tbuckley/cabot-search huggingface dataset:
Analyses of caspase-1-regulated transcriptomes in various tissues lead to identification of novel IL-1β-, IL-18- and sirtuin-1-independent pathways
Authors: Ya-feng Li, Gayani Nanayakkara, Yu Sun, Xinyuan Li, Luqiao Wang, Ramon Cueto, Ying Shao, Hangfei Fu, Candice Johnson, Jiali Cheng, Xiongwen Chen, Wenhui Hu, Jun Yu, Eric T. Choi, Hong Wang, Xiao-feng Yang
Journal: Journal of Hematology & Oncology (2017)

It is well established that caspase-1 exerts its biological activities through its downstream targets such as IL-1β, IL-18, and Sirt-1. The microarray datasets derived from various caspase-1 knockout tissues indicated that caspase-1 can significantly impact the transcriptome. However, it is not known whether all the effects exerted by caspase-1 on transcriptome are mediated only by its well-known substrates. Therefore, we hypothesized that the effects of caspase-1 on transcriptome may be partially independent from IL-1β, IL-18, and Sirt-1. To determine new global and tissue-specific gene regulatory effects of caspase-1, we took novel microarray data analysis approaches including Venn analysis, cooperation analysis, and meta-analysis methods. We used these statistical methods to integrate different microarray datasets conducted on different caspase-1 knockout tissues and datasets where caspase-1 downstream targets were manipulated. We made the following important findings: (1) Caspase-1 exerts its regulatory effects on the majority of genes in a tissue-specific manner; (2) Caspase-1 regulatory genes partially cooperates with genes regulated by sirtuin-1 during organ injury and inflammation in adipose tissue but not in the liver; (3) Caspase-1 cooperates with IL-1β in regulating less than half of the genes involved in cardiovascular disease, organismal injury, and cancer in mouse liver; (4) The meta-analysis identifies 40 caspase-1 globally regulated genes across tissues, suggesting that caspase-1 globally regulates many novel pathways; and (5) The meta-analysis identified new cooperatively and non-cooperatively regulated genes in caspase-1, IL-1β, IL-18, and Sirt-1 pathways. Our findings suggest that caspase-1 regulates many new signaling pathways potentially via its known substrates and also via transcription factors and other proteins that are yet to be identified.
Phase I/II Study of the Oral Isotype-Selective Histone Deacetylase (HDAC) Inhibitor MGCD0103 in Combination with Azacitidine in Patients (pts) with High-Risk Myelodysplastic Syndrome (MDS) or Acute Myelogenous Leukemia (AML).
Authors: Guillermo Garcia-Manero, Allen S. Yang, Francis Giles, Stefan Faderl, Farhad Ravandi, Jorge Cortes, Willie M. Newsome, Jean-Pierre Issa, Tracy-Ann Patterson, Marja Dubay, Zuomei Li, Hagop Kantarjian, Robert E. Martell
Journal: Blood (2006)
Improved Leukemia-Free and Overall Survival in Patients with Myelodysplastic Syndrome Receiving Iron Chelation Therapy: A Subgroup Analysis.
