tbuckley/cabot-search huggingface dataset:
The Landscape of Viral Expression Reveals Clinically Relevant Viruses with Potential Capability of Promoting Malignancy in Lower-Grade Glioma
Authors: Zheng Wang, Yajing Hao, Chuanbao Zhang, Zhiliang Wang, Xing Liu, Guanzhang Li, Lihua Sun, Jingshan Liang, Jianjun Luo, Dabiao Zhou, Runsheng Chen, Tao Jiang
Journal: Clinical Cancer Research (2016)

Purpose: RNA sequencing (RNA-seq) has recently proved to be effective for revealing novel virus-tumor associations. To get a thorough investigation of virus-glioma associations, we screened viruses in gliomas with RNA-seq data from the Chinese Glioma Genome Atlas project.Experimental Design: In total, 325 samples were enrolled into this study. Reads that failed to map to the human genome were aligned to viral genomes and screened for potential virus-derived transcripts. For quantification, VPKM was calculated according to mapped reads weighted by genome sizes and sequencing depth.Results: We observed that viruses tended to concertedly express in a certain subgroup of patients. Survival analysis revealed that individuals who were infected with Simian virus 40 (SV40) or woolly monkey sarcoma virus (WMSV) had a significantly shorter overall survival than those uninfected. A multivariate Cox proportional hazards model, taking clinical and molecular factors into account, was applied to assess the prognostic value of SV40 and WMSV. Both SV40 and WMSV were independent prognostic factors for predicting patient's survival in lower-grade gliomas. Subsequent gene analysis demonstrated that SV40 was correlated with regulation of transcription, whereas WMSV was correlated with cell-cycle phase, which indicated frequent proliferation of tumor cells.Conclusions: RNA-seq was sufficient to identify virus infection in glioma samples. SV40 and WMSV were identified to be prognostic markers for patients with lower-grade gliomas and showed potential values for targeting therapy. Clin Cancer Res; 23(9); 2177-85. ©2016 AACR.
Immune Mobilization of Autologous Peripheral Blood Progenitor Cells: IL-2 with GM-CSF and G-CSF Results in Effective Mobilization without Delay in Engraftment.
Authors: John M. Hill, Jia-Yan Wu, Susan M. Webber, Ortal Sharlin, Melinda Kendall, David McGregor, Marc J. Ernstoff, Zbigniew M. Szczepiorkowski, Kenneth R. Meehan
Journal: Blood (2006)
FRI0102 Characteristics of Functional Impairment in Patients with Long-Standing Rheumatoid Arthritis Based on Range of Motion of Joints: Multicenter Prospective Cohort Study for Evaluation of Joint Surgery on Physical Function
Authors: T. Kojima, H. Ishikawa, K. Nishida, S. Tanaka, N. Haga, M. Yukioka, H. Miyahara, J. Hashimoto, T. KImura, H. Oda, Y. Niki, M. Liu, M. Kojima, N. Ishiguro
Journal: Annals of the Rheumatic Diseases (2016)

<h3>Background</h3> Even now, in clinical practice, most of RA patients have long-standing disease and structural damage in their joints. Reconstructive joint surgery should be needed for further improvements of physical function for long-standing RA patients. It is very important to understand how much range of motion (ROM) should be needed to gain better physical function in each case. <h3>Objectives</h3> The purpose of this study is to explore the characteristics of functional impairment in RA patients who were needed joint surgery based on ROM of joints using multicenter prospective cohort. <h3>Methods</h3> We conducted this prospective study from 2012 to2015 (Study registration: UMIN000012649) We collected data on age, sex, disease duration, drug therapies, disease activity, and physical functional including HAQ-DI. Joint range of motion including shoulder, elbow, wrist, hip knee ankle was also measured. ROM in each joint by disability in HAQ-DI categories was compared by ANOVA with adjustment of age and sex. Association between ROM of each joint and no disability of daily activity in each 8 HAQ-DI categories was determined using ROC curve and logistic regression analysis. <h3>Results</h3> 460 patients who have data of ROM of any joints in registry were analyzed. Mean values for age, disease duration, DAS28-CRP and sex were 64.6 years, 16.9 years, 3.17, and 86.3% female, respectively. Median values for CRP was 0.2 mg/dl. We could find significant association between ROM and disability in HAQ-DI category based on area under the ROC curve. ROM of each joints had different impact on disability of each category (ie, ROC curve for category Arising, Fig. 1). The cut-off values of ROM of each joints for daily activity in each HAQ-DI category was shown in Table 1 using ROC curves (Table 1). Multivariate analysis adjusting disease activity, age, and sex, showed which joint had significant impact on disability of each category (Table 2). <h3>Conclusions</h3> ROMs of the joints were significantly associated with functional impairment. The information should be important for assessment of disability in patients with long-standing RA. The cut-off of ROM as shown in this study could be target of surgical procedure. It will be validated by further analysis of longitudinal data of this study. <h3>Acknowledgement</h3> This study was supported by grant from the Japanese Ministry of Health, Labour and Welfare. <h3>Disclosure of Interest</h3> None declared
PTU-108 Sustainibility of The Impact of Nutrition Support Team (NST) at a District General Hospital-5 Year Results: Abstract PTU-108 Table 1
Authors: K Eaton, E Copeland, H Roberts, M Patel, L Perry, S Gupta, A Tarn
Journal: Gut (2016)

