tbuckley/cabot-search huggingface dataset:
PD-1 Blockade with Pembrolizumab in Relapsed CLL Including Richter's Transformation: An Updated Report from a Phase 2 Trial (MC1485)
Authors: Wei Ding, Jennifer Le-Rademacher, Timothy G. Call, Sameer A. Parikh, Jose F. Leis, Tait D. Shanafelt, Rong He, Thomas M. Habermann, Yi Lin, Betsy R. Laplant, Andrew L Feldman, Thomas E. Witzig, Asher A. Chanan-Khan, Erik Asmus, Daniel L. Van Dyke, Michael J Conte, Deborah A. Bowen, Sutapa Sinha, Henan Zhang, Xin Liu, Charla R Secreto, Shulan Tian, Esteban Braggio, Ivana Micallef, Huihuang Yan, Neil E. Kay, Haidong Dong, Stephen M Ansell
Journal: Blood (2016)
Early Detection of Imminent Hematologic Relapse Due to BCR-ABL Kinase Domain Mutations in CML Patients on Imatinib Therapy by D-HPLC.
Authors: Thomas Ernst, Philipp Erben, Thomas Schenk, Martin C. Mueller, Michael Emig, Sebastian Kreil, Paul La Rosée, Ute Berger, Ruediger Hehlmann, Andreas Hochhaus
Journal: Blood (2005)
Erratum: Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma: a report from the International DLBCL Rituximab-CHOP Consortium Program Study
Authors: C Visco, Y Li, Z Y Xu-Monette, R N Miranda, T M Green, Y Li, A Tzankov, W Wen, W-m Liu, B S Kahl, E S G d'Amore, S Montes-Moreno, K Dybkær, A Chiu, W Tam, A Orazi, Y Zu, G Bhagat, J N Winter, H-Y Wang, S O'Neill, C H Dunphy, E D Hsi, X F Zhao, R S Go, W W L Choi, F Zhou, M Czader, J Tong, X Zhao, J H van Krieken, Q Huang, W Ai, J Etzell, M Ponzoni, A J M Ferreri, M A Piris, M B Møller, C E Bueso-Ramos, L J Medeiros, L Wu, K H Young
Journal: Leukemia (2014)
Expression of dUTP nucleotidohydrolase (dUTPase) and thymidylate synthase (TS) in stage III colon cancer patients treated with either bolus 5-FU or infusional 5-FU in the adjuvant setting: Results of a translational study of the PETACC-2 trial.
Authors: J. Stoehlmacher, C. Kohne, M. Mauer, E. Goekkurt, M. P. Lutz, D. E. Aust, A. Carrato, L. Bedenne, I. Popov, R. D. Ladner
Journal: Journal of Clinical Oncology (2011)

417 Background: Pts with stage III colon cancer have been treated with either infusional 5-FU or bolus 5- FU in the adjuvant setting (PETACC-2 trial). DUTPase and TS demonstrated potential as predictive markers for 5-FU efficacy in pts with advanced colorectal cancer. Here we aimed to explore whether TS or dUTPase protein levels may predict recurrence of disease for stage III colon pts treated with 5-FU. Methods: Tumor (T) blocks of 324 pts were analyzed for protein expression of dUTPase and TS. For analysis monoclonal antibodies DUT415 and TS106 were used. T were evaluated by two investigators as follows. Only nuclear staining for both, TS and dUTPase, was analyzed. If tumor cells (TC) showed a nuclear dUTPase expression in &gt;10% of cells, the sample was scored positive. Positive nuclear staining for &gt;20% of TC, when using the TS antibody, determined a positive sample. Results: Analysis for dUTPase was successful in 308 samples (95.1%, 308/324). 263 out of those 308 pts showed a positive dUTPase expression (85.3%). 297/324 samples (91.7%) could be evaluated for TS. In the TS group 62.3% (185/297) showed a positive expression for TS protein. In 281 cases analyses were successful for both TS and dUTPase. We observed a significant association between dUTPase and TS expression with a majotity of 71.4% (172/241) dUTPase positive T also being positive for TS as compared to 32.5% (13/40) of dUTPase negative T that showed positivity for TS protein expression (p&lt; 0.0001). Of pts with dUTPase positive T 64.7% showed no recurrence of disease as compared to 44.7% of those with dUTPase negative T 5 years after completion of therapy (HR 0.61 [95% CI 0.36, 1.03], p=0.06). No associations between TS and DFS were observed. Both TS and dUTPase expression did not correlate with OS in this patient cohort. Conclusions: High TS protein levels appeared to be significantly correlated with high protein levels of dUTPase in stage III colon cancer pts. Neither dUTPase nor TS protein levels appeared to be significantly associated with DFS or OS of stage III colon cancer pts that received adjuvant chemotherapy with 5-FU. No significant financial relationships to disclose.
