tbuckley/cabot-search huggingface dataset:
What caused your cancer? A survey of patients with early breast and bowel cancer
Authors: M. C. Gainford, M. R. Stockler, P. Butow, F. Boyle, A. Sullivan, P. Beale, S. Pendlebury, A. K. Nowak, V. M. Duric
Journal: Journal of Clinical Oncology (2008)

9563 Background: Views about causes of cancer might influence attitudes to conventional, complementary and alternative therapies. We sought patients’ views about the possible causes of their cancer. Methods: Participants in a study of preferences for adjuvant therapy completed the revised Illness Perception Questionnaire (rIPQ), rating 18 possible causes of their cancer on a 5 point Likert scale. The primary objective was to describe the perceived causes for the group. Secondary objectives were to describe causes by cancer type and gender. Two-tailed p-values <0.05 were considered statistically significant. Results: 304 patients completed the rIPQ: 178 with breast cancer and 126 with colon cancer (50% male). The causes endorsed most frequently (proportion of patients) were: stress or worry (50%), chance or bad luck (40%), ageing (34%), family problems or worries (33%), hereditary (31%), altered immunity (28%), pollution in the environment (28%), diet or eating habits (26%), overwork (26%), their emotional state (22%), their own behavior (16%), smoking (14%), their mental attitude (12%), their personality (10%), accident or injury (9%), poor medical care in the past (6%), alcohol (5%), a germ or virus (4%) When asked to nominate the most important cause of their cancer, 19% of colon cancer patients chose hereditary (24/99 responses) whilst 31% of breast cancer patients chose stress or worry (54/176 responses). Significantly more breast than colon cancer patients agreed that stress or worry (58% vs 40%), family problems (39% vs 23%), their emotional state (28% vs 14%) or mental attitude (15% vs 7%), an accident (12% vs 5%) or altered immunity (33% vs 21%) caused their cancer. Amongst colon cancer patients, significantly more men than women agreed that diet (42% vs 20%), ageing (40% vs 23%) and smoking (25% vs 7%) caused their cancers whilst more women agreed that family problems (33% vs 12%) were causative. Conclusions: Treating oncologists should appreciate that psychosocial issues are perceived to be major causes of cancer, particularly amongst breast cancer patients. Exploration of patient’s beliefs about causation may facilitate understanding of treatment choices. No significant financial relationships to disclose.
Faster ways of pursuing quality control using EHR (Electronic Health Record).
Authors: Ashish Dutta Dwary, Samip R. Master, Glenn Morris Mills, Richard P. Mansour
Journal: Journal of Clinical Oncology (2016)

169 Background: In this era of electronic health records (EHR), quality monitoring can be a fast repetitive process. Having access to the relational database of the EHR permits rapid case identification and quality indicator determination. We hereby describe evaluation of hepatitis B testing prior to rituximab administration, a quality measure as per ASCO guidelines. Methods: We connected SQL Query Manager with EPIC Clarity database. Using the object model for medication orders, location and department, we used SQL language to build a temporary dataset of all patients who have a completed order for a Rituximab infusion at a specific department location within the past 6 months. Using the dataset obtained in step 2, we created a smaller dataset with one row for each patient. We updated each unique patient row by updating columns for the count of completed Rituximab infusions, the first infusion date and the last infusion date. We then updated each row from a query of the order procedure and results object model. The unique patient id and component id are the key fields for this query. The Hepatitis B surface antigen and core antibody results were queried from up to 6 months prior to the initial rituximab dose. We looped through the dataset and compared the first Rituximab start date with the Hepatitis B testing date. If the testing date is before the drug administration date, a Boolean column was updated to indicate a 1 for passing the quality measure and a 0 for not passing. Finally, we reviewed that chart of any patients who fail the electronic quality measure check as some Hepatitis B testing may be represented in scanned results and these scanned results cannot be queried. Results: When the final SQL query runs, it takes less than a minute to see the result set. The query can be run at any interval or date range. Once the SQL procedure is created, there is essentially no labor and very low costs to run procedure at specific time intervals. Conclusions: Quality control is integral for improvement in patient care. Doing quality monitoring can be labor intensive, expensive, repetitive and time consuming. By using the relational database created and maintained by the EHR we can accomplish the quality control in faster way that is time and cost effective.
Value proposition for colorectal cancer (CRC) screening (SC) in underinsured populations (UP).
Authors: Afsaneh Barzi, Sarmad Sadeghi
Journal: Journal of Clinical Oncology (2014)