<h3>Introduction</h3> Although in 2010 Croydon University Hospital had Parenteral Nutrition (PN) team,it was felt patient care could be improved by broadening the team’s scope and extending its influence. Audit showed that despite Trust policy on PN use, it was non-compliant with NCEPOD recommendations. This was a key driver to form a Nutrition Support Team (NST) in October 2010. Our aims were to reduce inappropriate use of PN and emergency PN, ensure administration through central venous catheters and encourage EN where appropriate. This analysis was to check for sustainability of impact of NST after 5 years. <h3>Methods</h3> In 2010 NST members included a Chemical Pathologist, Gastroenterologist, Dietitian and Pharmacist. In 2012, a Consultant Biochemist, Dietitian joined the team. Protocols were drawn up, ratified and made available on a NST link on Trust Intranet. Patients requiring PN had to be discussed with NST. Radiology Department was contacted for timely insertion of peripheral inserted central venous catheters (PICC). Medical and nursing staff were trained on care of lines and appropriate use of PN. <h3>Results</h3> Results are shown in the Table. Use of peripheral cannulae for PN has gone down from 31% in 2009/10 to 4% in 2010/11 to 0% since 2011/12.Cost savings have been made in a number of areas. In 2010/11, savings of £20,671 were made. In 2013,NST advised and implemented a change in supplier of PN bags, resulting in total cost savings of £19,822. The total number of referrals for PN, number of inappropriate referrals, use of emergency PN, number of patients requiring PN for &lt;5 days has fallen while total number of days of PN and the mean have increased perhaps indicating more appropriate use of PN. <h3>Conclusion</h3> Our intervention resulted in safer,coordinated and appropriate delivery of PN which has been sustained over 5 years. The feedback from hospital management,clinical staff has been positive and encouraging. These results may be extrapolated to all hospitals that care for patients requiring parenteral nutrition. <h3>Disclosure of Interest</h3> None Declared
Prospective, Multicenter Clinical Trial of Everolimus as Primary Therapy in Waldenstrom Macroglobulinemia (WMCTG 09-214)
Authors: Steven P. Treon, Kirsten Meid, Christina Tripsas, Leonard T. Heffner, Herbert Eradat, Ashraf Z. Badros, Lian Xu, Zachary R. Hunter, Guang Yang, Christopher J. Patterson, Joshua Gustine, Jorge J. Castillo, Jeffrey Matous, Irene M. Ghobrial
Journal: Clinical Cancer Research (2016)

