tbuckley/cabot-search huggingface dataset:
Frequency of Axial Spondyloarthritis Diagnosis Among Patients Seen by US Rheumatologists for Evaluation of Chronic Back Pain
Authors: Atul Deodhar, Philip J. Mease, John D. Reveille, Jeffrey R. Curtis, Su Chen, Kailash Malhotra, Aileen L. Pangan
Journal: Arthritis & Rheumatology (2016)

To determine the proportion of patients with axial spondyloarthritis (SpA) among those with chronic back pain and ≥1 of 3 SpA features in the US.The study was conducted at rheumatology practices in the US. Patients were required to have chronic back pain for ≥3 months beginning at <45 years of age, no prior SpA diagnosis, and ≥1 of the following 3 SpA features: HLA-B27 positivity, current inflammatory back pain, and magnetic resonance imaging (MRI) or radiographic evidence of sacroiliitis. Medical history and physical examination findings, pelvic radiographs, MRIs of sacroiliac joints, C-reactive protein (CRP) level, and HLA-B27 status were obtained. Investigators were asked if a clinical diagnosis of axial SpA could be made based on the results. Data were also analyzed separately to determine if patients fulfilled the Assessment of SpondyloArthritis international Society (ASAS) criteria for axial SpA and/or modified New York criteria for ankylosing spondylitis (AS).A total of 751 patients were enrolled (46% were existing patients in rheumatology practices, 40% were new referrals, and 14% were self referred). Among patients with available data, 319 of 697 (46%) were diagnosed as having axial SpA by the investigator, and 348 of 744 (47%) fulfilled the ASAS criteria, of whom 238 were classified as having nonradiographic axial SpA and 108 as having AS; 2 had missing data. Using investigator's clinical diagnosis as the gold standard, the specificity and sensitivity of the ASAS criteria were 79% and 81%, respectively.Our findings indicate that among patients with chronic back pain for ≥3 months beginning at ages younger than 45 years, the presence of ≥1 of 3 SpA features is an effective way to identify those with possible axial SpA.
Abstract 15554: Improvement of Valvular Parameters Following Transcatheter Aoritc Valve Implantation versus Surgical Aortic Valve Replacement in Patients With Severe Aortic Stenosis: A Meta-Analysis
Authors: Hemang B Panchal, Saurabh Desai, Vijay Ramu, Timir Paul
Journal: Circulation (2013)

Background: Surgical aortic valve replacement (SAVR) is the standard of care for severe aortic valve stenosis (AS). In patients with high risk for surgery, transcatheter aortic valve implantation (...
P0837 : Efficacy of sofosbuvir and daclatasvir in HIV/HCV co-infected patients with advanced fibrosis
Authors: T.M. Antonini, J. Ursic Bedoya, E. Teicher, A. Coilly, E. de Martin, A.-M. Roque-Afonso, Y. Quertainmont, C. Goujard, J.-F. Delfraissy, D. Vittecoq, D. Samuel, J.-C. Duclos-Vallee
Journal: Journal of Hepatology (2015)
OP22 A significant reduction in “pro-inflammatory” CD14lo/CD16hi monocytes in paracetamol-induced acute liver failure: association with outcome and CCR2 expression
Authors: D Abeles, C G Antoniades, M S Longhi, N J Taylor, D L Shawcross, G Auzinger, W Bernal, N Heaton, J A Wendo, D Vergani
Journal: Gut (2010)

Introduction  Acute liver failure (ALF) shares many clinical and immunological features with severe sepsis. In severe sepsis the relative proportion of “pro-inflammatory” CD14lo/CD16hi monocytes (MO) is reduced, possibly due to recruitment into inflamed tissue. No data exist on monocyte subsets in paracetamol-induced ALF (PALF). Animal models of ALF suggest the importance of CC chemokine receptor (CCR) 2 mediated MO recruitment and in human PALF high circulating levels and hepatic expression of CC chemokine ligand 2 have been observed.  Aim  Investigate the relative composition of “pro-inflammatory” CD14hi/CD16lo, “intermediate” CD14hi/CD16hi and “classical” CD14lo/CD16hi MO subsets and the association of CCR2 expression, in patients with PALF.  Method  Blood was taken from five healthy controls and 20 patients with PALF within 24–48 hours of admission. Monoclonal antibodies against CD14, CD16 and CCR2 were used to determine MO subsets and CCR expression. Results are expressed as the percentage proportion of total MO and mean fluorescence intensity of CCR2 expression.  Results  Compared to healthy controls, a lower proportion of CD14lo/CD16hi MO was observed in PALF (2% vs 10%, p=0.01), CD14hi/CD16lo MO tended to be more highly represented (95% vs 82%, p  Conclusion  These are the first reported data defining the relative proportions of MO subsets in PALF. They show that the proportion of CD14lo/CD16hi MO is significantly reduced in PALF, the degree of which is predictive for outcome. This reduction may be due to early sequestration of these MO within the liver or other organs through CCR2 independent pathways.
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
Authors: Erfan Sayyari, Siavash Mirarab
Journal: Molecular Biology and Evolution (2016)

Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the MSC to compute (1) the local posterior probability (PP) that the branch is in the species tree and (2) the length of the branch in coalescent units. We evaluate the precision and recall of the local PP on a wide set of simulated and biological datasets, and show that it has very high precision and improved recall compared with multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene tree estimation error is low, but are underestimated when gene tree estimation error increases. Computation of both the branch length and local PP is implemented as new features in ASTRAL.
Change in perfusion patterns and its correlation to clinical outcomes following lung volume reduction surgery (LVRS) in COPD as assessed by single photon emission computer tomography (SPECT)
Authors: Henry Hoffmann, Didier Lardinois, Anke Mols, Anna-Maria Balestra, Flavio Forrer, Michael Tamm, Daiana Stolz
Journal: European Respiratory Journal (2011)

Background:  It is unknown whether SPECT adds to the assessment in LVRS. We evaluated the change in perfusion patterns and it9s correlation to clinical outcome in COPD patients undergoing LVRS.   Methods:  26 COPD patients (GOLD III-IV) meeting criteria for LVRS were evaluated by lung function, 6 MWD test, and SPECT preoperatively and 6 months after LVRS. CT scans with 8mm sections were performed with following 3D picture fusion. We calculated the perfusion pattern (low, intermediate, high) in% and the heterogeneity index, which was defined as the number of areas of high or intermediate perfusion in each of the 20 cuts added to 20 and divided by 20.   Results:  Mean age was 63.6±8.5 years, 19 male. FEV1% pred was 32.3±16.3, DLCO 31% ± 11, and the mean 6 MWD 328 m ± 120. As compared to the pre-operative values, post-operative, bilateral perfusion patterns improved (low 86.6%±7.6 vs. 78.6±11.9, p   Conclusion:  Lung SPECT perfusions pattern correlates with the clinical improvement and warrants evaluation as a pre-operative assessment tool in patients with COPD undergoing LVRS.
Long-term follow-up and factors of survival of HER-2 positive breast cancer patients treated either by neoadjuvant trastuzumab docetaxel (TAXHER-S01 study) or by neoadjuvant trastuzumab docetaxel carboplatin (GETN[A]1 study)
Authors: L. Favier, M. Liegard, S. Guiu, I. van Praagh, R. Largillier, B. Weber, D. Coeffic, B. Vasseur, B. Coudert
Journal: Journal of Clinical Oncology (2009)

e11507 Background: Almost 20% of breast cancers over express Her2, which is associated with a more aggressive phenotype and with a decreased survival. Nevertheless, trastuzumab (T) has been a revolutionary step in the adjuvant and in the metastatic treatments of Her2 positive breast cancers. Here, we focus on neoadjuvant T and try to determine the factors correlating with disease free survival and with overall survival in Her2 positive breast cancer treated with T based neoadjuvant chemotherapy. Methods: Data from two published T based neoadjuvant phases II were used: the TAX-HER trial which studied the use of 6 courses of 3 weekly docetaxel with weekly neoadjuvant T (scheme TH) (Coudert et. al. Annals of Oncology 2006) and the GET(N)A-1 trial which studied the use of 6 courses of 3 weekly docetaxel and carboplatin along with weekly neoadjuvant T (scheme TCH) followed by 3 weekly adjuvant T (Coudert et. al. JCO 2007). Moreover, additional patients from our institution and treated by neoadjuvant TH and adjuvant T were included. Survival curves were estimated using Kaplan-Meier methods and compared by log-rank test. Results: Data was available for 128 patients. 62 patients (48.4%) received neoadjuvant TH from whom 39 did not receive adjuvant T. 66 (51.6%) received neoadjuvant TCH and adjuvant T. Tumors characteristics were as followed: 65 (50.7%) SBR 1–2, 54 (42.19%) SBR 3, 49 (38.28%) hormonal receptors (RH) negative and 72 (56.25%) RH positive. The rate of pathological complete response (pCR) (Chevalier 1/2) was 39.6%. Overall survival (OS) for the entire cohort was 74,8 months. Relapse was defined as local, regional, metastatic relapse or death. Survival without relapse (SR) was 74.8 months. No difference was noted in OS and in SR according to the type of chemotherapy, TH or TCH. pCR did significantly influence SR (p = 0. 03) and survival without local recurrence (SLR) (p = 0.04) but neither OS nor survival without metastatic relapse (SMR). Multivariate analysis demonstrated that OS was correlated with node response (as defined by sataloff grade NA or NB) (p=0.0275) and the use of hormonal therapy in RH positive tumors (p=0.0724). [Table: see text]
Influence of Thymectomy, Splenectomy, and Gonadectomy on Incidence of Radiation-Induced Lymphoid Tumors in Strain C57 Black Mice&lt;xref ref-type="fn" rid="fn1"&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/xref&gt;
Authors: Henry S. Kaplan, M. D.
Journal: JNCI Journal of the National Cancer Institute (1950)

