tbuckley/cabot-search huggingface dataset:
Development and validation of a training module on the use of acetic acid for the detection of Barrett’s neoplasia
Authors: Fergus Chedgy, Kesavan Kandiah, Hugh Barr, John De Caestecker, Simon Dwerryhouse, Balint Eross, Charles Gordon, Susi Green, Andy Li, James Brown, Gaius Longcroft-Wheaton, Pradeep Bhandari
Journal: Endoscopy (2017)

<b>Background and study aims</b> Acetic acid chromoendoscopy (AAC) enhances the ability to correctly identify Barrett’s neoplasia, and is increasingly used by both expert and nonexpert endoscopists. Despite its increasing use, there is no validated training strategy to achieve competence. The aims of our study were to develop a validated training tool in AAC-assisted lesion recognition, to assess endoscopists’ baseline knowledge of AAC-assisted lesion recognition, and to evaluate the efficacy and impact of this training tool. <b>Methods</b> A validated assessment of 40 images and 20 videos was developed. A total of 13 endoscopists with experience of Barrett’s endoscopy but no formal training in AAC were recruited to the study. Participants underwent: baseline assessment 1, online training, assessment 2, interactive seminar, assessment 3. <b>Results</b> Baseline assessment demonstrated a sensitivity of 83 % and a negative predictive value (NPV) of 83 %. The online training intervention significantly improved sensitivity to 95 % and NPV to 94 % (<i>P</i> < 0.01). Further improvement was seen after a 1-day interactive seminar including live cases, with sensitivity increasing to 98 % and NPV to 97 %. <b>Conclusions</b> The data demonstrate the need for training in AAC-assisted lesion recognition as baseline performance, even by Barrett’s experts, was poor. The online training and testing tool for AAC for Barrett’s neoplasia was successfully developed and validated. The training intervention improved performance of endoscopists to meet ASGE PIVI standards. The training tool increases the endoscopist’s degree of confidence in the use of AAC. The training tool also leads to shift in attitudes of endoscopists from Seattle protocol towards AAC-guided biopsy protocol for Barrett’s surveillance.
Serum proteomic profiling distinguishes estrogen receptor (ER) positive and ER negative breast cancers
Authors: M. Sun, M. Sun, J. Lyons-Weiler, A. E. Lokshin, F. Modugno, J. Marks, W. L. Bigbee
Journal: Journal of Clinical Oncology (2005)

578 Background: ER (+) and ER (-) breast cancers have different clinical response to current therapies and distinct clinical outcomes. Identification of distinguishable serum protein profiles of these two breast cancer entities may facilitate biomarker discovery for disease diagnosis and elucidation of potential therapeutic targets. Method: Serum samples of 30 patients with ER (+) and 11 patients with ER (-) breast cancer were divided 70:30 into training and testing sets. Patients in both training and testing sets were frequency matched by age and race. Another independent sample set of 48 white postmenopausal women with ER (+) breast cancer was used to validate the finding. Samples were analyzed in duplicate on Ciphergen IMAC3-Cu ProteinChip arrays with PBSIIc SELDI-TOF-MS. Spectral preprocessing with Ciphergen ProteinChip and CiphergenExpress software included baseline subtraction, normalization to total ion current, and internal peak alignment. Averaged peak intensities of over 180 potential features (peaks) were submitted to Ciphergen Biomarker Patterns™ software (V.5) for scripted generation of multiple classification trees (CART). Two hundred and ten decision trees were generated for the two-group comparison using the training set. The performance of the best and top 10% classifiers from the training, testing, and validation set is reported. Conclusions: There are features in serum protein profiles that distinguish ER (+) from ER (-) breast cancer patients with a relatively high accuracy. An independent sample validation set with both ER (+) and ER (-) breast cancers is needed to further confirm this finding. A more specific serum protein profile needs to be identified for each group when they are compared with non-malignant sample sets. [Supported by DoD IDEA grant BC 021912 to AEL] No significant financial relationships to disclose.