Authors: Heather A. Leitch, Dominic H.C. Wong, Chantal S. Leger, Khaled M. Ramadan, Meaghan D. Rollins, Michael J. Barnett, Trisha A. Goodman, Karen K. Wong, Paul F. Galbraith, Linda M. Vickars
Journal: Blood (2007)
Outcome after Frontline Therapy with the Hyper-CVAD and Imatinib Mesylate Regimen for Adults with De Novo or Minimally Treated Philadelphia Chromosome (Ph) Positive Acute Lymphoblastic Leukemia (ALL)
Authors: Deborah A. Thomas, Hagop M Kantarjian, Jorge Cortes, Farhad Ravandi, Stefan Faderl, Dan Jones, Laurie A. Letvak, Partow Kebriaei, Richard E Champlin, Susan O’Brien
Journal: Blood (2008)
Impact of Epigenetic Therapy Versus Conventional Chemotherapy on Survival of Elderly Patients with Acute Myeloid Leukemia
Authors: Alfonso Quintás-Cardama, Hagop M Kantarjian, Guillermo Garcia-Manero, Farhad Ravandi, Mark Brandt, Stefan Faderl, Sherry Pierce, Gautam Borthakur, Jorge E. Cortes
Journal: Blood (2011)
Autologous Stem Cell Transplantation for NHL: 16 Years Follow- up
Authors: Cecilia Guillermo, Judith Lipschutz, Juan Zunino, Laura Topolansky, Alejandra Rocca, Mariana Stevenazzi, Andrea Diaz, Susana Perdomo, Ana Perdomo, Graciela M Lavagna, Hugo Isaurralde, Lilian Diaz, Martha Nese
Journal: Blood (2011)
Allogeneic CD19-CAR-T cell infusion after allogeneic hematopoietic stem cell transplantation in B cell malignancies
Authors: Jun Liu, Jiang F. Zhong, Xi Zhang, Cheng Zhang
Journal: Journal of Hematology & Oncology (2017)

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is considered the cornerstone in treatment of hematological malignancies. However, relapse of the hematological disease after allo-HSCT remains a challenge and is associated with poor long-term survival. Chimeric antigen receptor redirected T cells (CAR-T cells) can lead to disease remission in patients with relapsed/refractory hematological malignancies. However, the therapeutic window for infusion of CAR-T cells post allo-HSCT and its efficacy are debatable. In this review, we first discuss the use of CAR-T cells for relapsed cases after allo-HSCT. We then review the toxicities and the occurrence of graft-versus-host disease in relapsed patients who received CAR-T cells post allo-HSCT. Finally, we review clinical trial registrations and the therapeutic time window for infusion of CAR-T cells post allo-HSCT. The treatment of allogeneic CAR-T cells is beneficial for patients with relapsed B cell malignancies after allo-HSCT with low toxicities and complications. However, multicenter clinical trials with larger sample sizes should be performed to select the optimal therapeutic window and confirm its efficacy.
5-Azacytidine to Treat Acute Myeloid Leukemia In Elderly or Frail Patients: A Phase II Study (SAKK 30/07)
Authors: Jakob R. Passweg, Thomas Pabst, Sabine Blum, Mario Bargetzi, Hong Sun, Dominik Heim, Georg Stussi, Michael Gregor, Leda Leoncini, Sandrine Meyer-Monard, Peter Brauchli, Yves Chalandon
Journal: Blood (2010)
Yttrium-90 Ibritumomab Tiuxetan Is Feasible and Efficient in Unselected Patients. Definitive Results of a Large Retrospective Phase IV Study
Authors: Valentine Richez, Julie Abraham, Sandy Amorim, Charles Herbaux, Laure Philippe, Marc Andre, Anne Parcelier, Christophe Fruchart, Krimo Bouabdallah, Jérôme Cornillon, Sigrid Cherrier, Clementine Salvado, Bernard Drenou, Lucie Oberic, Philippe Quittet, Geoffroy Venton, Claire Calmettes, Safia Chebrek, Cedric Rossi, Arnaud Campidelli, Bruno Lioure, Sophie Auger, Lucille Altounian, Philippe Mineur, Erwin Woff, Frederic Peyrade
Journal: Blood (2015)
Outcome for Adolescent and Young Adults 16–21 years of age (AYA) with Acute Lymphoblastic Leukemia (ALL) Treated on the Children’ s Cancer Group (CCG) 1961 Study.
Authors: J. Nachman, N. Siebel, H. Sather, P. Steinherz, C. DeLaat, D. Fryer, L.A. Mattano, C. Hastings, C. Rubin, K. Bertolone, J. Franklin, T. Mitchell, L. Ettinger, A. Pyesmany, P.S. Gaynon
Journal: Blood (2004)
Cardiac T2* Magnetic Resonance Imaging (MRI) in Iron Overload and Ventricular Diastolic Function.
