tbuckley/cabot-search huggingface dataset:
Effect of Radiation on Levels of DNA Damage in Normal Mucosa of Colorectal Cancer Cases
Authors: J Sheridan, M Tosetto, J Gorman, H Mulcahy, D O'Donoghue, K Sheahan, J Armstrong, M Moriarty, J Hyland, D Gibbons, J O'Sullivan
Journal: Endoscopy (2006)

Background: Endogenous and exogenous DNA damage is repaired by four main pathways, two of which are Base-Excision Repair and Recombinational Repair. Defects in these pathways are linked with Colorectal Cancer (CRC). Radiotherapy results in DNA damage by causing double strand breaks (marked by mre11 expression) and indirect oxidative DNA damage (marked by 8-oxodG expression) is produced by the ionization of oxygen.
Association of Same-Day Discharge With Hospital Readmission After Appendectomy in Pediatric Patients
Authors: Sarah B. Cairo, Mehul V. Raval, Marybeth Browne, Holly Meyers, David H. Rothstein
Journal: JAMA Surgery (2017)

Appendectomy is the most common abdominal operation performed in pediatric patients in the United States. Studies in adults have suggested that same-day discharge (SDD) after appendectomy is safe and does not result in higher-than-expected hospital readmissions.To evaluate the influence of SDD on 30-day readmission rates following appendectomy for acute appendicitis in pediatric patients.This retrospective cohort study used the American College of Surgeons National Surgical Quality Improvement Program-Pediatric database to evaluate 30-day readmission rates among pediatric patients who underwent an appendectomy for acute, nonperforated appendicitis. The database provides high-quality surgical outcomes data from more than 80 participating US hospitals, including free-standing pediatric facilities, children's hospitals, specialty centers, children's units within adult hospitals, and general acute care hospitals with a pediatric wing. Patients selected for inclusion (n = 22 771) were between ages 0 and 17 years and underwent appendectomy for uncomplicated appendicitis between January 1, 2012, and December 31, 2015. Patients excluded were those discharged more than 2 days after surgery.Same-day discharge after appendectomy or discharge 1 or 2 days after surgery.The primary outcome was 30-day readmission. Secondary outcomes included surgical-site infections and other wound complications.Of the 20 981 patients, 4662 (22.2%) had SDD and 16 319 (77.8%) were discharged within 1 or 2 days after surgery. The patient cohort included 12 860 boys (61.3%) and 8121 girls (38.7%), with a mean (SD) age of 11.0 (3.56) years. There was no difference in the odds of readmission for patients with SDD compared with those discharged within 2 days (adjusted odds ratio [aOR], 0.82; 95% CI, 0.51-1.04; P = .06; readmission rate, 1.89% vs 2.33%). There was no significant difference in reason for readmission on the basis of discharge timing. Likewise, there was no difference in wound complication rate between patients with SDD and those discharged 1 or 2 days after surgery (aOR 0.75; 95% CI, 0.56-1.01; P = .06).In pediatric patients with acute appendicitis undergoing appendectomy, SDD is not associated with an increase in 30-day hospital readmission rates or wound complications when compared with discharge 1 or 2 days after surgery. Same-day discharge may be an applicable quality metric for the provision of safe and efficient care for pediatric patients with acute, nonperforated appendicitis.
Outcome of Patients with Relapsed/Refractory (R/R) Chronic Lymphocytic Leukemia (CLL) and/or 17p Deletion/TP53 Mutations Treated with Ibrutinib According to a Named Patient Program (NPP) in Italy: Preliminary Analysis of a Real Life Retrospective Study
Authors: Francesca Romana Mauro, Alessandra Tedeschi, Alfonso Piciocchi, Marina Motta, Emilia Iannella, Lucia Farina, Lydia Scarfo, Roberto Marasca, Marta Coscia, Agostino Cortelezzi, Luca Laurenti, Angela Melpignano, Pier Luigi Zinzani, Stefano Molica, Francesca Re, Alessandro Andriani, Donatella Iolanda Vincelli, Carlo Visco, Alessandro Gozzetti, Ester Maria Orlandi, Livio Trentin, Monica Tani, Catello Califano, Giuseppe Tagariello, Paolo Ghia, Maria Denise Caputo, Adriano Salaroli, Idanna Innocenti, Anna Frustaci, Candida Vitale, Marta Petullà, Paolo de Fabritiis, Marco Vignetti, Paola Fazi, Robin Foà
Journal: Blood (2016)
Physicians Interrupting Patients
Authors: James Kenneth Herstoff
Journal: JAMA (2017)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Colder temperature is associated with increased COPD morbidity
Authors: Meredith C. McCormack, Laura M. Paulin, Christine E. Gummerson, Roger D. Peng, Gregory B. Diette, Nadia N. Hansel
Journal: European Respiratory Journal (2017)