Plasma Circulating Ki-67 Index as a Biomarker and Prognostic Indicator in Patients with Chronic Lymphocytic Leukemia.
Authors: Jean-Marie Bruey, Zeev Estrov, Hagop M. Kantarjian, Wanlong Ma, Chen-Hsiung Yeh, William Weirda, Amber Donahue, Susan O'Brien, Michael Keating, Maher Albitar
Journal: Blood (2009)
The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data
Authors: Yukako Katsura, Craig E. Stanley, Sudhir Kumar, Masatoshi Nei
Journal: Molecular Biology and Evolution (2016)

The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented.
Impact of salvage regimens on response and overall survival in acute myeloid leukemia with induction failure
Authors: M Wattad, D Weber, K Döhner, J Krauter, V I Gaidzik, P Paschka, M Heuser, F Thol, T Kindler, M Lübbert, H R Salih, A Kündgen, H-A Horst, P Brossart, K Götze, D Nachbaur, C-H Köhne, M Ringhoffer, G Wulf, G Held, H Salwender, A Benner, A Ganser, H Döhner, R F Schlenk
Journal: Leukemia (2017)
NIK and the Alternative NF-κB Pathway in Human Lymphomas.
Authors: Lina Odqvist, Margarita Sanchez-Beato, Santiago Montes-Moreno, Cristina Gomez-Abad, Lydia Sanchez, Ana Rodriguez-Lopez, Jose Angel Martinez-Climent, Joaquin Martinez-Lopez, Francisco Javier Alves, Miguel A. Piris
Journal: Blood (2009)
The Chronic Kidney Disease-Epidemiology Collaboration-Cystatin C (CKD-EPI-CysC) Equation Has an Independent Prognostic Value for Overall Survival in Newly-Diagnosed Patients with Symptomatic Multiple Myeloma: Comparison with 3 Other Equations for GFR Estimation
Authors: Meletios A Dimopoulos, Efstathios Kastritis, Eirini Katodritou, Anastasia Pouli, Eurydiki Michalis, Dimitrios Christoulas, Maria Gkotzamanidou, Ioannis Papassotiriou, Konstantinos Zervas, Evangelos Terpos
Journal: Blood (2012)
Collagen Receptor-Mediated Mechanochemical Signaling Contributes to Human Pro-Angiogenic Mesenchymal Stem/Progenitor Cell-Induced Neo-Vasculogenesis
Authors: Mario Gimona, Rokhsareh Rohban, Thomas Lener, Doris Peckl-Schmid, Michaela Oeller, Katharina Schallmoser, Dirk Strunk, Eva Rohde
Journal: Blood (2012)
SOX11, CCND1, BCL1/Igh, and Igh-VDJ – a Plethora of Markers for Minimal Residual Disease in Mantle Cell Lymphoma: Which One to Choose?
Authors: Anita Tranberg Simonsen, Marie Schou, Camilla Darum Sørensen, Peter Hokland, Hans Bentzen, Charlotte Guldborg Nyvold
Journal: Blood (2014)
Integrating CT Myocardial Perfusion and CT-FFR in the Work-Up of Coronary Artery Disease
Authors: Adriaan Coenen, Alexia Rossi, Marisa M. Lubbers, Akira Kurata, Atsushi K. Kono, Raluca G. Chelu, Sabrina Segreto, Marcel L. Dijkshoorn, Andrew Wragg, Robert-Jan M. van Geuns, Francesca Pugliese, Koen Nieman
Journal: JACC. Cardiovascular imaging (2017)
The Impact of Histological Subtypes on Outcome in Patients with Mantle Cell Lymphoma Treated with or without Autologous Stem Cell Transplant.