Platelet Transfusion Refractoriness Pre-Allograft Is Associated with Higher Rates of Platelet Non-Engraftment and Graft Failure in Adult Allogeneic Haematopoietic Stem Cell Transplantation for Haematological Malignancies
Authors: Ashleigh Scott, Stephanie Buckby, Shoma Baidya, Cameron Curley, Kirk Lachlan Morris, Gail Pahn, Glen A Kennedy
Journal: Blood (2014)
Absolute Count of Myeloid Derived Suppressor Cells (MDSC) Is Able to Predict the Response to Early-PET In Hodgkin Lymphoma
Authors: Alessandra Romano, Nunziatina Parrinello, Calogero Vetro, Piera La Cava, Daniela Donnarumma, Concetta Conticello, Ugo Consoli, Paolo Fiumara, Annalisa Chiarenza, Giuseppe A Palumbo, Massimo Ippolito, Francesco Di Raimondo
Journal: Blood (2010)
A comparison of cetuximab-containing regimens for recurrent/metastatic squamous cell head and neck carcinoma: the clinical significance of weekly paclitaxel and cetuximab
Authors: K. Nakano, S. Marshall, S. Taira, Y. Sato, J. Tomomatsu, T. Sasaki, W. Shimbashi, H. Fukushima, H. Yonekawa, H. Mitani, K. Kawabata, S. Takahashi
Journal: Annals of Oncology (2016)
MPTH-61. A NOVEL TECHNIQUE TO EXPEDITE MOLECULAR GLIOMA TESTING
Authors: Justin Jordan, Julie Batten, Jochen Lennerz, Matthew Frosch, A. John Iafrate, Tracy Batchelor
Journal: Neuro-Oncology (2016)

Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is an important consideration for treatment decision-making in glioblastoma; it portends a better prognosis and predicts efficacy of temozolomide chemotherapy. MGMT promoter methylation status is especially valuable for treatment decision-making in elderly patients or when enrolling in certain clinical trials. Optimizing the delivery of this and other molecular information is critical to provide the best care for glioblastoma patients. We previously reported improved turn-around-time (TAT) with process interventions and now aim to present long-term follow up data, as well as preliminary results using a novel laboratory technique. Using the electronic medical record and pathology tracking system, we performed process mapping and multidisciplinary process intervention planning. We then modified the MGMT promoter methylation testing procedure to use ethanol-fixed specimens directly from the frozen pathology laboratory. Baseline average TAT from tumor resection to MGMT methylation result was 23.4 days (SD 5.6) during the two years (139 cases) prior to intervention, including 5 days (SD 2.6) from resection to neuropathological diagnosis, and 17.5 days (SD 4.1) from neuropathological diagnosis to MGMT result. After two process interventions and one year of follow up, the average TAT is 17.2 days (SD 5) (p<0.0001). Sixteen cases were tested using our novel fresh tissue method, and average TAT was 11.4 days (SD 6.4) (p<0.0001), a 51% reduction from baseline. Further, 50% of these cases were resulted prior to initial post-operative neuro-oncology consultation, compared to 10% during the baseline period (p=0.0107). While process intervention led to significant TAT reduction for MGMT methylation status, our novel technique resulted in marked additional improvement. Further, neuro-oncology consultations were molecularly-informed significantly more often. Machine failure led to delayed results in several cases, and we expect even better outcomes moving forward. Additional development of this novel technique is warranted.
P09.11 Role of PET [18F]-FDOPA in the evaluation of low grade gliomas
Authors: V. Villani, A. Chiaravalloti, A. Vidiri, S. Telera, C. M. Carapella, A. Pace
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.
Successful In Vitro Priming of EBV-Specific CD8+ T Cells Endowed with Strong Cytotoxic Function for Prophylaxis or Treatment of PTLD in EBV Seronegative Hosts.
