tbuckley/cabot-search huggingface dataset:
High-throughput glycomics for discovery of cancer biomarkers.
Authors: Taku Nakahara, Diane McCarthy, Yoshiaki Miura, Hidehisa Asada
Journal: Journal of Clinical Oncology (2012)

9 Background: While the importance of glycosylation in many cancers is well established, the use of glycomics in biomarker research has lagged behind genomics and proteomics. This is due, in part, to the lack of practical platforms capable of analyzing clinically relevant sample numbers. To address these challenges, we have developed a novel glycomics technology (the GlycanMap platform) that combines a high-throughput assay with custom bioinformatics and rapidly provides both biomarker candidates and information on the underlying biology. Methods: N-glycans were enzymatically released from their parent glycoproteins and captured on chemoselective beads. After washing to remove non-glycan components, purified glycans were derivatized to stabilize labile sialic acids and released from the beads. The steps described above were automated on a 96-well format robotics system to maximize throughput and reduce variability and can be performed in less than 24 hours. Released glycans were analyzed by MALDI-TOF MS using internal standards to facilitate quantitation. In addition to comparing individual glycans between groups, glycan changes were also analyzed with respect to known glycan biosynthetic pathways. Results: The automated assay was compatible with multiple biological sample types, including serum/plasma, tissue, and cell lysates. Human serum was used to assess assay performance and yielded 50-60 glycans with CVs of 10-15% and good linearity. The lower limit of detection was approximately 100 nM. The assay was applied to drug-treated colon cancer cells (HCT116) and revealed significant (&gt; 2-fold) changes in 17 glycans. Projection of these glycan changes on the known N-glycan pathway showed that the most significant changes occurred in the medial-Golgi. Conclusions: We have developed and optimized a high-throughput glycomics platform to facilitate large-scale biomarker studies and assured its practical performance in terms of sensitivity, repeatability, and linearity. Application of this assay to drug-treated colon cancer cells demonstrated that projection of individual glycan changes against known glycan pathways provided additional information about biological mechanism and relevance.
Radiofrequency ablation of hepatocellular carcinoma as bridge therapy to liver transplantation: A 10‐year intention‐to‐treat analysis
Authors: Min Woo Lee, Steven S. Raman, Nazanin H. Asvadi, Surachate Siripongsakun, Robert M. Hicks, Jeffrey Chen, Akeanong Worakitsitisatorn, Justin McWilliams, Myron J. Tong, Richard S. Finn, Vatche G. Agopian, Ronald W. Busuttil, David S.K. Lu
Journal: Hepatology (2017)

In a long-term (10-year) study of radiofrequency ablation (RFA) of hepatocellular carcinoma (HCC) as bridging therapy in patients listed for orthotopic liver transplantation (LT), we evaluated the impact of RFA on waiting list dropout rate, post-LT tumor recurrence, and long-term intention-to-treat, disease-specific survival (DSS). From March 2004 to October 2014, RFA was performed as the initial stand-alone bridge therapy to LT for 121 patients (men/women ratio, 83:38; mean age, 60.0 years) with 156 de novo HCCs (mean size, 2.4 cm). Follow-up period from initial RFA ranged from 1.3 to 128.0 months (median, 42.9 months). We assessed the overall and tumor-specific waiting list dropout rates, post-LT tumor recurrence, and 10-year post-LT and intention-to-treat survival rates. Dropout from the waiting list due to tumor progression occurred in 7.4% of patients. HCC recurrence after LT occurred in 5.6% of patients. The post-LT overall survival (OS) rate at 5 and 10 years was 75.8% and 42.2%, respectively, and the recurrence-free survival (RFS) rate was 71.1% and 39.6%, respectively. Intention-to-treat OS, RFS, and DSS rates for the entire study population at 5 and 10 years were 63.5% and 41.2%, 60.8% and 37.7%, and 89.5% and 89.5%, respectively.RFA as a first-line stand-alone bridge therapy to LT achieves excellent long-term overall and tumor-specific survivals, with a low dropout rate from tumor progression despite long wait list times and a sustained low tumor recurrence rate upon post-LT follow-up of up to 10 years. (Hepatology 2017;65:1979-1990).
Potent B-Cell Depletion by IMGN529, a CD37-Targeting Antibody-Maytansinoid Conjugate for the Treatment of B-Cell Malignancies,
Authors: Jutta Deckert, Sharon Chicklas, Yong Yi, Min Li, Jan Pinkas, Thomas Chittenden, Robert J. Lutz, Peter U. Park
Journal: Blood (2011)
H3K27me3 Level of the HIST1 Cluster Defines an Epigenetic Marker of Acute Myeloid Leukemia with Prognostic Value
Authors: Guillaume Tiberi, Aleksandra Pekowska, Claire Oudin, Adam Ivey, Thomas Prebet, Myriam Koubi, Frederique Lembo, Marie-Joelle Mozziconacci, Ghislain Bidaut, Aurelie Autret, Christian Chabannon, David Grimwade, Norbert Vey, Salvatore Spicuglia, Boris Calmels, Estelle Duprez
Journal: Blood (2014)
No association between static and dynamic postural control and ACL injury risk among female elite handball and football players: a prospective study of 838 players
Authors: Kathrin Steffen, Agnethe Nilstad, Tron Krosshaug, Kati Pasanen, Aleksander Killingmo, Roald Bahr
Journal: British Journal of Sports Medicine (2017)

