tbuckley/cabot-search huggingface dataset:
Update on the large-scale screening of ALK fusion oncogene transcripts in archival NSCLC tumor specimens using multiplexed RT-PCR assays.
Authors: Tianhong Li, Eric Huang, Sonal Desai, Laurel Beckett, Craig Stephens, Gary Zeger, Martin Karl Herbert Maus, Kathleen Danenberg, David R. Gandara
Journal: Journal of Clinical Oncology (2012)

7594 Background: The ALK inhibitor crizotinib offers a new standard of care for advanced NSCLC patients with EML4-ALK fusion oncogenes. We previously reported a 4.0% frequency of EML4-ALK fusion oncogene transcripts detected in 1889 NSCLC specimens in the RGI database (Li et al., ASCO 2011). Methods: Patented single and multiplexed RT-PCR assays suitable for rapid and accurate detection of all variants of ALK fusion oncogene transcripts were used as previously described, including all 9 known EML4-ALK fusion gene transcripts and ALK RNA levels (Danenberg, ASCO 2010). The sensitivity and specificity on archival formalin-fixed, paraffin-embedded tumor specimens are 99% and 100%, respectively. We here update the detection of EML4-ALK fusion transcripts in the RGI database. Results: Between 12/2009 and 09/2011, 4750 NSCLC specimens in the RGI database were tested for the presence of ALK fusion transcripts. We found 152 (3.2%) NSCLC cases with EML4-ALK fusion positivity, including 87 (57.2%) V1, 15 (9.9%) V2, 47 (30.9%) V3, and 3 (2.0%) V5a variants. Median age (range): 61.1 (33-96). Female: 74 (49%). All EML4-ALK-positive tumors were adenocarcinomas. No EGFR or K-Ras mutation was detected in ALK fusion-positive samples. Expression of chemotherapy-related biomarkers was available from 63 (female: 31, 49%) EML4-ALK-positive cases in the database: 43 (68%) had low TS level of &lt;2.33; 40 (63.5%) had low ERCC1 level of &lt;1.7, and 25 (40%) had low RRM1 level of &lt;0.97. Conclusions: This RT-PCR assay provides a tool for rapid, large-scale screening of NSCLC FFPE tissues for EML4-ALK fusion gene transcripts. The relative value of this RT-PCR assay as a companion diagnostic test for drugs targeting ALK merits evaluation in comparison with the FDA approved ALK FISH test.
Certain Effects of &lt;italic&gt;p&lt;/italic&gt;-Dimethylamino-azobenzene, Deficient Diet, and Hypotonic Media on Mitochondrial Enzymes in Experimental Rat-Liver Carcinogenesis
Authors: E CLERICI, G CUDKOWICZ
Journal: JNCI Journal of the National Cancer Institute (1956)

Certain Effects of p-Dimethylamino-azobenzene, Deficient Diet, and Hypotonic Media on Mitochondrial Enzymes in Experimental Rat-Liver Carcinogenesis Get access Enrico Clerici, Enrico Clerici Centro di Oncologia Sperimentale del Comitato Nazionale Ricerche, “Istituto del Cancro di Milano,”Milan, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar Gustavo Cudkowicz Gustavo Cudkowicz Centro di Oncologia Sperimentale del Comitato Nazionale Ricerche, “Istituto del Cancro di Milano,”Milan, Italy Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 16, Issue 6, June 1956, Pages 1459–1471, https://doi.org/10.1093/jnci/16.6.1459 Published: 01 June 1956 Article history Received: 03 October 1955 Published: 01 June 1956
Early Intervention in Lung Cancers With Rapid Plasma Genotyping for<i>EGFR</i>and<i>KRAS</i>Mutations
Authors: Ajit Venniyoor
Journal: JAMA Oncology (2016)

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 Oncology 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 Oncology journal
NRG Oncology/NSABP B-51/RTOG 1304: Phase III trial to determine if chest wall and regional nodal radiotherapy (CWRNRT) post mastectomy (Mx) or the addition of RNRT to breast RT post breast-conserving surgery (BCS) will reduce invasive cancer events in patients (pts) with positive axillary (Ax) nodes who are ypN0 after neoadjuvant chemotherapy (NC).
Authors: Eleftherios P. Mamounas, Hanna Bandos, Julia R. White, Thomas B. Julian, Atif J. Khan, Simona Flora Shaitelman, Mylin Ann Torres, Susan Ann McCloskey, Frank A. Vicini, Patricia A. Ganz, Soonmyung Paik, Nilendu Gupta, Joseph P. Costantino, Walter John Curran, Norman Wolmark
Journal: Journal of Clinical Oncology (2015)

