tbuckley/cabot-search huggingface dataset:
Steady State Haemoglobin Level Increases with the Proportion of Erythrocyte Membrane n-3 Fatty Acids in Sickle Cell Anaemia.
Authors: Iheanyi Okpala, Hongmei Ren, Obike Ibegbulam, Cynthia C. Ugochukwu, Kebreab Ghebremeskel, Michael Crawford
Journal: Blood (2004)
Autologous Stem Cell Transplantation (ASCT) As Upfront Treatment in Primary Central Nervous System Lymphoma (PCNSL): A Systematic Review and Comparative Analysis in Clinical Trials Setting
Authors: Mariana Nassif Kerbauy, Fabio Ynoe de Moraes, Lucila Nassif Kerbauy, Iracema Esteves, Guilherme Fleury Perini, Fabio Pires de Souza Santos, Andreza Alice Feitosa Ribeiro, Fabio Rodrigues Kerbauy, Nelson Hamerschlak
Journal: Blood (2016)
Association of γH2AX at Diagnosis with Chemotherapy Outcome in Patients with Breast Cancer
Authors: Sherry X. Yang, Eric C. Polley, Dat Nguyen
Journal: Theranostics (2017)

γH2AX plays a role in DNA damage response signaling and facilitates the repair of DNA double strand breaks. However, it remains unknown whether constitutive tumor γH2AX expression is associated with treatment outcome in patients. γH2AX status was detected in primary tumors from 24% of 826 patients with stage I, II and III breast cancer by immunohistochemistry; overall survival was analyzed by Kaplan-Meier method. At median follow-up of 176 months (range 13 - 282 months), we found substantial survival heterogeneity in γH2AX-positive patients (P=0.002) among uniform treatment groups including radiation or endocrine therapy alone and no-treatment, as well as chemotherapy alone (being worst), in contrast to γH2AX-negative patients (P=0.2). In the chemotherapy group (n=118), median survival was 63 months (95% confidence interval [CI], 29 - 83) in patients with γH2AX-positive tumors compared with 170 months (95% CI 94 - 235) in those with γH2AX-negative tumors (P=0.0017). γH2AX remained a poor prognosis factor in the group by multivariable analysis (adjusted hazard ratio 2.12, P=0.009). Our data demonstrate that constitutive γH2AX positivity is significantly associated with survival heterogeneity in patients among uniform treatment groups, and its expression at diagnosis independently predicts poor chemotherapy outcome in breast cancer.
Assessment of the Predictive Validity of Etiologic Stroke Classification
Authors: E. Murat Arsava, Johanna Helenius, Ross Avery, Mine H. Sorgun, Gyeong-Moon Kim, Octavio M. Pontes-Neto, Kwang Yeol Park, Jonathan Rosand, Mark Vangel, Hakan Ay
Journal: JAMA Neurology (2017)

The ability of present-day etiologic stroke classification systems to generate subtypes with discrete stroke characteristics is not known.To test the hypothesis that etiologic stroke subtyping identifies different disease processes that can be recognized through their different clinical courses.We performed a head-to-head evaluation of the ability of the Causative Classification of Stroke (CCS), Trial of Org 10172 in Acute Stroke Treatment (TOAST), and ASCO (A for atherosclerosis, S for small-vessel disease, C for cardiac source, and O for other cause) classification systems to generate etiologic subtypes with different clinical, imaging, and prognostic characteristics in 1816 patients with ischemic stroke. This study included 2 cohorts recruited at separate periods; the first cohort was recruited between April 2003 and June 2006 and the second between June 2009 and December 2011. Data analysis was performed between June 2014 and May 2016.Separate teams of stroke-trained neurologists performed CCS, TOAST, and ASCO classifications based on information available at the time of hospital discharge. We assessed the association between etiologic subtypes and stroke characteristics by computing receiver operating characteristic curves for binary variables (90-day stroke recurrence and 90-day mortality) and by calculating the ratio of between-category to within-category variability from the analysis of variance for continuous variables (admission National Institutes of Health Stroke Scale score and acute infarct volume).Among the 1816 patients included, the median age was 70 years (interquartile range, 58-80 years) (830 women [46%]). The classification systems differed in their ability to assign stroke etiologies into known subtypes; the size of the undetermined category was 33% by CCS, 53% by TOAST, and 42% by ASCO (P < .001 for all binary comparisons). All systems provided significant discrimination for the validation variables tested. For the primary validation variable (90-day recurrence), the area under the receiver operating characteristic curve was 0.71 (95% CI, 0.66-0.75) for CCS, 0.61 (95% CI, 0.56-0.67) for TOAST, and 0.66 (95% CI, 0.60-0.71) for ASCO (P = .01 for CCS vs ASCO; P < .001 for CCS vs TOAST; P = .13 for ASCO vs TOAST). The classification systems exhibited similar discrimination for 90-day mortality. For admission National Institutes of Health Stroke Scale score and acute infarct volume, CCS generated more distinct subtypes with higher between-category to within-category variability than TOAST and ASCO.Our findings suggest that the major etiologic stroke subtypes are distinct categories with different stroke characteristics irrespective of the classification system used to identify them. We further show that CCS generates discrete etiologic categories with more diverse clinical, imaging, and prognostic characteristics than either TOAST or ASCO.
EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas
Authors: Faizaan Mohammad, Simon Weissmann, Benjamin Leblanc, Deo P Pandey, Jonas W Højfeldt, Itys Comet, Chunqin Zheng, Jens Vilstrup Johansen, Nicolas Rapin, Bo T Porse, Andrey Tvardovskiy, Ole N Jensen, Nagore G Olaciregui, Cinzia Lavarino, Mariona Suñol, Carmen de Torres, Jaume Mora, Angel M Carcaboso, Kristian Helin
Journal: Nature Medicine (2017)
Inhibition of NHE1 Induced Apoptosis in Cytarabine Resistant Leukemia Cell Lines and Primary Leukemia Cells from AML Patients, Which Showed Increased Intracellular pH and NHE1 Activity
Authors: Shin Young Hyun, Young Kyung Kim, Ji Eun Jang, Yundeok Kim, Yu Ri Kim, June-Won Cheong, Kwang Yong Shim, Yoo Hong Min
Journal: Blood (2014)
More than 80% of US patients’ groups take industry funds, study finds
Authors: Michael McCarthy
Journal: BMJ (2017)

A study of 104 of the largest patient advocacy groups that are based in the US found that 83% received financial support from drug, device, and biotechnology companies. The study also found that 39% of the advocacy groups had a current or former executive of such a company on their governing board, with at least 12% having a former industry executive in a board leadership position.

In many cases, industry support for the groups was substantial, with at least 39% of the groups receiving donations totaling at least $1m a year, the researchers found. Only one of the 104 …
Inhibition of platelet function using liposomal nanoparticles blocks tumor metastasis
Authors: Yinlong Zhang, Jingyan Wei, Shaoli Liu, Jing Wang, Xuexiang Han, Hao Qin, Jiayan Lang, Keman Cheng, Yiye Li, Yingqiu Qi, Greg J Anderson, Saraswati Sukumar, Suping Li, Guangjun Nie
Journal: Theranostics (2017)

Extensive evidence has shown that platelets support tumor metastatic progression by inducing epithelial-mesenchymal transition of cancer cells and by shielding circulating tumor cells from immune-mediated elimination. Therefore, blocking platelet function represents a potential new avenue for therapy focused on eliminating metastasis. Here we show that liposomal nanoparticles bearing the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) can deliver a platelet inhibitor, ticagrelor, into tumor tissues to specifically inhibit tumor-associated platelets. The drug-loaded nanoparticles (CREKA-Lipo-T) efficiently blocked the platelet-induced acquisition of an invasive phenotype by tumor cells and inhibited platelet-tumor cell interaction in vitro. Intravenously administered CREKA-Lipo-T effectively targeted tumors within 24 h, and inhibited tumor metastasis without overt side effects. Thus, the CREKA-Lipo formulation provides a simple strategy for the efficient delivery of anti-metastatic drugs and shows considerable promise as a platform for novel cancer therapeutics.