Background Research on balance measures as potential risk factors for ACL injury is limited. Objective To assess whether postural control was associated with an increased risk for ACL injuries in female elite handball and football players. Method Premier league players were tested in the preseason and followed prospectively for ACL injury risk from 2007 through 2015. At baseline, we recorded player demographics, playing experience, ACL and ankle injury history. We measured centre of pressure velocity in single-leg stabilisation tests and reach distances in the Star Excursion Balance Test. To examine the stability of postural control measures over time, we examined their short-term and long-term reproducibility. We generated logistic regression models, 1 for each of the proposed risk factors. Results A total of 55 (6.6%) out of 838 players (age 21±4 years; height 170±6 cm; body mass 66±8 kg) sustained a non-contact ACL injury after baseline testing (1.8±1.8 years). When comparing normalised balance measures between injured and uninjured players in univariate analyses, none of the variables were statistically associated with ACL injury risk. Short-term and long-term reproducibility of the selected variables was poor. Players with a previous ACL injury had a 3-fold higher risk of sustaining a new ACL injury compared with previously uninjured players (OR 2.9, CI 1.4 to 5.7). Conclusions None of postural control measures examined were associated with increased ACL injury risk among female elite handball and football players. Hence, as measured in the current investigation, the variables included cannot be used to predict ACL injury risk.
A C3(H20) recycling pathway is a component of the intracellular complement system
Authors: Michelle Elvington, M. Kathryn Liszewski, Paula Bertram, Hrishikesh S. Kulkarni, John P. Atkinson
Journal: Journal of Clinical Investigation (2017)

An intracellular complement system (ICS) has recently been described in immune and nonimmune human cells. This system can be activated in a convertase-independent manner from intracellular stores of the complement component C3. The source of these stores has not been rigorously investigated. In the present study, Western blotting identified a band corresponding to C3 in freshly isolated human peripheral blood cells that was absent in corresponding cell lines. One difference between native cells and cell lines was the time absent from a fluid-phase complement source; therefore, we hypothesized that loading C3 from plasma was a route of establishing intracellular C3 stores. We found that many types of human cells specifically internalized C3(H2O), the hydrolytic product of C3, and not native C3, from the extracellular milieu. Uptake was rapid, saturable, and sensitive to competition with unlabeled C3(H2O), indicating a specific mechanism of loading. Under steady-state conditions, approximately 80% of incorporated C3(H2O) was returned to the extracellular space. These studies identify an ICS recycling pathway for C3(H2O). The loaded C3(H2O) represents a source of C3a, and its uptake altered the cytokine profile of activated CD4+ T cells. Importantly, these results indicate that the impact of soluble plasma factors should be considered when performing in vitro studies assessing cellular immune function.
RARE-48. PAPILLARY TUMOR OF THE PINEAL REGION IN PEDIATRIC POPULATION ASSOCIATED WITH TRISOMY 21: FIRST CASE REPORT AND LITERATURE REVIEW
Authors: Mansour Mathkour, Juanita Garces, Joshua Hanna, Ian Cormier, Olawale A.R. Sulaiman, Cuong J. Bui
Journal: Neuro-Oncology (2016)