TPS11112 Background: This phase III post-NC trial will evaluate if CWRNRT post Mx or whole breast irradiation (WBI) with RNRT after BCS significantly reduces the invasive breast cancer recurrence-free interval (IBCR-FI) rate in pts presenting with positive Ax nodes that are negative after NC. Secondary aims are OS, LRR-FI, DRFI, DFS-DCIS, and second primary cancer as well as comparing RT effect on cosmesis in reconstructed Mx pts. Correlative science examines RT effect by tumor subtype, molecular outcome predictors for residual disease pts, and predictors for the degree of reduction in loco-regional recurrence. Methods: Clinical T1-3, N1 IBC pts with positive Ax nodes (FNA or core needle biopsy) complete ≥ 12 wks of NC (anthracycline and/or taxane). HER2-positive pts receive anti-HER2 therapy (tx). After NC BCS or Mx is performed with a sentinel node biopsy ( ≥ 3 nodes) and/or Ax dissection with histologically negative nodes. ER/PR and HER-2 neu status before NC is required. Pts receive required systemic tx. Radiation credentialing with a facility questionnaire and a case benchmark is required. Randomization for Mx pts is to no CWRNRT or CWRNRT and for BCS pts to WBI or WBI RNRT. Statistics: 1636 pts to be enrolled over 5 yrs with definitive analysis at 7.5 yrs. Study is powered at 80% to test that RT reduces the annual hazard rate of events for IBCR-FI by 35% for an absolute risk reduction in the 5-yr cumulative rate of 4.6%. Intent-to-treat analysis with 3 interim analyses at 43, 86, and 129 events, with a 4th/final analysis at 172 events will occur. Accrual as of 1/15/15 is 96. Pt-reported outcomes focusing on RT effect will be provided by 736 pts before randomization and at 3, 6, 12, and 24 mths. Support: U10 CA 12027, 69651, -37377, -69974; -2166; -180868, -180822; CA189867; Elekta Clinical trial information: NCT01872975.
Is postoperative FEV1 (poFEV1) more accurately estimated by functional respiratory imaging (FRI) than by conventional methods
Authors: Annelies Janssens, Cedric Van Holsbeke, Wim Vos, Paul Van Schil, Elly Oostveen, Laurens Carp, Wilfried De Backer, Jan Van Meerbeeck
Journal: Journal of Thoracic Oncology (2013)
Phase I/II safety and antitumor activity of nivolumab in patients with advanced hepatocellular carcinoma (HCC): CA209-040.
Authors: Anthony B. El-Khoueiry, Ignacio Melero, Todd S. Crocenzi, Theodore Hobart Welling, Thomas Cheung Yau, Winnie Yeo, Akhil Chopra, Joseph Grosso, Lixin Lang, Jeffrey Anderson, Christine Marie Dela Cruz, Bruno Sangro
Journal: Journal of Clinical Oncology (2015)

LBA101 Background: Overexpression of PD-L1 in HCC has a poor prognosis. Safety and preliminary antitumor efficacy of nivolumab, a fully human IgG4 monoclonal antibody PD-1 inhibitor, was evaluated in a multiple ascending-dose, phase I/II study in patients (pts) with HCC. Methods: Pts with histologically confirmed advanced HCC with Child-Pugh (CP) score ≤ B7 and progressive disease (PD) on, intolerant of, or refusing sorafenib were enrolled. Dose escalation occurred in parallel cohorts based on etiology: no active hepatitis virus infection or virus-infected HCC pts. Pts received nivolumab 0.1 – 10 mg/kg intravenously for up to two years. The primary endpoint was safety. Secondary endpoints included antitumor activity using mRECIST criteria, pharmacokinetics, and immunogenicity. Results: The study has enrolled 41 pts with a CP score of 5 (n = 35) or 6 (n = 6), ECOG score of 0 (n = 26) or 1 (n = 15), 73% with extrahepatic metastasis and/or portal vein invasion, and 77% with prior sorafenib use. Eighteen pts remain on study, and 23 discontinued treatment due to PD (n = 17), complete response (CR; n = 2), drug-related adverse events (AEs; n = 2) and non-drug–related AEs (n = 2). Drug-related AEs of any grade occurred in 29 pts (71%; 17% grade 3/4), with ≥ 10% of pts experiencing aspartate aminotransferase (AST) increase and rash (each 17%), alanine aminotransferase(ALT) and lipase increase (each 15%), and amylase increase (12%). Grade 3 and 4 AEs ≥ 5% were AST increase (12%), ALT increase (10%) and lipase increase (5%). A dose-limiting toxicity occurred in an uninfected pt at 10 mg/kg; no maximum tolerated dose was defined in any cohort. Response was evaluable in 39 pts: 2 CR (5%) and 7 partial responses (PR; 18%). Response duration was 14–17+ months for CR, &lt; 1–8+ months for PR, and 1.5–17+ months for stable disease (SD). Overall survival (OS) rate at 6 months is 72%. Conclusions: Nivolumab has a manageable AE profile and produced durable responses across all dose levels and HCC cohorts, with a favorable 6-month OS rate. Updated safety, antitumor activity, and biomarker data will be presented. Clinical trial information: NCT01658878. [Table: see text]
Supportive and unsupportive behaviors of friends and families as experienced by cancer patients
Authors: C. Grange, R. Matsuyama, L. Lyckholm, T. J. Smith
Journal: Journal of Clinical Oncology (2006)

