tbuckley/cabot-search huggingface dataset:
A Clinical Measure of DNA Methylation Predicts Outcome in De Novo AML
Authors: Marlise R. Luskin, Phyllis Gimotty, Catherine Smith, Alison Loren, Maria Figueroa, Jenna Harrison, Zhuoxin Sun, Martin S Tallman, Elisabeth Paietta, Mark R Litzow, Ross L. Levine, Hugo F. Fernandez, Selina Luger, Martin Carroll, Stephen Master, Gerald Wertheim
Journal: Blood (2015)
Vitamin D levels in 70% of patients attending for colonoscopy in the UK and the Netherlands are suboptimal but consumption of salmon does not provide any significant improvement
Authors: G. Majsak-Newman, G. K. Pot, E. Maxwell, A. Geelen, L. J. Harvey, F. M. Nagengast, B. J. Witteman, P. C. van de Meeberg, R. Timmer, A. C. I. T. Tan, P. J. Wahab, A. Hart, E. Kampman, M. P. Williams, E. K. Lund
Journal: Gut (2009)
PTU-161 Systematic Review and Meta-Analysis on Complications Following Oesophageal Dilatation for Benign Oesophageal Strictures- Preliminary Results
Authors: SV Venkatachalapathy, N Burr, V Subramanian, S Everett
Journal: Gut (2016)

<h3>Introduction</h3> The incidence of benign oesophageal strictures is 0.5% in patients with dyspeptic symptoms.<sup>1</sup> It affects the quality of life by causing dysphagia, regurgitation and in severe cases weight loss. The first line of management is balloon or bougie dilatation. There is ambiguity about the complication rates associated with this procedure. We therefore did a systematic review and metanalysis on complications (bleeding and perforation) associated with endoscopic dilatation. <h3>Methods</h3> We searched several electronic databases including Pubmed for full journal articles published after 1990 reporting on the use of endoscopic dilatation using bougies or balloons in the treatment of beingn oesophageal strictures. We hand searched the reference lists of all retrieved articles. Cohort or prospective studies involving 10 or more adult patients were included in the analysis. Studies on corrosive/caustic strictures and radiological non-endoscopy guided diltations were excluded. We calculated the pooled proportion of patients who had a complication (perforation or bleed) to therapy in the selected studies. Heterogeneity between the studies was assessed using the <i>I</i><sup>2</sup> statistic. <h3>Results</h3> Our search identified 32 studies that were included in the final analysis (26 cohort studies and 6 randomised control trials). There were 11 studies that reported on balloon, 8 on bougie and 13 studies reported on both balloon and bougie dilatations. There were 18104 patients, 7195 balloon dilations and 15,936 bougie dilations. There were 7711 (42.5%) males and 7305 (40.3%) females. The pooled rate of perforation was 0.5% (95% CI, 0.3–0.8, I<sup>2</sup>–7.5%) and 0.3% (95% CI, 0.2–0.5, I<sup>2</sup>–41.1%) for balloon and bougie respectively. The rate of bleeding was 0.6% (95% CI 0.4–1.1, I<sup>2</sup>–17.1%), and 0.3% (95% CI, 0.2–0.8, I<sup>2</sup>–60.6%) for balloon and bougie dilatations respectively. <h3>Conclusion</h3> This large meta analysis on 18104 patients shows that the risk of perforation and bleeding is low and comparable in both endoscopic guided balloon and bougie dilatations. The rates are lower than the commonly accepted figure of 1% and should be reassuring to both patients and endoscopists. <h3>Reference</h3> 1 Breslin NP, Thomson ABR, Bailey RJ, <i>et al</i>. Gastric cancer and other en- doscopic diagnoses in patients with benign dyspepsia. <i>Gut</i> 2000;<b>46</b>. <h3>Disclosure of Interest</h3> None Declared
Gene Expression Profiling Signatures Allow the Identification of Unclassifiable Leukemic B-Cell Lymphoid Neoplasms
Authors: Alba Navarro, Guillem Clot, Alejandra Martinez-Trillos, Itziar Salaverria, David Martin-Garcia, Nicola Trim, Veronica Fernandez, Neus Villamor, Dolors Colomer, Magda Pinyol, Pedro Jares, Wendy N. Erber, Adrian Wiestner, Wyndham H. Wilson, Reiner Siebert, Marta Aymerich, Armando Lopez-Guillermo, Àlex Sánchez, Elias Campo, Estella Matutes, Sílvia Beà
Journal: Blood (2015)
New Prostate Cancer Grading System Predicts Long-term Survival Following Surgery for Gleason Score 8–10 Prostate Cancer
Authors: Won Sik Ham, Heather J. Chalfin, Zhaoyong Feng, Bruce J. Trock, Jonathan I. Epstein, Carling Cheung, Elizabeth Humphreys, Alan W. Partin, Misop Han
Journal: European Urology (2016)
Frequency of CD4+CD25hiFOXP3+ Regulatory T Cells Has Diagnostic and Prognostic Value as a Biomarker for Acute Graft-Versus-Host Disease.
