tbuckley/cabot-search huggingface dataset:
Abstract 19694: The Impact of Neointimal Tissue Morphology Evaluated by Optical Coherence Tomography on Development Process of Very Late In-stent Restenosis After Drug-eluting Stent: Four Serial Coronary Angiograms Study
Authors: Kenichi Fujii, Satoru Otsuji, Wataru Yamamoto, Kasumi Ishibuchi, Hiroto Tamaru, Shin Takiuchi, Katsuyuki Hasegawa, Rui Ishii, Shou Nakabayashi, Yorihiko Higashino
Journal: Circulation (2017)

Background: Recently, very late in-stent restenosis (VL-ISR) is occasionally observed beyond a few years after drug-eluting stents (DESs) implantation. This study evaluated the process of progressi...
SP0066 HOW TO IMPROVE YOUR TEACHING SKILLS
Authors: Loreto Carmona
Journal: Annals of the Rheumatic Diseases (2019)

<h3></h3> This is not an easy task to do in 20 minutes, but we will try to engage the attendee and to pass the message through. The most important take home message of this lecture will be that "it is the learning, not the teaching, what we must master". Good teachers are, therefore, mere facilitators of the learning process, not the stars. This lecture will have two parts, one dedicated to teaching in general and a second one on assessment (because assessment style drives learning behaviour). Four are the principles of teaching in medicine: 1) orientation not only to knowledge but to problem solving, 2) adaptation to needs, 3) evaluation of the efficacy of teaching, and 4) learning should be enjoyable. We will review each one of these principles and how to implement them in our daily teaching. Things like preparing a lesson plan, or tips to engage learners, will be part of this lecture. In the second part we will outline how to improve assessment and generate good questions. <h3>Disclosure of Interests:</h3> Loreto Carmona Grant/research support from: Abbvie, Actelion, Astellas, BMS, Eisay, Gebro Pharma, Grünenthal, Leo Pharma, Lilly, MSD, Novartis, Pfizer, Roche, Sanofi-Aventis and UCB Pharma, Paid instructor for: Novartis
AB0186 CORRELATIONS BETWEEN RENAL TRANSCRIPTOMIC PROFILES AND OUTOCOMES IN A MOUSE MODEL OF SYSTEMIC LUPUS ERYTHEMATOSUS
Authors: Pauline Montigny, Aurélie Degroof, Davide Brusa, Frederic Houssiau, Bernard Lauwerys
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background:</h3> Factors contributing to poor renal outcomes in lupus nephritis (LN) are poorly understood. In our previous research, we found an association between the presence of activated immune effectors in the lupus kidney and disease severity. Here we investigated correlations between patterns of renal genes expression and biological parameters of renal disease activity in a mouse model of systemic lupus erythematosus (SLE). <h3>Methods:</h3> We collected blood, urine, kidneys and spleens from 33 B6/Sle1.Sle2.Sle3 congenic mice, before disease onset at 3 months (n=8), and at different stages of disease progression, at 6 (n=7), 9-10 (n=12) and 17-18 (n=5) months. RNA was extracted from kidneys, and hybridized on Mouse Gene 2.0 ST exon arrays. Unsupervized hierarchical clustering studies and pathways analyses were performed on Genespring and DAVID softwares. Spleen and kidney CD8 T cell activation and differentiation markers were evaluated by flow cytometry (CD8, CD69, CD62L, CD44, CD122, CD25, CD44, CCR7, CD279, CD152, CD11a, CD103). Plasma urea and albuminuria were measured by immunoassay. <h3>Results:</h3> 712 (out of 33,793) transcripts were overexpressed in kidneys from diseased mice (age &gt; 6 months). These transcripts were significantly enriched in the following pathways: response to type I interferons, antigen processing and presentation, activation and regulation of B cells, complement activation, and regulation of cytotoxicity mediated by T cells. Proportions of renal CD8 T cells with an effector phenotype were significantly increased in the kidneys from 6 months and older compared to younger mice, and compared to paired spleens. Proportions of renal effector CD8 T cells correlated significantly with transcripts involved in interferon signature, adaptive immune responses, cytotoxic T cells, chemotaxis, and correlated negatively with pathways associated