18625 Background: Interpersonal support can help individuals manage stressors associated with cancer diagnosis and treatment. This study reveals cancer patients’ experiences with supportive and unsupportive behaviors of friends and families. Insufficient or inappropriate social support can negatively impact coping, quality of life and other patient outcomes. Methods: Eleven focus groups were conducted with 39 African-American and Caucasian cancer patients recruited from a university-affiliated cancer clinic, using established qualitative methodology. Data analysis included whole group analysis with a team of 4 researchers. Atlas Ti software was used to validate coding and establish intra-rater and inter-rater reliability. Results: Supportive behaviors included practical assistance (e.g., providing meals), family providing housing and daily care, family/friends who listen, prayer, and a social context that demonstrates positive attitudes. Unsupportive behavior included limitations of independence and withdrawal from patients due to fear or discomfort, as well as having to provide emotional support to family or friends. African-American participants were more likely than Caucasian participants to report family or community resources available for daily care and expressed greater concern about limitations to independence. Conclusions: Findings have implications for interventions to improve the quality of support provided to cancer patients from their caregivers and communities. Results can be used to inform family, friends and caregivers about the types of support valued by patients. [Table: see text] No significant financial relationships to disclose.
Association of Blood Donor Age and Sex With Recipient Survival After Red Blood Cell Transfusion
Authors: Michaël Chassé, Alan Tinmouth, Shane W. English, Jason P. Acker, Kumanan Wilson, Greg Knoll, Nadine Shehata, Carl van Walraven, Alan J. Forster, Timothy Ramsay, Lauralyn A. McIntyre, Dean A. Fergusson
Journal: JAMA Internal Medicine (2016)

While red blood cells (RBCs) are administered to improve oxygen delivery and patient outcomes, they also have been associated with potential harm. Unlike solid organ transplantation, the clinical consequences of donor characteristics on recipients have not been evaluated in transfusion medicine.To analyze the association of RBC donor age and sex with the survival of transfusion recipients.We established a longitudinal cohort by linking data from a blood collection agency with clinical and administrative data at 4 academic hospitals.Cox proportional hazards regression models were fitted to evaluate the risk of donor age and sex on transfusion recipient survival.Between October 25, 2006, and December 31, 2013, a total of 30 503 RBC transfusion recipients received 187 960 RBC transfusions from 80 755 unique blood donors. For recipients receiving an RBC unit from younger donors, the risk of death was increased compared with recipients receiving an RBC unit from a donor 40 to 49.9 years old (adjusted hazard ratio, 1.08; 95% CI, 1.06-1.10; P < .001 for donor age range 17-19.9 years and 1.06; 95% CI, 1.04-1.09; P < .001 for donor age range 20-29.9 years). Receiving an RBC transfusion from a female donor was associated with an 8% statistically significant increased risk of death compared with receiving an RBC transfusion from a male donor (adjusted hazard ratio, 1.08; 95% CI, 1.06-1.09; P < .001).Red blood cell transfusions from younger donors and from female donors were statistically significantly associated with increased mortality. These findings suggest that donor characteristics may affect RBC transfusion outcomes.
Smoking Habits of 21,612 Individuals in Texas
Authors: Helen Kirchoff, R. H. Rigdon
Journal: JNCI Journal of the National Cancer Institute (1956)

