tbuckley/cabot-search huggingface dataset:
Abstract 825: Development of RNA quality-control methods to improve tissue archiving and molecular diagnostic testing
Authors: Lauren M. Stanoszek, Erin L. Crawford, Thomas Blomquist, James C. Willey
Journal: Cancer Research (2010)

Abstract Biospecimen collection and processing methods practiced today yield clinical samples with a wide variation in RNA quality. Efforts to improve these methods are inadequate due to insufficient means to measure RNA quality. Improved RNA quality control (QC) measurement methods will enable establishment of cut-off criteria to determine which biospecimens will yield reliable RT-PCR results. Implementation of such criteria will enable existing banks of samples with variable RNA quality to be used for reverse transcriptase polymerase chain reaction (RT-PCR)-based diagnostic test development. Sources of inter-sample variation in RNA quality include RNA integrity, genomic DNA (gDNA) contamination, and substances that either a) interfere with RT efficiency and/or b) carry over to cDNA and cause gene-specific inhibition of PCR efficiency. An RNA integrity reference model was established by incubating A549 cell line populations at room temperature for different amounts of time following cytolysis. Between 0 and 100 min. post cytolysis, ACTB degradation, as well as the degradation of other major housekeeping genes, was more rapid than decline in RNA Integrity Number (RIN) Score, a measurement based on microcapillary electropheresis. Quantification of single-copy CC10 gene gDNA in RNA controlled for gDNA contamination and measurement of transcript abundance of each gene relative to known number of respective cDNA internal standards controlled for PCR inhibitors. The RT inhibition test uses a Reverse Transcription Standards Mixture (RTSM) that contains a known number of copies of ERCC (External RNA Control Consortium) RNA and cDNA standards. A known quantity of RTSM is added to an RNA sample and measurement of PCR product from the RNA standard relative to its cDNA standard following RT-PCR assesses RT efficiency. These RT-PCR tests have been implemented on an Agilent 2100 Bioanalyzer® and are being developed for implementation on high throughput RT-PCR platforms such as the Biotrove OpenArray® nanoarray and the Gene Express Standardized Expression Measurement (SEM) Center™. Improved methods for biospecimen collection will be selected and will then be used to identify which samples collected according to present methods are suitable for analysis by RT-PCR-based molecular diagnostic tests. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 825.
SP0141 Ask the Patient. Distinguishing Your Symptoms
Authors: C. Andrén
Journal: Annals of the Rheumatic Diseases (2014)

<h3>PER – the patients own registration</h3> In Sweden cooperates patients, at rheumatology clinics, with their doctor with the help of an IT tool called PER. It is an Internet based tool where patients answer questions about their health before they meet with their doctor. The patient may choose to register their answers on a computer at the clinic or at home on their own computer, I-pad, I-phone or android. The information they register goes directly into SRQ – Swedish rheumatology quality register that is nationwide. The physician can see the patients registration directly and use that and other information in the registry as a basis for decisions during the visit. The questions which the patient answers is about pain, quality of life, daily functioning, joint swelling and joint tenderness. Once registration is complete, the patient gets an overview showing the current registration, disease activity, medications, and test results. At the medical examination, the doctor makes his assessment of joints and disease activity. Together they go through the results of the registration, medical assessment and continued treatment using the overview. PER is used on about two thirds of all rheumatology clinics in Sweden. Studies show that both patients and physicians perceive several benefits of using PER. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.6198
PMO-221 Appropriateness of follow-up indications after colonic polyp removal: audit of current practice in a district general hospital
Authors: J K J Diss, A Hashim, D Arokianathan, J Colquhoun, G Tritto
Journal: Gut (2012)