Authors: John M. Magenau, Xuemei Qin, Isao Tawara, Clare E Rogers, Matthew Schlough, Daniel Bickley, Pil Sang Jang, Thomas M Braun, Kathleen Lowler, Dawn M Jones, Sung W Choi, Shin Mineishi, John E. Levine, James LM Ferrara, Sophie Paczesny
Journal: Blood (2009)
OC-009 Spyglass DS™ Cholangioscopy for Difficult Stones: Early Experience of Two UK Centres
Authors: NL Bekkali, R Sturgess, L Dwyer, S Direkze, GJ Webster
Journal: Gut (2016)

<h3>Introduction</h3> Endoscopic clearance of bile duct stones is achievable in &gt;90% with conventional ERCP (ASGE 2015). Additional techniques may be necessary for those patients with difficult stones, which may be due to stone location, size, or number. Cholangioscopy and intraductal lithotripsy may have a specific role in treating difficult stones. The Spyglass DS™ peroral cholangioscopy system was introduced in mid-2015, and here we report our early experience with this technique. <h3>Methods</h3> Spyglass DS cholangioscopy was available in the UK from May 2015. Cases referred to our 2 centres were assessed within a specialist HPB multidisciplinary meeting, and all cases deemed appropriate for Spyglass DS were prospectively followed. Patient demographics, indication for cholangioscopy, technical outcome and complications were recorded. <h3>Results</h3> Eight-four patients (54% female, median age 61 years (range 25–90)) underwent ERCP with plan for cholangioscopy. Indications were stones (83%), strictures (14%) and other (3%). The stones were extrahepatic (62%), intrahepatic (15%), cystic duct (15%), and intra + extrahepatic (8%). The total number of stones was &lt;5 in 58%, 5–10 in 18%, 11–15 in 9%, 16–20 in 9% and &gt;20 stones in 6%. The 70 patients with stones had undergone a median 2 ERCPs (range 1–7) prior to referral. At our centres duct clearance was achieved in 30% (n = 21/70) without need for cholangioscopy, using combinations of extraction balloon (100%), sphincteroplasty (69%) and mechanical lithotripsy (ML) (54%). Cholangioscopy was needed for 49 cases, in 46 patients. Cholangioscopy with electrohydraulic lithotripsy (EHL) led to complete stone clearance in 72% of patients (33/46), of whom 3 on second EHL. The remaining patients await a second EHL procedure. In the 18 patients with unsuccessful stone clearance to date, reasons included: stone size + density (n = 8 with stones &gt;15 mm); intrahepatic stones (n = 9); inability to apply EHL (n = 1). Overall, stone clearance was achieved in 54/67 (81%) of patients undergoing ERCP +/- cholangioscopy with EHL. The mean (SD) duration of ERCP + cholangioscopy + EHL was 93 (±28) minutes; 90% had propofol sedation, and 10% conscious sedation. No complications were observed. <h3>Conclusion</h3> In patients who have failed multiple attempts at endoscopic stone clearance, referral to a centre with availability of Spyglass DS cholangioscopy and EHL results in definitive stone clearance in 81% of patients. This success includes further conventional ERCP. Stone clearance with cholangioscopy may be achieved irrespective of site or size of stones, but failure of complete fragmentation with EHL may contribute to need for repeat procedures, and occasional failure. <h3>Disclosure of Interest</h3> None Declared
Prevention of Acute Graft-Versus-Host Disease Despite Compensatory Function of Lymphoid Organs In Vivo.
