tbuckley/cabot-search huggingface dataset:
Prediction of factors affecting clinical trial accrual at the Cancer Therapy and Research Center in San Antonio.
Authors: Praveena Iruku
Journal: Journal of Clinical Oncology (2017)

168 Background: Oncology is a very rapidly emerging science with need for more investigational drugs. It is highly essential to accrue patients into clinical trials to develop new drugs. According to the available data, about 38 % of the CTEP/NCI supporting oncology trials close due to inadequate accrual. In this study, we propose to develop a model that will predict clinical trial accrual and retrospectively validate the effectiveness of this model. Methods: Eligible studies included treatment and supportive care intervention studies either open or closed to accrual between 09/1999 and 012/2015 at our center. Data abstracted includes coordinating group, sponsor type, presence of competing trials, trial phase, disease category, single institutional study, author, primary purpose of the study, interventional modality, targeted therapy, advanced disease, randomization, presence of placebo, rare cancer category and new investigational agents. Statistical analysis was performed in the statistic software R (R Foundation for Statistical Computing, Vienna, Austria). We used Chi-square test and Fisher’s exact test. The significance level was set to alpha = 0.05. Results: Retrospective univariate analysis at our institution showed that the variables significantly associated with clinical accrual are: the type of sponsor, author of the trial, and the type of interventional modality. Using these variables, that were statistically significant in accrual of clinical trials, we then determined the strength of our model in measuring the performance of the predictors. Our prediction model had an AUC of 64.1 %. Conclusions: Clinical trial accrual is a key factor in the development of new drugs in Oncology. Our intention was to predict factors that may affect clinical trial accrual and develop a predictive model based on it. In the future, we want to use our predictive model in a prospective validation setting in order to guide our clinical trials portfolio. Data from multiple institutions will improve the validity of this model.
Real-world treatment patterns and characteristics in patients with chronic lymphocytic leukemia.
Authors: Brad Schenkel, Alex Rider, Brian Macomson, Pam Hallworth
Journal: Journal of Clinical Oncology (2017)

65 Background: CLL is the most prevalent form of adult leukemia. In recent years, there have been a number of newly approved therapies for the management of patients with CLL in both the 1 st line (1L) and relapsed/refractory settings, including ibrutinib (approved for 1L CLL, March 2016). Methods: USphysicians involved in CLL treatment decision-making were recruited into the Adelphi CLL Disease Specific Programme (February-May 2016). Physicians completed record forms on consecutively presenting patients &gt; 18 years currently on active CLL treatment. Descriptive statistics analyzed demographics, clinical characteristics, and antineoplastic treatment patterns. Results: 700 patients diagnosed with CLL for an average of 3.0 years were captured. Patients’ mean age was 68.3 years, 53% were male, 75% were Caucasian, 25% had 17p deletion, and 55% were Medicare insured. Of the 81 physicians, 35% were based in an academic hospital setting, 51% in a non-academic hospital setting, 4% in both, and 9% were office-based. Within the overall cohort, BR was the most common 1L regimen (25%), while ibrutinib was the most common 2 nd line (2L) regimen (42%). Among patients with 17p deletion, BR was the most common 1L regimen (25%) and ibrutinib was the most common 2L regimen (50%). Older patients ( ≥ 65) were most likely to receive BR at 1L (28%), while 1L younger patients ( &lt; 65) received FCR (24%). Conclusions: This analysis of real world treatment patterns identified BR, FCR, and ibrutinib as the most common 1L regimens in US CLL patients. Ibrutinib, BR, and idelalisib + rituximab were the most common 2L regimens. Choice of therapy varied depending on age and 17p deletion status. For example, FCR was more frequently used as 1L therapy in patients &lt; 65 years, and the proportion of ibrutinib use as 1L therapy was higher in those with 17p deletion. [Table: see text]
Detection of the BRAF<sup>V600E</sup> protein in human colon carcinomas by a mutation-specific antibody.
Authors: Thomas C. Smyrk, David Tougeron, Stephen N. Thibodeau, Shalini Singh, Andrea Muranyi, Kandavel Shanmugam, Thomas M. Grogan, Steven R. Alberts, Qian Shi, Frank A. Sinicrope
Journal: Journal of Clinical Oncology (2013)