Influence of Thymectomy, Splenectomy, and Gonadectomy on Incidence of Radiation-Induced Lymphoid Tumors in Strain C57 Black Mice Get access Henry S. Kaplan, M. D. Henry S. Kaplan, M. D. Department of Radiology, Stanford University School of Medicine, San Francisco 15, Calif. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 11, Issue 1, August 1950, Pages 83–90, https://doi.org/10.1093/jnci/11.1.83 Published: 01 August 1950 Article history Received: 10 April 1950 Published: 01 August 1950
STAT5A-Deficient Mice Demonstrate a Defect in Granulocyte-Macrophage Colony-Stimulating Factor–Induced Proliferation and Gene Expression
Authors: Gerald M. Feldman, Louis A. Rosenthal, Xiuwen Liu, Mark P. Hayes, Anthony Wynshaw-Boris, Warren J. Leonard, Lothar Hennighausen, David S. Finbloom
Journal: Blood (1997)
Incretin based drugs and the risk of pancreatic cancer: international multicentre cohort study
Authors: Laurent Azoulay, Kristian B Filion, Robert W Platt, Matthew Dahl, Colin R Dormuth, Kristin K Clemens, Madeleine Durand, David N Juurlink, Laura E Targownik, Tanvir C Turin, J Michael Paterson, Pierre Ernst
Journal: BMJ (2016)

To determine whether the use of incretin based drugs compared with sulfonylureas is associated with an increased risk of incident pancreatic cancer in people with type 2 diabetes.Population based cohort.Large, international, multicentre study combining the health records from six participating sites in Canada, the United States, and the United Kingdom.A cohort of 972,384 patients initiating antidiabetic drugs between 1 January 2007 and 30 June 2013, with follow-up until 30 June 2014.Within each cohort we conducted nested case-control analyses, where incident cases of pancreatic cancer were matched with up to 20 controls on sex, age, cohort entry date, duration of treated diabetes, and duration of follow-up. Hazard ratios and 95% confidence intervals for incident pancreatic cancer were estimated, comparing use of incretin based drugs with use of sulfonylureas, with drug use lagged by one year for latency purposes. Secondary analyses assessed whether the risk varied by class (dipeptidyl peptidase-4 inhibitors and glucagon-like peptide-1 receptor agonists) or by duration of use (cumulative duration of use and time since treatment initiation). Site specific hazard ratios were pooled using random effects models.During 2,024,441 person years of follow-up (median follow-up ranging from 1.3 to 2.8 years; maximum 8 years), 1221 patients were newly diagnosed as having pancreatic cancer (incidence rate 0.60 per 1000 person years). Compared with sulfonylureas, incretin based drugs were not associated with an increased risk of pancreatic cancer (pooled adjusted hazard ratio 1.02, 95% confidence interval 0.84 to 1.23). Similarly, the risk did not vary by class and evidence of a duration-response relation was lacking.In this large, population based study the use of incretin based drugs was not associated with an increased risk of pancreatic cancer compared with sulfonylureas. Although this potential adverse drug reaction will need to be monitored long term owing to the latency of the cancer, these findings provide some reassurance on the safety of incretin based drugs.
Control of menstrual bleeding during hemodialysis.
Authors: Newton J, Snowden Sa
Journal: BMJ (1976)

Patients with renal disease and undergoing hemodialysis frequently have excessive menstrual bleeding;  in 4 such patients following insertions of progesterone-releasing IUDs the total amount of menstrual bleeding was reduced and normal estrous cycles were observed.  The 4 women had been treated with Norethisterone previously but this treatment either failed to reduce bleeding or was accompanied by negative side effects.  After IUD insertion one patient was followed for 11 months and another for 16 months and regular cycles and normal bleeding were observed.  The other two patients had kidney transplants during the following 4th and 9th month and eventually died from a variety of complications.  Neither death was related to IUD use and during the 4 and 9 months in which they were followed their menstrual cycles and the amount of bleeding were normal.
Isolation and Characterization of Chicken Liver and Hepatoma Mc-29 Endoplasmic Reticulum and Golgi Apparatus Membranes and Biosynthesis of Their Glycoconjugates
Authors: E Gavazova, S Ivanov, H Chelibonova-Lorer
Journal: JNCI Journal of the National Cancer Institute (1987)