Authors: Andreas Beilhack, Stephan Schulz, Jeanette Baker, Georg F. Beilhack, Ryosei Nishimura, Gilad Landan, Enosh M. Baker, Edward I. Herman, Eugene C. Butcher, Christopher H. Contag, Robert S. Negrin
Journal: Blood (2005)
Phenotypic Differences amongst Subgroups of Patients with Myelofibrosis with Myeloid Metaplasia (MMM): Analysis of 458 MMM Patients.
Authors: Ruben Mesa, Joyce Niblack, Srdan Verstovsek, Sunni Barnes, Angelina Tan, Pamela Atherton, Jeffrey Sloan, Ayalew Tefferi
Journal: Blood (2006)
Anticoagulant therapy for symptomatic calf deep vein thrombosis (CACTUS): a randomised, double-blind, placebo-controlled trial
Authors: Marc Righini, Jean-Philippe Galanaud, Hervé Guenneguez, Dominique Brisot, Antoine Diard, Pascale Faisse, Marie-Thérèse Barrellier, Claudine Hamel-Desnos, Christine Jurus, Olivier Pichot, Myriam Martin, Lucia Mazzolai, Clarisse Choquenet, Sandrine Accassat, Helia Robert-Ebadi, Marc Carrier, Grégoire Le Gal, Bernadette Mermilllod, Jean-Pierre Laroche, Henri Bounameaux, Arnaud Perrier, Susan R Kahn, Isabelle Quere
Journal: The Lancet Haematology (2016)
SAT0192 Decreased Interleukin-6/STAT3, but Increased Interferon/STAT1 Signalling in Lymphocytes of Patients with Systemic Sclerosis (SSC)
Authors: C. Kittel, M. Skwarek, B. Heschel, J. Fantana, M. Aringer
Journal: Annals of the Rheumatic Diseases (2016)

<h3>Background</h3> Increased interleukin-6 (IL-6) was found in SSc skin, and early studies suggest therapeutic efficacy of IL-6 receptor blockade in SSc. Similarly, an increased interferon (IFN) signature was found in SSc patients. Accordingly, both IL-6 and interferons may be upregulated in SSc, and both act via Stat (signal transducer and activator of transcription) molecules, namely Stat3, and Stat1, respectively. <h3>Objectives</h3> To analyze the interleukin-6 (IL-6) receptor-Stat3 axis, as well as Stat1 and phosphorylated Stat1, in lymphocytes of patients with SSc. <h3>Methods</h3> PBMC of 30 patients with SSc and 42 healthy individuals (HC) were prepared. CRP, ESR, modified Rodnan skin score (mRSS) and the EULAR activity score were recorded. For determining the percentages of CD126 and CD130 positive cells, PBMC were directly stained with PE-labelled or control antibodies. Ex vivo and after 15 minutes of incubation with or without recombinant human interferon-γ (IFNγ) or interleukin-6 (IL-6), PBMC were fixed with formaldehyde (2%), permeabilized with methanol (80%), and stained with PE-labelled control antibodies or antibodies to Stat1 or phosphorylated Stat1 (pStat1) or pStat3, respectively. Stained cells were immediately analyzed on a Becton Dickinson FACSCalibur fluorocytometer, gating for lymphocytes. As a semiquantitative measure of Stat and pStat contents, mean fluorescence intensity (mfi) was used. Data were expressed as mean±SD. <h3>Results</h3> Both chains of the IL-6 receptor, CD126 and CD130, were expressed on decreased percentages of SSc lymphocytes (50.2±18.1% vs. 60.0±7.9%, p=0.0086, and 52.6±15.1% vs. 59.6±9.5%, p=0.0212, respectively). This translated into a diminished increase of pStat3 in SSc lymphocytes upon IL-6 