3576 Background: BRAF encodes a serine-threonine kinase that is a downstream effector of activated RAS. A point mutation (V600E) in BRAF occurs in a subset of colorectal cancers (CRCs) and is associated with adverse outcome and may predict non response to anti-EGFR antibodies. Detection of a BRAF V600E mutation in a CRC with microsatellite instability indicates a sporadic origin and excludes Lynch Syndrome. While BRAF V600E mutation status is determined using a DNA-based assay, antibodies against the BRAF V600E protein have recently been developed. We examined mutant BRAF V600E protein expression and its concordance with mutation status. Methods: Primary stage III colon carcinomas (50 BRAF V600E mutation carriers and 25 wild-type cases) were studied from a completed phase III adjuvant trial comparing FOLFOX +/- cetuximab (NCCTG N0147). In archival resection specimens, immunohistochemistry (IHC) was performed using a pan-BRAF antibody and a V600E mutation-specific antibody raised against an immunogenic synthetic peptide derived from the internal region of the BRAF V600E protein. BRAF V600E mutations in codon 15 were analyzed in extracted DNA using a multiplex, allele specific PCR–based assay. BRAF staining was scored independently by two pathologists blinded to mutation status. Results: In primary colon carcinomas stained with a pan-BRAF antibody, diffuse cytoplasmic staining for BRAF proteins was detected in 74 of 75 carcinomas with one case deemed non-evaluable. Using the mutation-specific BRAF V600E antibody, diffuse cytoplasmic staining was detected in 49 of 74 tumors without appreciable heterogeneity of expression. Among these 49 tumors expressing mutant BRAF V600E proteins, all (100%) were found to carry a BRAF V600E mutation according to a DNA-based assay. In contrast, absent BRAF V600E staining was observed in all 25 tumors that were found to have wild-type copies of BRAF V600E detected using a PCR-based assay. Conclusions: For the detection of mutant BRAF V600E , complete concordance was found between IHC and a DNA-based method in colon carcinomas. This finding supports the use of IHC as a simplified strategy to screen CRCs for mutant BRAF V600E proteins in routine clinical practice to inform clinical decision-making.
Abstract 16459: Underestimation of Aortic Stenosis Severity Using “Fusion” of Data From Computed Tomography and Doppler Echocardiography
Authors: Jan Minners, Stephan Dorfs, Philipp Ruile, Franz-Josef Neumann, Gregor Pache, Nikolaus Jander
Journal: Circulation (2016)

Introduction: 2D-transthoracic echocardiography does not account for the elliptical anatomy of the left ventricular outflow tract (LVOT) and may thereby underestimate LVOT area. Fusion of Multidete...
Chemotherapy use at the end of life: An analysis of the decision making process
Authors: F. Giorgi, R. Bascioni, M. Brugni, M. Safi, R. Berardi, L. Giustini, G. De Signoribus, R. Silva, S. Cascinu
Journal: Journal of Clinical Oncology (2004)

6081 Background: To evaluate the proportion of cancer patients (pts) receiving chemotherapy during the last 3 months of life and the factors influencing the decision to continue chemotherapy. Methods: We reviewed the clinical data of the pts followed in 4 oncology units and died in the year 2002. Results: Data of 292 pts were analyzed; the most frequent malignancies were NSCLC (57 pts), breast (33), colorectal (33), gastric (22). In the last 3 months of life 193 pts (66%) received chemotherapy, 98 (33%) in their last month of life; only 4 PR were documented and a clinical benefit was observed in 32 pts (10%). In the last month of life 12 out of 79 evaluable pts had grade 3–4 toxicities and there were 2 treatment-related deaths. The decision to continue chemotherapy in far advanced disease setting was suggested by the oncologist or by an external oncologist questioned for second opinion (2 cases). Twenty-three pts refused chemotherapy recommended by the oncologist and 8 pts requested chemotherapy instead of palliative care. There were differences among oncologists in the 4 oncology units: some were more palliative care oriented others were more aggressive, using chemotherapy until the last days of life. Data that supported the use of chemotherapy were scrutinized: in 30 cases there were good evidence-based informations (from phase 3 studies or meta-analysis), in 126 data ensued from phase 2 studies, in 3 from case reports, in 34 cases data were lacking. Conclusions: A high proportion of patients received chemotherapy in the last month of life without clinical benefit and significant side effects. The decision to continue chemotherapy was taken by the oncologist and was not always supported by reliable clinical studies. Rarely the patients requested chemotherapy contrasting with the oncologist's opinion. No significant financial relationships to disclose.
Baseline microcephaly prevalence in rural Guatemala: implications for neonatal screening for congenital Zika virus infection
Authors: Anne-Marie Rick, Gretchen Domek, Maureen Cunningham, Daniel Olson, Molly Lamb, Andrea Jimenez-Zambrano, Gretchen Heinrichs, Stephen Berman, Edwin Asturias
Journal: The Lancet Global Health (2017)

