tbuckley/cabot-search huggingface dataset:
Identification of cell-type-specific mutations in nodal T-cell lymphomas
Authors: T B Nguyen, M Sakata-Yanagimoto, Y Asabe, D Matsubara, J Kano, K Yoshida, Y Shiraishi, K Chiba, H Tanaka, S Miyano, K Izutsu, N Nakamura, K Takeuchi, H Miyoshi, K Ohshima, T Minowa, S Ogawa, M Noguchi, S Chiba
Journal: Blood Cancer Journal (2017)

Recent genetic analysis has identified frequent mutations in ten-eleven translocation 2 (TET2), DNA methyltransferase 3A (DNMT3A), isocitrate dehydrogenase 2 (IDH2) and ras homolog family member A (RHOA) in nodal T-cell lymphomas, including angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma, not otherwise specified. We examined the distribution of mutations in these subtypes of mature T-/natural killer cell neoplasms to determine their clonal architecture. Targeted sequencing was performed for 71 genes in tumor-derived DNA of 87 cases. The mutations were then analyzed in a programmed death-1 (PD1)-positive population enriched with tumor cells and CD20-positive B cells purified by laser microdissection from 19 cases. TET2 and DNMT3A mutations were identified in both the PD1+ cells and the CD20+ cells in 15/16 and 4/7 cases, respectively. All the RHOA and IDH2 mutations were confined to the PD1+ cells, indicating that some, including RHOA and IDH2 mutations, being specific events in tumor cells. Notably, we found that all NOTCH1 mutations were detected only in the CD20+ cells. In conclusion, we identified both B- as well as T-cell-specific mutations, and mutations common to both T and B cells. These findings indicate the expansion of a clone after multistep and multilineal acquisition of gene mutations.
Antibiotic Cycling and Antibiotic Mixing: which one best mitigates antibiotic resistance?
Authors: R. E. Beardmore, R. Pena-Miller, F. Gori, J. Iredell
Journal: Molecular Biology and Evolution (2017)

Can we exploit our burgeoning understanding of molecular evolution to slow the progress of drug resistance? One role of an infection clinician is exactly that: to foresee trajectories to resistance during antibiotic treatment and to hinder that evolutionary course. But can this be done at a hospital-wide scale? Clinicians and theoreticians tried to when they proposed two conflicting behavioral strategies that are expected to curb resistance evolution in the clinic, these are known as "antibiotic cycling" and "antibiotic mixing." However, the accumulated data from clinical trials, now approaching 4 million patient days of treatment, is too variable for cycling or mixing to be deemed successful. The former implements the restriction and prioritization of different antibiotics at different times in hospitals in a manner said to "cycle" between them. In antibiotic mixing, appropriate antibiotics are allocated to patients but randomly. Mixing results in no correlation, in time or across patients, in the drugs used for treatment which is why theorists saw this as an optimal behavioral strategy. So while cycling and mixing were proposed as ways of controlling evolution, we show there is good reason why clinical datasets cannot choose between them: by re-examining the theoretical literature we show prior support for the theoretical optimality of mixing was misplaced. Our analysis is consistent with a pattern emerging in data: neither cycling or mixing is a priori better than the other at mitigating selection for antibiotic resistance in the clinic.: antibiotic cycling, antibiotic mixing, optimal control, stochastic models.
Outcomes after HLA-Matched Sibling Transplants or Chemotherapy in Children with Acute Lymphoblastic Leukemia in a Second Remission after an Isolated Central Nervous System Relapse.
Authors: Mary Eapen, Mei-Jie Zhang, Elizabeth Raetz, Meenakshi Devidas, William L. Carroll, Arthur K. Ritchey, Julio C. Barredo, Kamar Godder, Stephan A. Grupp, Victor A. Lewis, Stella Davies, Bruce Camitta
Journal: Blood (2006)
Improved Outcome of Childhood Acute Lymphoblastic Leukemia (ALL) with Induction Failure Treated on the Japan Association of Childhood Leukemia Study (JACLS) ALL F-Protocol.
