tbuckley/cabot-search huggingface dataset:
The value of endoscopic ultrasonography in a PET/CT upfront model in staging esophageal cancer with respect to treatment decision.
Authors: Jan-Binne Hulshoff, Hiske E.M. de Boer, Walter Noordzij, Wouter B. Nagengast, Hendrik M. van Dullemen, Veronique E.M. Mul, John Theodorus Plukker
Journal: Journal of Clinical Oncology (2016)

25 Background: The optimal sequence of endoscopic ultrasonography (EUS) and positron emission tomography with computed tomography (PET/CT) in esophageal cancer (EC) is a matter of debate. The use of EUS with fine needle aspiration (FNA) after PET/CT seems to increase the efficacy of curative intended neoadjuvant or definitive chemoradiotherapy. Retrospectively, we assessed the impact of EUS in the PET/CT upfront model on the treatment decision making in EC patients. Methods: In the period 2009 to 2015, 298 EC patients were staged with hybrid PET/CT or PET with CT, and EUS if applicable, in a non-specific order to assess curability (T1-4a,N0-3M0). We determined the feasibility of EUS and whether the initial or additional EUS changed the primary decision suspicious incurable (T4b and M+) into curable disease or added extra nodal information leading to up/downstaging or exhibit suspected nodes at different lymph node stations. In addition, we assessed if EUS changed the radiation area (i.e. lymph nodes &gt; 3.5 cm from the defined radiation target volumes) in the PET/CT “upfront model”. Results: EUS was complete in 185 (62.1%) and incomplete due to stricture from a relative obstructing tumor in 59 (19.8%) patients. Fifty-four patients (18.1%) did not receive EUS because of stenosis (n = 46; 15.4%), patient dependent reasons (n = 4; 1.3%) or other reasons (n = 4; 1.3%). EUS after hybrid PET/CT or PET with CT (n = 244) gave additional information in 166 patients (68.0%); it changed the curability in 4 (1.6%), lead to nodal up and downstaging in respectively, 81 (33.2%) and 27 (11.1%) patients, changed the number of or lymph node station of suspected lymph nodes in an additional 58 patients (n = 23.8%), and FNA gave additional information in 34 (13.9%) patients. EUS after PET/CT ”upfront” changed the treatment plan in 90 patients (36.9%), including alteration in the radiation field (86; 35.2%) and curability (4; 1.6%). Conclusions: EUS gave additional information after PET/CT “up front” and altered the radiation field in about one third of the EC patients, suggesting a better yield of “EUS on indication” after PET/CT upfront.
Reassessment of a proposed molecular classification system for clear cell renal cell cancer (ccRCC): Results from a randomized phase II trial of pazopanib.
Authors: Martha P. Mims, Robert C. Gagnon, Yuan Liu, Elisabeth I. Heath, Primo Lara
Journal: Journal of Clinical Oncology (2012)

404 Background: Understanding the molecular basis of ccRCC heterogeneity could optimize the use of targeted therapies. Using consensus clustering and logical analysis of data (LAD) of gene expression data (Agilent), Brannon et al (Genes Cancer 2010) identified two distinct subtypes of ccRCC [ccA &amp; ccB] defined by a predictive gene set. Patients (pts) with ccA tumors had better disease-specific survival vs. ccB (8.6 vs 2.0 years, P = 0.002). We evaluated these results in an independent dataset. Methods: Gene expression analysis of archival FFPE samples obtained from pts in a randomized phase II trial of pazopanib in ccRCC (Hutson, JCO 2009) were done using Affy U133 plus chips. Corresponding probe sets from the Agilent and Affy platform were identified using Unigene ID’s (DAVID alignment tool). LAD was applied; pts were stratified into ccA/ccB. Kaplan-Meier analysis was used to compare progression-free survival (PFS) for pts stratified by ccA/ccB. Results: RNA was available for 46 pts. Of 110 genes, 108 were mapped to the Affy platform (probe closest to 3` was used). The 108 Affy genes were assessed for signal (present/absent calls) across the 46 samples. 74/108 genes were present in at least 20% (9/46) of pts, 96/108 genes were present in at least 1/46, and 12/108 were not present (0/46). No obvious patterns of expression were evident from heat maps of the 74 or 96 genes. LAD scoring was problematic due to loss of information imposed by using genes present. Of the total LAD patterns in the Brannon paper, 59% or 78% were available using 74 or 96 genes present. PFS based on ccA/ccB were not statistically distinct using either set of present genes. Conclusions: FFPE samples are routinely available from pts with ccRCC and could be used for gene expression studies which could inform clinical practice. Using the Affy platform and FFPE-RNA samples, stratification of ccRCC pts into ccA/ccB subtypes did not reveal PFS differences. While the analysis was confounded by differences in cross-study platform performance, results suggest that further investigation will be necessary to identify a robust set of genes that separates ccRCC into prognostic categories.