stimulation (Δmfi 17.2±12.1 vs. 20.5±9.3, p=0.03). In contrast, the IFNγ-induced increase in pStat1was more pronounced in SSc lymphocytes (Δmfi 10.5±11.2 vs. 4.8±3.7, p=0.0035), despite their increased Stat1 contents (mfi 51.2±27.4 vs. 16.7±9.1, p&lt;0.0001), thus suggesting activity of the IFN system in SSc. Somewhat unexpectedly, no differences were found between diffuse cutaneous (or anti-topoisomerase positive) and limited cutaneous (or anti-centromere-positive) SSc. <h3>Conclusions</h3> In combination of increased Stat1 and Stat1 phosphorylation and decreased IL-6 receptors, our results suggest activity of both the IFN/Stat1 and the IL-6/Stat3 axis in SSc, with a shift towards phosphorylated Stat1. <h3>Acknowledgement</h3> This work was supported by DFG grant AR-757/1–1. <h3>Disclosure of Interest</h3> C. Kittel: None declared, M. Skwarek: None declared, B. Heschel: None declared, J. Fantana: None declared, M. Aringer Consultant for: Chugai, Pfizer, Roche, Sanofi, Speakers bureau: Chugai, Pfizer, Roche
Continued Overall Survival Benefit After 5 Years' Follow-up with Bortezomib-Melphalan-Prednisone (VMP) Versus Melphalan-Prednisone (MP) in Patients with Previously Untreated Multiple Myeloma, and No Increased Risk of Second Primary Malignancies: Final Results of the Phase 3 VISTA Trial
Authors: Jesús F San Miguel, Rudolf Schlag, Nuriet K Khuageva, Meletios Athanasios Dimopoulos, Ofer Shpilberg, Martin Kropff, Ivan Spicka, Maria T Petrucci, Antonio Palumbo, Olga S Samoilova, Anna Dmoszynska, Kudrat M Abdulkadyrov, Michel Delforge, Bin Jiang, María-Victoria Mateos, Kenneth C. Anderson, Dixie-Lee Esseltine, Kevin Liu, William M Deraedt, Andrew Z Cakana, Helgi van de Velde, Paul G. Richardson
Journal: Blood (2011)
The Role of PIM1 in the Ibrutinib-Resistant ABC Subtype of Diffuse Large B-Cell Lymphoma
Authors: Hsu-Ping Kuo, Sidney Hsieh, Karl J. Schweighofer, Leo WK Cheung, Shiquan Wu, Mutiah Apatira, Mint Sirisawad, Karl Eckert, Yu Liang, Jeff Hsu, Betty Y. Chang
Journal: Blood (2015)
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Authors: Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
Journal: Genome biology (2016)

Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .
Essential medicines for universal health coverage
Authors: Veronika J Wirtz, Hans V Hogerzeil, Andrew L Gray, Maryam Bigdeli, Cornelis P de Joncheere, Margaret A Ewen, Martha Gyansa-Lutterodt, Sun Jing, Vera L Luiza, Regina M Mbindyo, Helene Möller, Corrina Moucheraud, Bernard Pécoul, Lembit Rägo, Arash Rashidian, Dennis Ross-Degnan, Peter N Stephens, Yot Teerawattananon, Ellen F M 't Hoen, Anita K Wagner, Prashant Yadav, Michael R Reich
Journal: The Lancet (2016)
Prostaglandin E2 (PGE2) Alters the Molecular and Functional Properties of Umbilical Cord Blood T Cells Via Modulating Wnt/β-Catenin Signaling
Authors: Lequn Li, Anoma Nellore, Sean McDonough, Ioannis Politikos, Haesook Kim, Sarah Nikiforow, Joseph H. Antin, Karen K. Ballen, Corey Cutler, Jerome Ritz, Vassiliki A. Boussiotis
Journal: Blood (2012)
Bone Marrow-Derived Cells Regenerate Kit+ Cardiac Stem Cells (CSCs) in Damaged Heart.