Treatment of Chronic Lymphocytic Leukemia Patients with Lenalidomide Induces Down-Regulation of miR342-3p Associated with Over-Expression of Tumor Suppressor RASSF4,
Authors: Emanuela M. Ghia, Lillian Werner, Danelle F. James, Donna Neuberg, Laura G Corral, Laura Z. Rassenti, Carlo M. Croce, Thomas J. Kipps
Journal: Blood (2011)
Adult weight gain and colorectal adenomas—a systematic review and meta-analysis
Authors: S. Schlesinger, K. Aleksandrova, L. Abar, A.R. Vieria, S. Vingeliene, E. Polemiti, C.A.T. Stevens, D.C. Greenwood, D.S.M. Chan, D. Aune, T. Norat
Journal: Annals of Oncology (2017)
Abstract P5-03-05: Development of a panel of serum-based protein biomarkers for the non-invasive detection of breast cancer in BI-RADS category 4 patients
Authors: KB Chapman, K Copeland, J Kidd, L Qiu, N Sheibani, O Tam, L Friedman, R Korn, J Fiorica, A Lourenco, S Suthers, L Hesterberg
Journal: Cancer Research (2017)

Abstract Background: Current breast cancer screening guidelines call for annual mammography for asymptomatic women age 45 to 54 and once every two years for women age 55 and older. Women with suspicious screening mammograms are recommended for a diagnostic mammogram and may also undergo MRI or ultrasound. Ultimately, suspicious findings unresolved by imaging typically result in the recommendation of a breast biopsy. Approximately 10% of suspicious diagnostic mammograms are recommended for breast biopsies and 67% to 95% of these biopsies yield negative results. With the goal of reducing the number of patients with benign pathology undergoing invasive biopsies, we conducted a screen for serum protein biomarkers and identified a novel panel for the non-invasive detection of breast cancer. Methods: Serum samples were collected at two sites from women with suspicious diagnostic mammogram findings (primarily BI-RADS category 4) undergoing biopsy for the evaluation of a potential malignancy. Serum samples from 100-patients (50 benign pathology and 50 malignant pathology) were evaluated on the SOMAscan Assay 1.3k, which measures levels of 1,310 different protein analytes. Statistical screening methodologies, such as individual t-tests with control for false discovery, were used to identify markers with the potential to distinguish benign from malignant pathology. The candidate markers were further studied and combined using generalized linear modeling to develop three potential diagnostic models. K-fold cross validation was used to guard against over fitting of the models. Results: A 15-marker model resulted in an AUC of 0.92 with a sensitivity of 90% and specificity of 76%. Two 6-marker models (with 4 markers in common) each resulted in AUC of 0.85, yielding a sensitivity of 90% with a specificity of 56% or 64%. Conclusions: This study reveals a novel panel of serum protein biomarkers that may allow for the non-invasive and sensitive detection of breast cancer in BI-RADS category 4 patients. A multicenter study is underway to further refine and validate this panel in a larger set of prospectively collected patient samples. Citation Format: Chapman KB, Copeland K, Kidd J, Qiu L, Sheibani N, Tam O, Friedman L, Korn R, Fiorica J, Lourenco A, Suthers S, Hesterberg L. Development of a panel of serum-based protein biomarkers for the non-invasive detection of breast cancer in BI-RADS category 4 patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-03-05.