Incidence of the BCR-ABL Kinase Domain Mutations in Imatinib Treated CML Patients: Russian Experience
Authors: Andrey V Misyurin, Elena N Misyurina, Alexey Krutov, Elena Aksenova, Irina Soldatova, Laura Kesaeva, Anna Turkina, Ekaterina Chelysheva, Valeri G Savchenko, Elena Parovichnikova
Journal: Blood (2011)
Vaccination Targeting Native Receptors to Enhance the Function and Proliferation of Chimeric Antigen Receptor (CAR)-Modified T Cells
Authors: Miyuki Tanaka, Haruko Tashiro, Bilal Omer, Natasha Lapteva, Jun Ando, Minhtran Ngo, Birju Mehta, Gianpietro Dotti, Paul R. Kinchington, Ann M. Leen, Claudia Rossig, Cliona M. Rooney
Journal: Clinical Cancer Research (2017)

Purpose: The multiple mechanisms used by solid tumors to suppress tumor-specific immune responses are a major barrier to the success of adoptively transferred tumor-specific T cells. As viruses induce potent innate and adaptive immune responses, we hypothesized that the immunogenicity of viruses could be harnessed for the treatment of solid tumors if virus-specific T cells (VST) were modified with tumor-specific chimeric antigen receptors (CAR). We tested this hypothesis using VZV-specific T cells (VZVST) expressing a CAR for GD2, a disialoganglioside expressed on neuroblastoma and certain other tumors, so that the live-attenuated VZV vaccine could be used for in vivo stimulation.Experimental Design: We generated GMP-compliant, GD2.CAR-modified VZVSTs from healthy donors and cancer patients by stimulation of peripheral blood mononuclear cells with overlapping peptide libraries spanning selected VZV antigens, then tested their ability to recognize and kill GD2- and VZV antigen-expressing target cells.Results: Our choice of VZV antigens was validated by the observation that T cells specific for these antigens expanded in vivo after VZV vaccination. VZVSTs secreted cytokines in response to VZV antigens, killed VZV-infected target cells and limited infectious virus spread in autologous fibroblasts. However, while GD2.CAR-modified VZVSTs killed neuroblastoma cell lines on their first encounter, they failed to control tumor cells in subsequent cocultures. Despite this CAR-specific dysfunction, CAR-VZVSTs retained functional specificity for VZV antigens via their TCRs and GD2.CAR function was partially rescued by stimulation through the TCR or exposure to dendritic cell supernatants.Conclusions: Vaccination via the TCR may provide a means to reactivate CAR-T cells rendered dysfunctional by the tumor microenvironment (NCT01953900). Clin Cancer Res; 23(14); 3499-509. ©2017 AACR.