Authors: Francesco Cerisoli, Lucio Barile, Roberto Gaetani, Letizia Cassinelli, Giacomo Frati, Alessandro Giacomello, Elisa Messina, Sergio Ottolenghi, Maria Cristina Magli
Journal: Blood (2006)
Involved Field Radiation Therapy Following Autologous Stem Cell Rescue for Hodgkin and Non-Hodgkin Lymphoma - Is It Efficacious?.
Authors: Tithi Biswas, Sughosh Dhakal, Sheema Chawla, Nikhil Uppal, Sarada Uppuliri, Ann G. Muhs, Jane Liseveld, Gordon Phillips, Louis S. Constine
Journal: Blood (2006)
Sustained Improvements in Transfusion Requirements, Fatigue and Thrombosis with Eculizumab Treatment in Paroxysmal Nocturnal Hemoglobinuria.
Authors: Gerard Socié, Peter Hillmen, Petra Muus, Jörg Schubert, Ulrich Dührsen, Antonio M. Risitano, Russell P. Rother, Robert A. Brodsky, Jeffrey Szer
Journal: Blood (2007)
Complement Activation and Complement-Mediated Killing of B Cells Promoted by Anti-CD20 Monoclonal Antibodies (mAb) Rituximab and Ofatumumab Are Rapid, and Ofatumumab Kills Cells More Rapidly and with Greater Efficacy.
Authors: Ronald P. Taylor, Andrew W. Pawluczkowycz, Paul V. Beum, Margaret A. Lindorfer, Frank Beurskens, Jan van de Winkel, Paul Parren
Journal: Blood (2007)
Predicting the chances of a live birth after one or more complete cycles of in vitro fertilisation: population based study of linked cycle data from 113 873 women
Authors: David J McLernon, Ewout W Steyerberg, Egbert R te Velde, Amanda J Lee, Siladitya Bhattacharya
Journal: BMJ (2016)

To develop a prediction model to estimate the chances of a live birth over multiple complete cycles of in vitro fertilisation (IVF) based on a couple's specific characteristics and treatment information. Population based cohort study. All licensed IVF clinics in the UK. National data from the Human Fertilisation and Embryology Authority register. All 253 417 women who started IVF (including intracytoplasmic sperm injection) treatment in the UK from 1999 to 2008 using their own eggs and partner's sperm. Two clinical prediction models were developed to estimate the individualised cumulative chance of a first live birth over a maximum of six complete cycles of IVF-one model using information available before starting treatment and the other based on additional information collected during the first IVF attempt. A complete cycle is defined as all fresh and frozen-thawed embryo transfers arising from one episode of ovarian stimulation. After exclusions, 113 873 women with 184 269 complete cycles were included, of whom 33 154 (29.1%) had a live birth after their first complete cycle and 48 925 (43.0%) after six complete cycles. Key pretreatment predictors of live birth were the woman's age (31 v 37 years; adjusted odds ratio 1.66, 95% confidence interval 1.62 to 1.71) and duration of infertility (3 v 6 years; 1.09, 1.08 to 1.10). Post-treatment predictors included number of eggs collected (13 v 5 eggs; 1.29, 1.27 to 1.32), cryopreservation of embryos (1.91, 1.86 to 1.96), the woman's age (1.53, 1.49 to 1.58), and stage of embryos transferred (eg, double blastocyst v double cleavage; 1.79, 1.67 to 1.91). Pretreatment, a 30 year old woman with two years of unexplained primary infertility has a 46% chance of having a live birth from the first complete cycle of IVF and a 79% chance over three complete cycles. If she then has five eggs collected in her first complete cycle followed by a single cleavage stage embryo transfer (with no embryos left for freezing) her chances change to 28% and 56%, respectively. This study provides an individualised estimate of a couple's cumulative chances of having a baby over a complete package of IVF both before treatment and after the first fresh embryo transfer. This novel resource may help couples plan their treatment and prepare emotionally and financially for their IVF journey.