with renal tubular cell functions. Finally, we found a correlation between biological parameters of kidney function (plasma urea, albuminuria) and transcripts involved in pro-fibrotic pathways, chemokines and adaptive immune responses. <h3>Conclusion:</h3> Our results confirm the link between the presence of activated immune effectors in the kidney and renal outcomes in a mouse model of SLE, similar to our previous observations in human LN, and warrant further functional studies on the role of kidney-infiltrating T and B cells in this model. <h3>Acknowledgement:</h3> This research was funded in part by grants from Fonds de la Recherche Scientifique – FNRS, Fondation Roi Baudouin and Fondation Saint-Luc. <h3>Disclosure of Interests:</h3> None declared
AB0246 PREDICTORS OF FATIGUE IN RHEUMATOID ARTHRITIS PATIENTSWHO RECEIVE BIOLOGICAL AND TARGETED SYNTHETIC DISEASE-MODIFYING ANTIRHEUMATIC DRUGS
Authors: Dalifer Freites Nuñez, Marta Redondo, Lydia Abasolo, Pia Lois, Isabel Hernandez, Cristina Vadillo, Leticia León
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Fatigue is one of the most frequent symptoms in patients with rheumatoid arthritis (RA), affecting more than 80% of them. Despite being a very disabling symptom, the variables that predict it are still unknown. <h3>Objectives</h3> To identify potential factors associated with fatigue. <h3>Methods</h3> Cross-sectional study. 60 patients were included, patients were being followed up in the rheumatology outpatient clinic of Hospital Clínico San Carlos, Madrid, Spain. Data were collected between July 2018 and January 2019. All patients met the ACR/EULAR 2010 criteria and they were in treatment with Biological agents or Targeted Synthetic DMARDs. <b>Main variable:</b> Fatigue was assessed by the Bristol Rheumatoid Arthritis Fatigue Multidimensional Questionnaire (BRAF-MDQ) and the Bristol Rheumatoid Arthritis Fatigue Numerical Rating Scale (BRAF-NRS). <b>Covariables:</b> Sociodemographic, clinical, Disease-related variables and treatment. <b>Statistical analysis.</b> A descriptive analysis was carried out for the different variables. To identify factors independently associated to BRAF-MDQ a multivariable linear regression was applied. Results were expressed as β with their corresponding 95% CI. A value of p &lt; 0.05 was accepted as statistically significant. <h3>Results</h3> A total of 60 patients, comprising of 53 females (88%) and 7 males (12%) with a mean age of 56.45±11.89 years and mean disease duration of 14.11±7.79 years were evaluated. RF was positive in 60% of patients. 65% of the patients were in active on work and 23% were retired. Regarding comorbidities, 43% had dyslipidemia, 42% hypertension, 17% hypothyroidism and 15% depression. The DAS28-ESR and SDAI scores of the patients were 2.68 ± 0.86, 8.56 ± 5.96 respectively. The rest of the clinical, treatment characteristics, and the scores of the fatigue instruments used in the study are shown in <b>Table 1</b>. Physical dimension was the most affected according to patients, who perceive an average severity and affectation, and insufficient coping. The factors affecting the total BRAF-MDQ was evaluated in multivariate analyze <b>Table 2.</b> We found that patients with Disability (p &lt;0.0001) and those in treatment with Non anti-TNF (p 0.048), experienced more fatigue while a positive RF (p 0.022) decreases overall fatigue. <h3>Conclusion</h3> Fatigue is a substantial symptom in RA patients and should be evaluated on the daily clinical practice. The results of our study indicated that disability and type of treatment were the dominant factors in the experience and degree of fatigue. Disease activity (DAS28 and SDAI) was not associated to fatigue. The evaluation and management of fatigue should be one of the objectives in the treatment of patients with RA <h3>Disclosure of Interests</h3> None declared
Abstract MP058: Racial and Gender Differences in Acute Ischemic Stroke Pre-hospital Documentation: Last Known Well, Pre-alert Notification and Stroke Severity, Paul Coverdell National Acute Stroke Program, 2012-2015
Authors: Erika Odom, Sallyann Coleman King, Xin Tong
Journal: Circulation (2017)