Due to global climate change, climatologists anticipate not only a rise in mean yearly ambient temperature, but also an increase in the frequency and intensity of variable weather patterns, including extreme hot and cold weather events [1, 2]. Overall mortality is higher during winter months [3, 4] and half of excessive deaths in the cold season are respiratory in nature [5]. Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide and is linked to high healthcare-associated financial burden [6, 7]. Identifying environmental factors that contribute to COPD morbidity is crucial to define adaptive strategies to improve outcomes. Cold temperatures lead to worse outcomes in those with COPD, even after accounting for other environmental factors <http://ow.ly/ltCG30bRWnT>
Comprehensive proteomic studies on ovarian cancer and biomarker discovery for molecular tumor typing
Authors: Atsuhiko Toyama, Takashi Shimada, Tetsuyoshi Sugita, Yutaka Aoki, Chikage Aoki, Yukari Umino, Atsushi Suzuki, Daisuke Aoki, Yataro Daigo, Yusuke Nakamura, Takaaki Sato
Journal: Cancer Research (2007)

604   Ovarian cancer is the most lethal gynecological malignancy, accounting up to 6% of death by cancer in women, yet there is no diagnostic marker with sufficient specificity to enable non-invasive diagnosis. Moreover, there is an increasing need for non-histological diagnosis to define the various tumor types, as it significantly affects the choice of post-operative chemotherapy. This study was aimed at identifying novel biomarkers for ovarian cancer, while focusing on making molecular profiles of tumor types; clear cell, endometrioid, serous and mucinous.  This is the first comprehensive study in human ovarian cancer using tissue samples from clinically diagnosed patients. The total protein contents of tissues were separated and visualized by 2-DE and individual protein spots were identified by peptide mass fingerprinting or MS/MS by AXIMA-QIT.  We have so far analyzed total proteins extracted from 40 clinical ovarian tumor samples and compared the expression patterns across the four tumor types. Meanwhile we identified, by peptide mass fingerprint, more than 10,000 spots harvested from 2D-E of 11 tumor samples to generate an integrated 2D-map database. Several proteins were identified that displayed tumor type specific expression pattern, collectively comprising protein expression profiles that may be used as a molecular diagnostic indicator. The result was validated by conventional bioassay as well as our custom-designed cDNA microarray. The list of candidates we demonstrated here together with the elaborate database will contribute to development of a new diagnostic tool for patients with early stage of ovarian cancers.
Radical chemoradiotherapy for patients with locally advanced esophageal cancer. Long-term follow up of an ambispective study
Authors: Milana Bergamino Sirven, Ana Ortega Franco, Gloria Hormigo, Luisa Aliste, Isabel Padrol, Manglio Rizzo, Mariona Calvo, Òlbia Serra, Núria Virgili, Glòria Creus, Maria Boladeras Ana, Leandre Farran, Marta Domenech Viñolas, Kevin Molina, Maria Borràs Josep, Maica Galán
Journal: Annals of Oncology (2017)
Dot map cartograms for detection of infectious disease outbreaks: an application to Q fever, the Netherlands and pertussis, Germany
Authors: Loes Soetens, Susan Hahné, Jacco Wallinga
Journal: Eurosurveillance (2017)

Geographical mapping of infectious diseases is an important tool for detecting and characterising outbreaks. Two common mapping methods, dot maps and incidence maps, have important shortcomings. The former does not represent population density and can compromise case privacy, and the latter relies on pre-defined administrative boundaries. We propose a method that overcomes these limitations: dot map cartograms. These create a point pattern of cases while reshaping spatial units, such that spatial area becomes proportional to population size. We compared these dot map cartograms with standard dot maps and incidence maps on four criteria, using two example datasets. Dot map cartograms were able to illustrate both incidence and absolute numbers of cases (criterion 1): they revealed potential source locations (Q fever, the Netherlands) and clusters with high incidence (pertussis, Germany). Unlike incidence maps, they were insensitive to choices regarding spatial scale (criterion 2). Dot map cartograms ensured the privacy of cases (criterion 3) by spatial distortion; however, this occurred at the expense of recognition of locations (criterion 4). We demonstrate that dot map cartograms are a valuable method for detection and visualisation of infectious disease outbreaks, which facilitates informed and appropriate actions by public health professionals, to investigate and control outbreaks.
Metastatic Neuroblastoma in Adult Patient, Presenting as a Super Scan on 68Ga-DOTANOC PET/CT Imaging
Authors: Dharmender Malik, Abhiram Jois, Harmandeep Singh, Girdhar S. Bora, Rajender Kumar Basher, Bhagwant Rai Mittal
Journal: Clinical Nuclear Medicine (2017)

