FNG), were selected for analysis. Slides were immunostained with a mouse monoclonal anti-PD-L1 antibody (405.9A11). The assay was validated using FFPE cell line controls known to be positive or negative for PD-L1 expression by flow cytometry. The presence of tumor cells with membranous staining was assessed. A case was considered positive when any tumor cell positivity was detected. Results: Positive membranous PD-L1 expression in tumor cells was observed in 10/34 (29%) primary ccRCCs. In 3 of these 10 cases (30%), the metastases were negative. In 2 cases the primary tumor was negative but the metastases were positive. In twenty-two cases, both the primary tumor and the corresponding metastasis were negative. The pattern of PD-L1 staining was highly heterogeneous in the primary tumors and was restricted to areas of highest FNG. The staining was more homogeneous in the metastases. PD-L1 expression by the tumor infiltrating immune cells is currently being evaluated. Conclusions: Discordant expression of PD-L1 between the primary tumor and the corresponding metastases was detected in 5/34 (15%) cases, suggesting that accurate assessment of predictive biomarkers for PD-1 blockade in ccRCC might require analysis of metastatic lesions. Analysis of a larger patient cohort is ongoing to confirm these findings.
Allogeneic Hematopoietic Cell Transplantation (AHCT) for Primary Cutaneous T Cell Lymphoma (CTCL): a Center for International Blood and Marrow Transplant Research (CIBMTR) Review
Authors: Mary Jo Lechowicz, Manza Agovi, Jeanette Carreras, Hillard M. Lazarus, Ginna G. Laport, Silvia Montoto, David G Maloney, Parameswaran Hari
Journal: Blood (2010)
Utility of Whole Exome Sequencing in Diagnosis of Pediatric Platelet Disorders: A Subanalysis of the Pediseq Study
Authors: Edward J Romasko, Sawona Biswas, Batsal Devkota, Jayaraman Vijayakumar, Sowmyra Jairam, Christopher S Thom, Matthew C Dulik, Laura K Conlin, Nancy B. Spinner, Ian D Krantz, Michele P. Lambert
Journal: Blood (2016)
Efficacy and safety of intrapatient dose escalation of sorafenib as first-line treatment for metastatic renal cell carcinoma (mRCC).
Authors: M. E. Gore, R. J. Jones, A. Ravaud, M. Kuczyk, T. Demkow, A. Bearz, N. Laferriere, U. P. Strauss, C. Porta
Journal: Journal of Clinical Oncology (2011)

4609^ Background: Previous data of intrapatient dose-escalated sorafenib in mRCC suggest that doses up to 800 mg bid were manageable with enhanced activity in terms of PFS and responses compared to the standard dose of 400 mg bid. This phase II study was conducted to investigate these earlier findings. Methods: Main eligibility criteria were metastatic and/or unresectable clear cell RCC; at least one measurable lesion, ECOG PS 0/1, MSKCC score good or intermediate, no prior systemic anticancer therapy. Patients (pts) were to receive sorafenib 400 mg bid for 4 weeks, then 600 mg bid for 4 weeks and 800 mg bid from month 3 to 6+, with response evaluated at 6 months. The primary endpoint was response rate (best overall response) within the first 6 months of treatment (≥4 months of treatment at the highest tolerated dose for all pts). Results: Of the 83 enrolled pts (65% male) who received ≥ one dose of sorafenib (safety population); 16 withdrew due to grade 1/2 toxicities and 67 had ≥ one post-baseline assessment (ITT population). Dose escalation per protocol was tolerated by 18 pts; all achieved clinical benefit (9-PR; 9-SD). The other 49 pts had dose escalations and reductions as tolerated throughout the study. Results for the ITT population and subgroups taking 400, 600, or 800 mg bid for the longest time while on study are shown (Table). Median age in the 400, 600, and 800 mg bid groups was 64.5, 58.5, and 57 years, respectively; other baseline characteristics were comparable. No clinically relevant differences in the severity or frequency of side effects were seen across the 3 groups. Conclusions: In the majority of pts dose escalation per protocol was not feasible. Pts in whom the sorafenib dose could be escalated above 400 mg bid appeared to have greater clinical benefit. 400 mg bid (n=25) 600 mg bid (n=12) 800 mg bid (n=20) ITT population (n=67)* Partial response n (%) 1 (4) 2 (16.7) 7 (35) 12 (17.9) Stable disease n (%) 15 (60) 10 (83.3) 13 (65) 46 (68.7) Clinical benefit (PR+SD) n (%) 16 (64) 12 (100) 20 (100) 58 (86.6) Median PFS mo (95% CI) 3.7 (1.8-9.5) 7.4 (6.3-12) 8.5 (5.6-14.9) 7.4 (6.3-9.7) PFS rate at 12 months % 18.7 33.3 46.4 35.9 * The dose for the longest time on treatment was 200 mg/day for 3 pts and 400 mg/day for 7 pts.
Quality improvement strategies in medical oncology: A qualitative analysis from a scoping review.
Authors: Bryan B. Franco, Laavanya Dharmakulaseelan, Simron Singh, Adam E. Haynes, Brian M. Wong, Matthew C. Cheung
Journal: Journal of Clinical Oncology (2016)

203 Background: In 2001, the Institute of Medicine (IOM) outlined imperatives to improve quality of care. Quality improvement (QI) has since become essential to cancer care but barriers still exist to the publication of and participation in QI initiatives, including limited recognition for QI and uncertainty with methodologies. We sought to identify strategies used in QI in scholarly medical oncology literature to provide practical guidance for QI. Methods: We conducted a scoping review using Arksey and O’Malley’s framework. A search of EMBASE and MEDLINE databases found 48,186 unique English citations published between January 2001 and August 2014. We utilized an iterative process to refine the inclusion criteria and two reviewers independently reviewed abstracts, resulting in the inclusion of 270 articles. The reviewers then extracted text segments relevant to QI strategies. A qualitative content analysis approach was used to accurately analyze and summarize this process-oriented data. Results: Fifty-four unique QI strategies identified were used alone or in combination to improve structures or processes of care. Five content categories of strategies that targeted structures of care emerged: 1) more methodical approaches (eg, lean thinking, supply-demand analyses), 2) participatory action research and similar strategies, 3) infrastructure to promote health care provider collaboration, 4) application or improvement of information technology (IT), and 5) progression towards a systematic assessment of all patients’ needs. We identified three categories of QI strategies for processes of care: 1) improving patient-clinician relationships or communications, 2) care navigation, and 3) telehealth. Conclusions: Our review identifiedQI strategies in published literature. Strategies were consistent with and expanded on the IOM’s redesign imperatives such as effective use of IT, development of better teams, and care coordination. Identification of strategies provides professionals with tools to engage in QI and may encourage support and recognition for QI. Future studies should examine the impact of different QI strategies on outcomes of care in oncology.