Abstract P6-08-05: Genome-wide identification of transcripts regulated by estrogen in MCF-7 cells using BrU-seq
Authors: J Sun, E Capobianco, N Tsinoremas, M Lippman
Journal: Cancer Research (2017)

Abstract Estrogen promotes estrogen receptor (ER)-positive breast cancer cell growth by modulating transcription through ligand activated ER. The spectrum of early ER target genes has been identified through gene expression microarray and more recently with RNA-seq analyses. These methods, although comprehensive, fall short in identifying many ER-regulated transcripts which are either not present in microarray; too abundant to determine estrogen regulated changes among steady-state pools of RNAs; or have very short half-lives and low abundance such as some non-coding RNAs, including RNAs generated by enhancers bound by ER (eRNAs). Global run-on sequencing (GRO-seq) has been used to identify ER target genes and eRNAs in breast cancer cells. It is technically cumbersome and is performed under non-physiological condition. We have applied BrU-seq technique to identify global transcripts regulated by estrogen in MCF-7 breast cancer cells. The newly synthesized RNAs in MCF-7 cells treated with or without estrogen for various time points, were labeled with 5'-bromo-uridine (BrU). The labeled RNAs were purified by immunoprecipitation using an anti-BrdU antibody and then subjected to RNA sequencing analysis, which provides greater sensitivity than regular RNA-seq analysis from steady-state total RNA samples. Robust estrogen-regulated transcripts can be detected within 30 min of treatment. Significantly more transcripts (both coding and non-coding RNAs) were identified as estrogen targets using BrU-seq analysis than RNA-seq analysis from total RNA pools. Many of these estrogen-regulated transcripts are located close to ER binding sites identified from ER ChIP-seq analysis, indicating a functional role for these ER binding sites in regulating RNA transcription. For estrogen targets identified through both analyses, the magnitude of expression changes (both up- and down-regulation) is usually greater from BrU-seq than from the regular RNA-seq analysis. The dynamics of RNA synthesis and degradation for some unstable RNAs (such as eRNAs) can be interrogated through our data set. Also, RNA pol II elongation rate can be deduced from some long ER target genes (&amp;gt;100 kb) such as GREB1. In addition to identifying estrogen targets, BrU-seq should be a very useful technique in assessing transcriptional changes triggered by various signal transduction pathways. Citation Format: Sun J, Capobianco E, Tsinoremas N, Lippman M. Genome-wide identification of transcripts regulated by estrogen in MCF-7 cells using BrU-seq [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-08-05.
Impact of Comorbidities at Diagnosis of Acute Myeloid Leukemia on One-Year Mortality
Authors: Mohamed L Sorror, Barry E. Storer, Mahmoud Elsawy, Amir T Fathi, Andrew Brunner, Aaron T. Gerds, Mikkael A. Sekeres, Sudipto Mukherjee, Bruno C. Medeiros, Paul Shami, Esteban Peña, Shylo Wardyn, Jennifer Whitten, Hannah Frenkel, Jeannine McCune, Stephanie J. Lee, Elihu H. Estey
Journal: Blood (2015)
Incidence and Risk Factors of Chronic Graft-Versus-Host Disease After Unrelated Cord Blood Transplant In Children and Adults. A Retrospective Study on Behalf of EUROCORD and Late-Effect Working Party of EBMT
Authors: Alessandro Crotta, Gerard Michel, Guillermo F. Sanz, Gerard Socie, Tracey A. O'Brien, William Arcese, Didier Blaise, Yves Bertrand, Miguel A. Diaz, Ajay J. Vora, Franca Fagioli, Giorgio Dini, Jean-Hugues Dalle, Mohamad Mohty, Myriam Labopin, Eliane Gluckman, André Tichelli, Vanderson Rocha