24 Background: SC for CRC is an effective preventive tool. In ASCO 2013 we reported that costs of SC are quickly offset by a reduction in the management costs of CRC rendering No Screening financially unsound. This is particularly relevant to the Medicaid and other UP where low reimbursements result in lower availability and inconsistent practice of SC creating an impediment to better outcomes and is a key part of outcome disparities. Methods: Twelve strategies (STs) and 1.4 million individuals were simulated to examine the role of participation (PA) in the SC on effectiveness and cost effectiveness of each SC ST. Individuals &gt; 50 with average risk of CRC and 1/1 male to female ratio were followed for up to 35 years with SC stopped at 75. PA was increased by 10% increments between 20% and 80%. Results: Our results demonstrated that FOBT and colonoscopy (CS) are consistently cost effective STs independently of the level of PA. The incremental cost effectiveness ratios (ICER) of CS relative to FOBT remain flat as PA increases. The absolute difference in life years gained between FOBT and CS ranges from 0.014 to 0.30. Sensitivity analysis reveals that costs of FOBT can be increased before CS becomes more cost effective. Conclusions: Given the limitations of resources within provider networks primarily supported by Medicaid, FOBT can be deployed as the SC modality of choice and efforts maybe focused on increasing PA. To this end, Medicaid can potentially offer more competitive reimbursement rates for fecal testing, thereby incentivizing providers. This will improve quality as reflected in the outcomes and is more pragmatic in terms of resources it requires. [Table: see text]
Characteristics of promoter methylation of O6-methylguanine-DNA methyltransferase (MGMT) gene in areca quid associated oral squamous cell carcinoma
Authors: Ling-Ling Hsieh, Kuo-Hao Huang, I-How Chen, Chun-Ta Liao, Hung-Ming Wang
Journal: Cancer Research (2007)

AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA

4997 

Cigarette smoking and areca quid (AQ) chewing are significantly associated with the high incidence of oral squamous cell carcinoma (OSCC) in Taiwan. Cigarette smoke contains many tobacco-specific nitrosamines, a class of alkylating N-nitroso compounds, can interact directly with DNA forming DNA adducts. Among these, O6-alkylguanine (O6-AlkG) is the most biologically significant mutagenic and carcinogenic DNA adducts lead to G:C to A:T transition mutation. The O6-methylguanine-DNA methyltransferase (MGMT) is a specific DNA repair enzyme for O6-AlkG by direct transfer of an alkyl group from DNA and restores the DNA structure to its predamaged state preventing the mutagenic and carcinogenic effects of alkylating N-nitroso compounds. When MGMT function is lost, the cells have a diminished capacity to repair alkylation damage to the base guanosine and are susceptible to tumorigenesis. On the other hand, such lost function can sensitize tumor cells to the effects of chemotherapy. We have reported an important contributive role for tobacco carcinogens in p53 mutation for a series of Taiwanese OSCCs and the most prevalent types of p53 mutation were G:C to A:T transitions. Recently, upregulation of MGMT was observed in cultured normal human oral keratinocytes treated with ripe areca nut extract (ANE) and several studies have found that cigarette smoking was significantly correlated with an increased frequency of promoter methylation for MGMT gene. Thus, this study was design to evaluate the effect of AQ chewing on the prevalence of promoter methylation for MGMT gene and mutation of p53 gene in OSCC with cigarette smoking history as well as the effect of chemotherapy on OSCC with promoter methylation of MGMT gene. The methylation status of MGMT promoter region was determined by bisulfie-denature high-performance liquid chromatography (DHPLC) in 231 male OSCCs. Promoter methylation of MGMT was observed in 46.67% (7/15), 13.39% (10/72), 8.33% (4/48), and 15.00% (6/40) for those with none, low, moderate and high AQ chewing history, respectively, indicating AQ could dramatically reduce promoter methylation of MGMT . However, the effect of AQ chewing on p53 mutation was not significant. Furthermore, promoter methylation of MGMT was associated with better disease-free (HR=0.51, 95% CI= 0.26-1.00) and overall survival (HR=0.43, 95% CI= 0.20-0.89) for advanced OSCC. In summary, AQ chewing could reduce promoter methylation of MGMT and promoter methylation of MGMT could sensitize tumor cells to the effects of chemotherapy for better outcome.
Activation of T and NK Cells Following Lenalidomide Therapy in Patients with Follicular Lymphoma.
Authors: Seema Rawal, Nathan Fowler, Min Zhang, Zhiqiang Wang, Tariq Muzzafar, Nusrat Harun, Veerabhadran Baladandayuthapani, Rakesh Sharma, David Delgado, Michael Wallace, Carla Heise, Linda Catherine Lacerte, Felipe Samaniego, R Eric Davis, Sattva S. Neelapu
Journal: Blood (2012)
Tract Sizes in Miniaturized Percutaneous Nephrolithotomy: A Systematic Review from the European Association of Urology Urolithiasis Guidelines Panel
Authors: Yasir Ruhayel, Abdulkadir Tepeler, Saeed Dabestani, Steven MacLennan, Aleš Petřík, Kemal Sarica, Christian Seitz, Andreas Skolarikos, Michael Straub, Christian Türk, Yuhong Yuan, Thomas Knoll
Journal: European Urology (2017)
The toxicity gap: Do real-life patients get hospitalized more during chemotherapy compared to trial patients?
Authors: Rebecca Michelle Prince, Monika K. Krzyzanowska, Eshetu G. Atenafu
Journal: Journal of Clinical Oncology (2014)