BackgroundMicrocephaly is the result of disturbance in early brain development and has various causes. Zika was identified in Central America in early 2015. Establishing baseline microcephaly rates in areas affected by Zika is important for the assessment of the burden and contribution of Zika to microcephaly in low-resource settings.MethodsWe undertook a retrospective review of records from a community wellness programme in rural Guatemala where trained community health workers obtained data on weight, length, and head circumference for infants aged 0 to 13 days, enrolled in the programme between August 1, 2014, and March 31, 2016. We estimated gestational age using a Z-score of zero for length on the modified Fenton growth curve. Z-scores for head circumference and weight, adjusted for gestational age and sex, were then calculated. We used univariate logistic regression to test associations between microcephaly and low weight (Z ≤−1), small size for gestational age (weight below 10th percentile for gestational age), and sex. We analysed head circumference Z-scores and microcephaly for changes over time using birth month as well as multiple time-breaks (we compared infants born before versus after April 30, 2015; October 31, 2015; and January 31, 2016) with Student t-tests, and logistic and linear regression.FindingsWe included 296 infants: mean head circumference Z-score was −0·68 (95% CI −0·78 to −0·58). 20 infants (6·8%) had a head circumference Z-score ≤–2 and were considered to have microcephaly, giving a microcephaly prevalence of 676 per 10 000 livebirths. One infant (0·3%) had a head circumference Z-score ≤–3. Weight ≤–1 SD (OR 4·59 (1·69–12·41, p=0·003) and small for gestational age (6·65, 1·88–23·55, p=0·003) were associated with microcephaly. Sex was not significantly associated with microcephaly. Birth month and time-breaks were not associated with microcephaly nor with head circumference Z score.InterpretationBaseline neonatal microcephaly present in this rural Guatemalan community before and during Guatemala's early Zika epidemic is more than 100 and 300 times higher than baseline rates reported before the Zika virus epidemic in Puerto Rico and Brazil, respectively. Increased microcephaly rate associated with Zika epidemics in other countries was not detectable in our study population, probably because data were collected early in the Zika epidemic. High baseline microcephaly rates have important implications for neonatal screening programmes to identify infants congenitally infected with Zika in low-income countries.FundingThe Center for Global Health at the University of Colorado and the Jose Fernando Bolanos Menendez Foundation provided funding for the wellness programme.
Preoperative radiochemotherapy treatment in advanced rectal carcinoma. Results of <b>8-year follow up</b>
Authors: W. Mermershtain, A. Gluzman, I. Gusakova, S. Walfisch, D. B. Geffen, Y. Cohen, S. Ariad
Journal: Journal of Clinical Oncology (2004)