<h3>Introduction</h3> Demand for colonoscopy is increasing worldwide due to the implementation of colon cancer screening programmes. According to current guidelines, the indication and timing for surveillance colonoscopy after removal of colonic adenomas are based on a risk estimation taking into account number and size of adenomas removed. In this study we audited the compliance with guidelines in the current practice of two district general hospital endoscopy services. <h3>Methods</h3> The study was conducted at the King George and Queen9s Hospitals in Essex (UK). All colonoscopies from June to August 2011 were retrospectively reviewed. All polyp-finding colonoscopies were selected and relevant data were retrieved from electronic records, patient notes and histopathology reports. The appropriate follow-up indication was established according to current British Society of Gastroenterology (BSG) guidelines, taking into account previous risk status, number and size of colonic adenomas. Finally the ideal indication was compared with the actual follow-up indication given to each patient. <h3>Results</h3> A total of 1438 colonoscopies were reviewed. Polyps were found and removed in 314 (22%). Only 205 were included in further analysis. The remaining 109 were excluded because further follow-up indication was based on different issues (12 IBD, 19 colon cancers, 34 technical problems, 21 unknown previous risk status, 23 referred for surgery). Of the included 205, 34 patients were given an appointment in 1 year (high risk), one in 2 years, 28 in 3 years (intermediate risk), 142 in 5 years or no follow-up (low risk). The follow-up indication was compliant with BSG guidelines in 136 (66.3%) cases. In 33 (16.1%) patients the follow-up appointment was scheduled too early and in 4 (2%) too late. The remaining 32 (15.6%) were booked for later decision in outpatient clinic. They belonged to the intermediate (No.=28) and high (No.=4) risk groups. Overall, in the 3-months period, 24 inappropriate colonoscopies and 32 extra outpatient appointments were scheduled for the following year alone. In a further step we reviewed 154 histopathology results of benign polyps and found that 22 (14.3%) more patients could have had their follow-up appointment modified on the basis of the final histopathology finding (2 earlier and 20 later). <h3>Conclusion</h3> The overall compliance with BSG guidelines in the evaluated period was 66.3% which is higher to that reported in previous studies. Nevertheless in only 3 months a significant inappropriate workload for endoscopy and outpatient clinics was generated. A more careful compliance with guidelines and a review of histopathology results could save a significant number of unnecessary colonoscopies and outpatient appointments. <h3>Competing interests</h3> None declared.
SAT0097 Assessing Significant Flares in Rheumatoid Arthritis: Validity of the Omeract Preliminary Flare Questionnaire (PFQ) in the Canadian Early Arthritis Cohort
Authors: S.J. Bartlett, C.O. Bingham, E. Choy, G. Boire, B. Haraoui, D. Lin, J.E. Pope, C. Thorne, C.A. Hitchon, D. Tin, E.C. Keystone, V. Bykerk
Journal: Annals of the Rheumatic Diseases (2014)