Smoking Habits of 21,612 Individuals in Texas Get access Helen Kirchoff, Helen Kirchoff Laboratory of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas Search for other works by this author on: Oxford Academic PubMed Google Scholar R. H. Rigdon R. H. Rigdon Laboratory of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 16, Issue 5, April 1956, Pages 1287–1304, https://doi.org/10.1093/jnci/16.5.1287 Published: 01 April 1956 Article history Received: 11 October 1955 Published: 01 April 1956
Prevalence, Neurohormonal Correlates, and Prognosis of Heart Failure Stages in the Community
Authors: Vanessa Xanthakis, Danielle M. Enserro, Martin G. Larson, Kai C. Wollert, James L. Januzzi, Daniel Levy, Jayashri Aragam, Emelia J. Benjamin, Susan Cheng, Thomas J. Wang, Gary F. Mitchell, Ramachandran S. Vasan
Journal: JACC Heart Failure (2016)
Pre-eclampsia paper raises dilemma for clinicians starting aspirin in high risk women
Authors: Junaid Rafi
Journal: BMJ (2016)

Bartsch and colleagues present a high impact paper quantifying the risk factors for pre-eclampsia.1 It will be useful in formulating guidelines for clinicians and especially community midwives in the UK to start aspirin at the booking appointment because, by the time a woman is seen in the antenatal clinic, it’s too …
Predictors of Outcome at Two Years in Patients with Rheumatoid Arthritis
Authors: Jane Reeback, Alan Silman
Journal: Journal of the Royal Society of Medicine (1984)

The prognostic value of clinical and laboratory measures in 72 patients with rheumatoid arthritis (RA), seen initially within 18 months of disease onset, in predicting function outcome after a further two years was assessed. Limitation of wrist extension was associated with a slow disease onset, a high articular index and a high latex titre. A reduction in global functional capacity, as measured by the Stanford Health Assessment Questionnaire, was associated with a high initial articular index and a high latex titre. Neither outcome was associated with the initial level of acute phase reactants nor with patient or physician's initial assessment of disease activity. It is concluded, first, that factors predicting early disability outcome in RA are not identical to those associated with continuing disease activity; and secondly, that patients' and physicians' judgment of disease activity at diagnosis do not carry any prognostic value for functional outcome two years later.
Selective Detection of the D-enantiomer of 2-Hydroxyglutarate in the CSF of Glioma Patients with Mutated Isocitrate Dehydrogenase
Authors: Juliya Kalinina, Jun Ahn, Narra S. Devi, Liya Wang, Yuancheng Li, Jeffrey J. Olson, Michael Glantz, Thomas Smith, Ella L. Kim, Alf Giese, Randy L. Jensen, Clark C. Chen, Bob S. Carter, Hui Mao, Miao He, Erwin G. Van Meir
Journal: Clinical Cancer Research (2016)

Elevation in D-2-Hydroxyglutarate (D-2HG) has recently emerged as a mandatory byproduct of mutated Isocitrate Dehydrogenase (IDH) genes 1 and 2 in glioma patients. The goal of the present study was to demonstrate the feasibility of detection of elevated levels of D-2HG in the cerebrospinal fluid (CSF) of glioma patients that carry point substitutions in the IDH gene.We developed a mass spectrometry (MS)-based platform to detect and quantify the D- and L-forms of 2HG in the CSF of glioma patients. Three independent cohorts of patients were analyzed, comprising a total of 176 samples derived from 84 patients. The levels of D- and L-2HG were used to stratify patients into IDH wild-type or IDH-mutated groups using an empirically obtained threshold of 0.69 μmol/L.Using this platform, a greater than 17-fold mean increase in D-2HG was observed in the CSF of patients with IDH mutant versus wild-type gliomas. The means for the D-2HG levels in CSF were 0.427 μmol/L in wild-type and 7.439 μmol/L in mutant groups. The C statistic for the receiver operator curve was 0.938, with 84% sensitivity, 90% specificity, and 89% accuracy to detect D-2HG. The levels of D- and L-2HG in CSF from wild-type patients varied by location of CSF draw (cisternal > ventricular > lumbar).Our findings demonstrate that the CSF of patients harboring IDH mutant gliomas contain increased levels of D-2HG, which can be reliably detected with a MS-based platform. Clin Cancer Res; 22(24); 6256-65. ©2016 AACR.
Point-of-Care Screening for Sickle Cell Disease By a Mobile Micro-Electrophoresis Platform
Authors: Ryan Ung, Yunus Alapan, Muhammad Noman Hasan, Megan Romelfanger, Ping He, Aaron Tam, Tolulope Rosanwo, Asya Akkus, Mehmet A Cakar, Kutay Icoz, Connie M. Piccone, Jane A Little, Umut A Gurkan
Journal: Blood (2015)
Case 29-1972
Authors: Richard C. Cabot, Benjamin Castleman, Robert E. Scully, Betty U. McNeely, Larry Nathanson, Alan L. Schiller
Journal: New England Journal of Medicine (1972)