3634 Background: Preoperative radiochemotherapy (RCT) may play an important role in decreasing local recurrence and possibly improving survival for advanced rectal carcinoma. Methods: 30 patients (pts) (median age 61.5) with advanced low rectal cancer, from 1995 to1998 were treated by RCT prior to surgery. Radiotherapy was administered to the pelvis using 10MV linear accelerator to the pelvis to a total dose of 45Gy given over five weeks. 5-FU (500mg/m2/day i.v.) was given concomitantly on days 1–3 and 29–31. Surgery was performed 2- 4 weeks after RCT and included abdominal perineal resection in 15 pts, anterior resection in 11 pts, transanal resection of tumor - 1 pt, explorative laparotomy - 1 pt and only 2 pts refused surgery. Results: There were no serious toxicities associated with RCT. Mild to moderate transient radiation dermatitis was noted in three pts, and grade II diarrhea in four pts. Postoperative pathologic staging was as follows: no tumor found (CR)- 4 pts, Dukes B1–5 pts, Dukes B2–17 pts, B3 (vaginal involvement)-1 pt, C2–2 pt, and D1–1 pt. The response rate was: CR –13%, PR –77%, NC –10%. The 5 and 8 year overall survival was 70% and 58% respectively. Necrosis and/or fibrosis was noted as a prominent histopathologic feature. Conclusions: Preoperative RCT in this series of 30 pts with advanced rectal cancer was well tolerated and associated with a high response rate. No significant financial relationships to disclose.
Survivorship care and weight management: Assessing patient attitudes and preferences toward provider involvement.
Authors: Robert Neff, Georgia Anne-Lee McCann, Kristen Carpenter, Jesse Mesenburg, David M. O'Malley
Journal: Journal of Clinical Oncology (2014)

e20589 Background: The aim of the study was to better understand gynecologic cancer patients’ attitudes and preferences regarding the role of their healthcare providers in managing weight loss in light of the current obesity epidemic. Methods: A cross-sectional design was used. Patients presenting to the Gynecologic Oncology (GO) ambulatory center at an NCI-designated Comprehensive Cancer Center were asked to complete a survey consisting of 49 items assessing knowledge about obesity and its health risks, health behaviors, and attitudes and preferences regarding provider involvement in weight management. Results: A total of 304 surveys were returned from among 350 distributed, yielding a participation rate of 87%. Excluding those without an identified cancer diagnosis (18%) and/or less than 50% complete data completion (<1%) yielded a final sample of 244. Diagnoses included endometrial (38%), ovarian (37%), cervical (16%), and vaginal/vulvar/other GYN malignancies (8%). Mean BMI was 31.6 (SD=9.6), with 50% surveyed classified as clinically obese (BMI>30, WHO). Participants identified as current or former smokers made up 37%. 80% reported having a primary care provider (PCP). Only 20% of obese individuals reported receiving weight loss (WL) counseling from their GOP, while 80% of smokers stated they received smoking cessation (SC) counseling. Obese patients were more likely to receive counseling than non-obese patients (p<0.001). Responses indicate that patients strongly expect health behaviors counseling (smoking, diet, WL) from their PCP and GOP, though expectations were higher for PCPs (paired t-tests, all p<.001). Neither obese nor non-obese patients reported they would be offended by GOP offering WL counseling and the patients were no more likely to be offended by a discussion of WL than by SC counseling (t(196)=1.63, p=.10). Conclusions: This is the first report of GO patients’ attitudes regarding obesity and WL. The present study highlights the low degree, to which patients report provider involvement in weight management, despite a strong expectation to the contrary. In addition, we showed that patients were not offended by providers counseling about weight related issues.
Risk of radiation pneumonitis in breast cancer patients treated with adjuvant taxanes and radiation
Authors: K. D. Voduc, S. Tyldesley, S. Chia
Journal: Journal of Clinical Oncology (2004)