Stroke is the fifth leading cause of death in the United States and a major cause of adult disability. Documentation of stroke-related factors that occur before arrival to the hospital or immediately upon arrival may be critical in determining patient eligibility for life-saving measures, including receipt of thrombolytic therapy (e.g., alteplase) and other neurointerventional treatment. There is a need to describe differences in documentation of pre-hospital measures, in order to improve overall stroke patient care. De-identified data for 216,129 stroke patients were reported by hospital personnel during the 2012-2015 Paul Coverdell National Acute Stroke Program. Chi-square tests were performed to examine the differences on demographic and pre-hospital measures by gender and race. The median age was greater for females than males (75 vs 68 years) and for whites than blacks (74 vs 63 years). A higher percentage of females had Medicare coverage than males (67.8% vs. 57.4%, p&lt;0.001), while blacks had higher Medicaid coverage than whites (12.8% vs. 4.2%, p&lt;0.0001). Females (49.9%) and blacks (48.8%) had the highest percentage of arrival by EMS. Among patients who arrived by emergency services, the percentage of blacks with advance notification of stroke was lower than whites (49.8% vs. 58.2%, p&lt;0.0001). Females (53.0%) were slightly less likely to have last known well time recorded than males (53.8%). Blacks were significantly less likely to have last known well time and stroke severity recorded compared whites (p&lt;0.0001). The median time interval between last known well and emergency department arrival for blacks were 4.8 hours, significantly longer than median time of 4.0 hours for whites (p&lt;0.001). Differences in documentation of pre-hospital measures, particularly between racial groups, suggest room for improvement in communication of information from the pre-hospital environment to emergency department staff, which may support access to critical links in the chain of stroke survival, including activation of stroke care teams who can provide swift access to life-saving treatment.
PF538 GENETIC EVOLUTION PATTERNS IN PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA TO SECONDARY ACUTE MYELOID LEUKEMIA: AN ANALYSIS OF 36 PAIRED SAMPLES
Authors: Y.‐J. Su, M.‐C. Kuo, P.‐N. Wang, J.‐H. Wu, T.‐H. Lin, T.‐Y. Huang, T.‐L. Lin, H. Chang, Y.‐S. Hung, L.‐Y. Shih
Journal: HemaSphere (2019)