Rough and smooth endoplasmic reticulum (ER) membranes and trans-Golgi apparatus (GA) fraction, intermediate GA fraction, and cis-GA fraction from White Leghorn chicken liver and hepatoma Mc-29 were isolated. Their purity was checked by electron microscopy and by determination of the activity of the marker enzymes. Rough and smooth membranes were also identified by calculation of the ratio between the content of RNA and the total phospholipids. It was found that the membrane fractions were pure enough. The tumor exhibited a decreased amount of ER and a small GA when compared with the ER and GA in the liver. The biogenesis of membrane glycoconjugates was followed by in vivo experiments either with [14C]glucosamine or by double labeling with [14C]N-acetylmannosamine and [3H]leucine. The radioisotope studies indicated that the synthesis rate of protein in liver and hepatoma rough ER was nearly the same, but in the tumor cells the glycosylation of the nascent polypeptide chain and the formation of glycolipids were significantly decreased.
Myelophthisis in solid tumors: Old aspects, new concepts (ONCOLGroup study)
Authors: M. Lujan, A. F. Cardona, A. Yepes, E. Carrasco-Chaumel, L. Reveiz, J. M. Otero
Journal: Journal of Clinical Oncology (2009)

e20672 Background: Myelophthisis is a form of bone marrow failure due to replacement of hematopoietic tissue by abnormal tissue, most commonly metastatic carcinomas. This results in extramedullary hematopoiesis, typically in the spleen leading to premature release of hematopoietic cells into the circulation. Peripheral blood findings of myelophthisis may include nucleated red blood cells, tear drop forms, giant platelets, and immature leukocytes. Overall, this picture is usually called leukoerythroblastosis. Methods: This retrospective study included 89 patients (pts) with solid tumors and myelophtisis that had been treated from 1991 to 2006 in a single reference center in Bogotá. We made a detailed analysis of pts characteristics and outcomes. Results: Mean age was 47.5±17.2 years, there was homogeneous gender distribution (F46/M43) and 62% pts had a PS ≥60%. Twenty-seven pts (30%) had breast cancer, pathology followed by primary unknown tumours (21%), rabdomiosarcoma (10%), prostate adenocarcinoma (10%), gastric carcinoma (7%) and others (22%). At the time when myelophtisis was documented 72% and 50% of pts had osseous and visceral metastasis respectively; 81 pts presented anaemia (Hb 9.8 ± 1.2 gr/dl), mean platelet count was 174,000 and mean leukocyte count was 24,283 ± 5,447. Forty-three pts received chemotherapy following the diagnosis of medullar infiltration, and normal leukocyte count was being seen in 40% of them after such treatment. Nine episodes of febrile neutropenia were found; median overall survival (OS) following the diagnosis of neoplasia and myelophtisis were 13.8 months and 2.2 months respectively. The factors related to lower survival rate were the presence of Hb ≤8.5 gr/dl (HR: 0,54, CI95% 0,32–0,95; p = 0.04), &gt;3 metastasis sites (HR: 0,67, CI95% 0,45–0,92; p = 0.03), visceral disease (HR: 0,72, CI95% 0,66–0,89; p = 0.04) and febrile neutropenia caused by chemotherapy (HR: 0,52, CI95% 0,37–0,60; p = 0.02). Conclusions: Myelophtisis is a serious condition modifying the OS of patients having solid tumours. Treatment for this subgroup should be selected bearing in mind its potential haematological toxicity. No significant financial relationships to disclose.
Follow-up of Coll2-1, Coll2-1 NO2 and myeloperoxidase in dog after transection of the cruciate ligament of the knee
Authors: Yves Henrotin, JP Pelletier, J Martel-Pelletier, J Caron, C Boileau, A Bosseloir, Michelle Deberg
Journal: Annals of the Rheumatic Diseases (2008)
Abstract 17076: Prognostic Implications of 12-Lead Surface ECG Characteristics in Patients With Cardiac Sarcoidosis and Preserved Ejection Fraction
Authors: Luke J Laffin, Amit R Patel, Gillian Murtagh, Zoe Yu, Amit V Patel, Catherine Bonham, Karima Addetia, Joshua D Moss, Douglas K Hogarth, Nadera Sweiss, Roberto M Lang, John F Beshai
Journal: Circulation (2014)

Introduction: Among patients with cardiac sarcoidosis (CS) and preserved left ventricular ejection fraction (LVEF), there is little evidence for risk stratification to guide device therapy, and the prognosis of these patients is not well defined. We sought to determine if 12-lead surface ECG characteristics predict adverse events (AE) in patients with biopsy proven extra-cardiac sarcoidosis, preserved LVEF, and late-gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR), demonstrating CS.