Rituximab in Neuromyelitis Optica Spectrum Disorders—Reply
Authors: Valentina Damato, Amelia Evoli, Raffaele Iorio
Journal: JAMA Neurology (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 Neurology 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 Neurology journal
431P First-line treatment of advanced nonsquamous non-small cell lung cancer (NSCLC) in China in the era of precision medicine
Authors: X. Zhang, Q. Zhou, Y. Song, G.Y. Chen, D.S. Zhong, Z. Yu, P. Yu, Y.P. Zhang, J.H. Chen, Y. Hu, G.S. Feng, X. Song, Q. Shi, L.L. Yang, P.H. Zhang, Y.-L. Wu
Journal: Annals of Oncology (2016)
Bortezomib-Doxorubicin-Dexamethasone (BDD) for Reversal of Acute Light Chain Induced Renal Failure (ARF) in Multiple Myeloma (MM). Results from a Phase II Study
Authors: Heinz Ludwig, Zdenek Adam, Roman Hajek, Richard Greil, Felix Keil, Niklas Zojer, Josef Thaler, Heinz Gisslinger, Alois Lang
Journal: Blood (2008)
Matched Sibling Transplants for Aplastic Anemia: Survival Advantage for Marrow Vs Peripheral Blood Transplants, In All Age groups
Authors: Andrea Bacigalupo, Gérard Socié, Hubert Schrezenmeier, Andre Tichelli, Anna Locasciulli, Monika Fuehrer, Antonio M. Risitano, Claudio Dufour, Jakob R. Passweg, Judith C. W. Marsh
Journal: Blood (2010)
P09.13 Clear cell renal carcinoma (CCRC) after diagnosis of Oligodendroglioma; real or false association?
Authors: A. Muggeri, B. Calabrese
Journal: Neuro-Oncology (2016)

histology over the entire cohort of diffuse glioma (p<0.0001).Sequencing analysis of 17/24 of the gemistocytic astrocytoma revealed IDH1R132H mutations in all, TP53 mutations in 15/17, ATRX mutations in 10/17 and NF1 mutations in 2/17 samples.The previously reported associations with PTEN mutations and epigenetic alterations of ERCC and RRAS were not detectable in our cohort.The finding of CCND2 gain could also provide the basis for novel therapeutic approaches: Up-regulation of CCND2 is already used as inclusion criterion for treatment with palbociclib in several clinical trials.Collectively, we provide evidence for a significant association of a particular genetic event, CCND2 gain or amplification, with the histologically defined variant gemistocytic astrocytoma, potentially allowing for a novel treatment approach.P09.
Immunoglobulin Free Light Chain Ratio Is an Independent Risk Factor for Progression of Smoldering Multiple Myeloma.
Authors: Angela Dispenzieri, Robert A. Kyle, Jerry A. Katzmann, Dirk Larson, Joanne Benson, Raynell Clark, L. Joseph Melton, Morie A. Gertz, Shaji K. Kumar, Rafael Fonseca, Diane F. Jelinek, S. Vincent Rajkumar
Journal: Blood (2007)
Urinary Prostaglandin D2 Metabolite Is a Novel Biomarker of Food Allergy
Authors: Tatsuro Nakamura, Shingo Maeda, Hiroaki Harada, Kosuke Aritake, Tatsuo Shimosawa, Yoshihiro Urade, Yutaka Yatomi, Takahisa Murata
Journal: Journal of Allergy and Clinical Immunology (2017)
Efficacy of ‘Off-the-Shelf’, Commercially-Available, Third-Party Mesenchymal Stem Cells (MSC) in Ex Vivo Cord Blood (CB) Co-Culture Expansion.