<h3>Background</h3> Rheumatoid arthritis (RA) flares are common, poorly defined, and understudied. A new tool is needed that can precisely and reliably measure significant RA flares that may signal need for evaluation for treatment change. Qualitative and quantitative research by the OMERACT RA Flare Group with an international group of scientists, patients and healthcare providers has led to the identification of an RA Flare Core Domain Set which was ratified by OMERACT 2012 attendees. <h3>Objectives</h3> To evaluate construct validity of the OMERACT Preliminary Flare Questionnaire in a large early RA observational trial. <h3>Methods</h3> 501 patients in the Canadian early ArThritis CoHort (CATCH) completed PFQs at two consecutive visits from 11-2011 through 5-2013. Flare status was classified using rheumatologist and patient evaluations as well as two criteria for using DAS scores that have been proposed. Patient completed PFQs for pain, physical function (PF), fatigue, stiffness, participation and coping over previous week using 11-point NRS scales, as well as HAQ, SF12, RADAI, WPAI and Patient Global. MDs provided clinical ratings. Inter-rater reliability was assessed using % agreement and kappa. Spearman correlations were calculated between PFQs and legacy items/scales. <h3>Results</h3> At enrollment, participants were mostly female (75%), white (83%), and 59% had &gt; HS education. Mean (SD) age was 55 (15) years and RA duration 6 (3) months. 33% of patients were classified as being in a flare by MDs; percentage agreement across 3 other classification methods ranged from 71-74% (kappa = 0.15-0.35). Irrespective of flare definition, correlations were strongest between PFQ pain and other pain scales (r9s=0.76-0.93); and moderate-strong correlations were evident among PFQ with other measures of PF (r9s=0.60-0.83), fatigue (r9s=0.59-0.88), stiffness (r=0.52-0.69), participation (r9s=0.49-0.86) and coping (r9s=0.42-0.83). <h3>Conclusions</h3> Using 4 different flare classification systems, there was substantial association among single item PFQs and legacy RA measures. These results from a large national observation study increase confidence in the construct validity of OMERACT PFQ items to assess core domains in early RA. Additional psychometric evaluation is needed to establish the reliability, validity, and responsiveness of the PFQ and relevant thresholds across a range of RA populations and settings prior to widespread use. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.3928
AB0153 Comparative proteomic analysis of neutrophils from patients with microscopic polyangiitis and granulomatosis with polyangiitis
Authors: T. Uchida, K. Nagai, T. Sato, N. Iizuka, M. Arito, Y. Takakuwa, H. Nakano, S. Ooka, M. Kurokawa, N. Suematu, K. Okamoto, S. Ozaki, T. Kato
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Both microscopic polyangiitis (MPA) and granulomatosis with polyangiitis (GPA) belong to ANCA-associated vasculitis (AAV), in which neutrophils are thought to be involved in their pathology. Clinically, it is often difficult to distinguish MPA from GPA. To discriminate between MPA and GPA, protein profiles of peripheral blood polymorphonuclear cells (PMNs) of MPA and GPA patients and healthy controls (HC) were analyzed. <h3>Objectives</h3> In this study, proteomic profilesof PMN of AAV patients and healthy controls (HC) were analyzed using two-dimensional difference gel electrophoresis (2D-DIGE), in order to confirm whether the profiles are useful to discriminate between AAV and HC, or MPA and GPA. <h3>Methods</h3> Proteins extracted from peripheral blood PMNs of 11 MPA patients, 9 GPA patients, and 10 HC were separated by two-dimensional difference gel electrophoresis (2D-DIGE). Differentially expressed protein spots were identified by mass spectrometry analysis. Then, to find biomarker candidates which discriminate between MPA and GPA, the obtained protein profiles were subjected to the multivariate data analysis using SIMCA-P+ containing principal component analysis (PCA) and orthogonal partial-least-squares-discriminate analysis (OPLS-DA), and subjected to the receiver operating characteristic (ROC) analysis. <h3>Results</h3> In all the 864 protein spots detected, intensity of 55 spots was found to be significantly different (<i>p</i> &lt; 0.05) among the three groups by an analysis of variance (ANOVA). 31 out of the 55 spots were identified by mass spectrometry. The OPLS-DA analysis revealed that the expression profile of the protein spots discriminated the AAV group from the HC group completely and also discriminated the MPA group from the GPA group completely. 13 protein spots were considered as biomarker candidates to distinguish between MPA and GPA. In those, spots whose intensity was higher in MPA than in GPA included actin with various p<i>I</i> values, while a considerable part of spots whose intensity was higher in GPA than MPA were proteins related with the activity of neutrophils. Among the candidate proteins, ROC analysis showed that a combination of neutrophil gelatinase-associated lipocalin and a kinase anchor protein 7 isoforms beta had a high diagnostic potential. <h3>Conclusions</h3> In the study, we determined that the protein profile of the neutrophil was clearly different between AAV and HC, and between MPA and GPA. In Particular, GPA was characterized by high expression level of the proteins associated with the activity of the neutrophil. <h3>Disclosure of Interest</h3> None Declared
AB1354 Observed dosing and refill compliance in bio-naÏve and bio-experienced ankylosing spondylitis patients treated with golimumab
Authors: L. Ellis, S. Haas, S. Bolge, N. Tandon
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Golimumab is a once-monthly, subcutaneously-administered, anti-TNF agent indicated for treatment of patients with ankylosing spondylitis (AS). Real-world dosing and refill compliance patterns of golimumab use in AS patients have not been reported previously. <h3>Objectives</h3> This study reports golimumab (GLM) dosing and refill compliance observed in ankylosing spondylitis (AS) patients. <h3>Methods</h3> This retrospective database analysis assessed GLM use in adult AS patients with ≥2 GLM prescriptions between 4/24/2009 and 12/31/2010; ≥1 AS diagnosis during the study period; continuous activity in the Source® LX database (≥6 months before; ≥6 months after the index GLM prescription); and a 28-31 day GLM supply. Refill compliance was defined as refills occurring ± 1 week of the expected 28-31 day (d) interval. The percent of compliant GLM refill intervals and the percent of patients demonstrating refill compliance at the 6th GLM dose were assessed in the overall population and in bio-naïve/bio-experienced subgroups. Descriptive statistics were used to characterize the study population (mean±SD, median, n and %). <h3>Results</h3> A total of 99 AS patients and 559 GLM refill intervals were studied. The sample was 53% male; mean age of 44 years with 72% bio-experienced. A 50 mg GLM dose was found in 99% of all fills. The mean ± SD refill interval for the overall population was 35.1±21.0 d with a median of 30 d. The refill interval of bio-experienced patients (34.8±18.7 d; median 30 d) was similar to bio-naïve patients (35.8±25.8 d; median 31 d). Refill compliance was observed in 79% of all intervals for the overall population. Refill compliance at the 6th GLM dose was achieved by 83% of patients overall. <h3>Conclusions</h3> In this retrospective analysis of a large national administrative claims database, 99% of GLM doses were 50 mg with approximately once monthly refill intervals. Overall refill compliance was observed in nearly 80% of all GLM refills and in greater than 80% of AS patients at the sixth GLM dose. Median refill interval and refill compliance appeared similar in bio-experienced and bio-naïve subgroups. Further study of these trends using additional data sources are desired to substantiate these preliminary findings. <h3>Disclosure of Interest</h3> L. Ellis Employee of: Janssen Scientific Affairs, LLC, S. Haas Consultant for: Janssen Scientific Affairs, LLC, S. Bolge Employee of: Janssen Scientific Affairs, LLC, N. Tandon Employee of: Janssen Scientific Affairs, LLC
A Multicenter Observational Study of Incretin-based Drugs and Heart Failure
Authors: Kristian B. Filion, Laurent Azoulay, Robert W. Platt, Matthew Dahl, Colin R. Dormuth, Kristin K. Clemens, Nianping Hu, J. Michael Paterson, Laura Targownik, Tanvir C. Turin, Jacob A. Udell, Pierre Ernst
Journal: New England Journal of Medicine (2016)