Authors: Muhammad I. Zulfiqar, Dennis D. Weisenburger, Fausto R. Loberiza, Julie M. Vose, Philip J. Bierman, R. Gregory Bociek, James O. Armitage
Journal: Blood (2007)
TECHNITIUM-99m-SESTAMIBI SCANNING (MIBI) CORRELATES WITH DISEASE ACTIVITY IN PATIENTS (PTS) WITH MULTIPLE MYELOMA UNDERGOING AUTOLOGOUS PERIPHERAL BLOOD STEM CELL TRANSPLANTATION (PBSCT).
Authors: Natalie S. Callander, William T. Phillips, Darlene F. Metter, Leonel Ochoa-Bayona, Cesar O. Freytes, Sharon A. Primeaux
Journal: Blood (2004)
Prevalence and Clinical Significance of the MYD88 (L265P) Somatic Mutation in Patients with Waldenström Macroglobulinemia, IgM-Monoclonal Gammopathy of Undetermined Significance or Other Mature B-Cell Neoplasms.
Authors: Marzia Varettoni, Luca Arcaini, Silvia Zibellini, Emanuela Boveri, Sara Rattotti, Roberta Riboni, Alessandro Corso, Ester Orlandi, Maurizio Bonfichi, Manuel Gotti, Cristiana Pascutto, Silvia Mangiacavalli, Lucia Morello, Maria Luisa Guerrera, Giorgio Croci, Valeria Fiaccadori, Marco Paulli, Mario Cazzola
Journal: Blood (2012)
Hyaluronic Acid Conjugated Magnetic Prussian Blue@Quantum Dot Nanoparticles for Cancer Theranostics
Authors: Yongbo Yang, Lijia Jing, Xiaoda Li, Li Lin, Xiuli Yue, Zhifei Dai
Journal: Theranostics (2017)

A multifunctional nanotheranostic agent was developed by conjugating both hyaluronic acid and bovine serum albumin coated CuInS 2 -ZnS quantum dots onto the surface of magnetic Prussian blue nanoparticles.The obtained nanoagent could serve as an efficient contrast agent to simultaneously enhance near infrared (NIR) fluorescence and magnetic resonance (MR) imaging greatly.The coexistence of magnetic core and CD44 ligand hyaluronic acid was found to largely improve the specific uptake of the nanoagent by CD44 overexpressed HeLa cells upon applying an external magnetic field.Both NIR fluorescence and MR imaging in vivo proved high accumulation of the nanoagent at tumor site due to its excellent CD44 receptor/magnetic dual targeting capability.After intravenous injection of the nanoagent and treatment of external magnetic field, the tumor in nude mice was efficiently ablated upon NIR laser irradiation and the tumor growth inhibition was more than 89.95%.Such nanotheranostic agent is of crucial importance for accurately identifying the size and location of the tumor before therapy, monitoring the photothermal treatment procedure in real-time during therapy, assessing the effectiveness after therapy.
Pre-B Cell Acute Lymphoblastic Leukemia Cells Carrying a Bcr/Abl Translocation Retain Sensitivity to Minor Histocompatibility Antigen Specific T Cells but Are Resistant to Natural Killer Cells: Implications for Manipulation of Graft Versus Leukemia Effects.
Authors: Craig A. Mullen, Andrew Campbell, Faith Young, Craig T. Jordan
Journal: Blood (2006)
The t(14;18) Is Associated with Germinal Center Phenotype Subset of the Diffuse Large B-Cell Lymphoma Patients in Egypt.
