tbuckley/cabot-search huggingface dataset:
The Exposome Paradigm in Human Health: Lessons from the Emory Exposome Summer Course
Authors: Megan M. Niedzwiecki, Gary W. Miller
Journal: Environmental Health Perspectives (2017)

Summary: The environment plays a major role in human health, yet tools to study the health impacts of complex environmental exposures are lacking. In 2005, Christopher Wild introduced the concept of the exposome, which encompasses environmental exposures and concomitant biological responses throughout the life course. Exposome-based approaches have the potential to enable novel insights into numerous research questions in environmental health sciences. To promote and develop the concept of the exposome, the Health and Exposome Research Center: Understanding Lifetime Exposures (HERCULES) Exposome Research Center at Emory University held the first Emory Exposome Summer Course from 13–17 June 2016. https://doi.org/10.1289/EHP1712
A multicenter non-interventional study exploring the impact of sarcopenia on the outcomes of colorectal cancer patients treated with chemotherapy plus bevacizumab – avawatchers
Authors: Leen Mortier, Pieter-Jan Cuyle, Bénédicte Naessens, Koen Hendrickx, Jochen Decaestecker, de Vyver Jan Van, Eric Van Cutsem
Journal: Annals of Oncology (2017)
Pleomorphic invasive lobular breast carcinoma: Prognosis and characteristics compared with classical invasive lobular breast carcinoma.
Authors: Christine H. Choi, Ying Liu, Kevin Kalinsky, Eileen Connolly
Journal: Journal of Clinical Oncology (2016)

e13094 Background: Pleomorphic lobular carcinoma (PLC) is a rare type of invasive lobular breast carcinoma that has traditionally been thought to have a worse prognosis as compared to classical lobular carcinoma (cILC), but prior studies are small with conflicting results. We seek to examine differences in clinical characteristics and progression-free and overall survival between PLC and cILC to guide treatment decisions. Methods: From retrospective review of all women with invasive breast carcinoma seeking care at a single institution from 1998-2012, 146 women with PLC and 262 women with cILC were identified. Analysis was performed to examine differences in clinicopathologic variables and progression-free and overall survival between the two groups. Results: On average, the PLC group had a significantly higher pathological stage, prevalence of lymphovascular invasion, proportion of node positive disease and proportion of mastectomy as compared to lumpectomy. There were no differences in age at diagnosis, tumor size, or mean number of positive nodes. Differences in race, subtype, grade, chemotherapy, hormonal therapy and radiation therapy were difficult to assess between the two groups as the cILC group had a higher proportion of missing data in those categories. On survival analysis, median follow-up was 60 months. In the PLC group there were 30 recurrences (21%), and in the cILC group there were 40 recurrences (15%), (chi-square p-value 0.175), as defined by STEEP criteria with the exception of death. In the PLC group, there were 27 deaths from all causes (18%), and in the cILC group there were 56 deaths from all causes (21%), (chi-square p-value 0.477). Results of multivariate cox proportional hazards models are ongoing. Conclusions: In this largest cohort of women in the literature with PLC as compared to cILC, although the PLC group had some high risk clinicopathologic characteristics, there were no differences in rates of recurrences or death. Outcomes: PLC vs. cILC Classical Pleomorphic Chi-square P- value n = 262 n = 146 Recurrence (STEEP criteria without Death) 40 (15%) 30 (21%) 0.175 None 222 (85%) 116 (79%) Death 56 (21%) 27 (18%) 0.477 None 205 (79%) 119 (82%)
Rituximab-dose-dense chemotherapy with or without high-dose chemotherapy plus autologous stem-cell transplantation in high-risk diffuse large B-cell lymphoma (DLCL04): final results of a multicentre, open-label, randomised, controlled, phase 3 study
Authors: Annalisa Chiappella, Maurizio Martelli, Emanuele Angelucci, Ercole Brusamolino, Andrea Evangelista, Angelo Michele Carella, Caterina Stelitano, Giuseppe Rossi, Monica Balzarotti, Francesco Merli, Gianluca Gaidano, Vincenzo Pavone, Luigi Rigacci, Francesco Zaja, Alfonso D'Arco, Nicola Cascavilla, Eleonora Russo, Alessia Castellino, Manuel Gotti, Angela Giovanna Congiu, Maria Giuseppina Cabras, Alessandra Tucci, Claudio Agostinelli, Giovannino Ciccone, Stefano A Pileri, Umberto Vitolo
Journal: The Lancet Oncology (2017)
Validity of sentinel lymph node biopsy in breast cancer patients after neoadjuvant chemotherapy
Authors: H. Jinno, S. Asaga, M. Sakata, T. Kubota, M. Kitajima, M. Mukai, A. Kubo, T. Ikeda
Journal: Journal of Clinical Oncology (2007)