Authors: Patrizia Comoli, Franco Locatelli, Chiara Frasson, Sabrina Basso, Massimo Labirio, Antonia Moretta, Daniela Montagna, Fabrizio Ginevri, Rita Maccario
Journal: Blood (2005)
The VEGF-C/Flt-4 Axis Promotes Invasion and Metastasis of Cancer Cells
Authors: Jen-Liang Su, Pan-Chyr Yang, Jin-Yuan Shih, Ching-Yao Yang, Lin-Hung Wei, Chang-Yao Hsieh, Chia-Hung Chou, Yung-Ming Jeng, Ming-Yang Wang, King-Jen Chang, Mien-Chie Hung, Min-Liang Kuo
Journal: Cancer Cell (2007)
High-dose chemotherapy for inflammatory breast cancer: impact of immunohistochemical status on survival outcome
Authors: L. Boudin, C. Chabannon, R. Sabatier, F. Bertucci, P. Sfumato, C. Tarpin, M. Provansal, G. Houvenaegel, E. Lambaudie, A. Tallet, R. Michel, E. Charafe-Jauffret, B. Calmels, C. Lemarie, B. Jean-Marie, J.-M. Extra, P. Viens, A. Gonçalves
Journal: Annals of Oncology (2016)
A retrospective multicenter characterization of patients with metastatic renal cell carcinoma: the Sicilian “real-world” experience
Authors: L. Incorvaia, G. Badalamenti, S. Rizzo, G. Cicero, G. Rinaldi, V. Bazan, A. Marchese, C. Ancona, D. Piazza, M. Spada, A. Butera, R. Valenza, L. Blasi, F. Verderame, V. Adamo, L. Di Cristina, N. Borsellino, A. Savarino, F. Zerilli, A. Russo
Journal: Annals of Oncology (2016)
Effects of nanoliposomal irinotecan (nal-IRI; MM-398) ± 5-fluorouracil and leucavorin (5-FU/LV) on quality of life (QoL) in patients (pts) with metastatic pancreatic adenocarcinoma (mPAC) previously treated with gemcitabine-based therapy: results from the phase 3 NAPOLI-1 study
Authors: D. Melisi, D. Melisi, J.T. Siveke, J. Blanc, D.D. Von Hoff, A. Wang-Gillam, L. Chen, C. Becker, K. Mamlouk, F. De Jong, R. Hubner
Journal: Annals of Oncology (2016)
Is baseline neutrophil to lymphocyte ratio (NLR) an independent prognostic biomarker for progression free survival (PFS) and overall survival (OS) in metastatic colorectal cancer (mCRC)? Analysis of the AGITG MAX study
Authors: C.I. Diakos, K. Wilson, R. Asher, V. Gebski, S. Yip, G. van Hazel, B. Robinson, A. Broad, T.J. Price, J. Simes, N. Tebbutt, S. Clarke
Journal: Annals of Oncology (2016)
BMET-04. EVALUATION OF SURVIVAL FOLLOWING STEREOTACTIC RADIOSURGERY (SRS) FOR MELANOMA BRAIN METASTASES
Authors: Esther Kim, Shilpa Kailas, Aryan Sarparast, Andrew Keller, Gurjaspreet Bhattal, Joshua Dajac, Tiffanie Do, Rahim Ismail, Talayesa Buntinx-Krieg, Zoran Pavlovic, Jacqueline Babb, Naren Ramakrishna
Journal: Neuro-Oncology (2016)

We examined the impact of patient and tumor-specific factors on overall expected survival in patients with melanoma brain metastases treated with stereotactic radiosurgery (SRS). A single-institution IRB-approved retrospective analysis was conducted on 54 patients who underwent SRS for brain metastases from pathologically confirmed melanoma between November 2008 and January 2014. Patients included in the study were treated with linear accelerator-based SRS and had at least one follow-up MRI. Patients with primary intracranial tumors were excluded. Survival was defined as the interval from initial SRS treatment to death. Kaplan-Meier plots with 95% confidence intervals were used to assess survival estimates, and Log-Rank tests were used to calculate significance. Multiple parameters were evaluated for effect on survival including Karnofsky Performance Status (KPS), extracranial disease, number of initial metastases, and B-raf V600-E status. The median overall survival estimate was 6.44 months. There was a significant difference in median survival between patients with KPS ≥70 (6.77 months) and KPS <70 (3.19 months, p=0.03), inactive (9.46 months) versus active extracranial disease prior to initial SRS treatment (3.71 months, p=0.04), and 1-2 initial metastases (9.63 months) versus 3-4 initial metastases pairwise (3.29 months, p=0.008). There was no significant difference in survival in patients with positive versus negative B-raf V600E status (p=0.58). Although patients with melanoma brain metastases generally exhibit poor outcomes, parameters such as initial higher performance status, absence of extracranial disease, and fewer initial brain metastases were associated with increased survival post-SRS. These prognostics factors should be individually considered when treatment modality decisions are made for patients with brain metastases from a primary melanoma. The assessment of the impact of the B-raf V600E mutation was limited by the limited number of patients with these abnormalities in this study.