624 Background: In 2001, Taghian et al (JNCI 2001;93:1806–11) published a retrospective cohort study of 41 breast cancer patients treated with adjuvant paclitaxel and radiotherapy (RT). The crude rate of radiation pneumonitis was 15%, significantly higher than the expected rate of 1%. This result raised considerable concern regarding the safety of this treatment. The goal of this study was to conduct a review of breast cancer patients treated with paclitaxel and RT at the BC Cancer Agency, and to determine the risk of radiation pneumonitis at this institution. The results of this study can be used to develop safe guidelines for use of this treatment. Methods: This study is a retrospective review of breast cancer patients treated with adjuvant paclitaxel and radiotherapy at the BCCA. Patients received 4 cycles of adjuvant AC and then 4 cycles of paclitaxel, RT is usually given sequentially after paclitaxel. All patients had stage II-III, node positive, and ER- breast cancer. The number of chemotherapy cycles, RT technique and dose, and pulmonary symptoms 1–12 months following RT were recorded. Radiation pneumonitis is defined as Grade 2 or 3 toxicity on the RTOG scale. Results: A total of 77 women who initiated treatment from Apr. 2000 –Jun. 2002 were identified. Of these 77 women, 53 received sequential adjuvant RT. 91% completed all 4 cycles of paclitaxel, 100% received the prescribed dose of radiation. All patients had at least 3 months of follow-up following completion of RT. With this sample size, the power to detect a change in pneumonitis risk from 1% to 15% exceeds 80% (alpha = 0.05). 10 patients (19%) reported pulmonary symptoms within a year of RT. 1 patient was diagnosed with heart failure from anthracycline. 1 patient had pleural effusions from metastases. 1 patient was diagnosed with radiation pneumonitis and improved with steroids. 7 patients had episodes of dyspnea or dry cough that resolved without treatment. Thus, the crude rate of Grade 1 and Grade 2–4 pulmonary toxicity was 13% and 2% respectively. Conclusions: The incidence pneumonitis is not significantly increased for breast cancer patients treated with adjuvant paclitaxel and adjuvant sequential RT. No significant financial relationships to disclose.
Research on Gun Violence vs Other Causes of Death
Authors: Lavi Oud
Journal: JAMA (2017)

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Health utility scores (HUS) and health-related quality of life (HRQoL) in stage 4 lung cancer (S4LC) patients with brain metastases (BM).
Authors: Vivian Tam, Brandon C Tse, Tiffany Tse, Lin Lu, Emily Tam, Michael Borean, Catherine Labbé, Mark Doherty, Penelope Ann Bradbury, Natasha B. Leighl, M Catherine Brown, Wei Xu, Doris Howell, Geoffrey Liu, Grainne O'Kane
Journal: Journal of Clinical Oncology (2017)

24 Background: Novel therapies have improved the survival of S4LC patients, particularly those with EGFR or ALK alterations. As BM are common among such patients, determining whether HUS appropriately capture BM-specific HRQoL is crucial in economic analyses. We evaluated the relationship between the FACT-Brain (Br) HRQoL, presence of BM, and HUS. Methods: This cross-sectional study of S4LC outpatients at a comprehensive cancer centre assessed FACT-Br and EQ-5D-3L-derived HUS. Correlational analyses, stratified by BM status, were performed between HUS and each of FACT-Br and its subscales: FACT-General (G), physical well-being (PWB), social well-being (SWB), emotional well-being (EWB), functional well-being (FWB), and brain cancer (BrC). Linear regression interaction models assessed whether BM modified the associations between FACT-Br or its subscales and HUS. Results: The 65 BM and 42 non-BM patients had similar demographics: median age (range) was 62 (30-83) years, 61% were female, 55% were Caucasian, and 54% were EGFR/ ALK+. Mean± standard error of the mean (SEM) values of HUS were similar between BM and non-BM groups (0.77±0.02 vs. 0.78±0.02; p=0.49). However, 40 BM patients with stable brain disease had higher HUS than the 14 with progressive disease (0.81 vs. 0.69; p=0.007). Mean±SEM values for FACT-Br, FACT-G, and BrC were 148±2.6, 79±1.5, and 69±1.3, respectively, with no differences between BM and non-BM groups. With the exception of SWB, FACT-Br and its subscales were each individually correlated with HUS (all p&lt;0.001 unless specified), including between HUS and PWB (all patients: r=0.58; BM only: r=0.60; non-BM only: r=0.54), FACT-Br (all: r=0.55; BM: r=0.55; non-BM: r=0.54), FACT-G (all: r=0.51; BM: r=0.49; non-BM: r=0.55), and BrC (all: r=0.49; BM: r=0.51; non-BM: r=0.44, p=0.003). Having BM did not modify these relationships (each interaction, p&gt;0.35). Conclusions: The FACT-Br HRQoL measures and the majority of its subcomponents moderately correlate with HUS but are not specific to patients with BM. Progression of CNS disease greatly alters HUS. EQ-5D-3L-derived HUS are a useful index of HRQoL in S4LC.