11023 Background: Sentinel lymph node biopsy (SLNB) is a potential alternative procedure to conventional axillary lymph node dissection (ALND) in clinically node-negative breast cancer patients. Neoadjuvant chemotherapy (NAC) is a standard of care for patients with locally advanced breast cancer and indications of NAC have been widespread to operable breast cancer patients to facilitate breast conserving surgery. However, the validity of SLNB in breast cancer patients who received NAC is still controversial. Methods: Forty-six patients with stage II or III breast cancer who were treated with NAC from January 2002 to May 2006 were included in the study. Consecutive 122 patients who had SLNB without NAC during the same period were used as a control group. All patients underwent SLNB followed by completion ALND. Sentinel lymph node (SLN) was detected using a combined method of injecting isosulfan blue dye and small-sized technetium- 99m-labeled tin colloid (particle size: 200–400 nm in diameter) peritumorally and subcutaneously. SLNs were evaluated by means of H&amp;E and immunohistochemical staining. Results: SLNs were successfully identified in 42/46 patients (91.3%) treated with NAC and 112/113 patients (99.1%) without NAC (p=0.01). Metastases in the SLNs were found in 16/42 patients (38.1%) with NAC and 32/112 patients (28.6%) without NAC (p=0.2). There were 5 false negative cases (false negative rate: 23.8%) in the NAC group and 2 false negative cases (false negative rate: 5.9%) in the control group (p=0.05). Accuracy of SLNB in the NAC group was also significantly inferior to the control group (88.1% vs. 98.2%, p&lt;0.01). The presence of clinically positive axillary lymph nodes before NAC was not correlated with false negative rate. Conclusions: These data suggest that NAC might be considered a contraindication to SLNB even in patients with clinically negative axillary lymph nodes before NAC. No significant financial relationships to disclose.
Ranking of Hospitals Performing Advanced Abdominal Laparoscopic Procedures
Authors: Clifford W. Deveney
Journal: JAMA Surgery (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 Surgery HomeNew OnlineCurrent IssueFor Authors Podcast 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 Surgery journal
Frequency and impact of tumor genotyping in clinical practice of patients with advanced biliary tract cancers (ABTCs)
Authors: Stephanie Reyes, Nora Horick, Jeffrey Clark, Janet Murphy, Lawrence Blaszkowsky, Jill Allen, David P. Ryan, Theodore Hong, Jennifer Wo, Ryan Nipp, Aparna Parikh, Jason Faris, Eunice Kwak, Aralee Galway, Michelle Knowles, Rahmi Oklu, Iafrate A. John, Jochen Lennerz, Dianne Finkelstein, Darrell Borger, Andrew Zhu, Lipika Goyal
Journal: Annals of Oncology (2017)
Do nonmelanoma skin cancer survivors use tanning beds more often than the general public?
Authors: Lauren Wiznia, Leah M Ferrucci, Susan T Mayne, Anees B. Chagpar
Journal: Journal of Clinical Oncology (2013)

e20017 Background: Tanning bed use increases the incidence of nonmelanoma skin cancer (NMSC), however utilization of indoor tanning after diagnosis in this population is not well-studied. We sought to determine if tanning bed use among NMSC survivors differed from the general population. Methods: The National Health Interview Survey is an annual population-based survey that is representative of the civilian US population. We utilized the 2010 cancer supplement to evaluate self-reported tanning bed use in the previous 12 months in self-reported NMSC survivors compared to individuals without a history of skin cancer. Results: In 2010, 24,941 people were surveyed, 1.85% of whom had a self-reported history of NMSC. On univariate analysis, NMSC survivors were significantly less likely to use tanning beds in the previous 12 months (2.16 vs. 5.61%, p &lt; 0.001). On multivariate analysis, however, NMSC survivors were equally likely to use tanning beds as those who had never had skin cancer (see Table). Conclusions: When controlling for other sociodemographic factors, NMSC survivors were no less likely to use tanning beds than the general population. These findings suggest a need to better educate NMSC survivors about the increased risk of future skin cancers with ongoing tanning bed use. [Table: see text]
Targeted therapies in 54 patients with Erdheim-Chester disease, including follow-up after interruption (the LOVE study)
Authors: Fleur Cohen Aubart, Jean-François Emile, Fabrice Carrat, Frédéric Charlotte, Neila Benameur, Jean Donadieu, Philippe Maksud, Ahmed Idbaih, Stéphane Barete, Khê Hoang-Xuan, Zahir Amoura, Julien Haroche
Journal: Blood (2017)
Book: In Your Right Mind
Authors: K. McKenzie
Journal: BMJ (1999)