Papillary tumors of the pineal region (PTPRs) are rare tumors arising from the subcomissural organ (SCO), only recently codified in 2007 by the WHO. PTPRs most commonly occur in the third decade, with exceedingly rare presentation in pediatric populations. We present the fourth youngest case of a PTPR and the first pediatric case presentation associated with trisomy 21. A 10-year-old female with trisomy 21 presented with behavioral alterations, progressive disequilibrium, difficulty executing simple tasks and ‘staring spells’ of one month’s duration. MRI revealed a heterogeneously enhancing cystic mass occupying the posterior portion of the third ventricle with extension into the midbrain and associated hydrocephalus. Ventriculostomy was performed with biopsy and concurrent CSF sampling that demonstrated findings consistent with PTPR. The patient proceeded to right occipital craniotomy for gross total resection. Postoperative MRI revealed findings consistent with possible residual tumor. She is currently one month post-surgery with complete resolution of her symptoms, and active follow-up at our clinic. Diagnosis and management of PTPRs is rapidly accruing data in the literature, given the recent characterization of this tumor entity. However, relatively little is known about the presentation of PTPRs in pediatric populations. PTPRs have been linked with a number of chromosomal and genetics abnormalities, which is pertinent in our patient’s case. Due to age and the developmental changes of the CNS in children, the application of adult treatment protocols may not be possible; however the principle of complete surgical resection is standardized across age groups.
Bendamustine for Relapsed/Refractory Classical Hodgkin Lymphoma After High Dose Chemotherapy and or Allogeneic Transplant: A Study of Fondazione Italiana Linfomi (FIL)
Authors: Antonella Anastasia, Carmelo Carlo-Stella, Paolo Corradini, Flavia Salvi, Chiara Rusconi, Alessandro Pulsoni, Stefan Hohaus, Patrizia Pregno, Simonetta Viviani, Ercole Brusamolino, Stefano Luminari, Laura Giordano, Armando Santoro
Journal: Blood (2012)
Reducing unnecessary testing on admission in autologous stem cell transplant (SCT) patients.
Authors: Brett Glotzbecker, Deborah Yolin-Raley, Sara Close, Robert Soiffer, Joseph H. Antin, Joseph O. Jacobson, Edwin Alyea
Journal: Journal of Clinical Oncology (2012)

185 Background: Health care institutions are identifying strategies to reduce unnecessary testing, employ better utilization of resources, and decrease risk. At Dana-Farber Cancer Institute (DFCI), patients admitted for autologous SCT have standard testing, including CXR, completed within 42 days of hospital admission. Despite previous work-up, routine CXR is often ordered on admission. We questioned if this repeat CXR was clinically necessary. A retrospective review from 2010 showed that 69 of 130 (53%) asymptomatic SCT patients had CXR obtained on the day of admission. Two patients had findings of possible atelectasis vs. infiltrate on admission CXR. No further work up or antibiotics were initiated. After count recovery, one of the two patients had a chest CT for evaluation of fevers, showing only atelectasis. Based on these results, we aimed to reduce admission CXR without clinical indication to less than 5% by July 1, 2012. Methods: A multidisciplinary group was formed to map existing processes leading to admission CXR. Areas where previous standard testing were not readily available and areas of redundancy were identified. Changes to the EMR allowing easier access to pre-transplant results were made and a written and oral education program for PAs and nocturnists was created. Study Population: All elective patients admitted to the bone marrow transplant PA service (BMT-PA) for autologous SCT for multiple myeloma or lymphoma between 11/1/11-5/30/12. Results: The intervention (changing the EMR and establishing an education program) resulted in a reduction of admission CXR in asymptomatic patients from 53.3% to 5.5% (target 5.0%). During the study period, 144 patients were admitted to the BMT-PA service. Of those, 8 had CXR without indication. All CXR were ordered by Nocturnists, two prior to the intervention and six in the last four weeks of the observation period. Conclusions: The reduction of unnecessary CXR in asymptomatic SCT patients has had a considerable reduction in overall costs, nearly $58,000 to date, as well as reduced delays in initiating chemotherapy, radiation exposure, overall resource utilization, and patient inconvenience. Through this simple intervention, this reduction was easily obtained.
Ultrastructural characterization of hyperactive endothelial cells, pericytes and fibroblasts in hypertrophic and nodular port-wine stain lesions
Authors: L. Gao, R. Yin, H. Wang, W. Guo, W. Song, J.S. Nelson, W. Tan, G. Wang
Journal: British Journal of Dermatology (2017)