Authors: Nobuhiro Suzuki, Keiko Yumura-Yagi, Junichi Hara, Makoto Yoshida, Shinichiro Nishimura, Tooru Kudoh, Akio Tawa, Ikuya Usami, Akihiko Tanizawa, Hiroki Hori, Yasuhiro Ito, Ryosuke Miyaji, Yoshihiro Komada, Megumi Oda, Keizo Horibe
Journal: Blood (2006)
Membrane Fluidity's Role In Platelet Function In Patients with Myeloproliferative Neoplasms
Authors: Viola Maria Popov, Ana Maria Vladareanu, Horia Bumbea, Sanziana Radesi, Maria Minodora Iordache, Radu Gologan, Eugenia Kovacs, Tudor Savopol, Mihaela Georgeta Moisescu, Minodora Onisai
Journal: Blood (2010)
Possible Involvement of γδ-T Cells in the Development of Chronic Graft-Versus-Host Disease after Allogeneic Hematopoietic Stem Cell Transplantation.
Authors: Ki-Ryang Koh, Hirohisa Nakamae, Kensuke Ohta, Hongzhang Li, Hideo Koh, Takahiko Nakane, Yasunobu Takeoka, Asao Hirose, Kiyoyuki Hagihara, Erina Sakamoto, Mika Nakamae, Yoshiki Terada, Takahisa Yamane, Masayuki Hino
Journal: Blood (2007)
The Interferon Score Towards Interferon Alpha Tailored Therapy In Essential Thrombocythemia
Authors: Novella Pugliese, Novella Pugliese, Concetta Quintarelli, Biagio De Angelis, Luana Marano, Santa Errichiello, Nicola Esposito, Maddalena Raia, Claudio Cerchione, Luigi Del Vecchio, Marco Picardi, Vincenzo Martinelli, Fabrizio Pane
Journal: Blood (2013)
Outcome and Risk Factors of Hodgkin Lymphoma Patients with Relapse or Progression After Autologous Stem Cell Transplant: A Report From the German Hodgkin Study Group (GHSG).
Authors: Bastian von Tresckow, Horst Müller, Dennis A. Eichenauer, Jan Peter Glossmann, Andreas Josting, Boris Böll, Beate Klimm, Michael Fuchs, Peter Borchmann, Andreas Engert
Journal: Blood (2012)
MN1 Inhibits Myeloid Differentiation by Transcriptional Repression of EGR2
Authors: Michael Heuser, Eric Yung, Courteney Lai, Bob Argiropoulos, Florian Kuchenbauer, Gyeongsin Park, Grace Lin, Piper Jessica, Sarah Vollett, Malina Leung, Arnold Ganser, R. Keith Humphries
Journal: Blood (2010)
Development of a Bispecific Antibody-Releasing Stem Cell System for the Eradication of Acute Myeloid Leukemia Blasts Via Redirected Immune Effector Cells
Authors: Roberta Aliperta, Marc Cartellieri, Anja Feldmann, Claudia Arndt, Stefanie Koristka, Irene Michalk, Martin Bornhäuser, Armin Ehninger, Gerhard Ehninger, Michael P. Bachmann
Journal: Blood (2014)
Pre-Clinical Activity of the Novel, First-in-Class p97 Inhibitor, CB-5083, in Multiple Myeloma
Authors: Blake T. Aftab, Daniel J Anderson, Ronan Le Moigne, Stevan Djakovic, Eugen Dhimolea, Megan Murnane, Emily King, Julie Rice, Steve Wong, Brajesh Kumar, Eduardo Valle, Mary-Kamala Menon, Szerenke Kiss von Soly, Jinhai Wang, Bing Yao, Ferdie Soriano, Martin Kampmann, Diego Alcost-Alvear, Marta Chesi, Leif Bergsagel, F. Michael Yakes, Han-Jie Zhou, David Wustrow, Thomas G. Martin, Jeffrey L. Wolf, Constantine S. Mitsiades, Mark Rolfe
Journal: Blood (2014)
Impact of Different In Vivo T Cell Depletion Strategies on Outcomes Following Hematopoietic Stem Cell Transplantation for Idiopathic Aplastic Anaemia: A Study on Behalf of the EBMT SAA Working Party
Authors: Sujith Samarasinghe, Simona Iacobelli, Cora Knol, Rose-Marie Hamladji, Gerard Socie, Mahmoud Aljurf, Mickey Koh, Henrik Sengeloev, Jean-Hugues Dalle, Stephen Robinson, Andrea Bacigalupo, Joan H Veelken, Dietrich Beelen, Ghulam J Mufti, John A Snowden, Didier Blaise, Judith C.W. Marsh, Carlo Dufour, Antonio M Risitano
Journal: Blood (2015)
High Response Rate to Lenalidomide in Relapsed/Refractory Aggressive Non-Hodgkin’s Lymphoma with Prior Stem Cell Transplant.