Methods: Forty-eight patients (age 54 +/- 11 years, 63% female), referred for CMR to evaluate for CS between April 2008 and December 2012, were found to have LGE and preserved LVEF (>50%). Medical records, including ICD interrogations, were reviewed and patients contacted to determine AE (death, ventricular fibrillation, or sustained ventricular tachycardia). ECG characteristics assessed include ventricular rate, PR interval, QRS duration, QT interval, corrected QT interval (QTc), axis deviation, ventricular hypertrophy, and the presence of a bundle branch block, among others. In the setting of a bundle branch block, 40ms was subtracted from the QTc interval, in-line with previous studies. AE-free survival analysis was performed, comparing patients with and without a prolonged QTc (>440ms). Patients with CS and AE were compared to those with no AE using a student’s t-test.

Results: Ten of forty-eight patients with CS had an AE during follow-up (average of 2.6 years). AE-free survival was significantly less for those patients with QTc >440ms (p=0.002). Patients with CS and AE have longer QTc intervals compared to those without AE (462 vs. 435ms, p=0.003). Other ECG characteristics were not significantly different.

Conclusions: In patients with CS and preserved LVEF, a QTc greater than 440ms is a negative prognostic marker and may play a role in risk stratification to guide device therapy.

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A Phase Ib Study of Everolimus, 5-Fluorouracil (5-Fu) and Pelvic Radiotherapy (Rt) As Neo-Adjuvant Treatment for Locally Advanced Rectal Cancer (Larc)
Authors: F. Bertolini, E. Pettorelli, B. Meduri, S. Zironi, A. Fontana, F. Gelsomino, E. Mazzeo, R. Depenni, A. Spallanzani, P.F. Conte, G. Luppi
Journal: Annals of Oncology (2014)
Quantitative evaluation of human bone mesenchymal stem cells rescuing fulminant hepatic failure in pigs
Authors: Dongyan Shi, Jianing Zhang, Qian Zhou, Jiaojiao Xin, Jing Jiang, Longyan Jiang, Tianzhou Wu, Jiang Li, Wenchao Ding, Jun Li, Suwan Sun, Jianzhou Li, Ning Zhou, Liyuan Zhang, Linfeng Jin, Shaorui Hao, Pengcheng Chen, Hongcui Cao, Mingding Li, Lanjuan Li, Xin Chen, Jun Li
Journal: Gut (2016)

<h3>Objective</h3> Stem cell transplantation provides a promising alternative for the treatment of fulminant hepatic failure (FHF). However, it lacks fundamental understanding of stem cells' activities. Our objective was to clarify stem cell-recipient interactions for overcoming barriers to clinical application. <h3>Design</h3> We used an in-house large-animal (pig) model of FHF rescue by human bone marrow mesenchymal stem cells (hBMSCs) and profiled the cells' activities. The control and transplantation groups of pigs (n=15 per group) both received a D-galactosamine (D-Gal) injection (1.5 g/kg). The transplantation group received hBMSCs via intraportal vein infusion (3×10<sup>6</sup> cells/kg) immediately after D-Gal administration. The stem cell-recipient interactions were quantitatively evaluated by biochemical function, cytokine array, metabolite profiling, transcriptome sequencing and immunohistochemistry. <h3>Results</h3> All pigs in the control group died within an average of 3.22 days, whereas 13/15 pigs in the transplantation group lived &gt;14 days. The cytokine array and metabolite profiling analyses revealed that hBMSC transplantation suppressed D-Gal-induced life-threatening cytokine storms and stabilised FHF within 7 days, while human-derived hepatocytes constituted only ∼4.5% of the pig hepatocytes. The functional synergy analysis of the observed profile changes indicated that the implanted hBMSCs altered the pigs' cytokine responses to damage through paracrine effects. Delta-like ligand 4 was validated to assist liver restoration in both pig and rat FHF models. <h3>Conclusions</h3> Our results delineated an integrated model of the multifaceted interactions between stem cells and recipients, which may open a new avenue to the discovery of single molecule-based therapeutics that simulate stem cell actions.