There is concern that antidiabetic incretin-based drugs, including dipeptidyl peptidase 4 (DPP-4) inhibitors and glucagon-like peptide 1 (GLP-1) analogues, can increase the risk of heart failure. Ongoing clinical trials may not have large enough samples to effectively address this issue. We applied a common protocol in the analysis of multiple cohorts of patients with diabetes. We used health care data from four Canadian provinces, the United States, and the United Kingdom. With the use of a nested case-control analysis, we matched each patient who was hospitalized for heart failure with up to 20 controls from the same cohort; matching was based on sex, age, cohort-entry date, duration of treated diabetes, and follow-up time. Cohort-specific hazard ratios for hospitalization due to heart failure among patients receiving incretin-based drugs, as compared with those receiving oral antidiabetic-drug combinations, were estimated by means of conditional logistic regression and pooled across cohorts with the use of random-effects models. The cohorts included a total of 1,499,650 patients, with 29,741 hospitalized for heart failure (incidence rate, 9.2 events per 1000 persons per year). The rate of hospitalization for heart failure did not increase with the use of incretin-based drugs as compared with oral antidiabetic-drug combinations among patients with a history of heart failure (hazard ratio, 0.86; 95% confidence interval [CI], 0.62 to 1.19) or among those without a history of heart failure (hazard ratio, 0.82; 95% CI, 0.67 to 1.00). The results were similar for DPP-4 inhibitors and GLP-1 analogues. In this analysis of data from large cohorts of patients with diabetes, incretin-based drugs were not associated with an increased risk of hospitalization for heart failure, as compared with commonly used combinations of oral antidiabetic drugs. (Funded by the Canadian Institutes of Health Research; ClinicalTrials.gov number, NCT02456428.).
Convenient Ambulatory Care — Promise, Pitfalls, and Policy
Authors: Ji Eun Chang, Suzanne C. Brundage, Dave A. Chokshi
Journal: New England Journal of Medicine (2015)

The authors describe the rapid expansion of retail clinics and urgent care centers in the United States, and they discuss their potential cost advantages and their potential threats to quality of care. They also review the current regulation of these new models of care.
OC-036 Neuronavigated Repetitive Cerebellar Stimulation Produces Long-Lasting Activation of Human Cortical Swallowing Projections
Authors: D H Vasant, S Mistry, V Jayasekeran, E Michou, S Hamdy
Journal: Gut (2013)

