tbuckley/cabot-search huggingface dataset:
A population-based analysis of outcomes in cancer patients who do not satisfy clinical trial eligibility criteria (CTEC).
Authors: Winson Y. Cheung, Hagen F. Kennecke, Howard John Lim, Daniel John Renouf, Sharlene Gill, Ozge Goktepe, Caroline Speers
Journal: Journal of Clinical Oncology (2013)

6502 Background: Trials have stringent inclusion and exclusion criteria to maintain internal validity. However, study findings are often applied to patients in routine practice who do not meet CTEC. Our aim was to characterize the outcomes and magnitude of treatment benefit in these patients. Methods: Patients diagnosed with stage III colon cancer from 2006 and 2008, referred to 1 of 5 regional cancer centers in British Columbia, and assessed for adjuvant chemotherapy (AC) within 12 weeks of surgery were analyzed. Patients were considered trial-eligible (TE) if aged 18 to 79 years, ECOG 0/1, CEA &lt;10, did not receive prior chemotherapy or radiation, and had adequate blood counts and normal cardiac, liver and kidney function. All other patients were deemed trial-ineligible (TI). Results: A total of 820 patients were identified: median age was 69 years (range 60-76), 423 (52%) were men, 365 (45%) were ECOG 0/1 and 592 (72%) received AC. Among patients treated with AC, 370 (63%) were TE and 222 (37%) were TI. Compared to TI patients, those who were TE were younger (63 vs 70 years, p&lt;0.01) and more likely to receive combination regimens rather than single agent AC (56 vs 33%, p&lt;0.01). Outcomes were significantly different among patients who were TE, TI, and those who did not receive AC (Table). In multivariate analyses that adjusted for known prognostic factors such as age, ECOG and T and N stages, both TI patients and those not treated with AC had worse outcomes than TE patients (HR for colon cancer death 1.32, 95%CI 0.86-2.02 and 2.77, 95%CI 1.92-3.99, respectively, p trend &lt;0.01; HR for all cause death 1.24, 95%CI 0.85-1.80 and 2.95, 95%CI 2.17-4.00, respectively, p trend &lt;0.01). Conclusions: In this population-based cohort, colon cancer patients who did not fit CTEC were frequently treated with AC. Outcomes in this TI group were inferior to those in the TE group, but they were better than the subset that did not receive AC. Broadening CTEC to include a segment of the TI population should be considered as there appears to be benefit in selected individuals. [Table: see text]
PREVALENCE OF INTESTINAL METAPLASIA AND DYSPLASIA IN PATIENTS WITH VERRUCOUS GASTRITIS AT A TERTIARY REFERRAL HOSPITAL
Authors: H Uchima, M Albert, C Rosales, L Torrealba, V Piñol, M Figa, C Huertas, M Hombrados, L Peries, L Gutierrez, R Louvriex, S Arjona, X Aldeguer
Journal: Endoscopy (2018)

Verrucous Gastritis (VG), also known as chronic erosive gastritis is a type of gastritis with characteristic endoscopic features such as numerous small elevated lesions with a central umbilical-like depression (“octopus sucker” gastritis). The association between verrucous gastritis and gastric dysplasia is not well known, as well as the risk factors for the development of this entity.
Standardization of Ki-67 assessment for breast cancer patients with preoperative endocrine therapy.
Authors: Yoshio Mizuno, Hiroyuki Takayanagi, Hiroaki Abe, Kazuhiko Sato
Journal: Journal of Clinical Oncology (2012)