Authors: Hasan A. Abdel-Ghaffar, Sherin M. Abdel-Aziz, Doaa A. Shahin, Ezzat S. Sobki Board, Nadia I. Attwan, Youssef A. Al-Tonbary, Nader G. Abraham
Journal: Blood (2007)
MIB-1 Labeling Index As a Prognostic Factor in Patients with Follicular Lymphoma Treated with R-CHOP Therapy
Authors: Eri Yamamoto, Naoto Tomita, Seiji Sakata, Naoko Tsuyama, Kengo Takeuchi, Yuki Nakajima, Kazuho Miyashita, Takayoshi Tachibana, Hirotaka Takasaki, Masatsugu Tanaka, Chizuko Hashimoto, Hideyuki Koharazawa, Katsumichi Fujimaki, Jun Taguchi, Hiroshi Harano, Shigeki Motomura, Yoshiaki Ishigatsubo
Journal: Blood (2012)
Abstract A65: A novel small-molecule IAP antagonist, AZD5582, draws Mcl-1 down-regulation for induction of apoptosis through targeting of cIAP1 and XIAP in human pancreatic cancer
Authors: Eun-Yeung Gong, Eun Young Lee, Jai-Hee Moon, Jae-Sik Shin, Seung-Woo Hong, Soo-A Jung, Ih-Yeon Hwang, Jeong Hee Kim, Dong-Hoon Jin, Tae Won Kim
Journal: Cancer Research (2016)

Abstract Inhibitor of apoptosis proteins (IAPs) plays an important role in controlling cancer cell survival. IAPs have therefore attracted considerable attention as potential targets in anticancer therapy. In this study, we investigated the anti-tumor effect of AZD5582, a novel small-molecule IAP inhibitor, in human pancreatic cancer cells. Treating human pancreatic cancer cells with AZD5582 differentially induced apoptosis, dependent on the expression of p-Akt and p-XIAP. Moreover, the knockdown of endogenous Akt or XIAP via RNA interference in pancreatic cancer cells, which are resistant to AZD5582, resulted in increased sensitivity to AZD5582, whereas ectopically expressing Akt or XIAP led to resistance to AZD5582. Additionally, AZD5582 targeted cIAP1 to induce TNF-α-induced apoptosis. More importantly, AZD5582 induced a decrease of Mcl-1 protein, a member of the Bcl-2 family, but not that of Bcl-2 and Bcl-xL. Interestingly, ectopically expressing XIAP and cIAP1 inhibited the AZD5582-induced decrease of Mcl-1 protein, which suggests that AZD5582 elicits Mcl-1 decrease for apoptosis induction by targeting of XIAP and cIAP1. Taken together, these results indicate that sensitivity to AZD5582 is determined by p-Akt-inducible XIAP phosphorylation and by targeting cIAP1. Furthermore, Mcl-1 in pancreatic cancer may act as a potent marker to analyze the therapeutic effects of AZD5582. Citation Format: Eun-Yeung Gong, Eun Young Lee, Jai-Hee Moon, Jae-Sik Shin, Seung-Woo Hong, Soo-A Jung, Ih-Yeon Hwang, Jeong Hee Kim, Dong-Hoon Jin, Tae Won Kim. A novel small-molecule IAP antagonist, AZD5582, draws Mcl-1 down-regulation for induction of apoptosis through targeting of cIAP1 and XIAP in human pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr A65.
Increased Marrow CD57+ Cytotoxic T Cells Is a Powerful Prognostic Marker for Survival in Patients with Relapsed Multiple Myeloma (MM) Receiving Thalidomide.
Authors: Linda R. Mileshkin, Peter Gambell, Victoria Beshay, Yoshihiro Hayakawa, Mark Smyth, Melanie Trivett, Paul J. Simmons, Alvin Milner, Jerome B. Zeldis, Miles Prince
Journal: Blood (2005)
Spatiotemporal AED Location Optimization
Authors: Timothy C.Y. Chan, Christopher L.F. Sun, Derya Demirtas, Laurie J. Morrison, Steven C. Brooks
Journal: Circulation (2015)

Background: Mathematical optimization can be used to plan future AED placement to maximize out-of-hospital cardiac arrest (OHCA) coverage. Many public access AEDs are placed in locations without 24/7 access. AED coverage can be overestimated unless temporal availability is considered.   
Objective: To develop a new spatiotemporal AED location optimization model that accounts for both spatial and temporal information.   