Background: Chronic myelomonocytic leukemia (CMML) are associated with a tendency to secondary acute myeloid leukemia (sAML) progression. Aims: We sought to examine the patterns of genetic evolution by analyzing a cohort of matched paired samples collected at initial diagnosis and at sAML transformation. Methods: Mutational analyses of 33 genes related to myeloid neoplasms on paired bone marrow samples from 36 patients with CMML at both diagnosis and sAML phase were performed. The samples were analyzed by PCR‐based assays followed by direct sequencing and/or next generation sequencing (NGS). The allele frequency of mutated genes was determined by variant allele frequency with NGS and/or pyrosequencing for validation. Results: Mutational analyses on the 36 paired CMML/sAML samples showed that 92% of patients had at least one mutated gene at initial diagnosis. Gene mutations involving epigenetic regulators (65%), myeloid transcription factors (52%), spliceosome (50 %), and signaling pathway (47%) were frequently detected, followed by BCOR (11%), NPM1 (6%) and SETBP1 (6%), mutations of cohesin complex were rare (3%), and none had TP53 , WT‐1 or BCORL1 mutations. Co‐existed mutations with different gene classes were present in 78% of CMML patients at diagnosis. The median time from CMML to sAML was 7.2 months (ranged from 1 to 89.6 months). At sAML transformation, 97% of patients had at least one mutated gene, mutation frequencies of epigenetic regulators (62%) and spliceosome (56%) remained mostly unchanged at sAML phase. Acquisition of additional gene mutations was observed in 47% of patients during sAML progression, in which signaling pathway mutations emerged most frequently (RTK/RAS/JAK‐STAT: 5/3/1), followed by transcription factors (3 acquiring RUNX1 mutations and 3 CEBPa ). Emergence of new mutant subtypes of the same genes with or without disappearance of pre‐existed mutants was found in 3 RUNX1 , and one each for CBL, PTPN11 and TET2 mutated patients during sAML progression. In addition, 8 patients had apparently increase in allele burden (&gt;20%) for 6 genes. Loss of mutations was found in 4 (11%) patients during sAML progression, one each for PTPN11 , JAK2 V617F, CSF3R and TET2 . Eight patients had apparently decrease in allele burden (&gt;20%) for 4 different genes ( N‐RAS , PTPN11 , CBL and RUNX1 ). Summary/Conclusion: The present study on a relative large cohort of matched paired CMML/sAML samples showed that genetic evolution from CMML to sAML exhibited different patterns, including stable mutations, acquisition of new mutations, subclone selection or expansion of pre‐existed clones. Loss of mutation might occur but infrequently.
Fast and accurate genomic analyses using genome graphs
Authors: Goran Rakocevic, Vladimir Semenyuk, Wan-Ping Lee, James Spencer, John Browning, Ivan J. Johnson, Vladan Arsenijevic, Jelena Nadj, Kaushik Ghose, Maria C. Suciu, Sun-Gou Ji, Gülfem Demir, Lizao Li, Berke Ç. Toptaş, Alexey Dolgoborodov, Björn Pollex, Iosif Spulber, Irina Glotova, Péter Kómár, Andrew L. Stachyra, Yilong Li, Milos Popovic, Morten Källberg, Amit Jain, Deniz Kural
Journal: Nature Genetics (2019)
Abstract 18980: Effect of Severe Renal Dysfunction and Diffuse Interstitial Fibrosis on Left Ventricular Remodeling After TAVR
Authors: Jeremy Hill, Kimi Sato, Yash Jobanputra, Samir Kapadia, Amar Krishnaswamy, Stephanie Mick, Brian Griffin, Scott Flamm, Wael Jaber, Zoran Popovic, Deborah H Kwon
Journal: Circulation (2017)

Introduction: Severe renal dysfunction (SRD) has been shown to have increased diffuse interstitial myocardial fibrosis (DIF). It is unclear how SRD and DIF impact left ventricular remodeling follow...
Abstract 14738: Acute Effects of Diets Rich in Almonds and Walnuts on Endothelial Function in Humans
Authors: Ravindra Bhardwaj, Shanthi Manivannan, Wissam Gharib, Bradford Warden, Gerry Hobbs, Abnash Jain
Journal: Circulation (2012)

Background: Omega-3 fatty acid and Linolenic acid (ALA) reduces cardiovascular disease (CVD) risk, possibly by favorably changing vascular inflammation and endothelial dysfunction. Objective: The o...
METTL3 promote tumor proliferation of bladder cancer by accelerating pri-miR221/222 maturation in m6A-dependent manner
Authors: Jie Han, Jing-zi Wang, Xiao Yang, Hao Yu, Rui Zhou, Hong-Cheng Lu, Wen-Bo Yuan, Jian-chen Lu, Zi-jian Zhou, Qiang Lu, Ji-Fu Wei, Haiwei Yang
Journal: Molecular Cancer (2019)