e11007 Background: Change in Ki-67 levels is a predictive marker of breast cancer, and it has been widely investigated in patients treated with preoperative endocrine therapy. Several studies have compared Ki-67 expression in untreated specimens obtained by core needle biopsy (CNB) and surgery. We conducted a retrospective study to assess Ki-67 expression between these two specimen types. Methods: 307 patients underwent primary operations for early breast cancer at Tokyo-West Tokushukai Hospital from August 2008 to October 2011. Among them, 193 patients who underwent CNB prior to the operation were enrolled. Patients with ductal carcinoma in situ and those undergoing neoadjuvant chemotherapy were excluded. A cutoff value of 20% was used as the Ki-67 positive criterion. We also examined ER, PgR, and HER2 expression and compared it with Ki-67 expression. Statistical significance for concordance rates between the two types of specimens was evaluated by Wilcoxon t-test. To evaluate the consequences of formalin and genetic heterogeneity, parameters such as operative method and tumor size were analyzed using chi-square test. We reexamined Ki-67 expression in the central laboratory among the Ki-67 discordant group to evaluate the discordance between the pathologist’s judgments. Results: The Ki-67 expression concordance rate between the two types of specimens was 77.7%, which was significantly lower than that for ER, PgR, and HER2 expression at 94.8%, 88%, and 91%, respectively. No significant differences in the operative method (mastectomy vs. breast conserving surgery) or tumor size (≤2cm vs. &gt;2cm) were observed between the groups. We reexamined Ki-67 expression in the Ki-67 discordant group and found that the Ki-67 concordance rate had improved to 93.8%. Conclusions: The Ki-67 expression concordance rate between the two types of specimens was significantly lower than that of ER, PgR, and HER2 expression. However, a reexamination of Ki-67 expression in the central laboratory revealed no significant difference, suggesting the need for a standard pathological assessment of Ki-67 expression to clinically use Ki-67 as a predictive marker.
SPYGLASS CHOLEDOCHOSCOPY IN AN 8 YEARS-OLD GIRL WITH AN ACUTE PANCREATITIS AND ANOMALOUS PANCREATICOBILIARY JUNCTIO
Authors: C Mangas, J Martínez, L Compañy, FA Ruiz, JA Casellas, J Ramón Aparicio
Journal: Endoscopy (2018)

Anomalous pancreaticobiliary junction is a congenital malformation that describes an abnormal junction of the pancreatic duct and the common bile duct that occurs outside the duodenal wall to form a long common channel (> 15 mm).
EVALUATION OF THE ENDOSCOPIC TREATMENT OF ACHALASIA
Authors: S Elaboudi, I Benelbarhdadi, FZ Ajana
Journal: Endoscopy (2018)

Pneumatic dilation (PD) is considered the first line therapy for achalasia. The aim of our study is to demonstrate the efficiency of this treatment and to evaluate the predictive factors of its success and those of symptom recurrence.
Gastroesophageal Reflux Monitoring
Authors: Amit Patel, C. Prakash Gyawali
Journal: JAMA (2018)

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Abstract P367: Association Between Resting Heart Rate and Progression of Valvular Calcification
Authors: Kojo Amoakwa, Oluwaseun E Fashanu, Martin Tibuakuu, Di Zhao, Eliseo Guallar, Seamus P Whelton, Wesley T O’Neal, Wendy S Post, Matthew J Budoff, Erin D Michos
Journal: Circulation (2018)

Background: Mitral annular calcification (MAC) and aortic valvular calcification (AVC) are progressive and linked to increased cardiovascular disease (CVD) morbidity and mortality. Few known modifiable risk factors associated with the progression of MAC and AVC exist. Resting heart rate (RHR) is an established independent risk factor for CVD. Due to the potential hemodynamic effects of RHR on development or progression of valve calcification, we assessed whether RHR is associated with the incidence and progression of MAC and AVC in a community-based cohort free of CVD and atrial fibrillation at baseline. Methods: We obtained RHR from baseline 12-lead electrocardiograms of 5,498 MESA cohort participants. We studied RHR as a continuous variable (per 1 SD increment) and also categorized at clinical cut points of &lt; 60, 60 - 69, 70 - 79, and ≥ 80 bpm. MAC and AVC were quantified (using Agatston scoring) from cardiac computed tomography scans obtained at baseline and at follow-up examinations 2 or 3. We examined associations between RHR and incident MAC/AVC and annual change in MAC/AVC scores, after adjusting for demographics, CVD risk factors, physical activity, and atrioventricular nodal blocker medication use. We used progressively adjusted parametric survival models for incident MAC/AVC and linear regression models for annual change in MAC/AVC. Results: At baseline, participants had a mean age of 62±10 years and mean RHR of 63±10 bpm; 12.3% and 8.9% had prevalent AVC and MAC [Agatston Units (AU) &gt;0], respectively. Over a median follow up time of 2.3 years, 4.1% and 4.5% developed incident AVC and MAC, respectively. Each 10 bpm higher RHR was significantly associated with incident MAC [Hazard Ratio 1.18 (95% CI 1.03-1.36)], but not incident AVC. However, RHR (per 10 bpm) was associated with AVC progression [β coeff 1.62 (0.45-2.80) AU/year], but not MAC progression. The association of RHR on annual change in AVC was modified by age and sex (p-interactions 0.006 and &lt;0.02, respectively) but not race/ethnicity. Each 10 bpm higher RHR was significantly associated with AVC progression for age &gt; 62 years [β coeff 2.94 (0.55, 5.34) AU/year] and male sex [3.49 (1.31, 5.67) AU/year]. The association between RHR and AVC progression was not significant for age ≤ 62 or female sex. Similar trends were seen using clinical cut-points for RHR. Conclusion: Higher RHR predicted incident MAC and AVC progression independent of traditional CVD risk factors. Future studies are needed to determine whether this association is causal and whether modification of RHR through lifestyle or pharmacologic interventions can reduce valvular calcium progression.
Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding
Authors: Gabriella E. Martyn, Beeke Wienert, Lu Yang, Manan Shah, Laura J. Norton, Jon Burdach, Ryo Kurita, Yukio Nakamura, Richard C. M. Pearson, Alister P. W. Funnell, Kate G. R. Quinlan, Merlin Crossley
Journal: Nature Genetics (2018)
Etude NORMO: Efficacité, sécurité d'emploi et acceptabilité d'une solution de lavage intestinal en 2 litres (macrogol + électrolytes + ascorbate) versus 4 litres de macrogol + électrolytes
Authors: T Ponchon, JY Danielou, D Heresbach, RL Vitte, F Genuist, C Dugué
Journal: Endoscopy (2009)