STMC-23. ETHICAL PERSPECTIVES ON UNPROVEN STEM CELL TRANSPLANTS IN NEURO-ONCOLOGICAL DISEASE
Authors: David Cote, Timothy Smith, Annelien Bredenoord, Marike Broekman
Journal: Neuro-Oncology (2016)

The application of stem cell transplants in clinical practice has become increasingly common, and many neurological diseases, including malignant brain tumors, are being targeted for intervention with stem cell transplants. The transplant procedures currently being carried out are frequently unregulated and may endanger patients. In most cases, patients undergoing such operations are not included in a clinical trial, and often do not provide genuinely informed consent. We performed a systematic search of the PubMed database to identify articles that referenced the use of the ethics of stem cell transplants in the treatment of neurooncological disease. Few recent articles have been written from a neurosurgical perspective on the ethics of stem cell transplants, despite the fact that many unproven stem cell transplants are currently being carried out by neurosurgeons. There are many relevant ethical issues at hand when discussing stem cell transplants, which include regulatory oversight, data sharing, the nature of investigation (e.g., clinical trial vs. non-trial), informed consent, risk-benefit ratios and the therapeutic misconception, and patient vulnerability. Unproven stem cell therapies for neurooncological disease are currently being offered outside the structure of well-designed clinical trials. Some of these therapies may be ethically dubious, and could jeopardize progress in the field. Here, we provide a series of discussion points for neurosurgeons to consider as they evaluate new stem cell interventions for neurooncological disease, based primarily on the recently updated guidelines put forth by the International Society for Stem Cell Research. Our hope is that this discussion may help guide the translation of stem cells from the laboratory into the neurosurgical clinic in an ethically sound manner for improved treatment of patients harboring brain tumors. [Submitted on behalf of the Ethics Committee of the World Federation of Neurosurgical Societies].
Epigenetic modulation in well differentiated (WD) and dedifferentiated (DD) liposarcoma (LPS): a novel therapeutic approach
Authors: A. Constantinidou, J. Selfe, T. Khin, S. Popov, E. Missiaglia, E. Aladowicz, R. Al-Saadi, D. Olmos, R.L. Jones, D.C. Strauss, A. Hayes, W. van der Graaf, I. Judson, J. Shipley
Journal: Annals of Oncology (2016)
TMOD-19. PROPERTIES OF COGNITIVE DEVELOPMENT OF CHILDREN WITH CEREBELLAR TUMOR
Authors: Varvara Chizhova, Anastasia Shcheglova
Journal: Neuro-Oncology (2016)

The aim of the study was to estimate the influence of brain tumor and tumor’s localization on children’s cognitive development. Two groups of children participated in research: 1) children with cerebellar tumor (N=19, aged 10-14); 2) control group of healthy children developing normally (N=30, aged 10-14). K-ABC-II (Kaufman Assessment Battery for Children, 2nd Ed.); CANTAB (Cambridge Neuropsychological Test Automated Battery; Cambridge Cognition), selected subtests: SWM (spatial working memory). Analysis of covariance indicated that group of children with cerebellar tumor scored significantly lower in overall intelligence, verbal memory and spatial memory. These data show that the cerebellar tumor has negative impact on intelligence, verbal memory and spatial memory. The study of the group of children with cerebellar tumor did not reveal any relationship between spatial memory and verbal memory scores, and intelligence and spatial memory scores as in control group. Those results may suggest that the spatial memory and verbal memory decline independently of each other and the fact that reduction of spatial memory is not related to the decrease in intelligence. The study was supported by the Russian Foundation for Basic Research, project 15-06-08680. Keywords: memory, verbal memory, spatial memory, cognitive development, brain tumor, cerebellum.
Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin
Authors: Amit Kumar, Chandrasekhar Natarajan, Hideaki Moriyama, Christopher C. Witt, Roy E. Weber, Angela Fago, Jay F. Storz
Journal: Molecular Biology and Evolution (2017)

If the fitness effects of amino acid mutations are conditional on genetic background, then mutations can have different effects depending on the sequential order in which they occur during evolutionary transitions in protein function. A key question concerns the fraction of possible mutational pathways connecting alternative functional states that involve transient reductions in fitness. Here we examine the functional effects of multiple amino acid substitutions that contributed to an evolutionary transition in the oxygenation properties of avian hemoglobin (Hb). The set of causative changes included mutations at intradimer interfaces of the Hb tetramer. Replacements at such sites may be especially likely to have epistatic effects on Hb function since residues at intersubunit interfaces are enmeshed in networks of salt bridges and hydrogen bonds between like and unlike subunits; mutational reconfigurations of these atomic contacts can affect allosteric transitions in quaternary structure and the propensity for tetramer–dimer dissociation. We used ancestral protein resurrection in conjunction with a combinatorial protein engineering approach to synthesize genotypes representing the complete set of mutational intermediates in all possible forward pathways that connect functionally distinct ancestral and descendent genotypes. The experiments revealed that 1/2 of all possible forward pathways included mutational intermediates with aberrant functional properties because particular combinations of mutations promoted tetramer–dimer dissociation. The subset of mutational pathways with unstable intermediates may be selectively inaccessible, representing evolutionary roads not taken. The experimental results also demonstrate how epistasis for particular functional properties of proteins may be mediated indirectly by mutational effects on quaternary structural stability.
Clinical characteristics in colorectal cancer harboring BRAF V600E and non-V600E mutations
Authors: E. Shinozaki, Y. Miki, M. Ueno, M. Igarashi, K. Chin, D. Takahari, M. Ogura, T. Ichimura, I. Nakayama, H. Osumi, T. Wakatsuki, T. Matsushima, K. Yamaguchi
Journal: Annals of Oncology (2016)
Donor Th17 and Th1 Contribute to Chronic Graft-Versus-Host Disease
Authors: Hisakazu Nishimori, Haruko Sugiyama, Koichiro Kobayashi, Yoshiko Yamasuji, Sachiyo Kadohisa, Kengo Takeuchi, Mitsune Tanimoto, Yoshinobu Maeda
Journal: Blood (2010)
The role of pre-treatment plasma Epstein-Barr virus (EBV) DNA as a predictive biomarker of induction chemotherapy for stage IVA or IVB nasopharyngeal carcinoma (NPC) patients – A Subgroup Analysis on Taiwan Cooperative Oncology Group (TCOG) 1303 study
Authors: H.-F. Kao, C.-F. Hsiao, S.-C. Lai, C.-W. Wang, J.-Y. Ko, P.-J. Lo, T.-J. Lee, T.-W. Liu, R.-L. Hong
Journal: Annals of Oncology (2016)
Clinical Implications of Killer Cell Immunoglobulin-Like Receptor (KIR) Genotypes on Autologous Peripheral Blood Stem Cell Transplantation for Acute Myelogenous Leukemia Patients.
Authors: Heeje Kim, Young Choi, Tai-Hyang Lee, Dong-Hoon Hahn, Hoei-Sung Gang, Woo-Sung Min
Journal: Blood (2008)
Visualization of Posttraumatic Splenosis on Chemokine Receptor CXCR4-Targeted PET/CT
Authors: Thorsten Derlin, Hans-Jürgen Wester, Frank M. Bengel, Katja Hueper
Journal: Clinical Nuclear Medicine (2017)

The C-X-C motif chemokine receptor 4 (CXCR4) is expressed by a variety of inflammatory and malignant cells. We report the case of a 54-year-old woman with recurrent urinary tract infection who underwent a Ga-pentixafor PET/CT for detection of occult infectious foci. As a secondary finding, multiple CXCR4 abdominal lesions could be seen, consistent with the diagnosis of long-known posttraumatic splenosis. It is important to be aware that CXCR4-directed imaging may identify splenic tissue based on the presence of inflammatory cells and that both benign and malignant cells may show CXCR4 expression to avoid misinterpretation.
A randomized phase 2 trial of nab-paclitaxel plus gemcitabine, ± capecitabine, cisplatin (paxg regimen) in unresectable or borderline resectable pancreatic adenocarcinoma: the ghost regimen strikes back
Authors: M. Reni, S. Zanon, G. Balzano, P. Passoni, A. Costantino, C. Pircher, M. Chiaravalli, R. Nicoletti, P.G. Arcidiacono, G. Pepe, S. Crippa, C. Doglioni, C. Fugazza, D. Ceraulo, M. Falconi, L. Gianni
Journal: Annals of Oncology (2016)