Authors: Julie M. Vose, Joseph M. Tuscano, Glen Justice, Izidore S. Lossos, Annette Ervin-Haynes, Kenichi Takeshita, Dennis Pietronigro, Jerome B. Zeldis, Thomas M. Habermann
Journal: Blood (2007)
Induction of metastasis, cancer stem cell phenotype, and oncogenic metabolism in cancer cells by ionizing radiation
Authors: Su Yeon Lee, Eui Kyong Jeong, Min Kyung Ju, Hyun Min Jeon, Min Young Kim, Cho Hee Kim, Hye Gyeong Park, Song Iy Han, Ho Sung Kang
Journal: Molecular Cancer (2017)

Radiation therapy is one of the major tools of cancer treatment, and is widely used for a variety of malignant tumours. Radiotherapy causes DNA damage directly by ionization or indirectly via the generation of reactive oxygen species (ROS), thereby destroying cancer cells. However, ionizing radiation (IR) paradoxically promotes metastasis and invasion of cancer cells by inducing the epithelial-mesenchymal transition (EMT). Metastasis is a major obstacle to successful cancer therapy, and is closely linked to the rates of morbidity and mortality of many cancers. ROS have been shown to play important roles in mediating the biological effects of IR. ROS have been implicated in IR-induced EMT, via activation of several EMT transcription factors—including Snail, HIF-1, ZEB1, and STAT3—that are activated by signalling pathways, including those of TGF-β, Wnt, Hedgehog, Notch, G-CSF, EGFR/PI3K/Akt, and MAPK. Cancer cells that undergo EMT have been shown to acquire stemness and undergo metabolic changes, although these points are debated. IR is known to induce cancer stem cell (CSC) properties, including dedifferentiation and self-renewal, and to promote oncogenic metabolism by activating these EMT-inducing pathways. Much accumulated evidence has shown that metabolic alterations in cancer cells are closely associated with the EMT and CSC phenotypes; specifically, the IR-induced oncogenic metabolism seems to be required for acquisition of the EMT and CSC phenotypes. IR can also elicit various changes in the tumour microenvironment (TME) that may affect invasion and metastasis. EMT, CSC, and oncogenic metabolism are involved in radioresistance; targeting them may improve the efficacy of radiotherapy, preventing tumour recurrence and metastasis. This study focuses on the molecular mechanisms of IR-induced EMT, CSCs, oncogenic metabolism, and alterations in the TME. We discuss how IR-induced EMT/CSC/oncogenic metabolism may promote resistance to radiotherapy; we also review efforts to develop therapeutic approaches to eliminate these IR-induced adverse effects.
Non-Pathogenic Anti-Heparin/PF4 Antibodies Generated by Low Molecular Weight Heparins Mediate Procoagulant Effects.
Authors: Jeanine M. Walenga, Debra Hoppensteadt, Evangelos Litinas, Harry L. Messmore, Bruce E Lewis, Gundu Rao, Russell Hull, Jawed Fareed
Journal: Blood (2010)
Characterization of a Bone Marrow Derived Mesenchymal Cell Line from Nude Rat Assembling Tumor Stem/Progenitor Cell Properties In Vitro and In Vivo.