Purpose: Everolimus inhibits mTOR, a component of PI3K/AKT prosurvival signaling triggered by MYD88 and CXCR4-activating mutations in Waldenstrom macroglobulinemia.Experimental design: We evaluated everolimus in a prospective, multicenter study of 33 symptomatic, previously untreated Waldenstrom macroglobulinemia patients. Intended therapy consisted of everolimus (10 mg/day) until progression or unacceptable toxicity. Dose deescalation was permitted. The study was registered at www.clinicaltrials.gov (NCT00976248).Results: At best response, median serum IgM levels declined from 4,440 to 1,360 mg/dL (P < 0.0001), median hemoglobin rose from 10.8 to 12 g/dL (P = 0.001), and median bone marrow disease burden declined from 75% to 52.5% in serially biopsied patients. The ORR and major response rates were 72.7% and 60.6%, respectively. Among genotyped patients, nonresponders associated with wild-type MYD88 and mutated CXCR4 status. Median time to response was 4 weeks. Discordance between serum IgM levels and bone marrow disease burden was remarkable. With a median follow-up of 13.1 (range, 1.6-64.6 months), the median time to progression was 21 months for all patients and 33 months for major responders. Discontinuation of everolimus led to rapid serum IgM rebound in 7 patients and symptomatic hyperviscosity in 2 patients. Toxicity led to treatment discontinuation in 27% of patients, including 18% for pneumonitis.Conclusions: Everolimus is active in previously untreated Waldenstrom macroglobulinemia. IgM discordance is common, and treatment cessation can often lead to rapid serum IgM rebound. Pneumonitis also appears more pronounced in untreated versus previously treated Waldenstrom macroglobulinemia patients. The risks and benefits of everolimus should be carefully weighed against other primary Waldenstrom macroglobulinemia therapy options. Clin Cancer Res; 23(10); 2400-4. ©2016 AACR.
OP0298 Anti-Citrullinated Protein Antibodies Promote Synovial Fibroblasts Migration and Adhesion through A Peptidylarginine Deiminases (PAD) Dependent Pathway
Authors: M. Sun, V. Joshua, A. Haj Hensvold, S.B. Catrina, C. Ospelt, V. Malmström, K. Amara, M. Engström, H. Wähämaa, B. Rethi, A.I. Catrina
Journal: Annals of the Rheumatic Diseases (2016)

<h3>Background</h3> Synovial fibroblasts (SFs) contribute to rheumatoid arthritis (RA) pathogenesis by growing into the synovial space and by producing pro-angiogenic and tissue remodelling factors, chemokines and inflammatory cytokines that recruit and stimulate various immune cells. We have recently demonstrated that anti-citrullinated proteins antibodies (ACPAs) promote osteoclast development. In the present work we investigated whether ACPAs can also modulate SFs. <h3>Methods</h3> SFs were isolated from synovial tissue of RA patients by enzymatic digestion. Polyclonal ACPA and others non-ACPA IgGs were separated from plasma of RA patients by affinity purification on cyclic citrullinated peptide (CCP)-2 column. Monoclonal ACPAs were generated from synovial B-cells. Antibodies were tested in scratch-assays for SF migration and the results were evaluated by NIH ImageJ software. SF adhesion was analyzed by xCELLigence System Real-Time Cell Analyzer (ACEA bioscience). ACPA-induced signalling pathways were examined using inhibitors of phosphoinositide 3-kinase (PI3K), phosphatase and tensin homolog (PTEN), G-protein coupled receptors, focal adhesion kinase (FAK) and peptidylarginine deiminases (PAD) in the migration assays. Protein phosphorylations were monitored by western blot. <h3>Results</h3> Polyclonal ACPAs but not others IgGs induced both SFs migration (a fold increase of 2.6±0.5, mean±SD, p&lt;0,05) and SFs adhesion (a fold increase of 1.3±0.1 at 6 hours, p&lt;0.05). Similar effects were observed with two (D10 and B02) out of three tested monoclonal ACPAs, with a fold increase of the migration index of 2.4±0.4 for D10 antibody and 2.2±0.4 for B02 antibody (p&lt;0.05 for both). IL-8, a chemokine that is upregulated in developing ostecolasts by ACPAs, synergistically increased the ACPA-induced SF migration. Inactivation of the PAD enzymes completely abolished the ACPA-induced SFs migration. GPCR and PI3K blocking completely abolished ACPAs effects, indicating an important role for GPCR and PI3K but not for FAK in the ACPA effects. <h3>Conclusions</h3> ACPAs promote SFs migration and adhesion acting synergistically with IL-8 through a PAD-dependent pathway. Our findings suggest that SFs may have a potential role in the ACPA-dependent disease propagation from the bone marrow to synovial tissue. <h3>Disclosure of Interest</h3> None declared
Impaired consciousness in patients with absence seizures investigated by functional MRI, EEG, and behavioural measures: a cross-sectional study
Authors: Jennifer N Guo, Robert Kim, Yu Chen, Michiro Negishi, Stephen Jhun, Sarah Weiss, Jun Hwan Ryu, Xiaoxiao Bai, Wendy Xiao, Erin Feeney, Jorge Rodriguez-Fernandez, Hetal Mistry, Vincenzo Crunelli, Michael J Crowley, Linda C Mayes, R Todd Constable, Hal Blumenfeld
Journal: The Lancet Neurology (2016)
Unrelated Donor KIR B/X Genotype Reduces Relapse and Improves Progression-Free Survival after HLA-Matched Allogeneic Transplantation for Relapsed/Refractory Non-Hodgkin Lymphoma
Authors: Veronika Bachanova, Daniel J. Weisdorf, Tao Wang, Steven G.E. Marsh, Elizabeth Trachtenberg, Michael D Haagenson, Stephen R. Spellman, Guethlein A. Lisbeth, Martha Ladner, Peter Parham, Jeffrey S. Miller, Sarah A. Cooley
Journal: Blood (2014)
Elucidating the interplay between IgG-Fc valency and FcγR activation for the design of immune complex inhibitors
Authors: Daniel F. Ortiz, Jonathan C. Lansing, Laura Rutitzky, Elma Kurtagic, Thomas Prod’homme, Amit Choudhury, Nathaniel Washburn, Naveen Bhatnagar, Christopher Beneduce, Kimberly Holte, Robert Prenovitz, Matthew Child, Jason Killough, Steven Tyler, Julia Brown, Stephanie Nguyen, Inessa Schwab, Maurice Hains, Robin Meccariello, Lynn Markowitz, Jing Wang, Radouane Zouaoui, Allison Simpson, Birgit Schultes, Ishan Capila, Leona Ling, Falk Nimmerjahn, Anthony M. Manning, Carlos J. Bosques
Journal: Science Translational Medicine (2016)