We report a case of 23-year-old man who presented with complaints of progressive abdominal distension for the past 3 months along with the loss of appetite and weight and had a large solid cystic mass in the left half of the abdominal cavity revealed on ultrasonography and contrast-enhanced CT of the abdomen. Subsequent biopsy and histopathology revealed it to be neuroblastoma. 68Ga-DOTANOC PET/CT scan performed to rule out distant metastasis showed intense radiotracer uptake distributed throughout the skeleton, mimicking a super scan.
Reply: Clinical Metagenomics for the Diagnosis of Hospital-acquired Infections: Promises and Hurdles
Authors: Kathryn M. Pendleton, John R. Erb-Downward, Yuwei Bao, William R. Branton, Nicole R. Falkowski, Duane W. Newton, Gary B. Huffnagle, Robert P. Dickson
Journal: American Journal of Respiratory and Critical Care Medicine (2017)
Dose reduction (DR) due to chemotherapy induced peripheral neuropathy (CIPN) in breast cancer (BC) patients (pts) in the neoadjuvant/adjuvant settings.
Authors: Bhavana Bhatnagar, Steven Gilmore, Olga G. Goloubeva, Lulu Wang, Michelle Medeiros, Saranya Chumsri, Katherine Hanna Tkaczuk, Martin J. Edelman, Ting Bao
Journal: Journal of Clinical Oncology (2013)

e20574 Background: CIPN is a common and potentially dose-limiting complication of many effective cytotoxic agents. Taxanes are the cornerstone of treatment in BC. Limited data are available regarding the prevalence and severity of DR due to CIPN following taxane use. Methods: Charts of 123 consecutive newly diagnosed BC pts treated with a taxane as part of standard neoadjuvant/adjuvant chemotherapy at the University of Maryland Greenebaum Cancer Center between 01/01/2008 and 12/31/2011 were reviewed. Treating physicians followed standard recommendations for DR. Results: Median age at diagnosis was 53 years (range, 32-78), 120 female/3 male, 48 Caucasian (C), 70 African-American (AA), 5 had a history of alcohol abuse, and 20 had a diagnosis of diabetes mellitus (DM). Seventy pts received docetaxel, 46 paclitaxel, 7 received both or nab-paclitaxel. Fifty (40%) pts required DR, with 21 (17%) due to CIPN and 29 (23%) due to other causes. The median relative dose intensity (received dose/planned dose) for the 21 CIPN-induced dose reduction pts was 88% (range, 62%-97%). A multivariable logistic regression model was used to compare pts who did and did not require DR based on the following possible risk factors: taxane received, DM, alcohol use, and race. Based on the effects estimated by statistical model, there was no difference between pts who did and did not undergo DR with regard to factors listed. However, diabetic pts were over twice as likely to require DR (OR = 2.4, 95% CI: 0.6-10.2, p=0.06). The univariable logistic regression model for 50 pts who had undergone DR revealed possible differences in developing CIPN between C and AA patients. The chances of DR due to CIPN are higher in AA pts (OR=4.3, 95% CI: 1.1-16.7, p=0.03). Pts who received paclitaxel are more likely to require DR due to CIPN than those treated with docetaxel (OR=10.4, 95% CI: 2.7-39.6, p=0.001). Conclusions: 1. CIPN-induced dose-reduction occurred in 17% of our study population. 2. The median relative dose intensity was 88%. 3. DM may increase the overall risk of dose reduction, and AA, paclitaxel therapy may confer a higher risk of CIPN-induced dose reduction.
Abstract 157: Metabolomic Profiling of AMP-Signaling Stress: Effects of Metformin on Wild Type and Adenylate Kinase AK1-/- Transgenic Mice
Authors: Emirhan Nemutlu, Song Zhang, Andre Terzic, Petras Dzeja
Journal: Circulation Research (2012)