Authors: Mengyu Wang, Jingfang Ju, Stein Saeboe-Larssen, Svein-Ole Mikalsen, Elena Olsen, Jahn M. Nesland, Oystein Fodstad, Gunhild Maelandsmo, Gunnar Kvalheim
Journal: Blood (2006)
Changes in the serum proteome associated with docetaxel chemotherapy
Authors: N. D. James, D. Ward, A. Martin, D. Barton, J. Dunn, E. Porfiri
Journal: Journal of Clinical Oncology (2006)

20036 Background: Trapeze is a randomised phase II clinical study involving Docetaxel chemotherapy ± Zoledronic Acid and strontium 89 for the treatment of hormone refractory prostate cancer. A proteomic sub-study is designed to identify novel biomarkers to monitor treatment. Methods: Surface-Ehanced Laser Desorption/Ionisation (SELDI) time-of-flight mass spectrometry combines retentate chromatography and mass spectrometry in a high-throughput platform for proteomic profiling of biological samples. A biofluid such as serum is applied to a ‘proteinchip array’, certain proteins will bind and non-binding species are removed by washing. The bound proteins are vaporised using a laser and detected by mass spectrometry. The peak intensities in the resulting “profiles” can be compared between patient cohorts to identify potential biomarkers. Results: The serum from 6 patients was analysed both before and after 2 cycles of chemotherapy using copper loaded IMAC30 proteinchip arrays. The intensities of 103 peaks were compared between pre- and post-treatment and 11 were found to differ significantly (p &lt; 0.01, paired t-test). Hierarchical clustering was able to distinguish pre- and post-treatment sera. Initial results show these changes to continue in sequential samples taken from the same patient. Conclusions: Chemotherapy produces significant and detectable changes in the serum proteome. This is a significant difference from a recent lung cancer study carried out in our Institution (submitted separately), which showed no detectable changes in pre and post operative lung cancer patients once acute post-operative changes had settled. Work is currently underway to identify the discriminatory proteins in the SELDI profiles. The current Trapeze study accrual rate of approximately 10 patients per month will mean that 80 patients will be included in this treatment cohort by May 2006 and subject to initial findings, individual proteins of interest will be identified and followed throughout the phase II and subsequent phase III to determine if they can be used to assess patients individual response to chemotherapy and provide a biomarker to monitor prostate cancer therapy. No significant financial relationships to disclose.
Non-Inferior Survival of Black Versus White Patients and Superior Outcomes for Black Females Compared to Other Race/Gender Groups Following Allogeneic Transplantation for Hematologic Malignancy: A Single Center Multivariable Analysis of 475 Allografted Patients
Authors: Asad Bashey, Xu Zhang, Katelin Jackson, Stacey Brown, Melhem Solh, Lawrence E. Morris, H. Kent Holland, Scott R. Solomon
Journal: Blood (2015)
Days of Pheresis Needed for Harvesting CD34+ Cells for Autologous Hematopoietic Stem Cell Transplantation Is Associated with Speed of Neutrophil Recovery and the Development of Secondary AML/MDS.
Authors: Shahbaz Malik, Brian J. Bolwell, Robert Dean, Ronald Sobecks, Matt Kalaycio, John Sweetenham, Brad Pohlman, Steve Andresen, Lisa Rybicki, Shawnda Tench, Priscilla Figueroa, Edward Copelan
Journal: Blood (2009)
Extreme Effectiveness of Operative Resection with or without Radiotherapy as a First Line Treatment for Localized Orbital Malt Lymphoma.
Authors: Yoshihiro Yakushijin, Toshio Kodama, Ikue Takaoka, Masaki Otsuka, Takaaki Hato, Masaki Yasukawa, Shigeru Fujita
Journal: Blood (2004)
Enhanced Recovery After Surgery
Authors: Olle Ljungqvist, Michael Scott, Kenneth C. Fearon
Journal: JAMA Surgery (2017)

Enhanced Recovery After Surgery (ERAS) is a paradigm shift in perioperative care, resulting in substantial improvements in clinical outcomes and cost savings.Enhanced Recovery After Surgery is a multimodal, multidisciplinary approach to the care of the surgical patient. Enhanced Recovery After Surgery process implementation involves a team consisting of surgeons, anesthetists, an ERAS coordinator (often a nurse or a physician assistant), and staff from units that care for the surgical patient. The care protocol is based on published evidence. The ERAS Society, an international nonprofit professional society that promotes, develops, and implements ERAS programs, publishes updated guidelines for many operations, such as evidence-based modern care changes from overnight fasting to carbohydrate drinks 2 hours before surgery, minimally invasive approaches instead of large incisions, management of fluids to seek balance rather than large volumes of intravenous fluids, avoidance of or early removal of drains and tubes, early mobilization, and serving of drinks and food the day of the operation. Enhanced Recovery After Surgery protocols have resulted in shorter length of hospital stay by 30% to 50% and similar reductions in complications, while readmissions and costs are reduced. The elements of the protocol reduce the stress of the operation to retain anabolic homeostasis. The ERAS Society conducts structured implementation programs that are currently in use in more than 20 countries. Local ERAS teams from hospitals are trained to implement ERAS processes. Audit of process compliance and patient outcomes are important features. Enhanced Recovery After Surgery started mainly with colorectal surgery but has been shown to improve outcomes in almost all major surgical specialties.Enhanced Recovery After Surgery is an evidence-based care improvement process for surgical patients. Implementation of ERAS programs results in major improvements in clinical outcomes and cost, making ERAS an important example of value-based care applied to surgery.