Methods: We identified all atraumatic public-location OHCAs occurring in Toronto, Canada from Jan. 2006 – Aug. 2014. We gathered location and operating hours data for 4898 buildings that were used as potential sites for AED placement. We extended a previously published spatial optimization model, which identifies locations to place AEDs that maximize the number of historical OHCAs occurring within 100 m of an AED. The new spatiotemporal model finds AED locations that maximize the number of OHCAs occurring within 100 m of an available AED, considering when the OHCAs occurred (“actual coverage”). We then compared the spatial and spatiotemporal models on actual coverage of out-of-sample OHCAs using 10-fold cross validation. Statistical analysis was performed using McNemar’s test.   
Results: We identified 2440 atraumatic public-location OHCAs. AED locations chosen by the spatiotemporal model outperformed those chosen by the spatial model by 26.1% in actual coverage (p<0.001). The figure shows coverage improvement at all times of day: daytime (11.2%), evening (37.4%), and night (292.3%). Equivalently, 40.2% fewer AEDs are needed when using the spatiotemporal model to reach the same level of actual coverage provided by AEDs located according to the spatial model.   
Conclusion: Spatiotemporal optimization can maximize actual OHCA coverage by accounting for AED availability when identifying future AED locations. The largest gains occurred during the evening and night, which is when the largest coverage losses were experienced by Toronto’s existing AEDs.
High-Dose Methotrexate and Early Intensification of Therapy Do Not Improve 3 Year EFS in Children and Adolescents with Disseminated Lymphoblastic Lymphoma. Results of the Randomized Arms of COG A5971
Authors: Minnie Abromowitch, Amanda Termuhlen, Myron Chang, Sherrie L. Perkins, Thomas Gross, Howard J. Weinstein, Jonathan Finlay
Journal: Blood (2008)
Co-Expression of a Suicide Gene in CAR-Redirected T Cells Enables the Safe Targeting of CD44v6 for Leukemia and Myeloma Eradication
Authors: Monica Casucci, Benedetta Nicolis di Robilant, Laura Falcone, Barbara Camisa, Pietro Genovese, Bernhard Gentner, Luigi Naldini, Barbara Savoldo, Fabio Ciceri, Claudio Bordignon, Gianpietro Dotti, Chiara Bonini, Attilio Bondanza
Journal: Blood (2012)
Clofarabine Plus Anthracycline Combinations in Acute Myeloid Leukemia (AML) Salvage.
Authors: Stefan Faderl, Alessandra Ferrajoli, Farhad Ravandi-Kashani, Srdan Verstovsek, William G. Wierda, Gautam Borthakur, Deborah Thomas, Jorge Cortes, Steven M. Kornblau, Zeev Estrov, Michael Andreeff, Miloslav Beran, Francis Giles, Xuelin Huang, Monica Kwari, Hagop M. Kantarjian
Journal: Blood (2006)
Addition of cladribine to the standard induction treatment improves outcomes in a subset of elderly acute myeloid leukemia patients. Results of a randomized Polish Adult Leukemia Group (PALG) phase II trial
Authors: Agnieszka Pluta, Tadeusz Robak, Agata Wrzesien‐Kus, Bozena Katarzyna Budziszewska, Kazimierz Sulek, Ewa Wawrzyniak, Magdalena Czemerska, Malgorzata Zwolinska, Aleksandra Golos, Aleksandra Holowiecka‐Goral, Slawomira Kyrcz‐Krzemien, Jaroslaw Piszcz, Janusz Kloczko, Monika Mordak‐Domagala, Andrzej Lange, Małgorzata Razny, Krzysztof Madry, Wieslaw Wiktor‐Jedrzejczak, Sebastian Grosicki, Aleksandra Butrym, Kazimierz Kuliczkowski, Krzysztof Warzocha, Jerzy Holowiecki, Sebastian Giebel, Richard Szydlo, Agnieszka Wierzbowska
Journal: American Journal of Hematology (2017)

Abstract Intensive induction chemotherapy using anthracycline and cytarabine backbone is considered the most effective upfront therapy in physically fit older patients with acute myeloid leukemia (AML). However, outcomes of the standard induction in elderly AML are inferior to those observed in younger patients, and they are still unsatisfactory. As addition of cladribine to the standard induction therapy is known to improve outcome in younger AML patients. The present randomized phase II study compares efficacy and toxicity of the DAC (daunorubicin plus cytarabine plus cladribine) regimen with the standard DA (daunorubicin plus cytarabine) regimen in the newly diagnosed AML patients over 60 years of age. A total of 171 patients were enrolled in the study (DA, 86; DAC, 85). A trend toward higher complete remission (CR) was observed in the DAC arm compared to the DA arm (44% vs. 34%; P = .19), which did not lead to improved median overall survival, which in the case of the DAC group was 8.6 months compared to in 9.1 months in the DA group ( P = .64). However, DAC appeared to be superior in the group of patients aged 60‐65 (CR rate: DAC 51% vs. DA 29%; P = .02). What is more, a subgroup of patients, with good and intermediate karyotypes, benefited from addition of cladribine also in terms of overall survival ( P = .02). No differences in hematological and nonhematological toxicity between the DA and DAC regimens were observed.