Metabolic drugs frequently target mitochondrial functions and AMP signaling. Metformin, one of the most prescribed anti-diabetic medications, exerts its glucose lowering effect through mild interference with mitochondrial energy metabolism triggering homeostatic adenylate kinase (AK)-catalyzed AMP and downstream AMPK signaling. However, metabolomic signature of drug-induced “therapeutic mitochondrial toxicity" and energetic imbalance-induced AMP signaling are poorly understood. This work was aimed to determine metabolomic representation of metformin-induced mitochondrial and AMP signaling stress by comparing wild type and AK1-deficient mice with compromised AMP-signaling. Metabolomic profiling of plasma and urine samples from wild type mice treated with metformin revealed distinct metabolic signature suggesting altered energy, Krebs cycle, lipid and ketone body metabolism, with higher levels of creatinine, malate, α-ketoglutarate, FFA, glycerol, glycerol-3-phosphate, 3-hydroxybutyrate and hypoxanthine. Contrary to expectations glucose lowering effect of metformin was greater in energetically and AMP-signaling compromised AK1-/- mice. Metformin action on AK1 deficient mice was characterized by increased levels of creatinine, lactate, alanine, FFA, phosphoserine, acetoacetate, 3-hydroxybutyrate, malate and α-ketoglutarate indicating broader alterations in energy, glycolytic, Krebs cycle, ketone body, lipid and amino acid metabolism. At baseline, livers from AK1-/- mice had higher AMP/ADP and pAMPKα/AMPKα ratios compared to wild type. There were no significant sustained changes in global nucleotide ratios after metformin treatment. Overall metabolomic profile of AK1-/- mice indicate larger disturbances in energetic and substrate metabolic networks after metformin treatment compared to wild type. Thus, this study revealed specific metabolomic signatures of metformin therapeutic action and mitochondrial toxicity indicating that genetic and metabolic background modulate individual response to metformin treatment.
Targeting Vascular Endothelial-Cadherin in Tumor-Associated Blood Vessels Promotes T-cell–Mediated Immunotherapy
Authors: Yang Zhao, Ka Ka Ting, Jia Li, Victoria C. Cogger, Jinbiao Chen, Anna Johansson-Percival, Shin Foong Ngiow, Jeff Holst, Georges Grau, Shom Goel, Thorleif Muller, Elisabetta Dejana, Geoff McCaughan, Mark J. Smyth, Ruth Ganss, Mathew A. Vadas, Jennifer R. Gamble
Journal: Cancer Research (2017)

T-cell infiltration of solid tumors is associated with improved prognosis and favorable responses to immunotherapy. Mechanisms that enable tumor infiltration of CD8+ T cells have not been defined, nor have drugs that assist this process been discovered. Here we address these issues with a focus on VE-cadherin, a major endothelial cell-specific junctional protein that controls vascular integrity. A decrease in VE-cadherin expression is associated with tumor pathology. We developed an oligonucleotide-based inhibitor (CD5-2), which disrupted the interaction of VE-cadherin with its regulator miR-27a, resulting in increased VE-cadherin expression. Administration of CD5-2 in tumor-bearing mice enhanced expression of VE-cadherin in tumor endothelium, activating TIE-2 and tight junction pathways and normalizing vessel structure and function. CD5-2 administration also enhanced tumor-specific T-cell infiltration and spatially redistributed CD8+ T cells within the tumor parenchyma. Finally, CD5-2 treatment enhanced the efficacy of anti-PD-1 blocking antibody. Our work establishes a role for VE-cadherin in T-cell infiltration in tumors and offers a preclinical proof of concept for CD5-2 as a therapeutic modifier of cancer immunotherapy via effects on the tumor vasculature. Cancer Res; 77(16); 4434-47. ©2017 AACR.
Use of a web-based app to improve breast cancer symptom management and aromatase inhibitor adherence: A pilot randomized controlled trial.
Authors: Ilana Graetz, Caitlin N McKillop, Edward J. Stepanski, Gregory A. Vidal, Lee Steven Schwartzberg
Journal: Journal of Clinical Oncology (2017)