Thomas Stuttaford, Tonmoy Sharma Faber and Faber, £9.99, pp 377 ISBN 057119348X Rating: ![Graphic][1]</img> ![Graphic][2]</img> This book was written by Tom Stuttaford, veteran medical columnist of the Times , to help the layperson and the clinician to speak the same language His wish is to demystify psychiatry and to open it up to the general public so that they would not be baffled if they were to be told that their nearest and dearest is “depressed, but not clinically depressed.” The book … [1]: /embed/inline-graphic-1.gif [2]: /embed/inline-graphic-2.gif
Abstract P331: Metabolic Dynamics and Phosphometabolomic Fingerprinting Using <sup>18</sup> O-Assisted <sup>31</sup> P NMR and Mass Spectrometry
Authors: Petras Dzeja, Emirhan Nemutlu, Song Zhang, Andre Terzic
Journal: Circulation Research (2011)

Evaluation of disease phenotypes and drug effects requires knowledge not only metabolite levels but also their turnover rates from which metabolic fluxes and status of the whole energetic system can be determined. Oxygen-18-assited 31 P NMR and mass spectrometric technique uniquely allow simultaneous measurements of phosphorus-containing metabolite levels and their turnover rates. This includes simultaneous recordings of 18 O-labeling rates reflecting ATP synthesis (γ-ATP) and ATP utilization (Pi), phosphotransfer fluxes through adenylate kinase (β-ATP/ADP), creatine kinase (CrP) and glycolytic pathways (G-6-P) as well as Krebs cycle associated mitochondrial nucleotide turnover (γ/β-GTP), substrate shuttle (G-3-P) and glycogen metabolism (G-1-P). Metabolomic and fluxomic profiling of hearts and body fluids of phosphotransfer enzyme deficient transgenic animals using 18 O-assisted GC/MS, 1 H and 18 O-assisted 31 P NMR indicate selective metabolic perturbations and adaptations in the whole energetic system. Adenylate kinase and creatine kinase deficiencies were associated with altered metabolomic profiles, increased mitochondrial capacities and redistribution of phosphotransfer flux through glycolytic and guanine nucleotide systems. These phosphometabolomic alterations were more expressed when animals were subjected to treadmill exercise, mitochondria-targeting drugs such as metformin and high-fat diet. Metabolite turnover rates are correlated with heart performance unveiling robustness and dynamics rearrangements in cell bioenergetics infrastructure. Glycerophosphate, G-3-P, metabolic dynamics is altered in transgenic animal models indicating defects in substrate shuttle and supply of reducing equivalents to mitochondria. This is of importance since G-3-P metabolic abnormalities and metabolic arrest are linked to human diseases such as sudden death syndrome. Thus, our study demonstrates that phosphometabolomic and fluxomic profiling is a valuable tool for metabolic phenotyping of transgenic animal models of human diseases as well as for plasma biomarker identification and monitoring of treatment efficacy and drug toxicity.
Periprocedural Bleeding and Thromboembolic Events With Dabigatran Compared With Warfarin
Authors: Jeff S. Healey, John Eikelboom, James Douketis, Lars Wallentin, Jonas Oldgren, Sean Yang, Ellison Themeles, Hein Heidbuchel, Alvaro Avezum, Paul Reilly, Stuart J. Connolly, Salim Yusuf, Michael Ezekowitz
Journal: Circulation (2012)