Opioid system in L-DOPA-induced dyskinesia
Authors: Jing Pan, Huaibin Cai
Journal: Translational Neurodegeneration (2017)

L-3, 4-Dihydroxyphenylalanine (L-DOPA)-induced dyskinesia (LID) is a major clinical complication in the treatment of Parkinson's disease (PD). This debilitating side effect likely reflects aberrant compensatory responses for a combination of dopaminergic neuron denervation and repeated L-DOPA administration. Abnormal endogenous opioid signal transduction pathways in basal ganglia have been well documented in LID. Opioid receptors have been targeted to alleviate the dyskinesia. However, the exact role of this altered opioid activity is remains under active investigation. In the present review, we discuss the current understanding of opioid signal transduction in the basal ganglia and how the malfunction of opioid signaling contributes to the pathophysiology of LID. Further study of the opioid system in LID may lead to new therapeutic targets and improved treatment of PD patients.
Pathogen control at the intestinal mucosa – H<sub>2</sub>O<sub>2</sub>to the rescue
Authors: Ulla G. Knaus, Rosanne Hertzberger, Gratiela G. Pircalabioru, S. Parsa M. Yousefi, Filipe Branco dos Santos
Journal: Gut Microbes (2017)

Intestinal infections are a global challenge, connected to malnutrition and inadequate hygiene in developing countries, and to expanding antibiotic resistance in developed countries. In general, a healthy host is capable of fighting off gut pathogens or at least to recover from infections quickly. The underlying protective mechanism, termed colonization resistance, is provided by indigenous commensal communities (microbiota) that are shaped and aided by the host's epithelial and innate immune system. Commensal-pathogen interactions are governed by competition for a suitable niche for replication and stable colonization, nutrient availability, species-specific alterations of the metabolic environment, changes in oxygen tension and release of chemicals and proteinaceous toxins (bacteriocins). This protective intestinal milieu is further reinforced by antimicrobial factors and chemicals secreted by the epithelial barrier, by dendritic cell sensing and by homeostasis between T-cell subsets (Treg/Th17) in the lamina propria. The 3 players (host-microbiota-pathogen) communicate via direct interactions or secreted factors. Our recent manuscript illustrates that reactive oxygen species (ROS) are an integral part of colonization resistance and should be considered an interkingdom antivirulence strategy.
Conventional and Pretargeted Radioimmunotherapy with Bismuth-213 to Target and Treat CD20-Expressing Non-Hodgkin Lymphoma: A Preclinical Model for Consolidation Therapy to Eradicate Minimal Residual Disease.
Authors: Steven I. Park, Jaideep Shenoi, John M. Pagel, Donald K. Hamlin, Nural Orgun, Aimee L. Kenoyer, Shani M. Wilbur, Amanda Axtman, D. Scott Wilbur, Yukang Lin, Darrell R. Fisher, Ajay K. Gopal, Damian J. Green, Oliver W. Press
Journal: Blood (2009)