e12044 Background: For postmenopausal women with hormone receptor-positive breast cancer, use of aromatase inhibitors (AI) significantly reduces the risk of cancer recurrence and improves survival, but many patients are nonadherent due to adverse side effects. We conducted a pilot randomized controlled trial of a web-enabled application (app) to provide real-time symptom monitoring between visits and facilitate management of treatment-related adverse symptoms among patients with hormone receptor-positive breast cancer and a new AI prescription. Methods: Patients were randomized into two groups: (1) App+Reminder: had access to the app and received weekly reminders via text or email to use it, or (2) App: had access to the app but did not receive reminders. The app asked patients about their AI use in the last 7 days and about new symptoms related to the treatment. New symptoms with severity in a clinically-relevant range or AI nonadherence triggered email alerts to the patient’s providers. The main analyses compared AI adherence and changes in quality of life. Results: We enrolled 44 patients, 21 in the App+Reminder and 23 in the App group; 83% of patients approached agreed to participate, 23% were African-American, and 32% were over the age of 65. Overall, 74% of participants in the App+Reminder group used the app at least once per week compared with 38% in the App group (p&lt;0.01). Reported AI adherence 8 weeks after initiation was significantly higher among those in the App+Reminder group compared with the App group (100% vs. 72%, p=0.01). Using a differences-in-differences analysis, we found that the decrease in quality of life 8 weeks after AI initiation was substantially larger, but not statistically significant, in the App group compared with App+Reminder (difference=7.6, p=0.191). Conclusions: Use ofa web-enabled app to provide real-time monitoring of AI adherence and treatment-related symptoms with weekly reminders significantly improves short-term AI adherence and may limit reductions in quality of life.If short-term gains in adherence persist, this low-cost intervention could improve survival outcomes for women with hormone receptor-positive breast cancer. Clinical trial information: NCT02957526.
Reduction in Subtypes and Sizes of Myocardial Infarction With Ticagrelor in PEGASUS-TIMI 54
Authors: Marc P Bonaca, Stephen D Wiviott, David A Morrow, P. Gabriel Steg, Christian Hamm, Deepak L Bhatt, Robert F Storey, Julia Kuder, Sabina A Murphy, Giulia Magnani, Andrej Budaj, Pierre Theroux, Jose C Nicolau, Alexander Parkhomenko, Jose Lopez-Sendon, Mikael Dellborg, Rafael Diaz, Frans Van de Werf, Ramon Corbalan, Eva C Jensen, Eugene Braunwald, Marc S Sabatine
Journal: Circulation (2015)
Hemophilia Lend-Lease Program in Italy Successfully Meets Albania Factor Needs
Authors: Louis M. Aledort, Michele De Luca, Maria Jose Caldes Pinilla, Alberto Zanobini, Simona Carli, Anila Godo, Ogerta Manastirliu, Gentian Kolaj, Tatiana Caja, Vera Neziri
Journal: Blood (2016)
Mutational burden of tumors with primary site unknown.
Authors: Laurie M. Gay, David Fabrizio, Garrett Michael Frampton, Caitlin F. Connelly, James Sun, Sugganth Daniel, Julia Andrea Elvin, Shakti Ramkissoon, Eric Allan Severson, James Suh, Jo-Anne Vergilio, Philip J. Stephens, Jeffrey S. Ross
Journal: Journal of Clinical Oncology (2017)

3039 Background: Higher levels of tumor mutational burden (TMB) can predict sensitivity to immunotherapies (IO), which are FDA approved to treat NSCLC, melanoma, and urothelial carcinoma (Ca). TMB may be a biomarker for sensitivity to IO, irrespective of tumor type. TMB has not been explored widely for tumors of unknown primary site, but may reveal additional treatment options. Methods: Comprehensive genomic profiling of DNA from FFPE tissue samples was performed using hybrid-capture, next-generation sequencing. TMB was calculated by counting all coding short variant alterations (base substitutions and indels), including synonymous alterations, and subtracting from this functionally oncogenic or germline alterations (per ExAC, dbSNPT, or internal algorithmic analysis). To calculate the TMB per Mb, the total number of relevant mutations is divided by the coding region of the bait set (0.8 Mb, 1.1 Mb, or 1.2 Mb). High, intermediate, and low TMB were defined as ≥20 mut/Mb, ≥6 and &lt;20 mut/Mb, or &lt;6 mut/Mb, respectively. Tumor types with &gt;100 samples were analyzed. Results: From a database of 102,878 samples sequenced during routine clinical care, 6116 samples for which the primary tumor site was unclear at sequencing were identified. Table shows TMB metrics (mut/Mb) and median patient age for these cohorts. Conclusions: Significant numbers of patients with each tumor type have high TMB that may indicate benefit from IO, excepting GIST. As expected, urothelial tumors have higher than average TMB and more patients have high TMB. SCC tumors are commonly TMB high (23%), as are tumors difficult to define histologically (15%). For ACUP or CUP, the most common tumors, 8-11% have high TMB. Analysis of responses to treatment with IO are ongoing. [Table: see text]