Introduction: La visualisation de la totalité de la muqueuse grâce à une bonne préparation colique est le gage d'une coloscopie réussie. De nombreux patients se plaignent de devoir boire les 4L de préparation généralement recommandés. La conséquence peut en être une mauvaise acceptabilité et donc, potentiellement, une moindre place de la coloscopie dans le dépistage du cancer colorectal.
AN INUSUAL BRIDGEABLE COMPLICATION IN A CHANGED-OVER-TIME METAL STENT
Authors: M Hernandez-Tejero, J Santos, M Cimavilla, R Torres, A Carbajo, R Sánchez-Ocaña, J García-Alonso, S Sevilla, C De la Serna, P Gil, M Pérez-Miranda
Journal: Endoscopy (2018)

A 57-year-old-woman with obstructive jaundice secondary to chronic pancreatitis. She was underwent an ERCP in which it was diagnosed a benign stenosis of common bile duct as well as pancreatic duct. Endoscopic drainage was undertaken with two stents, a fully-covered metal stent (SEMS) for bile duct and a plastic stent (PPS) for the Wirsung. A 6 months follow-up was planned to remove both stents, but the patient did not appear. After 3-years the patient reappear. PPS was removed without difficulties but it was not feasible to remove SEMS because it had missed its cover and it was working as a bare metal stent impossible to displaced without damaging. Moreover, SEMS had a lot of mud so it must be removed to avoid a subsequent abnormal functioning. In order to make possibe a deferred removal, we performed a placing of a second SEMS inside the previous one. Endoscopically, we tought we had successfully introduced the second SEMS, but when we verified the fluoroscopic placement we realized that the first half of the stent was in the correct position (inside the metal stent previously placed), but the second furthest half which we could not see with the scope was in a parallel position in relation to the first SEMS (it would have left the first stent through a lateral-side hole). We proceeded to pull out the second SEMS from its wrong position without complications. We had a completely new stent and still a patient that carried a stent that was about to dysfunction, so we decided to reintroduce the new SEMS inside an OASIS, after lubricating, and using it again. Firstly, we tried to push the stent with a grasping tripod, but it was not enough stiff, so we changed it for a biopsy forceps whose stiffness allowed us finally push the stent inside the another one in the correct planned position. This case reports a method to reuse a stent with material that we usually have in the endoscopic unit.
Abstract MP28: Cardiorespiratory Fitness Attenuates Risk of Cancer in Obese
Authors: Puneet Narayan, Peter F Kokkinos, Charles Faselis, Jonathan Myers, Anubhav Kumar, Pamela Karasik, Hans Moore
Journal: Circulation (2018)