Authors: Simon N. Robinson, Paul J. Simmons, Nathalie Brouard, Shannon Kidd, Hong Yang, William K. Decker, Dongxia Xing, David Steiner, Jingjing Ng, Michael Thomas, Richard E. Champlin, Marcos de Lima, Chitra M. Hosing, Laurence Cooper, Harjeet Singh, Patrick A. Zweidler-McKay, Elizabeth J. Shpall
Journal: Blood (2007)
Phase 2 Trial of the Farnesyltransferase Inhibitor Tipifarnib in Previously Untreated Older Adults with AML and Baseline Presence of a Specific 2-Gene Expression Signature Ratio
Authors: Jeffrey E Lancet, Eric Feldman, Matthew C Foster, Ivana Gojo, Olatoyosi Odenike, Rami S. Komrokji, Roger Strair, Scott H. Kaufmann, Roland Knoblauch, J. D. Karkera, John J Wright, Judith E. Karp
Journal: Blood (2012)
T-cell repertoires in refractory coeliac disease
Authors: Julia Ritter, Karin Zimmermann, Korinna Jöhrens, Stefanie Mende, Anke Seegebarth, Britta Siegmund, Steffen Hennig, Kremena Todorova, Andreas Rosenwald, Severin Daum, Michael Hummel, Michael Schumann
Journal: Gut (2017)

Refractory coeliac disease (RCD) is a potentially hazardous complication of coeliac disease (CD). In contrast to RCD type I, RCD type II is a precursor entity of enteropathy-associated T-cell lymphoma (EATL), which is associated with clonally expanding T-cells that are also found in the sequentially developing EATL. Using high-throughput sequencing (HTS), we aimed to establish the small-intestinal T-cell repertoire (TCR) in CD and RCD to unravel the role of distinct T-cell clonotypes in RCD pathogenesis.DNA extracted from duodenal mucosa specimens of controls (n=9), active coeliacs (n=10), coeliacs on a gluten-free diet (n=9), RCD type I (n=8), RCD type II (n=8) and unclassified Marsh I cases (n=3) collected from 2002 to 2013 was examined by TCRβ-complementarity-determining regions 3 (CDR3) multiplex PCR followed by HTS of the amplicons.On average, 106 sequence reads per sample were generated consisting of up to 900 individual TCRβ rearrangements. In RCD type II, the most frequent clonotypes (ie, sequence reads with identical CDR3) represent in average 42.6% of all TCRβ rearrangements, which was significantly higher than in controls (6.8%; p<0.01) or RCD type I (6.7%; p<0.01). Repeat endoscopies in individual patients revealed stability of clonotypes for up to several years without clinical symptoms of EATL. Dominant clonotypes identified in individual patients with RCD type II were unique and not related between patients. CD-associated, gliadin-dependent CDR3 motifs were only detectable at low frequencies.TCRβ-HTS analysis unravels the TCR in CD and allows detailed analysis of individual TCRβ rearrangements. Dominant TCRβ sequences identified in patients with RCD type II are unique and not homologous to known gliadin-specific TCR sequences, supporting the assumption that these clonal T-cells expand independent of gluten stimulation.
Early Normalization of Serum Free Light Chain Is Associated with Prolonged Time to Progression Following Bortezomib ± Pegylated Liposomal Doxorubicin Treatment of Relapsed/Refractory Multiple Myeloma.
Authors: Robert Orlowski, Heather Sutherland, Joan Bladé, Jesús San Miguel, Roman Hájek, Arnon Nagler, Pieter Sonneveld, Andrew Spencer, Tadeusz Robak, Suneel Mundle, Donghan Luo, Sen Hong Zhuang, Jean-Luc Harousseau
Journal: Blood (2007)
Re-differentiation of radioiodine-refractory <i>BRAF</i> V600E-mutant thyroid carcinoma with dabrafenib: A pilot study.