An engineered trivalent Fc drug candidate is a potent inhibitor of FcγR-driven immune cell activation and autoimmune diseases in animal models.
A Variant Form of Chronic Granulomatous Disease Caused by A Mutation in the Exon 9 of CYBB Gene Revealed by A Burkholderia Cepacia Invasive Infection.
Authors: Nizar Mahlaoui, Carolina Prando, Stephane Blanche, Alain Fischer, Jean-Laurent Casanova, Jacinta Bustamante
Journal: Blood (2009)
High prevalence of viral hepatitis in a series of splenic marginal zone lymphomas from Romania
Authors: B Fetica, B Pop, M L Blaga, A Fulop, D Dima, M T Zdrenghea, C I Vlad, A S Bojan, P Achimas-Cadariu, C I Lisencu, A Irimie, D D Weisenburger
Journal: Blood Cancer Journal (2016)

High prevalence of viral hepatitis in a series of splenic marginal zone lymphomas from Romania
Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep
Authors: Robert VanBuren, Ching Man Wai, Jisen Zhang, Jennifer Han, Jie Arro, Zhicong Lin, Zhenyang Liao, Qingyi Yu, Ming-Li Wang, Francis Zee, Richard C. Moore, Deborah Charlesworth, Ray Ming
Journal: Genome biology (2016)

The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity π syn = 0.00017, tenfold lower than the autosomal region (π syn = 0.0017) and 12-fold lower than the Y-linked region (π syn = 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes < X-linked genes < autosomal genes; papaya shows an unprecedented pattern of X-linked genes < autosomal genes < Y-linked genes.
Practical Experience of Thromboprophylaxis After Lower Limb Replacement – Rivaroxaban Versus Enoxaparin
Authors: Kyoung Ha Kim, Nam Seok Ham, Yang Ki Kim, Hyung Suk Choi, You Sung Suh, Young Woo Jeon, Han Jo Kim, Se Hyung Kim, Sang Byung Bae, Sung Kyu Park, Jong-Ho Won, Dae Sik Hong, Hee Sook Park
Journal: Blood (2012)
SP0109 How To Perform Clinical History and Physical Examination?
Authors: M. Doherty
Journal: Annals of the Rheumatic Diseases (2016)