Introduction: An association exists between being overweight and obese and an increased risk of certain types of cancers. In recent years even though there has been a decline in cancer rates in the general population, cancer rates in the overweight and obese have increased. Specific factors that may protect obese individuals against cancer have not been identified. Hypothesis: We assessed the hypothesis that improved cardiorespiratory fitness (CRF) will attenuate the risk of obesity associated cancer. Methods: We studied a total of 6,830 obese Veterans aged 56.2 ±10.4 years, of whom 67.2% (6471 of 6830) were African-American, 94.7% (4581 of 6830) males, 57.4% (3921 of 6830 smokers, 94.4% (6439 of 6830) with a past history of alcohol or drug use and 60.0% (4100 of 6830) were on statins. Obesity was defined as body mass index (BMI) ≥30.0 kg/m 2 and mean BMI for the cohort was 34.4±4.2 kg/m 2 . None of the patients had a diagnosis of cancer at baseline. Participants completed a maximal exercise tolerance test (ETT) as a part of clinical evaluation at either the Department of Veterans Affairs Medical Centers in Washington, DC or Palo Alto, CA and metabolic equivalents (METs) were estimated based on peak exercise time and treadmill grade. Based on these METs achieved on ETT, patients were divided into 4 age-based CRF categories (mean ± SD): least-fit (4.8±1.3 METs; n=1978), low-fit (6.8±1.2 METs; n=2210), moderately-fit (8.3±1.2 METs; n=1674), and high-fit (11.1±2.2 METs; n=968). Multivariable Cox models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for incidence of cancer across these age-based fitness categories for the entire obese cohort, using least-fit as the reference group. The models were adjusted for age, race, gender, smoking, alcohol and drug use. Results: During a median follow-up of 11.1 years, 9.5% (646 of 6830) of the cohort developed cancer with an event rate of 8.0 per 1000-person years of follow-up. An inverse and graded association was observed between CRF and cancer rates. The adjusted risk of cancer was 15% lower for each 1-MET increase in exercise capacity (HR=0.85; CI: 0.82-0.89). When incidence rates were assessed across CRF categories using the least fit as the referent group, the incidence of cancer was 31% lower in the moderately-fit group (HR=0.69; 95% CI: 0.56-0.86) and 81% lower in the high-fit group (HR=0.19; 95% CI: 0.12-0.29). Conclusions: CRF was inversely associated with rate of cancer in obese Veterans. For each 1-MET increase in fitness, cancer rate was 15% lower.
Candida auris: epidemiological situation, laboratory capacity and preparedness in European Union and European Economic Area countries, 2013 to 2017
Authors: Anke Kohlenberg, Marc J Struelens, Dominique L Monnet, Diamantis Plachouras
Journal: Eurosurveillance (2018)

During 2013-2017, 620 cases of Candida auris were reported in the European Union/European Economic Area - 466 (75.2%) colonisations, 110 (17.7%) bloodstream infections, 40 (6.5%) other infections and four cases (0.6%) of unknown colonisation/infection status - the majority from four large outbreaks. Survey results showed that several countries lacked laboratory capacity and/or information on the occurrence of cases at national level. To prevent further spread, adequate laboratory capacity and infection control preparedness is required in Europe.
C19-Diterpenoid alkaloid arabinosides from an aqueous extract of the lateral root of Aconitum carmichaelii and their analgesic activities
Authors: Qinglan Guo, Huan Xia, Xianhua Meng, Gaona Shi, Chengbo Xu, Chenggen Zhu, Tiantai Zhang, Jiangong Shi
Journal: Acta Pharmaceutica Sinica B (2018)

Eight new C19-diterpenoid alkaloid arabinosides, named aconicarmichosides E-L (1-8), were isolated from an aqueous extract of the lateral roots of Aconitum carmichaelii (Fu Zi). Their structures were determined by spectroscopic and chemical methods including 2D NMR experiments and acid hydrolysis. Compounds 1-8, together with the previously reported four neoline 14-O-arabinosides from the same plant, represent the only examples of glycosidic diterpenoid alkaloids so far. At a dose of 1.0 mg/kg (i.p.), as compared with the black control, compounds 1, 2, and 4-6 exhibited analgesic effects with >65.6% inhibitions against acetic acid-induced writhing of mice. Structure-activity relationship was also discussed.
ROLE OF DOUBLE BALLOON ENTEROSCOPE AS AN INITIAL METHOD IN DIAGNOSIS AND TREATMENT OF PATIENTS WITH OBSCURE GASTROINTESTINAL BLEEDING
Authors: M Wahba, A Farag, O Ashoush, W Aerf, M Fawzi
Journal: Endoscopy (2018)