METTL3 is known to be involved in all stages in the life cycle of RNA. It affects the tumor formation by the regulation the m6A modification in the mRNAs of critical oncogenes or tumor suppressors. In bladder cancer, METTL3 could promote the bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner. Recently, METTL3 was also found to affect the m6A modification in non-coding RNAs including miRNAs, lincRNAs and circRNAs. However, whether this mechanism is related to the proliferation of tumors induced by METTL3 is not reported yet. Quantitative real-time PCR, western blot and immunohistochemistry were used to detect the expression of METTL3 in bladder cancer. The survival analysis was adopted to explore the association between METTL3 expression and the prognosis of bladder cancer. Bladder cancer cells were stably transfected with lentivirus and cell proliferation and cell cycle, as well as tumorigenesis in nude mice were performed to assess the effect of METTL3 in bladder cancer. RNA immunoprecipitation (RIP), co-immunoprecipitations and RNA m6A dot blot assays were conducted to confirm that METTL3 interacted with the microprocessor protein DGCR8 and modulated the pri-miR221/222 process in an m6A-dependent manner. Luciferase reporter assay was employed to identify the direct binding sites of miR221/222 with PTEN. Colony formation assay and CCK8 assays were conducted to confirm the function of miR-221/222 in METTL3-induced cell growth in bladder cancer. We confirmed the oncogenic role of METTL3 in bladder cancer by accelerating the maturation of pri-miR221/222, resulting in the reduction of PTEN, which ultimately leads to the proliferation of bladder cancer. Moreover, we found that METTL3 was significantly increased in bladder cancer and correlated with poor prognosis of bladder cancer patients. Our findings suggested that METTL3 may have an oncogenic role in bladder cancer through interacting with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner. To our knowledge, this is the first comprehensive study that METTL3 affected the tumor formation by the regulation the m6A modification in non-coding RNAs, which might provide fresh insights into bladder cancer therapy.
Abstract 15735: The Value of Biomarkers of Angiogenesis and Endothelial Dysfunction in Predicting the Response to CD34+ Cell Therapy in Non-Ischemic Dilated Cardiomyopathy Patients
Authors: Gregor Zemljic, Martina Jaklic, Andraz Cerar, Sabina Frljak, Gregor Poglajen, Francois Haddad, Bojan Vrtovec
Journal: Circulation (2018)

Introduction: Although there is evidence of beneficial effects of CD34+ therapy in non-ischemic dilated cardiomyopathy (DCM), the individual patient response is highly variable. Hypothesis: We inve...
Telomere length and recurrence risk after curative resection in women with adenocarcinoma of the lung: A prospective cohort study.
Authors: Eric S. Kim, Yuanqing Ye, Ara A. Vaporciyan, Jinliang Xing, Maosheng Huang, Jian Gu, Jack A. Roth, Scott Michael Lippman, Xifeng Wu
Journal: Journal of Clinical Oncology (2013)