Presentation of CaseA 56-year-old woman was admitted to the hospital because of numbness of the feet.Nine months previously, after a European trip, she had diarrhea for several weeks, with spontaneous recovery, and at the same time became aware of numbness of the feet. An examination by a physician was negative. The numbness gradually progressed to the level of the knees, accompanied by muscular weakness in the lower extremities, with occasional crampy pain in the legs on climbing stairs. During the week before entry she experienced fecal urgency, and incontinence occurred twice. For several days she had a mild, . . .
The art of medicine
Authors: Mark Edmondstone
Journal: BMJ (2016)

Without doubt he had carcinoid syndrome. The patient had levels of 5-hydroxyindoleacetic acid (5-HIAA) way above those required to confirm the diagnosis. The history was textbook-typical. All that remained was to answer his many questions and formulate a management plan. I realised my knowledge of carcinoid syndrome had not been refreshed since MRCP days, and, …
Itinerant Patient
Authors: DERRICK L. LATOS
Journal: Annals of Internal Medicine (1973)

Comments and Corrections1 November 1973Itinerant PatientDERRICK L. LATOS, M.D., OLIVER P. MATTHEWS, M.D.DERRICK L. LATOS, M.D.Search for more papers by this author, OLIVER P. MATTHEWS, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-79-5-765_2 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: A 28-year-old man of Italian descent was seen in the Vanderbilt University Hospital Emergency Room on 16 January 1973. He complained of severe pain and swelling in both legs and pleuritic midsternal pain that had occurred while he was traveling by bus from Florida to New York. He gave a history of recurrent thrombophlebitis and pulmonary emboli, which necessitated inferior vena cava umbrella insertion in early 1970 and cava ligation in December 1970. He moved to Florida because of the finding of cryoglobulinemia during a New York City hospitalization and claimed that a cervical node biopsy showed... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited ByMore on "Munchausen Syndrome"RICHARD B. DEVEREUX, M.D., THOMAS R. MILLER, M.D. 1 November 1973Volume 79, Issue 5Page: 765-765KeywordsBiopsyEmergency departmentHospitalizationsInferior vena cavaInflammationLigation assay Issue Published: 1 November 1973 PDF DownloadLoading ...
Retrospective study of chemotherapy for non-small cell lung cancer, complicated pleural effusion
Authors: Yasuto Ueda, Masaaki Yanai, Hiroki Izumi, Tomohiro Sakamoto, Naoki Kinoshita, Kenichi Takeda, Haruhiko Makino, Masahiro Kodani, Tadashi Igishi, Eiji Shimizu
Journal: Annals of Oncology (2015)
<i>Annals</i> Graphic Medicine - The Price of Progress
Authors: Grace E. Farris
Journal: Annals of Internal Medicine (2016)

Web Exclusives5 July 2016Annals Graphic Medicine - The Price of ProgressFREEGrace E. Farris, MDGrace E. Farris, MDSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/G16-0003 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAffiliations: Disclosures: The author has disclosed no conflicts of interest. Form can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=G16-0003.Author/Illustrator Information: Grace E. Farris, MD, is an instructor of medicine at Harvard Medical School and a hospitalist at Beth Israel Deaconess Medical Center in Boston, Massachusetts.Corresponding Author: Grace E. Farris, MD, Beth Israel Deaconess Medical Center, Palmer Baker Span 2, 330 Brookline Avenue, Boston, MA 02215; e-mail, [email protected]harvard.edu.Author Contributions: Drafting of the article: G.E. Farris.Critical revision for important intellectual content: G.E. Farris.Final approval of the article: G.E. Farris. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 5 July 2016Volume 165, Issue 1Page: W1-W4KeywordsConflicts of interestDisclosureHealth careHospitalists ePublished: 5 July 2016 Issue Published: 5 July 2016 Copyright & PermissionsCopyright © 2016 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Dengue virus sero-cross-reactivity drives antibody-dependent enhancement of infection with zika virus
Authors: Wanwisa Dejnirattisai, Piyada Supasa, Wiyada Wongwiwat, Alexander Rouvinski, Giovanna Barba-Spaeth, Thaneeya Duangchinda, Anavaj Sakuntabhai, Van-Mai Cao-Lormeau, Prida Malasit, Felix A Rey, Juthathip Mongkolsapaya, Gavin R Screaton
Journal: Nature Immunology (2016)