Dabigatran reduces ischemic stroke in comparison with warfarin; however, given the lack of antidote, there is concern that it might increase bleeding when surgery or invasive procedures are required.The current analysis was undertaken to compare the periprocedural bleeding risk of patients in the Randomized Evaluation of Long-Term Anticoagulation Therapy (RE-LY) trial treated with dabigatran and warfarin. Bleeding rates were evaluated from 7 days before until 30 days after invasive procedures, considering only the first procedure for each patient. A total of 4591 patients underwent at least 1 invasive procedure: 24.7% of patients received dabigatran 110 mg, 25.4% received dabigatran 150 mg, and 25.9% received warfarin, P=0.34. Procedures included: pacemaker/defibrillator insertion (10.3%), dental procedures (10.0%), diagnostic procedures (10.0%), cataract removal (9.3%), colonoscopy (8.6%), and joint replacement (6.2%). Among patients assigned to either dabigatran dose, the last dose of study drug was given 49 (35-85) hours before the procedure on comparison with 114 (87-144) hours in patients receiving warfarin, P<0.001. There was no significant difference in the rates of periprocedural major bleeding between patients receiving dabigatran 110 mg (3.8%) or dabigatran 150 mg (5.1%) or warfarin (4.6%); dabigatran 110 mg versus warfarin: relative risk, 0.83; 95% CI, 0.59 to 1.17; P=0.28; dabigatran 150 mg versus warfarin: relative risk, 1.09; 95% CI, 0.80 to 1.49; P=0.58. Among patients having urgent surgery, major bleeding occurred in 17.8% with dabigatran 110 mg, 17.7% with dabigatran 150 mg, and 21.6% with warfarin: dabigatran 110 mg; relative risk, 0.82; 95% CI, 0.48 to 1.41; P=0.47; dabigatran 150 mg: relative risk, 0.82; 95% CI, 0.50 to 1.35; P=0.44.Dabigatran and warfarin were associated with similar rates of periprocedural bleeding, including patients having urgent surgery. Dabigatran facilitated a shorter interruption of oral anticoagulation.URL: http://www.clinicaltrials.gov. Unique identifier: NCT00262600.
No Differences in the Treatment Outcome in T-Cell Acute Lymphoblastic Leukemia/Lymphoma Regarding the Initial Bone Marrow Blasts Count: Results of the Russian Acute Lymphoblastic Leukemia (RALL) Study Group
Authors: Elena N. Parovichnikova, Vera V. Troitskaya, Andrey N. Sokolov, Larisa A. Kuzmina, Sergey Bondarenko, Olga Baranova, Zalina Akhmerzaeva, Mikhail Rusinov, Sergei M Kulikov, Valery G Savchenko
Journal: Blood (2016)
Influence of ultrasound contrast agents on spectral Doppler analysis in recipients of liver transplantation
Authors: Young Seo Cho, Kyoung Won Kim, Hye Young Jang, Bo Hyun Kim, Jeongjin Lee, Gi Won Song, Sung Gyu Lee, Dagvasumberel Munkhbaatar
Journal: Clinical and Molecular Hepatology (2017)

Background/Aims Clinical validation is required to determine whether Doppler measurements are comparable before and after administering ultrasound contrast agent (USCA). The purpose of this study is to explore whether the use of USCA affects spectral Doppler analysis in recipients of liver transplantation (LT). Methods For this study, 36 patients were examined using Doppler ultrasonography (US) along with a contrast-enhanced US for surveillance of vascular complications after LT. The following spectral Doppler US parameters were measured before and after administration of USCA: peak systolic velocity, end-diastolic velocity, resistive index, and systolic acceleration time of the graft hepatic artery; peak flow velocity of the graft portal vein; and peak flow velocity and venous pulsatility index of the graft hepatic vein. Results The mean peak systolic and end-diastolic velocities of the hepatic artery and the peak flow velocity of the portal and hepatic veins were increased after intravenously administration of the USCA, ranging from 10% to 13%. However, the changes were not statistically significant (P=0.097, 0.103, 0.128, and 0.190, respectively). There were no significant differences in other measured parameters, including the resistive index (P=0.205) and systolic acceleration time (P=0.489) of the hepatic artery and venous pulsatility index (P=0.494) of the hepatic vein. Conclusions The measured velocities of graft hepatic vessels tended to increase after administration of USCA, but without statistical significance. The comparison of serial Doppler parameters with or without injection of USCA is valid during Doppler surveillance in recipients of LT. Keywords: Doppler shift; Liver transplantation; Microbubbles
<i>BRAF</i> fusions in clinically advanced non-small cell lung cancer: An emerging target for anti-<i>BRAF</i> therapies.
Authors: Venkataprasanth P. Reddy, Laurie M. Gay, Julia Andrea Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Sugganth Daniel, Eric Allan Severson, Siraj Mahamed Ali, Alexa Betzig Schrock, Jon Chung, Garrett Michael Frampton, David Fabrizio, Phil Stephens, Vincent A. Miller, Jeffrey S. Ross
Journal: Journal of Clinical Oncology (2017)