<h3>Introduction</h3> Animal studies, human brain imaging and more recently Transcranial Magnetic Stimulation (TMS) suggest a role for the cerebellum in human swallowing. Moreover, paired-pulse cerebellar-cortical TMS delivered in rapid succession (50–200 ms intervals) facilitates pharyngeal motor cortex excitability. We therefore hypothesised that high-frequency (5–20 Hz) repetitive TMS (rTMS) of the cerebellum could modulate pharyngeal motor cortex excitability producing long-lasting changes that may prove to be therapeutically useful for dysphagia after stroke. <h3>Methods</h3> In 17 healthy adults (6 female, age range 18–61 yrs), anatomical MR brain scans were acquired. Thereafter participants were intubated with an intraluminal catheter to record pharyngeal electromyography and underwent TMS cortical mapping with neuronavigation to co-localise pharyngeal motor representation bilaterally, hand motor cortex and the cerebellar site which evoked the largest pharyngeal motor response. Subjects were then randomised to receive one of 5 neuronavigated cerebellar rTMS interventions (Sham, 1 Hz, 5 Hz, 10 Hz and 20 Hz, at least 1 week apart) to the cerebellar site evoking the largest baseline pharyngeal responses to single-pulse cerebellar TMS. Bihemispheric pharyngeal cortical excitability (ipsilateral and contralateral cortex to cerebellum site) was measured at baseline and for up to one hour post cerebellar rTMS intervention. Abductor pollicis brevis (APB) recordings were used as control. Interventional data were compared to sham using repeated measures ANOVA. <h3>Results</h3> Cerebellar rTMS was tolerated well and delivered at an average intensity of 55% of stimulator output. Compared to Sham, 10Hz cerebellar rTMS increased pharyngeal cortical excitability (F (1.16) = 8.3, *<i>p</i> = 0.01), with maximal size and durational effects seen primarily in the contralateral pharyngeal cortex (+72%, **<i>p</i> = 0.02, <i>Figure 1</i>). By contrast, 1Hz (F (1.16) = 0.3, <i>p</i> = 0.60), 5Hz (F (1.16) = 0.5, <i>p</i> = 0.48), and 20Hz rTMS (F (1.16) = 1.3, <i>p</i> = 0.27) cerebellar conditioning did not significantly alter pharyngeal excitability compared to Sham. APB responses were not significantly different to sham after any intervention. <h3>Conclusion</h3> Our data show for the first time that high-frequency (10Hz) cerebellar stimulation can produce long-lasting increases in human pharyngeal motor cortex excitability, with larger and longer-lasting effects of the intervention primarily seen in the contralateral projection. Hence 10 Hz cerebellar rTMS may play a therapeutic role in the treatment of dysphagia after hemispheric stroke. <h3>Disclosure of Interest</h3> None Declared
1165 CLINICAL UTILITY OF THE ARCHITECT HCV AG ASSAY FOR EARLY TREATMENT RESPONSE MONITORING IN PATIENTS WITH CHRONIC HEPATITIS C GENOTYPE 1 INFECTION
Authors: J. Vermehren, S. Süsser, A. Berger, D. Perner, K.H. Peiffer, S. Zeuzem, C. Sarrazin
Journal: Journal of Hepatology (2012)
Endoscopic diagnosis of secondary rectal teratoma in a young woman with constipation and positive fecal occult blood test
Authors: A. Federico, A. Gravina, A. Tiso, A. Miranda, F. D’Armiento, M. Mascolo, S. Maurea, M. Romano
Journal: Endoscopy (2010)

In the literature there are several reports of primary teratomas of the rectum [1]; however, the incidence of ovarian teratoma with secondary rectal involvement is extremely rare (10 cases in the literature in the past 100 years) [2]. Ovarian teratoma is usually a benign lesion, containing a diversity of tissues including hair, teeth, bone, and thyroid [3]. It is mostly detected in the childbearing years, and up to 15 % of women have bilateral lesions. The prevalence of complications is < 5 %, and the complications include torsion, rupture, infection, and malignant transformation [4] [5].
Case 5-2007
Authors: Didier Raoult, Suhny Abbara, Davinder S. Jassal, Richard L. Kradin
Journal: New England Journal of Medicine (2007)

A 53-year-old man was admitted to the hospital with a 4-month history of worsening fatigue, dyspnea, weight loss, and sweats. Four years earlier, aortic-valve replacement surgery had been performed for severe aortic insufficiency, which recurred 3 months later, requiring replacement of the prosthetic valve. Evaluation during the current admission showed splenomegaly and an abnormal echocardiogram. A procedure was performed.
Communicating in Organizations, Part IV
Authors: Jay A. Harolds
Journal: Clinical Nuclear Medicine (2012)

E-mail messages and face-to-face meetings both are important methods of communication, and each has its own advantages and disadvantages. Conducting informal one-on-one meetings well is important to the success of a leader or manager. However, the follower can also do many things to optimize the success of a one-on-one discussion with his superior.
A COMPUTER-BASED METHOD FOR DETECTION AND LOCALIZATION OF PERFUSION DEFECTS ON RESTING PLANAR THALLIUM-201 SCINTIGRAPHY
Authors: Dalila Bellil, Jamshid Maddahi, Ken Van Train, Allan S. Lew, Prediman Shah, Daniel Berman
Journal: Clinical Nuclear Medicine (1987)

Bellil, Dalila; Maddahi, Jamshid; Train, Ken Van; Lew, Allan S.; Shah, Prediman; Berman, Daniel Author Information