Port wine stain (PWS) is a congenital vascular malformation of human skin involving the superficial vascular plexus,1-4 but the molecular pathogenesis of these lesions remains incompletely understood.5-8 We herein performed a transmission electron microscopy (TEM) study to determine the main pathological characteristics and ultrastructure of various cell types, including endothelial cells (ECs), pericytes, fibroblasts and keratinocytes, in hypertrophic and nodular PWS. The study was approved by the Investigational Review Board at the Xijing Hospital, Xi'an, China.

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Results of a 10-year retrospective search in two university institutes of pathology: Concordance of HER-2/neu expression of primary breast carcinomas and their metachronous distant metastases
Authors: D. Luftner, H. Dilk, P. Henschke, R. Geppert, M. Dietel, H. Stein, K. Wernecke, K. Possinger, B. Heine
Journal: Journal of Clinical Oncology (2004)

670 Background: The dogma of clonality between primary solid tumors and their later distant metastases is more and more weakened by the evidence of clonal changes in the course of the diseases. The diagnosis of HER-2/neu positivity for selection of stage IV breast cancer patients for trastuzumab therapy is done on the primary tumor. Changes of HER-2/neu expression may lead to a wrong selection of patients for a life-prolonging therapy. Methods: The archives of 2 university institutes of pathology were searched for pairs of tissue blocks of primary breast carcinomas and their metachronous metastases. 80 pairs dating from 1994–2003 were identified and stained for HER-2/neu expression using the method and scoring system of the DAKO HercepTest. Results: Characteristics of the primary breast cancers were as follows: 73% invasive ductal, T1/T2 tumors 45% and 37%, N1/N2 stage 48% and 42%. Biopsies were distributed as follows: Viscera 9%, bone 10%, soft tissue 78%, rest others. A total of 47.7% of the primary lesions were HER-2/neu positive (DAKO +2/+3) while 59.0% of the distant metastases showed +2/+3 expression. The concordance between the HER-2/neu expression of the primary tumors and their distant metastases was moderate with a concordance index kappa of 0.52 (0 = weak concordance, 1.0= strong concordance). The McNemar test for changes from HER-2/neu negative primaries to HER-2/neu positive metastases (17.9%) as compared to reverse changes from HER-2/neu positive primaries to HER-2/neu negative metastases (6.4%) showed a p-value of p=0.063 in favour of preferential changes from negative primaries to positive metastases, just missing statistical significance. Conclusions: Clonal changes between primary breast carcinomas and their distant metastases are more frequent than generally assumed, but do not question the current practice. A simple option to reassure the current HER-2/neu status would be serum testing for HER-2/neu with a level > 50 ng/ml (normal < 15 ng/ml) indicating HER-2/neu positive metastatic spread. No significant financial relationships to disclose.
Effectiveness of Targeted Food Elimination Diet in Management of Pediatric Eosinophilic Esophagitis (EoE): A Retrospective Review.
Authors: Shalini Thiru, Stephanie L. Vakaljan, Mary E. Sherlock, Mary Zachos, Elyanne Ratcliffe, Robert Issenman, Nikhil Pai, Jason A. Ohayon
Journal: Journal of Allergy and Clinical Immunology (2017)
Rituximab, Endoxan, Ganciclovir, Dexamethasone, Tocilizumab Sequential Treatment In Kaposi's Sarcoma-Associated Herpesvirus (KSHV) -Related Multicentric Castleman Disease. A Case Report with 8 Months Follow-up
Authors: Francesco Iuliano, Tecla Mingrone, Stefania Infusino, Alessia Perricelli, Angelo Pomillo, Maria Luci, Massimo Di Maio
Journal: Blood (2010)
Long-Term Outcomes from a Pediatric Subgroup of Tenor I: 10 Years Follow up
Authors: Benjamin Ortiz, Bradley E. Chipps, Robert S. Zeiger, Tmirah Haselkorn, Aimee Foreman, Farid Kianifard, Brandee Paknis, Stanley J. Szefler
Journal: Journal of Allergy and Clinical Immunology (2017)
Analysis of clinical factors in relationship to treatmenteffects of erlotinib in non small cell lung cancer (NSCLC)patiients
Authors: Jana Skřičková, Marcela Tomíšková, Irena Vašutová, Bohdan Kadlec, Jana Kaplanová, Lenka Babičková, Pavel Turčáni, Tomáš Nebeský, Leoš Křen, Lucie Burešová
Journal: European Respiratory Journal (2008)