Utility of Oncotype DX risk assessment in patients with invasive lobular carcinoma (ILC).
Authors: Michaela L. Tsai, Joel E Money, Marsha J Finkelstein, Tamera J Lillemoe, Barbara Susnik, Erin V Grimm, Sung-hae L Kang, Karen K Swenson
Journal: Journal of Clinical Oncology (2014)

28 Background: Oncotype DX (Genomic Health, Redwood City, CA) is a breast cancer assay that uses reverse transcriptase polymerase chain reaction (RT-PCR) to measure gene expression in paraffin-embedded tumor tissue, which correlates with recurrence risk. This test is used to guide chemotherapy decisions in patients with estrogen receptor-positive breast cancer. Invasive lobular carcinoma (ILC) is a distinct histologic subtype, inherently estrogen receptor rich, that has not been the unique focus of prior studies validating Oncotype DX. The study purpose was to determine if there are certain features of ILC that predict uniformly low Oncotype DX Recurrence Scores (RS) such that Oncotype DX testing may be unnecessary, saving patients time and financial resources. Methods: A search was conducted of all ILC cases having Oncotype DX testing in our hospital pathology database. The Oncotype DX RS, histologic tumor characteristics (including subtype and grade), immunohistochemical (IHC) analyses of estrogen receptor (ER)/progesterone receptor (PR) percent (by image analysis), E-cadherin expression, and Ki-67 levels were obtained for each case. Discriminant analysis was used to test the hypothesis that tumors classified as low or high risk based on the Oncotype DX RS would differ significantly on a linear combination of selected variables. Results: From 2006 to 2013, 158 cases of ILC having Oncotype DX testing were identified; 90 low risk (RS &lt;18), 66 intermediate risk (RS 18 – 30) and 2 high risk (RS &gt; 30). Discriminant analysis showed that PR% followed by Ki-67 provided the greatest contribution to discriminating between low versus high RS. A subset of 57 cases (~ 36%) with predicted probabilities &gt; 86% for either low or high RS yielded 96.5% correct classification, 92.3% sensitivity, and 97.7% specificity. Conclusions: Our analytical model may be useful in predicting high versus low recurrence risk in some patients with ILC. If validated, this provides a faster and less expensive alternative to Oncotype DX testing in certain patients with ILC.