109 Background: Toxicity related hospitalizations during chemotherapy are poorly reported in the literature. We sought to compare “real world” versus clinical trial rates of hospitalizations among patients with metastatic non-small cell lung cancer (mNSCLC) receiving chemotherapy. We hypothesised that hospitalization rates in real life patients would be significantly higher. Methods: We conducted a systematic review of Medline and EMBASE (1946-June 2013) to identify articles reporting hospitalization rates during chemotherapy in patients with cancer. Both observational studies and clinical trials were eligible. This report focuses on patients with mNSCLC receiving palliative chemotherapy as data was available for this clinical scenario in both the observational and clinical trial setting, allowing comparison. Study results were abstracted using a standardised form. Summary statistics were used to describe results and the chi-square test used to compare hospitalization rates. Results: The search identified 61 articles (all published after 1987), of which 16 were clinical trials and 45 were observational (“real world”) studies. Nine studies examined chemotherapy in mNSCLC - four observational studies and five randomised trials. The four observational studies included 7,456 patients; three included patients on any chemotherapy while the other focused on doublet regimens. Of the five randomised trials which included 3,962 patients, three treated patients with platinum doublets and two used single-agent chemotherapy. The real life cohort was older (70 years vs. 62 years). The aggregate hospitalization rate among real life patients was significantly higher than among trial patients (49% vs. 16%, OR=7.7, 95% CI 7-8.5, p-value &lt; 0.0001). Performance status and type of chemotherapy were associated with hospitalization during chemotherapy in clinical trials while type of chemotherapy was a risk factor in observational studies. Conclusions: Clinical trials in mNSCLC consistently report lower rates of hospitalization than real life cohorts of patients undergoing similar therapies but very few clinical trials report this information.
Methotrexate (MTX) rechallenge for recurrent primary CNS lymphoma (PCNSL).
Authors: E. Pentsova, L. M. DeAngelis, A. M. P. Omuro
Journal: Journal of Clinical Oncology (2011)