Authors: Stephen M. Rothenberg, David G McFadden, Edwin Palmer, Gilbert H Daniels, Lori J. Wirth
Journal: Journal of Clinical Oncology (2013)

6025 Background: Resistance to radioactive iodine is a leading cause of mortality in differentiated thyroid carcinoma. The MAPK pathway is a major determinant of iodine uptake into thyroid carcinoma cells. Mutations in BRAF activate this pathway, resulting in resistance to radioactive iodine. A pilot study using the MEK1/2 inhibitor, selumetinib, (Ho, ASCO 2012) increased radioiodine uptake in a subset of thyroid cancers. Methods: This is a single institution, single arm pilot study investigating the potential for the BRAF inhibitor dabrafenib to induce radioiodine uptake in metastatic, BRAF-mutant, radioiodine-refractory papillary thyroid carcinoma (PTC). The primary endpoint is increased radioiodine uptake demonstrated on a 4mCi 131-I whole body scan. Patients with increased uptake receive 14 additional days of dabrafenib followed by treatment with 150mCi 131-I. Secondary endpoints include safety and tolerability and clinical benefit as measured by decreases in serum thyroglobulin and objective response rate per modified RESIST 1.1. Results: To date, 7 patients have been enrolled. All had negative 131-I scans within 14 months of enrollment. No dose adjustments for toxicity have been needed. One patient developed reversible hypophosphatemia and a second developed a benign skin lesion. 3 of 5 evaluable patients developed radioiodine uptake after 28 days of dabrafenib, and new radioiodine-avid lesions were demonstrated in all three after receiving a therapeutic dose of 131-I. All three patients demonstrated increases in thyroglobulin levels during treatment with dabrafenib. Conclusions: This initial data suggests that a subset of patients with radioiodine-resistant BRAF-mutant PTC demonstrate new iodine uptake following treatment with dabrafenib. Reuptake may correlate with increases in thyroglobulin, suggestive of re-differentiation. It is not yet known whether increased uptake of radioactive iodine will translate into a radiographic response. Two patients failed to convert to radioiodine-sensitive disease; it is possible that BRAF inhibition was incomplete in these patients and/or determinants other than BRAF mutation status contribute to radioiodine sensitivity. Clinical trial information: NCT01534897.
Efficiency of the Neonatal Screening Program for Sickle Cell Disease. the Belgian Experience
Authors: Phu-Quoc Le, Alina Ferster, Françoise Vertongen, Christiane Vermylen, Anna Vanderfaeillie, Catherine Heijmans, Ba-Cuong Nguyen, Malou Ngalula Mijinga, Beatrice Gulbis
Journal: Blood (2010)
Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples
Authors: Luciano G Martelotto, Timour Baslan, Jude Kendall, Felipe C Geyer, Kathleen A Burke, Lee Spraggon, Salvatore Piscuoglio, Kalyani Chadalavada, Gouri Nanjangud, Charlotte K Y Ng, Pamela Moody, Sean D'Italia, Linda Rodgers, Hilary Cox, Arnaud da Cruz Paula, Asya Stepansky, Michail Schizas, Hannah Y Wen, Tari A King, Larry Norton, Britta Weigelt, James B Hicks, Jorge S Reis-Filho
Journal: Nature Medicine (2017)
Crossing kingdoms: Using decellularized plants as perfusable tissue engineering scaffolds
Authors: Joshua R. Gershlak, Sarah Hernandez, Gianluca Fontana, Luke R. Perreault, Katrina J. Hansen, Sara A. Larson, Bernard Y.K. Binder, David M. Dolivo, Tianhong Yang, Tanja Dominko, Marsha W. Rolle, Pamela J. Weathers, Fabricio Medina-Bolivar, Carole L. Cramer, William L. Murphy, Glenn R. Gaudette
Journal: Biomaterials (2017)

Despite significant advances in the fabrication of bioengineered scaffolds for tissue engineering, delivery of nutrients in complex engineered human tissues remains a challenge. By taking advantage of the similarities in the vascular structure of plant and animal tissues, we developed decellularized plant tissue as a prevascularized scaffold for tissue engineering applications. Perfusion-based decellularization was modified for different plant species, providing different geometries of scaffolding. After decellularization, plant scaffolds remained patent and able to transport microparticles. Plant scaffolds were recellularized with human endothelial cells that colonized the inner surfaces of plant vasculature. Human mesenchymal stem cells and human pluripotent stem cell derived cardiomyocytes adhered to the outer surfaces of plant scaffolds. Cardiomyocytes demonstrated contractile function and calcium handling capabilities over the course of 21 days. These data demonstrate the potential of decellularized plants as scaffolds for tissue engineering, which could ultimately provide a cost-efficient, "green" technology for regenerating large volume vascularized tissue mass.