The GALS (gait, arms, legs, spine) screen is useful to detect musculoskeletal (MSK) abnormality as part of a general assessment (1). However, for a person with MSK complaints a more detailed assessment is required to determine the diagnosis and impact on the patient. A thorough history alone usually suggests the single most likely cause for the patient9s problem(s). The examination that follows should be a targeted assessment in which the practitioner selects the required skills from a range of competencies according to specific elements in the history (i.e. not a uniform set of identical procedures in each patient). The overall assessment needs to be holistic and individualised as the enquiry proceeds, since the impact of any condition is person specific and influenced by many factors (e.g. psychosocial factors, illness perceptions, sleep, comorbidity etc.). This presentation will cover key principles and considerations related both to the history and examination (2). Examples include: (1) in the <i>history:</i> determination of pain localisation and features that associate with radiated pain; important pain and stiffness characteristics that differentiate mechanical usage-related pain, inflammatory pain, acute crystal synovitis pain, destructive bone pain and neurogenic pain; non-specific symptoms of inflammation (2) in the <i>examination:</i> usual order of inspection at rest, inspection during movement, then palpation at rest and during movement; contrasting clinical findings that differentiate joint and peri-articular problems; detection of "stress pain" (pain worse in tight-pack positions but reduced/absent in loose-pack positions - the most sensitive sign of inflammation); examination for effusion, soft-tissue and firm swelling; use of resisted active movements and stress tests for peri-articular lesions. With experience, following a thorough history and examination the combined aspects of the history and examination which differentiate between major categories of MSK conditions permit pattern recognition and a confident clinical diagnosis in the majority of cases. A simple way of assembling the clinical findings to enable them increasingly to point to a likely single diagnosis will be presented. EULAR learning resources available at http://www.eular.org/edu_training_dvd.cfminclude: (1) The "GALS" screen and (2) Principles of the musculoskeletal history and examination. <h3>Disclosure of Interest</h3> None declared
Adding formoterol to budesonide did not increase serious asthma events and reduced exacerbations
Authors: Matthew B. Stanbrook
Journal: Annals of Internal Medicine (2016)

ACP Journal Club15 November 2016Adding formoterol to budesonide did not increase serious asthma events and reduced exacerbationsMatthew B. Stanbrook, MD, PhDMatthew B. Stanbrook, MD, PhDToronto Western Hospital, University of Toronto, Toronto, Ontario, Canada (M.B.S.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/ACPJC-2016-165-10-056 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Source CitationPeters SP, Bleecker ER, Canonica GW, et al. Serious asthma events with budesonide plus formoterol vs. budesonide alone. N Engl J Med. 2016;375:850-60. https://pubmed.ncbi.nlm.nih.gov/27579635Clinical Impact RatingsAllerg & Immunol: Pulmonology: References1 Nelson HS, Weiss ST, Bleecker ER, et al; SMART Study Group. The Salmeterol Multicenter Asthma Research Trial: a comparison of usual pharmacotherapy for asthma or usual pharmacotherapy plus salmeterol. Chest. 2006;129:15-26. [PMID: 16424409] Google Scholar2 Castle W, Fuller R, Hall J, Palmer J. Serevent nationwide surveillance study: comparison of salmeterol with salbutamol in asthmatic patients who require regular bronchodilator treatment. BMJ. 1993;306:1034-7. [PMID: 8098238] Google Scholar3 Global Initiative for Asthma (GINA). 2016 GINA report: global strategy for asthma management and prevention. http://ginasthma.org/2016-gina-report-global-strategy-for-asthma-management-and-prevention/ (accessed 12 Oct 2016). Google Scholar4 Chowdhury BA, Seymour SM, Levenson MS. Assessing the safety of adding LABAs to inhaled corticosteroids for treating asthma. N Engl J Med. 2011;364:2473-5. [PMID: 21714647] Google Scholar5 Ducharme FM, Ni Chroinin M, Greenstone I, Lasserson TJ. Addition of long-acting beta2-agonists to inhaled steroids versus higher dose inhaled steroids in adults and children with persistent asthma. Cochrane Database Syst Rev. 2010;(4):CD005533. [PMID: 20393943] Google Scholar6 Wechsler ME, Kunselman SJ, Chinchilli VM, et al; National Heart, Lung and Blood Institute's Asthma Clinical Research Network. Effect of beta2-adrenergic receptor polymorphism on response to longacting beta2 agonist in asthma (LARGE trial): a genotype-stratified, randomised, placebo-controlled, crossover trial. Lancet. 2009;374:1754-64. [PMID: 19932356] Google Scholar Author, Article, and Disclosure InformationAffiliations: Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada (M.B.S.)This article was published at Annals.org on 1 November 2016. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 15 November 2016Volume 165, Issue 10Page: JC56KeywordsAdolescentsAsthmaChildrenEmergency departmentFood and Drug AdministrationHazard ratioHospitalizationsIntubationReproducibilitySafety ePublished: 15 November 2016 Issue Published: 15 November 2016 Copyright & PermissionsCopyright © 2016 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...