2025 Background: The prognosis of PCNSL recurring after MTX +/- whole brain radiotherapy (WBRT) is poor, with reported objective response rates (ORR) of 26-53% and 1y overall survival (OS) of 35-57%. Salvage chemotherapies for lymphoma are usually based on the use of different agents to avoid cross-resistance. However, because MTX is much more active than other agents in PCNSL, a MTX re-challenge has been proposed as a salvage strategy for recurrent disease. In this study, we report our experience with MTX re-challenge in recurrent PCNSL. Methods: We reviewed records from 295 pts included in a prospective database and identified 38 histologically confirmed PCNSL pts who had responded to MTX at initial diagnosis and received MTX re-challenge as salvage treatment. Results: At the start of MTX re-challenge, the median age was 66y (range 41-82), median KPS was 80 (range 50-100), 22 were women. Median time from initial diagnosis to disease progression leading to MTX re-challenge was 26m. Twenty-seven pts were at first relapse and 11 were at second or later relapse, after failing other chemotherapy regimens. A total of 15 pts had received WBRT. At re-challenge, MTX was given in combination with other agents to 33 pts and as single agent to 5. In 33 pts, the MTX dose was 3.5g/m2; in the remainder, a different dose (2.5-8g/m2) was used. In 12 pts, a regimen identical to the initial therapy (MTX, procarbazine, vincristine) was used; 26 pts received a different regimen. Grades 3/4 toxicities at re-challenge included pneumopathy in 2 and nephrotoxicity in 3 pts; hematotoxicity varied according to the combination used. A complete response was seen in 27 (71%) pts, partial response in 5 (13%) and disease progressed in 6 (16%); ORR=84%. At median followup of 15m, the median progression free survival (PFS) was 12m (95% CI 10-19). The 1y OS was 74% (CI 54-86); median OS: 23m. MSKCC RPA class predicted PFS (p=0.007) and OS (p=0.048). Conclusions: In this pt population selected by previous MTX response, MTX re-challenge was a safe and effective strategy, suggesting chemosensitivity was retained. Efficacy compared favorably to other salvage treatment options, suggesting MTX re-challenge should be considered in all patients with recurrent PCNSL who previously responded to MTX.
Salivary markers in renal cell carcinoma.
Authors: Alexandra Dudek, Lauren Appleyard, Tim S. O'Brien, Simon Chowdhury, Penny Champion, Ben Challacombe, Gordon Kooiman, Guy Carpenter
Journal: Journal of Clinical Oncology (2014)

489 Background: Kidney cancer ranks number 8 among cancer diagnoses in the UK with around 9,600 new diagnoses made each year (Cancer Research UK. Risks and causes of kidney cancer. http://www.cancerresearchuk.org/cancer-help/type/kidney-cancer/about/risks-and-causes-of-kidney-cancer). This study aimed to identify overexpressed proteins in human saliva that could serve as markers for renal cell carcinoma. Methods: Saliva was collected from 144 participants (95 male and 28 female).; 123 RCC patients (85%) and 21 healthy controls (15%), Total salivary protein levels were determined by BCA protein assay. Then 10ug of total saliva protein were evaluated via Western blotting on 4-12% Bis-Tris SDS-PAGE gels. Blots were probed for albumin as well as for three proteins associated with RCC; profilin1, 14-3-3 zeta, and endogenous avidin binding protein (EABP). Additionally, 6 saliva samples were evaluated via quantitative proteomics in a Tandem mass tag (TMT) labelling experiment comparing 4 RCC patients vs. 2 renal cyst patients. Results: Profilin1 levels were determined visually on a scale of 0 to 3 depending on band intensities on Western blots. Cancer patients had a higher percentage of levels 2 and 3 with 62 patients (50.4%). The control group only had 2 patients at level 2 (9.5%) and none at level 3. No difference in profilin1 levels was seen between metastatic vs. non-metastatic disease. Differences were seen in gender and histology, with female and non-CC patients having higher profilin levels. There is a potential link between profilin1 levels and surgical or drug treatment. 14-3-3 zeta could not be detected in saliva with these analyses. Albumin was present across all samples. EABP was found in 40.6% of cancer patients vs. 0% of controls; however no clear trend was seen with respect to disease burden, histology, or gender. Proteomic analysis gave a total of 33 hits showing raised protein levels of up to 20x higher in cancer patients vs. controls. Profilin1 was 2x and 14-3-3 zeta 5x more prevalent. Conclusions: This study has successfully identified profilin1 as a detectable salivary marker for renal cell carcinoma. [Table: see text]
The use of breast MRI in early-stage breast cancer: Findings after implementation of an institutional protocol at a county hospital.
Authors: Stewart Whitney, Nestor Arita, Jessica LaCross, Brian Lassinger, Elizabeth Bonefas, Kathy Liscum, Eric Jay Silberfein
Journal: Journal of Clinical Oncology (2014)