Targeting the Risks of Specific Antiplatelet Alloimmunization in the Populations of Sub-Saharan Africa, Asia, and Oceania.
Authors: Cecile Kaplan-Gouet, Andre Bigot, Gisele Imandy, Ferdinand M’Bayo, Hoa B. Khanh, Claude Tetaria, Corinne Martageix, Liliane Halle
Journal: Blood (2004)
Dose-dence adjuvant chemotherapy in early breast cancer: the results of 15 years of follow-up
Authors: S. Giraudi, M.G. Cavazzini, A. Michelotti, A. De Censi, F. Testore, M. Benasso, M.R. Sertoli, C. Bighin, S. Pastorino, A. Levaggi, A. D'Alonzo, M. Lambertini, F. Poggio, E. Blondeaux, B. Conte, P. Pronzato, L. Del Mastro
Journal: Annals of Oncology (2016)
Interim analysis of a phase I dose escalation trial of the antibody drug conjugate (ADC) AGS15E (ASG-15ME) in patients (Pts) with metastatic urothelial cancer (mUC)
Authors: D. Petrylak, E. Heath, G. Sonpavde, S. George, A.K. Morgans, B.J. Eigl, J. Picus, S. Cheng, S.J. Hotte, E. Gartner, M. Vincent, R. Chu, B. Anand, K. Morrison, L. Jackson, A. Melhem-Bertrandt, E.Y. Yu
Journal: Annals of Oncology (2016)
Effect of Lenalidomide (LEN) Exposure on AML-Free Survival and Overall Survival in LEN-Treated Patients (Pts) with IPSS Low- or Intermediate-1-Risk Myelodysplastic Syndromes (MDS) with Del(5q)
Authors: Mikkael A. Sekeres, Arlene S. Swern, Alan F. List, Pierre Fenaux, Mary M. Sugrue
Journal: Blood (2015)
Ruxolitinib Plus Pomalidomide in Myelofibrosis: Updated Results from the Mpnsg-0212 Trial (NCT01644110)
Authors: Frank Stegelmann, Holger Hebart, Markus Bangerter, Denise Wolleschak, Martin Griesshammer, Steffen Koschmieder, Nikolas von Bubnoff, Robert Möhle, Thomas Kindler, Andreas Hochhaus, Florian H. Heidel, Andreas Reiter, Christof Scheid, Rebecca Kirschbaum, Regina Reim, Ulrike Sutter, Katrin Vetter, Hartmut Döhner, Richard F. Schlenk, Konstanze Döhner
Journal: Blood (2016)
Effectiveness of Elimination Diets in Treating Eosinophilic Gastroenteritis
Authors: Miori Sato, Akio Yoshida, Motoko Mitsui, Miyuki Ohta, Yumiko Miyaji, Shinichiro Inagaki, Tatsuki Fukuie, Masami Narita, Katsuhiro Arai, Kenji Matsumoto, Yukihiro Ohya, Ichiro Nomura
Journal: Journal of Allergy and Clinical Immunology (2017)
Tacrolimus and Mycophenolate Mofetil as Post-Grafting Immunosuppression After Conditioning with Fludarabine and Low-Dose Total Body Irradiation for Recipients of HLA-Matched Sibling or Unrelated Donor Hematopoietic Cell Transplants in Patients with Paroxysmal Nocturnal Hemoglobinuria.
Authors: Tara Gregory, Mark W. Brunvand, Peter A. McSweeney, Scott I. Bearman, Michael Maris, Jeffrey Matous
Journal: Blood (2009)