Analysis of clinical factors in relationship to treatment
effects of erlotinib in non small cell lung cancer (NSCLC)
patiients An analysis is presented of clinical factors in
relationship to the treatment with erlotinib in non-small cell
lung cancer.
Treatment of Relapse After Allogeneic Hematopoietic Stem-Cell Transplantation for Myelodysplastic Syndrome: A Large-Scale Study On Behalf of the Société Française De Greffe De Moelle Et De Thérapie Cellulaire (SFGM-TC)
Authors: Romain Guièze, Gandhi Damaj, Marie Robin, Mohamad Mohty, Mauricette Michallet, Reza Tabrizi, Yves Beguin, Didier Blaise, Claude-Eric Bulabois, Faezeh Legrand, Anne Huynh, Jérôme Cornillon, Nathalie Contentin, Felipe Suarez, Bruno Lioure, Natacha Maillard, Laurence Clement, Gaelle Guillerm, Marie T Rubio, Federico Garnier, Ibrahim Yakoub-Agha
Journal: Blood (2012)
Lenalidomide Maintenance after Front Line Therapy Substantially Prolongs Progression Free Survival in High Risk CLL: Interim Results of a Phase 3 Study (CLL M1 study of the German CLL Study Group)
Authors: Anna Maria Fink, Jasmin Bahlo, Robrecht Sandra, Othman Al-Sawaf, Ali Aldaoud, Holger Hebart, Kathleen Jentsch-Ulrich, Steffen Doerfel, Kirsten Fischer, Clemens Martin Wendtner, Thomas Noesslinger, Paolo Ghia, Francesc Bosch, Arnon P. Kater, Karl-Anton Kreuzer, Hartmut Dohner, Michael Kneba, Stephan Stilgenbauer, Sebastian Boettcher, Barbara Eichhorst, Michael Hallek
Journal: Blood (2016)
The Nature of the P Value
Authors: Stuart J Pocock, Gregg W Stone
Journal: New England Journal of Medicine (2016)