5 Background: Breast MRI has recently become standard-of-care in many practices, however, its proper utility in the preoperative management of early-stage breast cancer has not been fully elucidated. Our program recently instituted a protocol to obtain breast MRI at the time of diagnosis of breast cancer. We report the outcomes of this new approach in patients with surgically resected, early-stage breast cancer. Methods: An institutional database was queried for all patients that underwent surgery after a new histopathologic diagnosis of either noninvasive or invasive breast cancer from November 2012, the time of protocol implementation, through March 2014. Patients that received neoadjuvant treatment and patients with stage IV disease were excluded. Demographic, diagnosti,c and clinical data were extracted and analyzed using summary statistics and student’s t-test. Results: Fifty-eight patients met criteria. The median size of the index lesion on mammogram, ultrasound, MRI, and final surgical pathology was 1.2, 1.4, 2.1, and 1.3 cm, respectively. MRI size was significantly larger than mammogram, ultrasound, and final surgical pathology size (p &lt; 0.05). The median time between initial pathologic diagnosis and breast MRI was 16 days. MRI identified 20 additional lesions in 19 (33%) patients leading to 14 additional biopsies and the diagnosis of two additional invasive and two noninvasive cancers. The median time between initial pathologic diagnosis and final report of these 14 biopsies was 36 days. Nine (64%) of the 14 patients that underwent a second biopsy went on to have a partial mastectomy, all with negative margins. Of the remaining five patients that went on to have total mastectomy, all but one were offered partial mastectomy but desired reconstruction. Conclusions: In this cohort of patients with early-stage breast cancer, MRI overestimated the size of the index lesion when compared to other imaging modalities and final surgical pathologic size. The use of MRI did not alter the surgical management in the majority of cases and increased the time from initial diagnosis to definitive surgical management. More studies are needed to determine the role of breast MRI in early-stage breast cancer.
Impact of relapse site on oncological outcomes after radical nephroureterectomy for upper urinary tract urothelial carcinoma.
Authors: Shinichi Yamashita, Akihiro Ito, Koji Mitsuzuka, Yoshihide Kawasaki, Ichiro Shintaku, Tatsuo Tochigi, Fumihiko Soma, Takashige Namima, Shinnosuke Katoh, Shozo Ota, Atsushi Kyan, Kazuhiko Orikasa, Atsushi Takeda, Kenji Numahata, Masataka Aizawa, Naomasa Ioritani, Hisanobu Adachi, Naoki Kawamorita, Yasuhiro Kaiho, Yoichi Arai
Journal: Journal of Clinical Oncology (2016)

426 Background: Most upper urinary tract urothelial carcinomas (UTUC) are invasive and advanced with a poor prognosis. Patients often relapse after treatment with radical nephroureterectomy (RNU). However, little is known about an association between sites of recurrence after RNU and oncological outcomes. The present study retrospectively evaluated the impact of a first recurrence site on survival. Methods: A total of 650 patients with UTUC treated by RNU at 12 institutions that participated in the Tohoku Urological Evidence-Based Medicine Study Group between 2000 and 2011 were initially enrolled. Patients who experienced relapse other than intravesical recurrence after RNU were included in this study. Those who had metastasis at the time of UTUC diagnosis or missing data regarding the time and location of relapse were excluded. Finally, 173 patients were eligible to participate in this study. Survival rates were analyzed using Kaplan-Meier curves and the log-rank test, and factors predicting survival were assessed using multivariate analyses. Results: The median follow-up after relapse was nine months. The cancer-specific survival rates at one and two years after relapse were 49% and 22%, respectively. Cancer in 59 (34%), 32 (18%), 23 (13%), and 94 (53%) patients recurred in the lung, liver, bone and lymph nodes, and 23 (13%) had local recurrence. The one-year cancer-specific survival rates were 44%, 27%, 22% and 52% among patients with metastasis of the lungs, liver, bone and lymph nodes respectively, and 41% among those with local recurrence. The survival rate was worse among 48 patients with metastasis at multiple sites, than in those with metastasis at a single site. Fourteen (8%) patients with a single lymph, lung or local recurrence survived for over three years after a first relapse. Multivariate analyses selected the liver, bone and local recurrence as critical factors for cancer-specific survival. Conclusions: Liver or bone metastasis was a negative prognostic factor for UTUC with relapse after RNU. Information about recurrence sites might be helpful for patient counseling.