Being “penny-wise but pound foolish” in cancer immunotherapy research: the urgent need for mouse cancer models to reflect human modifying factors
Authors: William J. Murphy
Journal: Journal for ImmunoTherapy of Cancer (2016)

Inbred mice are the mainstay for preclinical cancer assessment of potential therapeutics, especially immune-based approaches. However, the use of young, lean, inbred mice housed under specific-pathogen-free conditions does not mirror the human cancer scenario. This commentary discusses some of the issues in evaluating immunotherapeutics in mice given recent advances.
Heparin-Induced Thrombocytopenia Antibodies Do Not Predict Adverse Outcomes in End-Stage Renal Disease Patients on Dialysis.
Authors: Lars M. Asmis, Jodi B. Segal, Laura C. Plantinga, Nancy E. Fink, Jonathan S. Kerman, Thomas S. Kickler, Josef Coresh, Lawrence B. Gardner
Journal: Blood (2004)
The spread and clinical impact of ST14CC-PBP3 type IIb/A, a clonal group of non-typeable Haemophilus influenzae with chromosomally mediated β-lactam resistance—a prospective observational study
Authors: V. Månsson, D. Skaare, K. Riesbeck, F. Resman
Journal: Clinical Microbiology and Infection (2016)
Augmented Preparative Regimens Using Total Body Irradiation or BCNU Prior to Autologous Stem Cell Transplant (AuSCT) Are Well-Tolerated and Yield Substantial Rates of Progression-Free Survival in Patients with Poor Risk Hodgkin Lymphoma (HL) or Diffuse Large B-Cell Lymphoma (DLBCL).
Authors: David S. Ritchie, John F. Seymour, Sarah Thompson, Michael McManus, Miles Prince
Journal: Blood (2005)
World Changing
Authors: Ellen J. Plumb
Journal: Annals of Internal Medicine (2015)

On Being a Doctor21 April 2015World ChangingEllen J. Plumb, MDEllen J. Plumb, MDFrom Thomas Jefferson University, Philadelphia, Pennsylvania.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/M14-2076 Audio Reading - “World Changing” Audio. Michael A. LaCombe, MD, Annals Associate Editor, reads "World Changing," by E.J. Plumb. Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Like many physicians, I can tell you the exact moment when I decided to become a healer. It involved an experience with a man in Uganda dying of AIDS in a house made of mud crumbling back into the earth. It involved a 21-year-old me as an undergraduate anthropology researcher, helpless in my confrontation of the agony of death. It was a powerful, pivotal moment that changed my life, a tangible whisper that ignited a deep sense of powerlessness that ultimately pushed me away from public health and onto the path of medicine.Becoming a physician was not easy. I ... Author, Article, and Disclosure InformationAffiliations: From Thomas Jefferson University, Philadelphia, Pennsylvania.Corresponding Author: Ellen J. Plumb, MD, 1015 Walnut Street, Suite 401, Philadelphia, PA 19107; e-mail, ellen.[email protected]edu. PreviousarticleNextarticle Advertisement Audio Reading - “World Changing” Audio. Michael A. LaCombe, MD, Annals Associate Editor, reads "World Changing," by E.J. Plumb. Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ FiguresReferencesRelatedDetails Metrics 21 April 2015Volume 162, Issue 8Page: 594-595KeywordsAnxietyEmotionsFearForecastingMemoryPrevention, policy, and public healthResidencyUndergraduatesUrineWalking ePublished: 21 April 2015 Issue Published: 21 April 2015 Copyright & PermissionsCopyright © 2015 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Searching Polymorphic Markers Associated with the Genetic Predisposition To Develop Therapy-Related Myelodysplastic Syndromes and Acute Myelogenous Leukemia T-(MDS/AML) after Myeloablative Chemotherapy.
Authors: Mar M. Tormo, Vicent V. Guillem, Manuel M. Mata, Marcos M. Gonzalez, Josep J. Nomdedeu, Jordi J. Esteve, Maria Jose M.J. Calasanz, Maria Jose M.J. Terol, Isabel I. Marugan, Carlos C. Solano
Journal: Blood (2005)