Journal: Blood (2010)
Screening for Depression Through a Glass Darkly
Authors: H. George Nurnberg
Journal: JAMA Internal Medicine (2017)

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TET2 Mutations Are Highly Associated with RUNX1-RUNX1T1 Translocations and NPMc+ in Childhood AML: a Report from Children's Oncology Group AAML03P1, AAML0531 and NCI/COG Target AML Initiative
Authors: Matthew A. Kutny, Todd A. Alonzo, Yi-Cheng Wang, Rhonda Ries, Jason E. Farrar, Jaime M. Guidry Auvil, Malcolm A. Smith, Daniela S. Gerhard, Tanja M. Davidsen, Patee Gesuwan, Leandro C. Hermida, Marco A Marra, Andrew J. Mungall, Richard Moore, William Long, Yussanne Ma, Stuart Zong, E. Anders Kolb, Alan S. Gamis, Soheil Meshinchi
Journal: Blood (2015)
Deficiency of the hepatokine selenoprotein P increases responsiveness to exercise in mice through upregulation of reactive oxygen species and AMP-activated protein kinase in muscle
Authors: Hirofumi Misu, Hiroaki Takayama, Yoshiro Saito, Yuichiro Mita, Akihiro Kikuchi, Kiyo-aki Ishii, Keita Chikamoto, Takehiro Kanamori, Natsumi Tajima, Fei Lan, Yumie Takeshita, Masao Honda, Mutsumi Tanaka, Seiji Kato, Naoto Matsuyama, Yuya Yoshioka, Kaito Iwayama, Kumpei Tokuyama, Nobuhiko Akazawa, Seiji Maeda, Kazuhiro Takekoshi, Seiichi Matsugo, Noriko Noguchi, Shuichi Kaneko, Toshinari Takamura
Journal: Nature Medicine (2017)
Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence
Authors: Jeanna A. Bugaytsova, Oscar Björnham, Yevgen A. Chernov, Pär Gideonsson, Sara Henriksson, Melissa Mendez, Rolf Sjöström, Jafar Mahdavi, Anna Shevtsova, Dag Ilver, Kristof Moonens, Macarena P. Quintana-Hayashi, Roman Moskalenko, Christopher Aisenbrey, Göran Bylund, Alexej Schmidt, Anna Åberg, Kristoffer Brännström, Verena Königer, Susanne Vikström, Lena Rakhimova, Anders Hofer, Johan Ögren, Hui Liu, Matthew D. Goldman, Jeannette M. Whitmire, Jörgen Ådén, Justine Younson, Charles G. Kelly, Robert H. Gilman, Abhijit Chowdhury, Asish K. Mukhopadhyay, G. Balakrish Nair, Konstantinos S. Papadakos, Beatriz Martinez-Gonzalez, Dionyssios N. Sgouras, Lars Engstrand, Magnus Unemo, Dan Danielsson, Sebastian Suerbaum, Stefan Oscarson, Ludmilla A. Morozova-Roche, Anders Olofsson, Gerhard Gröbner, Jan Holgersson, Anders Esberg, Nicklas Strömberg, Maréne Landström, Angela M. Eldridge, Brett A. Chromy, Lori M. Hansen, Jay V. Solnick, Sara K. Lindén, Rainer Haas, Andre Dubois, D. Scott Merrell, Staffan Schedin, Han Remaut, Anna Arnqvist, Douglas E. Berg, Thomas Borén
Journal: Cell Host & Microbe (2017)
Prognostic Value of cMYC Gene Abnormalities in Diffuse Large B Cell Lymphoma Treated with Chemo-Immunotherapy
Authors: Ana Batlle López, Sonia Glez de Villambrosia, Santiago Montes-Moreno, Francisco Mazorra, Andrés Insunza, Anabel Sáez, Carlos Montalban, Lydia Sánchez, Juan F. Garcia, Eva González-Barca, A López, MC Ruiz-Marcellan, Manuela Mollejo, Carlos Grande, Cherie H. Dunphy, ED His, Ronald S. Go, Carlo Visco, Zijun Y. Xu-Monette, Ken H. Young, Miguel Piris, Eulogio Conde
Journal: Blood (2011)
SAR 650984, a Therapeutic Anti-CD38 Monoclonal Antibody, Blocks CD38-CD31 Interaction in Multiple Myeloma
Authors: Gang An, Hua Jiang, Chirag Acharya, Mike Y Zhong, Ti Cai, Guang Yang, Zhili Song, Joachim Theilhaber, Francisco Adrian, Yu-Tzu Tai, Kenneth C. Anderson
Journal: Blood (2014)
Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance
Authors: Whijae Roh, Pei-Ling Chen, Alexandre Reuben, Christine N. Spencer, Peter A. Prieto, John P. Miller, Vancheswaran Gopalakrishnan, Feng Wang, Zachary A. Cooper, Sangeetha M. Reddy, Curtis Gumbs, Latasha Little, Qing Chang, Wei-Shen Chen, Khalida Wani, Mariana Petaccia De Macedo, Eveline Chen, Jacob L. Austin-Breneman, Hong Jiang, Jason Roszik, Michael T. Tetzlaff, Michael A. Davies, Jeffrey E. Gershenwald, Hussein Tawbi, Alexander J. Lazar, Patrick Hwu, Wen-Jen Hwu, Adi Diab, Isabella C. Glitza, Sapna P. Patel, Scott E. Woodman, Rodabe N. Amaria, Victor G. Prieto, Jianhua Hu, Padmanee Sharma, James P. Allison, Lynda Chin, Jianhua Zhang, Jennifer A. Wargo, P. Andrew Futreal
Journal: Science Translational Medicine (2017)

Immune checkpoint blockade produces clinical benefit in many patients. However, better biomarkers of response are still needed, and mechanisms of resistance remain incompletely understood. To address this, we recently studied a cohort of melanoma patients treated with sequential checkpoint blockade against cytotoxic T lymphocyte antigen-4 (CTLA-4) followed by programmed death receptor-1 (PD-1) and identified immune markers of response and resistance. Building on these studies, we performed deep molecular profiling including T cell receptor sequencing and whole-exome sequencing within the same cohort and demonstrated that a more clonal T cell repertoire was predictive of response to PD-1 but not CTLA-4 blockade. Analysis of CNAs identified a higher burden of copy number loss in nonresponders to CTLA-4 and PD-1 blockade and found that it was associated with decreased expression of genes in immune-related pathways. The effect of mutational load and burden of copy number loss on response was nonredundant, suggesting the potential utility of a combinatorial biomarker to optimize patient care with checkpoint blockade therapy.
Abstract B29: Reorganization of signaling modules revealed in human colorectal cancer using single-cell mass cytometry
Authors: Alan J. Simmons, Cherie R. Scurrah, Eliot T. McKinley, Charles A. Herring, Jonathan M. Irish, Mary K. Washington, Robert J. Coffey, Ken S. Lau
Journal: Cancer Research (2017)

Abstract Cellular heterogeneity poses a significant challenge to understanding tissue level phenotypes, and confounds conventional bulk analyses. To facilitate the analysis of signaling at the single-cell level in human tissues, we, for the first time, applied mass cytometry using CyTOF (Cytometry Time-of-Flight) to formalin-fixed paraffin-embedded (FFPE) normal and diseased intestinal specimens. We developed and validated FFPE-DISSECT (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue), a single-cell approach for preserving and characterizing native signaling states from embedded solid tissue samples. We applied FFPE-DISSECT coupled to mass cytometry to demonstrate differential TNF-α signaling in intestinal enterocytes, goblet cells and enteroendocrine cells, implicating the role of the RAS-RAF-MEK-ERK signaling pathway in goblet cell identity. In addition, application of FFPE-DISSECT, mass cytometry, and data-driven computational analyses of human colorectal cancer specimens confirmed reduction of differentiation and revealed quantitative changes in inter- and intra-tumoral heterogeneity with regards to the modular regulation of signaling pathways. Our single-cell approach, applied in conjunction with genomic annotation such as microsatellite and K-Ras and B-RAF status, allows rapid and detailed characterization of cellular heterogeneity from clinical repositories of embedded human tissues. Citation Format: Alan J. Simmons, Cherie R. Scurrah, Eliot T. McKinley, Charles A. Herring, Jonathan M. Irish, Mary K. Washington, Robert J. Coffey, Ken S. Lau. Reorganization of signaling modules revealed in human colorectal cancer using single-cell mass cytometry. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B29.