Authors: Jane Hankins, Claudia Hillenbrand, Vijay Joshi, Ralf Loeffler, Ruitian Song, Russell Ware, Eileen Hansbury, Martha Rieman, Nicole Mortier, Matt Smeltzer, Chin-Shang Li, M. Beth McCarville
Journal: Blood (2007)
Pre-Emptive Rituximab Treatment for Epstein-Barr Virus (EBV) Reactivation After Allogeneic Hematopoietic Stem Cell Transplantation (HSCT): High Incidence of Infections and Delayed Immune Reconstitution
Authors: Anna D. Petropoulou, Raphael Porcher, Regis Peffault de Latour, Alienor Xhaard, Patricia Ribaud, Gerard Socie, Marie Robin
Journal: Blood (2010)
Toll-Like Receptors 2 and 4 Are Involved in the Induction of Graft-Versus-Host-Disease in Mice.
Authors: Axel Nogai, Markus M. Heimesaat, Marc Thiele, Stefan Bereswill, Eckhard Thiel, Ulf B. Goebel, Lutz Uharek
Journal: Blood (2006)
Increased D-Dimer Levels and Residual Venous Thrombosis Are Associated with Late Recurrence of Deep Venous Thrombosis
Authors: Bruna Moraes Mazetto, Fernanda Andrade Orsi, Mariane Flores-Nascimento, Sandra Silveira, Luis Fernando Bittar, Kiara Zapponi, Marina Pereira Colella, Erich Vinicius De Paula, Joyce Maria Annichino-Bizzacchi
Journal: Blood (2015)
Evaluation of the Role of STAT3 in the Self-Renewal of Primitive Chronic Myelogenous Leukemia (CML) Stem Cells.
Authors: Severine Marti N-Lannerée, Marie-Laure Bonnet, Caroline Mayeur-Rousse, Angelina Bertrand, Marie-Claude Meunier, Lydia Roy, Francois Guilhot, Isabelle Dusanter-Fourt, Ali G Turhan
Journal: Blood (2008)
Imatinib Therapy for Chronic Myeloid Leukemia Patients Who Relapse after Allogeneic Stem Cell Transplantation: A Molecular Analysis.
Authors: Francesca Palandri, Giovanni Martinelli, Marilina Amabile, Francesca Bonifazi, Giuseppe Bandini, Fabio Benedetti, Emilio Usala, Emanuele Angelucci, Mario Tiribelli, Renato Fanin, Marco Sorio, Mario Arpinati, Nicoletta Testoni, Sadia Falcioni, Maria Benedetta Giannini, Angela Poerio, Simona Soverini, Fabrizio Pane, Gianantonio Rosti, Sante Tura, Michele Baccarani
Journal: Blood (2004)
Low incidence of acute hepatitis C virus infection among Southern Spanish HIV-infected individuals
Authors: María Mancebo, Juan Macías, Nicolás Merchante, Luis M. Real, Fernando Lozano, Lara Domínguez, María J. Álvarez-Ossorio, Fernando Saussol, Pilar Rincón, Juan A. Pineda, Karin Neukam
Journal: Journal of Infection (2017)
Airway and serum biochemical correlates of refractory neutrophilic asthma
Authors: Rafeul Alam, James Good, Donald Rollins, Mukesh Verma, HongWei Chu, Tuyet-Hang Pham, Richard J. Martin
Journal: Journal of Allergy and Clinical Immunology (2017)

Despite progress in the diagnosis and management of asthma, many patients have poorly controlled or refractory asthma (RA). The mechanism of this RA is not well understood.We sought to explore the relationship between neutrophils and other biomarkers of RA.Sixty patients with RA, 30 patients with nonrefractory asthma (NRA), and 20 healthy subjects were enrolled. We performed a comprehensive characterization of these study subjects, which included laboratory and pulmonary function studies, chest computed tomography, and bronchoscopy with bronchoalveolar lavage (BAL). We analyzed BAL fluid and serum for a total of 244 biomolecules using a multiplex assay and correlated them with clinical and other laboratory parameters.RA was significantly different from NRA with regard to pulmonary function indices, bronchial basement membrane thickness, and BAL fluid neutrophil and lymphocyte counts but not eosinophil counts. BAL fluid neutrophil counts negatively and positively correlated with forced vital capacity and age, respectively. Of the 244 biomolecules studied, 52 and 14 biomolecules from BAL fluid and serum, respectively, were significantly different among the study groups. Thirteen of these 52 molecules correlated with BAL fluid neutrophil counts. BAL fluid from 40% of patients with RA was positive for a pathogenic microbe. Infection-negative neutrophilic RA was associated with an increase in levels of select biomarkers of inflammation in the serum, suggesting the presence of systemic inflammation.RA was associated with increased numbers of neutrophils and proneutrophilic biomolecules in the airways. Subclinical infection was present in 40% of patients with RA, which likely contributed to neutrophilic inflammation. A subgroup of patients with noninfected neutrophilic RA was associated with systemic inflammation.