1532 Background: We hypothesized that telomere length in peripheral blood would have significant predictive value for risk of recurrence after curative resection in non-small cell lung cancer (NSCLC). Methods: This prospective study included 473 patients with histologically confirmed early stage NSCLC who underwent curative resection at MD Anderson Cancer Center between 1995 and 2008. Relative telomere length (RTL) of peripheral leukocytes was measured by real-time PCR. The risk of recurrence was estimated as hazard ratios (HRs) and 95% confidence intervals (CIs) using a multivariable Cox proportional hazard regression model. Results: Median duration of follow-up was 61 months and 151 patients (32%) had developed recurrence at time of analysis. Patients who developed recurrence had significantly longer mean RTL compared to those without recurrence (1.13 vs 1.07, P=0.046). A subgroup analysis indicates that women had longer RTL compared to males (1.12 vs 1.06, P=0.025), and the patients with adenocarcinoma demonstrated longer RTL compared to those with other histologic types (1.11 vs 1.05, P=0.042). To determine if longer RTL in women and adenocarcinoma subgroup would predict risk of recurrence, multivariate Cox analysis adjusting for age, gender, stage, pack year and treatment regimens was performed. Longer telomeres were significantly associated with higher risk of developing recurrence in female (HR=2.25; 95% CI, 1.02-4.96, P=0.044) and adenocarcinoma subgroups (HR=2.19; 95% CI, 1.05-4.55, P=0.036). The increased risk of recurrence due to long RTL was more apparent in females with adenocarcinoma (HR=2.67; 95% CI, 1.19-6.03, P=0.018). Conclusions: This is the first prospective study to suggest that long RTL is associated with recurrence in early stage NSCLC after curative resection. Women and adenocarcinoma appear to be special subgroups in which telomere biology may play an important role. (Supported by NCI CA 111646, CA 55769, and CA 70907.)
Suicide Among Older Adults Living in or Transitioning to Residential Long-term Care, 2003 to 2015
Authors: Briana Mezuk, Tomohiro M. Ko, Viktoryia A. Kalesnikava, David Jurgens
Journal: JAMA Network Open (2019)

Almost 25% of Medicare beneficiaries live in residential long-term care (LTC) (eg, independent or assisted living facility or nursing home). There are few reliable statistics on completed suicide in LTC, in part because of data limitations.To estimate the number of suicides associated with residential LTC (ie, among persons in a facility, transitioning into or out of a facility, or otherwise associated with LTC) among adults 55 and older and, secondarily, to identify whether machine learning tools could improve the quality of suicide surveillance data.Cross-sectional epidemiologic study (conducted in 2018) of restricted-access data from the National Violent Death Reporting System (NVDRS) (2003-2015) using restricted-access case narratives from suicides and undetermined deaths among adults 55 years and older in 27 states. Participants were all suicides and undetermined deaths (N = 47 759) among persons 55 years and older.Long-term care cited in the coroner/medical examiner case narrative, whether as a reason for self-harm or the injury location, identified using machine learning natural language processing (NLP) algorithms plus manual review of texts.Number and characteristics (eg, demographics, health history, and means of injury) of suicides associated with LTC. The κ statistic was used to estimate the reliability of the existing NVDRS injury location codes relative to cases identified by the algorithm.Among 47 759 persons 55 years and older (median age, 64 years; 77.6% male; 90.0% non-Hispanic white), this study identified 1037 suicide deaths associated with LTC, including 428 among older adults living in LTC, 449 among older adults transitioning to LTC, and 160 otherwise associated with LTC. In contrast, there were only 263 cases coded with the existing NVDRS location code "supervised residential facility," which had poor agreement with cases that the algorithm identified as occurring in LTC (κ statistic, 0.30; 95% CI, 0.26-0.35).Over a 13-year period, approximately 2.2% of suicides among adults 55 years and older were associated with LTC in some manner. Clinicians, administrators, and policy makers should consider ways to promote the mental health and well-being of older adults experiencing functioning limitations and their families. Natural language processing may be a useful way to improve abstraction of variables in the NVDRS.
SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-Scale Single Cell RNA-Seq Data
Authors: Xianwen Ren, Liangtao Zheng, Zemin Zhang
Journal: Genomics Proteomics & Bioinformatics (2019)

Abstract Clustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate and efficient clustering are of pressing need. Here we proposed Spearman subsampling-clustering-classification (SSCC), a new clustering framework based on random projection and feature construction, for large-scale scRNA-seq data. SSCC greatly improves clustering accuracy, robustness, and computational efficacy for various state-of-the-art algorithms benchmarked on multiple real datasets. On a dataset with 68,578 human blood cells, SSCC achieved 20% improvement for clustering accuracy and 50-fold acceleration, but only consumed 66% memory usage, compared to the widelyused software package SC3. Compared to k-means, the accuracy improvement of SSCC can reach 3-fold. An R implementation of SSCC is available at https://github.com/Japrin/sscClust.