9072 Background: Although far less common than BRAF V600E base substitutions (subs) classically associated with melanomas and colorectal carcinomas, BRAF subs occur in 1-2% of non-small cell lung cancer (NSCLC). BRAF fusions are emerging treatment targets for Spitzoid melanomas and other solid tumors. The frequency of BRAF fusions and targeting potential in NSCLC has not been widely described. Methods: Hybridization capture-based comprehensive genomic profiling (CGP) was performed on 17,128 NSCLC FFPE samples sequenced to a mean coverage depth of &gt; 550X for up to 315 cancer-related genes plus 37 introns from 19 genes frequently rearranged in cancer. Genomic alterations (GA) included short variant (SV) base subs and insertions/deletions, copy number alterations, and rearrangements/fusions. Tumor mutational burden (TMB; mut/Mb) was calculated on up to 1.1 Mb of sequenced DNA. Results: BRAF fusions were identified in 42/17,128 (0.2%) NSCLC profiled. Median patient age was 67 (range 44-93 yrs). Of the BRAF fusion positive NSCLC, 55% were female. Biopsies were obtained from primary lung tumor (48%) and metastatic sites (52%). The most frequent 5’ partners were AGK, DOCK4, and TRIM24. Multiple novel BRAF fusions were identified. The genes most frequently co-altered with BRAF fusions were TP53(67%), CDKN2A(31%), EGFR (29%) and CDKN2B (26%). Overall TMB in the BRAFfusion positive cohort was low (median 3.8 mut/Mb), although 3/42 cases (7%) had &gt; 20 mut/Mb. Of the BRAF fusion driven NSCLC, 10 cases (24%) featured EGFR SV alterations. Two BRAF fusion/ EGFR SV cases featured primary exon 19 deletion and T790M mutation. Examples of BRAF fusion driven NSCLC responding to a combination of BRAFand MEK inhibitors (MEKi) will be presented. Conclusions: NSCLC BRAF fusions are a rare GA that may be associated with acquired resistance in a subset of EGFR-mutated NSCLC progressing on anti- EGFR TKI therapies. Given clinical evidence for the activity of targeted therapy approaches, molecular eligibility for clinical trials of MEKi should include these variants. The clinical evidence for responsiveness of BRAF fusion driven NSCLC provides an opportunity to personalize treatments and improve clinical outcomes for patients.
Abstract 4915: Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing
Authors: Priscila Mayrink Miranda, Fabio A. Marchi, Maísa Pinheiro, Luiz Paulo Kowalski, Silvia Regina Rogatto
Journal: Cancer Research (2015)

Abstract Head and neck squamous cell carcinomas (HNSCC) often affect patients over 60 years, although epidemiological studies have shown an increased incidence in young adults (18-45 years), especially those having oropharynx and oral cavity tumors. There is no consensus regarding the etiology, clinical course and prognosis of HNSCC in young patients that often do not have the risk factors frequently described as associated with the disease (alcohol consumption, smoking and HPV infection). Despite its importance, studies with this group of patients are scarce, mainly focusing on the molecular aspects involved in the development and progression of the disease. In this study, we evaluated 36-paired samples (6 oral cavity, 12 oropharyngeal carcinomas and 18 matched blood samples) by whole exome sequencing (WES) aiming to identify molecular markers useful to clinical practice. Libraries were prepared (Illumina Nextera exome Enrichment kit) for WES using the high quality DNA from tumor tissue and peripheral blood of each patient (HiSeq2500, Illumina). The coverage reached an average of 55x per sample. We used an in-house pipeline for cleaning, mapping and SNP calling revealing an average of 36,494 SNPs per sample. A paired comparison of normal and tumor samples was performed considering only the exclusive variants in tumors, after exclusion of the common variants, based on 1000 Genomes (http://www.1000genomes.org/), project and 6500 exomes (evs.gs.washington.edu/). It was identified 248 variants distributed in 169 genes, with 184 (74%) classified as new (variant not described) and 64 (26%) as rare (population frequency ≤0.1%). Three genes, ZNF717, HYDIN and KCNJ12, presented higher frequency of SNPs and were enriched to head and neck carcinoma (p = 1,9×10-9) and calcium (p = 1.82×10-3) pathways. Considering only tongue samples (4 cases) from non-smokers and HPV negative patients, the ZNF717 and HYDIN genes remained among those with the highest frequency of SNPs [non-smokers: HYDIN (23 SNPs) and ZNF77 (24 SNPs); HPV-negative: HYDIN (6 SNPs) and ZNF77 (5 SNPs)]. These genes are putative drivers in young patients with HNSCC. Financial Support: FAPESP (2013/06897-2) and INCiTO (FAPESP: 2008/57887-9 and CNPq 573589/08-9) Citation Format: Priscila Mayrink Miranda, Fabio A. Marchi, Maísa Pinheiro, Luiz Paulo Kowalski, Silvia Regina Rogatto. Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4915. doi:10.1158/1538-7445.AM2015-4915