New G-CSF-Dependent Signaling Pathway and Its Role In Patients with Severe Congenital Neutropenia and Acute Myeloid Leukemia
Authors: Julia Skokowa, Elena Chirvon, Lan Dan, Kshama Gupta, Ana Gigina, Marlene Reuter, Annette Müller Brechlin, Kais Hussein, Esteban Carrizosa, Janis Burkhardt, Hans Kreipe, Karl Welte
Journal: Blood (2010)
Characterization of Tcra and Tcrb Repertoires in Acute Myeloid Leukemia Patients before and after Combined Haploidentical and Umbilical Cord Blood Transplant
Authors: Houda Alachkar, Poh-Yin Yew, Rui Yamaguch, Kazuma Kiyotani, Hongtao Liu, Andrew S. Artz, Amittha Wickrema, Koen van Besien, Michael R Bishop, Satoru Miyano, Wendy Stock, Yusuke Nakamura
Journal: Blood (2014)
Immunotherapy with Donor Leukocyte Infusions (DLIS) in Relapsed Hodgkin’s Disease (HD) Following Allogeneic Stem Cell Transplantation (ALLO-SCT): CD3+ Cell Dose, GVHD and Disease Response.
Authors: Paolo Anderlini, Sandra A. Acholonu, Grace-Julia Okoroji, Rima Saliba, Sergio A. Giralt, Naoto Ueno, Michele L. Donato, Borje S. Andersson, Richard E. Champlin
Journal: Blood (2004)
Reply to Runqiang Yuan and Hongxing Huang's Letter to the Editor re: Ernesto R. Cordeiro Feijoo, Arjun Sivaraman, Eric Barret, et al. Focal High-intensity Focused Ultrasound Targeted Hemiablation for Unilateral Prostate Cancer: A Prospective Evaluation of Oncologic and Functional Outcomes. Eur Urol 2016;69:214–20
Authors: Arjun Sivaraman, Eric Barret
Journal: European Urology (2017)
A Genetic Variation in the Heme Oxygenase-1 Gene Predicts the Outcome of HLA-Fully-Matched Unrelated Bone Marrow Transplantation
Authors: Eriko Morishita, Keiko Maruyama, Akiyoshi Takami, Makoto Onizuka, Takakazu Kawase, Yasuo Morishima, Takahiro Fukuda, Yoshihisa Kodera, Shigeki Ohtake, Akihiro Yachie, Shinji Nakao
Journal: Blood (2011)
Lack of clastogenicity of combretastatin A-4 (CA4) - microtubule destabilizing agent, in human peripheral blood lymphocytes in vitro
Authors: Devaki N. Sadhu, Laxman Desai, Scott Young, Joseph C. Randall
Journal: Cancer Research (2005)

3433  The purpose of this study is to determine whether CA4 or CA4-glucuronide (CA4G) can induce aneuploidy or chromosome damage in cultured human lymphocytes. CA4 is a naturally occurring derivative of the South African willow tree (combretum caffrum), which binds tubulin and inhibits microtubule assembly. Microtubules are involved in the maintenance of the cytoskeleton and in the separation of sister chromatids during mitosis. Classic microtubule destabilizing agents, such as colchicine, have been shown to cause metaphase arrest and programmed cell death in rapidly dividing cells. The phosphate prodrug of CA4 (CA4 phosphate, CA4P) is in clinical trials in patients with malignant neoplasms or aberrant retinal neovasculature. Initial dose range-finding work was done to determine appropriate stock concentrations based on solubility and toxicity in cultured lymphocytes. In the main chromosome study, test concentrations were 50, 250 and 500 μg/mL for CA4 and 50, 500 and 5000 μg/mL for CA4G. An increase in the number of structural chromosome aberrations was not observed at any of the test concentrations, with or without metabolic activation (rat liver homogenates). A confirmatory assay using a longer duration of exposure (24 hours) in the absence of metabolic activation yielded similar results. Exposure of cells to positive control agents (Mitomycin C and cyclophosphamide) had a significant increase in the number of chromosome breaks compared to the negative controls. Under