Obscure GI bleeding (OGIB) had been defined as bleeding of unknown origin that persists or recurs after an initial negative investigation. Identifying the source of OGIB represents a diagnostic challenge. Conventional diagnostic methods, such as push enteroscope, small-bowel follow-through, radionuclide scanning, and angiography, all have their own inherent limitations. Double balloon enteroscope (DBE) was designed specifically for diagnosis of various small bowel diseases as well as therapeutic intervention. Due to our limited resources and unaffordability of capsule endoscopy the aim of the study to assess feasibility and efficacy of DBE as an initial diagnostic and therapeutic tool for OGIT.
Identifying biomarkers from SELDI-TOF MS data of ovarian cancer
Authors: Deukwoo Kwon, Mahlet Tadesse, Naijun Sha, Ruth Pfeiffer, Marina Vannucci
Journal: Cancer Research (2007)

590   In recent years, there has been an increased interest in using protein mass spectroscopy to identify molecular markers to discriminate diseased from healthy individuals. Existing methods are tailored towards classifying observation into nominal categories. Sometimes, however, the outcome of interest may be measured ordered scale. Ignoring this natural ordering may result in loss of information. In this paper, we propose a Bayesian model for the analysis of mass spectrometry data with ordered outcome. The  method provides a unified approach for identifying relevant  markers and predicting class membership. This is accomplished by  building a stochastic search variable selection method with an  ordinal outcome model. We apply the methodology to mass spectrometry data on ovarian cancer cases and healthy individuals. We also utilize wavelet-based techniques to denoise the mass spectra prior to  analysis. We identified protein markers associated with being healthy, a low grade case, or a high grade case. For comparison, we repeated  the analysis using conventional classification procedures and  found improved predictive accuracy with our method.  One of the most predictive peaks,  m/z  value 3,271 we believe is  inter-alpha tyrpsin inhibitor heavy chain 4 (ITIH4), that has been found to predict ovarian cancer in the previous studies.
The prognostic role of inflammatory markers in patients with metastatic colorectal cancer treated with bevacizumab.
Authors: Stephen John Clarke, Matthew E. Burge, Kynan Feeney, Kristian Jones, Peter Gibbs, Mark P. Molloy, Gavin M. Marx, Timothy Jay Price, William Reece, Eva Segelov, Niall C. Tebbutt
Journal: Journal of Clinical Oncology (2018)

719 Background: Bevacizumab (BEV) with fluoropyrimidine-containing chemotherapy is well-established for patients (pts) with mCRC. There is a need for reproducible, validated, inexpensive and accessible prognostic markers to aid in treatment selection. Pre-treatment levels of systemic inflammatory markers including the neutrophil to lymphocyte ratio (NLR) have been shown retrospectively to be prognostic in many tumors. This study aimed to prospectively evaluate the relationship between NLR and treatment outcomes in previously untreated mCRC pts receiving BEV-based therapy. Methods: ASCENT (NCT01588990) is an open-label, single arm, phase-IV, multi-center study. Pts received 1st-line BEV+XELOX or mFOLFOX6 in phase A (PhA) with planned continuation of BEV+FOLFIRI beyond 1st progression in phase B (PhB). Primary analysis: association of NLR with progression free survival (PFS). Secondary analyses: overall survival (OS) and safety. Sub-study: safety in pts with intact primary in situ (PIS) and resected primary tumor (RPT). Results: 128 pts started PhA; median age 63.5 years (range: 26-84), 70(55%) females, 51(40%) PIS, 71(56%) and 56(44%) were PS 0 and ≥ 1; respectively. 53(41%) pts entered PhB. The median baseline (b) NLR was 3.2 (range: 1.5-20.4) with 32(25%) pts having a baseline level &gt; 5. The hazard ratio (HR) for PFS by NLR &gt; 5 vs ≤5 was 1.4 (95% CI: 0.9-2.2; p = 1.01). Median PFS was 9.2 months (mo; 95% CI: 7.9-10.8) for PhA and 6.7 mo (95% CI: 3.0-8.2) for PhB. HR for OS based on baseline NLR &gt; 5 vs ≤5 was 1.6 (95% CI: 1.0-2.7; p = 0.052). Based on a multivariate model, the 12-month predicted OS probability for pts with PS 0, no metastatic liver disease and ≤ 3 sites of other metastatic disease, was 87% in pts with bNLR ≤ 5 and 79% in pts with bNLR &gt; 5. Median OS was 25 mo (95% CI: 19.2-29.7) for the full analysis set and 14.9 mo for PhB. Treatment related toxicities were numerically and qualitatively consistent with prior experience. There were 4(3%) instances of GI perforation, of which, 3(6%) occurred in the PIS group. Conclusions: Consistent with previous studies, the trend was towards worse PFS and OS in pts with higher bNLR, but the association was not proven. Clinical trial information: NCT01588990.