identify potential new collaborators. 2 Nevertheless, under the terms of approval of our retrospective study by the institutional review board, we are not permitted to release patient-level data.Our retrospective study includes not only patients in different clinical trials but also patients who received "standard of care" treatment that was not determined by a specific clinical protocol.Different consents apply to the different populations included in the analysis; therefore, in order to perform our retrospective study, we applied for and received specific approval from the institutional review board under internal protocol 2281 of the Fred Hutchinson Cancer Research Center.Furthermore, Hourigan and colleagues request disclosure of patient-level data pertaining to a large number of individual patient-related factors, some of which were not collected at the time of the chart review or included in the analysis.Although we agree that some of these factors might be worth examining, to collect, analyze, and release such information would require time and another institutional review board application.In response to the other questions by Hourigan et al., bone marrow biopsies with cytogenetic analysis were performed before transplantation in all the patients with myelodysplasia.In our system, we do not have a way of determining how many patients are considered for transplantation but do not undergo transplantation.The study by Walter et al. included transplants from both related and unrelated donors, and a total of 152 patients in that study were also involved in our study.With the goal of sharing data among various institutions in the future, we are willing to submit a new institutional review board application and collaborate with Hourigan and colleagues or others.
Comparisson of Molecular Mechanisms Altered by Treatment with Different Drugs (Doxorubicin, Melphalan, Bortezomib, Aplidin and Arsenic Trioxide) in Multiple Myeloma Patients Using Oligonucleotide Microarrays.
Authors: Patricia Maiso, Norma C. Gutierrez, Ricardo Lopez-Perez, Gema Mateo, Isabel M. Isidro, Encarna Ferminan, Xonia Carvajal-Vergara, Juan C. Montero, Jesus M. Hernandez, Atanasio Pandiella, Jesus F. San Miguel
Journal: Blood (2004)
HCT.CI in Autologous Stem Cell Transplantation. Predicting Early and Late Transplant Related Mortality
Authors: Mariano Berro, Maria M Rivas, Jorge Alberto Arbelbide, Ana Lisa Basquiera, Adriana Vitriu, Maria Cecilia Foncuberta, Alejandro Requejo, Nicolas Fernandez Escobar, Vera Milovic, Sebastian Yantorno, Juliana Martinez Rolon, Juan Garcia, Pablo Andres Garcia, Jose Trucco, Lucia Bet, Milagros Selagowsky, Gonzalo Bentolila, Gonzalo Ariel Ferini, Gastón Caeiro, Gustavo Daniel Kusminsky
Journal: Blood (2016)
An Anti-Apoptotic Molecule, Anamorsin, Functions in Both Iron-Sulfur Protein Assembly and Cellular Iron Homeostasis
Authors: Akira Tanimura, Yuri Kondo, Hirokazu Tanaka, Itaru Matsumura, Tomohiko Ishibashi, Takao Sudo, Yusuke Satoh, Takafumi Yokota, Sachiko Ezoe, Kenji Oritani, Hirohiko Shibayama, Yuzuru Kanakura
Journal: Blood (2011)
DRES-03. EXPRESSION OF DRUG RESISTANCE GENES ASSOCIATED WITH HYPOXIA IN HUMAN GLIOMA
Authors: Tatsuya Abe, Yukiko Nakahara, Motofumi Kouguchi, Hiroshi Ito, Tomihiro Wakamiya, Ikuko Morisaki, Yasutomo Momii, Hirotaka Fudaba, Minoru Fujiki
Journal: Neuro-Oncology (2016)

The brain tumor cells can survive regardless of hypoxia and undernutrition. Hypoxia is known to be causes of resistance to radio-chemotherapy, increased recurrence and poor prognosis. Recent reports demonstrated that cancer stem cells (CSCs) exist in hypoxic lesion of the tumor. In this study, we examined the mechanism of drug resistance under hypoxic condition. Most of brain tumor patients are treated by temozolomide (TMZ) as chemotherapy. The efficiency and resistance of TMZ are associated with the O6-methylguanine-DNA methyltransferase (MGMT) gene. In addition, MGMT expression is induced by hypoxia, and regulated by N-myc downstream regulated gene 1 (NDRG1). We investigated the expression of these genes in glioma cell lines (GCs), CSCs, and clinical specimens detected by molecular hypoxia imaging (PET). The expression of MGMT and NDGR1 was induced by hypoxia in GCs. Hypoxic clinical specimens also showed the increased expression of these genes. Thus, it is suggested that the improvement of hypoxia could lead to overcome the resistance of treatments.