the test conditions employed, CA4 and CA4G did not induce chromosome aberrations and are non-clastogenic. There was also no evidence of CA4-induced aneuploidy, which is consistent with a previous report that microtubule-destabilizing agents cannot induce aneuploidy in cultured a549 cells (Chen and Horwitz, 2002). In contrast, Taxol® stabilizes tubulin and induces aneuploidy and errors in mitosis, (micronuclei with > 1 centromere) in cultured human lymphocytes (Digue, Orsiere, DeMeo, Duffaud, Favre and Botta, 1998). These results suggest that CA4 and other microtubule destabilizing agents are less likely to cause aneuploidy and aberrant mitosis than microtubule stabilizing agents.
Trends in the Incidence of HIV-Related Hematologic Malignancies in the Era of Combination Antiretroviral Therapy and Predictors of HIV-Related Non-Hodgkin's Lymphoma Development and Survival.
Authors: Linda R Taggart, Pierre K Isogai, Nancy Risebrough, Nicole Mittmann, Anita R Rachlis, Kevin R Imrie, Matthew C Cheung
Journal: Blood (2009)
Clinical Outcomes with Unfractionated Heparin or Low-Molecular-Weight Heparin as Bridging Therapy in Patients on Long-Term Oral Anticoagulants: Results from the REGIMEN Registry.
Authors: A.C. Spyropoulos, A.G.G. Turpie, A.S. Dunn, J. Spandorfer, J. Douketis, A. Jacobson, F.J. Frost
Journal: Blood (2004)
Does arousal enhance apical amplification and disamplification?
Authors: M. E. Larkum, W. A. Phillips
Journal: Behavioral and Brain Sciences (2016)

Abstract We summarize evidence that input to the apical tufts of neocortical pyramidal cells modulates their response to basal input. Because this apical amplification and disamplification provide intracortical mechanisms for prioritization, Mather and colleagues' arguments suggest that their effects are enhanced by noradrenergic arousal. Though that is likely, it has not yet been adequately studied. Their article shows that it should be.
Mutations in sphingosine-1-phosphate lyase cause nephrosis with ichthyosis and adrenal insufficiency
Authors: Svjetlana Lovric, Sara Goncalves, Heon Yung Gee, Babak Oskouian, Honnappa Srinivas, Won-Il Choi, Shirlee Shril, Shazia Ashraf, Weizhen Tan, Jia Rao, Merlin Airik, David Schapiro, Daniela A. Braun, Carolin E. Sadowski, Eugen Widmeier, Tilman Jobst-Schwan, Johanna Magdalena Schmidt, Vladimir Girik, Guido Capitani, Jung H. Suh, Noëlle Lachaussée, Christelle Arrondel, Julie Patat, Olivier Gribouval, Monica Furlano, Olivia Boyer, Alain Schmitt, Vincent Vuiblet, Seema Hashmi, Rainer Wilcken, Francois P. Bernier, A. Micheil Innes, Jillian S. Parboosingh, Ryan E. Lamont, Julian P. Midgley, Nicola Wright, Jacek Majewski, Martin Zenker, Franz Schaefer, Navina Kuss, Johann Greil, Thomas Giese, Klaus Schwarz, Vilain Catheline, Denny Schanze, Ingolf Franke, Yves Sznajer, Anne S. Truant, Brigitte Adams, Julie Désir, Ronald Biemann, York Pei, Elisabet Ars, Nuria Lloberas, Alvaro Madrid, Vikas R. Dharnidharka, Anne M. Connolly, Marcia C. Willing, Megan A. Cooper, Richard P. Lifton, Matias Simons, Howard Riezman, Corinne Antignac, Julie D. Saba, Friedhelm Hildebrandt
Journal: Journal of Clinical Investigation (2017)

Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease cases. A mutation in 1 of over 40 monogenic genes can be detected in approximately 30% of individuals with SRNS whose symptoms manifest before 25 years of age. However, in many patients, the genetic etiology remains unknown. Here, we have performed whole exome sequencing to identify recessive causes of SRNS. In 7 families with SRNS and facultative ichthyosis, adrenal insufficiency, immunodeficiency, and neurological defects, we identified 9 different recessive mutations in SGPL1, which encodes sphingosine-1-phosphate (S1P) lyase. All mutations resulted in reduced or absent SGPL1 protein and/or enzyme activity. Overexpression of cDNA representing SGPL1 mutations resulted in subcellular mislocalization of SGPL1. Furthermore, expression of WT human SGPL1 rescued growth of SGPL1-deficient dpl1Δ yeast strains, whereas expression of disease-associated variants did not. Immunofluorescence revealed SGPL1 expression in mouse podocytes and mesangial cells. Knockdown of Sgpl1 in rat mesangial cells inhibited cell migration, which was partially rescued by VPC23109, an S1P receptor antagonist. In Drosophila, Sply mutants, which lack SGPL1, displayed a phenotype reminiscent of nephrotic syndrome in nephrocytes. WT Sply, but not the disease-associated variants, rescued this phenotype. Together, these results indicate that SGPL1 mutations cause a syndromic form of SRNS.
Common Dimensional Reward Deficits Across Mood and Psychotic Disorders: A Connectome-Wide Association Study
Authors: Anup Sharma, Daniel H. Wolf, Rastko Ciric, Joseph W. Kable, Tyler M. Moore, Simon N. Vandekar, Natalie Katchmar, Aylin Daldal, Kosha Ruparel, Christos Davatzikos, Mark A. Elliott, Monica E. Calkins, Russell T. Shinohara, Danielle S. Bassett, Theodore D. Satterthwaite
Journal: American Journal of Psychiatry (2017)

Anhedonia is central to multiple psychiatric disorders and causes substantial disability. A dimensional conceptualization posits that anhedonia severity is related to a transdiagnostic continuum of reward deficits in specific neural networks. Previous functional connectivity studies related to anhedonia have focused on case-control comparisons in specific disorders, using region-specific seed-based analyses. Here, the authors explore the entire functional connectome in relation to reward responsivity across a population of adults with heterogeneous psychopathology.In a sample of 225 adults from five diagnostic groups (major depressive disorder, N=32; bipolar disorder, N=50; schizophrenia, N=51; psychosis risk, N=39; and healthy control subjects, N=53), the authors conducted a connectome-wide analysis examining the relationship between a dimensional measure of reward responsivity (the reward sensitivity subscale of the Behavioral Activation Scale) and resting-state functional connectivity using multivariate distance-based matrix regression.The authors identified foci of dysconnectivity associated with reward responsivity in the nucleus accumbens, the default mode network, and the cingulo-opercular network. Follow-up analyses revealed dysconnectivity among specific large-scale functional networks and their connectivity with the nucleus accumbens. Reward deficits were associated with decreased connectivity between the nucleus accumbens and the default mode network and increased connectivity between the nucleus accumbens and the cingulo-opercular network. In addition, impaired reward responsivity was associated with default mode network hyperconnectivity and diminished connectivity between the default mode network and the cingulo-opercular network.These results emphasize the centrality of the nucleus accumbens in the pathophysiology of reward deficits and suggest that dissociable patterns of connectivity among large-scale networks are critical to the neurobiology of reward dysfunction across clinical diagnostic categories.