Beyond the margins: real-time detection of cancer using targeted fluorophores
Authors: Ray R. Zhang, Alexandra B. Schroeder, Joseph J. Grudzinski, Eben L. Rosenthal, Jason M. Warram, Anatoly N. Pinchuk, Kevin W. Eliceiri, John S. Kuo, Jamey P. Weichert
Journal: Nature Reviews Clinical Oncology (2017)
The Efficacy and Safety of RAD (Lenalidomide, Adriamycin and Dexamethasone) In Newly Diagnosed Multiple Myeloma – First Results of a Phase II Trial by the German DSMM Group
Authors: Stefan Knop, Christian Langer, Monika Engelhardt, Lars O Muegge, Albrecht Reichle, Christoph Röllig, Martin Gramatzki, Wolf Roesler, Max S Topp, Carmen Wesemeier, Bernd Hertenstein, Isrid Sturm, Tobias Dechow, Martin Kortüm, Marianne Sauerwein, Hermann Einsele, Ralf Bargou
Journal: Blood (2010)
Similar Outcomes among African-Americans (AA) and Whites after Autologous Hematopoietic-Cell Transplantation (Auto HCT) for Multiple Myeloma (MM)
Authors: Parameswaran Hari, Navneet S. Majhail, Anna Hassebroek, Mei-Jie Zhang, Fareeha Siddiqui, Paulette Mehta
Journal: Blood (2008)
A Chemical Genetic Analysis of Platelet Activation Identifies An Antithrombotic Allosteric Modulator That Acts through Helix 8 of Par1
Authors: Louisa M. Dowal, Derek Sim, James R Dilks, Price Blair, Sarah Beaudry, Bradley Denker, George Koukos, Athan Kuliopulos, Robert Flaumenhaft
Journal: Blood (2010)
Hematologic Findings and Transfusion Therapy in Severe Pediatric Plasmodium Falciparum Malaria: Results from a Prospective Observational Study in Uganda
Authors: Christine Cserti-Gazdewich, Aggrey Dhabangi, Charles Musoke, Nicolette Nabukeera-Barungi, Henry Ddungu, Arthur Mpimbaza, Isaac Ssewanyana, Walter H. Dzik
Journal: Blood (2008)
MPTH-30ATRX CAN OCCUR IN IDH WILD-TYPE GBM
Authors: Anastasia Vernadou, Evangelia Skarpidi, Georgios Rigakos, Sotirios Papadopoulos, Vasileios Kourvelos, Stefanos Labropoulos, Evangelia Razis
Journal: Neuro-Oncology (2015)

BACKGROUND: ATRX (alpha thalassemia/ mental retardation syndrome X-linked) is a transcriptional regulatory protein which contains an ATPase/helicase domain. In gliomas loss of ATRX expression has been recently described and is mostly restricted to IDH mutant tumors who seem to have a significantly better prognosis. ATRX loss is thought to be extremely rare in IDH wild type (WT) tumors and in that setting one group reported H3F3A mutation. METHODS: Tissue samples of 23 patients with IDH wild-type malignant gliomas were analyzed for ATRX expression using immunohistochemistry. ATRX status was associated with clinical characteristics, histology and other molecular markers (MGMT, BRAF, EGFR). RESULTS: Median age in all patients was 49,3 years. Loss of ATRX expression was detected in 4 out of 23 patient tumors. All ATRX loss patients were primary glioblastomas. Median survival in ATRX mutated gliomas is 237 weeks which was longer than overall survival in gliomas with retained ATRX (88 weeks). All of our patients underwent concurrent chemoradiotherapy with temozolomide. One out of four ATRX loss tumors was BRAF mutated, three out of four ATRX loss patients tested for EGFR were found to be wild type and the two ATRX mutated patients tested for MGMT were methylated. CONCLUSION: ATRX mutation can occur in IDH wild-type patients. In that setting it appears to be associated with a better outcome. Our data is hypothesis generating. Tumors with IDH WT/ ATRX loss should be evaluated prospectively in a larger cohort and possibly checked for H3F3A mutation.
A Novel Intravenous Catheter with Self-Operating Pretransfusion Blood Sampling for Enhanced Transfusion Safety: Retrospective Risk Analysis and Prospective Phase II Trial in Emergency Care
Authors: Michael Notter, Ariane Storch, Ellen Richter-Loeseke, Hans-Richard Arntz, Johannes Fakler, Eckhard Thiel, Ephrath Lahmer-Naim, Adolf Pfaff, Jan Breckwoldt
Journal: Blood (2008)
Incidence and prognostic impact of ASXL2 mutations in adult acute myeloid leukemia patients with t(8;21)(q22;q22): a study of the German-Austrian AML Study Group
Authors: N Jahn, M Agrawal, L Bullinger, D Weber, A Corbacioglu, V I Gaidzik, L Schmalbrock, F Thol, M Heuser, J Krauter, G Göhring, A Kündgen, W Fiedler, M Wattad, G Held, C-H Köhne, H-A Horst, M Lübbert, A Ganser, R F Schlenk, H Döhner, K Döhner, P Paschka
Journal: Leukemia (2017)