tbuckley/cabot-search huggingface dataset:
FRI0333 ASSESSING SYSTEMIC SCLEROSIS CARDIAC INVOLVEMENT USING MAGNETIC RESONANCE T1-MOLLI MAPPING
Authors: Sue-Ann Ng, Stephanie Marchesseau, John Carson Allen, John Totman, Andrea Low
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Patients with systemic sclerosis (SSc) and symptomatic cardiac involvement have a disease-associated mortality of 20% in 10 years. Prevalence of subclinical cardiac involvement is 15%-35%. Early diagnosis and monitoring is therefore critical in the management of SSc-associated cardiac involvement. Conventional cardiac magnetic resonance imaging (cMRI) T1-weighted sequence with late gadolinium contrast has good accuracy for detecting localized fibrosis but not diffuse fibrosis that occurs in SSc. Modified look-locker inversion recovery (T1-MOLLI) mapping, a novel cMRI sequence, has been used to detect and quantify diffuse fibrosis in aortic stenosis. T1-MOLLI values have also been correlated with the degree of biopsy-quantified fibrosis. <h3>Objectives</h3> To investigate whether cMRI T1-MOLLI is able to detect fibrosis associated with SSc cardiac involvement. <h3>Methods</h3> We recruited 16 patients fulfilling the 2013 ACR/EULAR criteria for SSc and 17 healthy age-matched (within 5 years) controls. Patients underwent cMRI T1-MOLLI mapping on the Siemens Biograph mMR 3.0T (Erlanger, Germany). T1-MOLLI values were compared between SSc patients and healthy controls using student t-test and statistical significance was taken to be p&lt;0.05. <h3>Results</h3> Demographics and clinical features of our study cohort are as shown in Table 1. Two (12.5%) SSc patients were symptomatic with palpitations or had arrhythmia requiring treatment. Eleven (68.8%) SSc patients had elevated T1 MOLLI values, using a normal cut-off threshold of 1284 ms. Mean cardiac T1 values were significantly higher in SSc patients (1329 ± 88.0 ms) than in controls (mean T1 = 1238 ± 93.7 ms, p=0.0075), indicating the presence of cardiac fibrosis. Conclusion: cMRI T1-MOLLI mapping demonstrated that SSc patients who were predominantly asymptomatic showed evidence of cardiac fibrosis. cMRI T1-MOLLI is potentially a useful diagnostic and monitoring tool for SSc cardiac disease. <h3>Disclosure of Interests</h3> None declared
Atrial Fibrillation Detection With Wearable Devices—Reply
Authors: James E. Ip
Journal: JAMA (2019)

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FRI0289 THE CYCLOPHOSPHAMIDE-SPARING ROLE OF AN INTENSIFIED B-CELLS DEPLETION PROTOCOL IN ANCA-ASSOCIATED VASCULITIS
Authors: Dario Roccatello, Savino Sciascia, Roberta Fenoglio, Daniela Rossi
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background:</h3> ANCA-associated vasculitis (AAV) are systemic diseases with relapsing chronic course. The management of AAV requires the use of immunosuppressive drugs whose use is associated with potential toxicity. <h3>Objectives:</h3> This case-control study aims to evaluate the immunosuppressive-sparing effect of rituximab (RTX) used with cyclophosphamide (CYC), compared to a traditional regimen based on high-dose CYC. <h3>Methods:</h3> 26 patients (pts) with AAV with a necrotising extracapillary glomerulonephritis were prospectively enrolled. 13 pts received the intensified protocol of B-lymphocyte depletion therapy (IBCDT) "4+2" with RTX and CYC (4 weekly infusions of RTX followed by 2 monthly followed by prednisone tapered to 5 mg/day in 3 months). 13 pts treated with the high-dose CYC treatment protocol followed by azathioprine as maintenance therapy were enrolled as controls. <h3>Results:</h3> In the 13 cases treated with the IBCDT we observed a significant reduction in mean values of parameter of disease activity. After administration of RTX, a significant reduction of the mean s-creatinine values and BVAS was observed. All pts had full B-cell depletion on peripheral blood after the first IBCDT protocol after 1 year. No further maintenance therapy was given. In the cases, a response was observed in 8/13 cases. 4 pts did not respond and a death was observed for cardiovascular causes. No significant difference was observed in terms of response to therapy between the two groups. The IBCDT allows a significant reduction in the cumulative dose of CYC to which each patient was exposed during follow-up, reaching statistical significance levels (p &lt;0.001). Calculated on a monthly basis, the "4+2" protocol allowed an average reduction in the CYC cumulative dose equivalent to 827 mg/month. <h3>Conclusion:</h3> In a selected sample of patients with AAV with renal involvement, the IBCT regimen appeared to be non inferior in terms of the efficacy when compared to CYC-based standard regimens. Moreover, the IBCDT regimen allowed a net reduction in the cumulative average dose of CYC to which pts are exposed, quantifiable in approximately 1g/month. <h3> Disclosure of Interests:</h3> None declared
Diagnostic Value of Cerebrospinal Fluid Neurofilament Light Protein in Neurology
Authors: Claire Bridel, Wessel N. van Wieringen, Henrik Zetterberg, Betty M. Tijms, Charlotte E. Teunissen, José C. Alvarez-Cermeño, Ulf Andreasson, Markus Axelsson, David C. Bäckström, Ales Bartos, Maria Bjerke, Kaj Blennow, Adam Boxer, Lou Brundin, Joachim Burman, Tove Christensen, Lenká Fialová, Lars Forsgren, Jette L. Frederiksen, Magnus Gisslén, Elizabeth Gray, Martin Gunnarsson, Sara Hall, Oskar Hansson, Megan K. Herbert, Joel Jakobsson, Jan Jessen-Krut, Shorena Janelidze, Gudmundur Johannsson, Michael Jonsson, Ludwig Kappos, Mohsen Khademi, Michael Khalil, Jens Kuhle, Mikael Landén, Ville Leinonen, Giancarlo Logroscino, Ching-Hua Lu, Jan Lycke, Nadia K. Magdalinou, Andrea Malaspina, Niklas Mattsson, Lieke H. Meeter, Sanjay R. Mehta, Signe Modvig, Tomas Olsson, Ross W. Paterson, Josué Pérez-Santiago, Fredrik Piehl, Yolande A. L. Pijnenburg, Okko T. Pyykkö, Oskar Ragnarsson, Julio C. Rojas, Jeppe Romme Christensen, Linda Sandberg, Carole S. Scherling, Jonathan M. Schott, Finn T. Sellebjerg, Isabella L. Simone, Tobias Skillbäck, Morten Stilund, Peter Sundström, Anders Svenningsson, Rosanna Tortelli, Carla Tortorella, Alessandro Trentini, Maria Troiano, Martin R. Turner, John C. van Swieten, Mattias Vågberg, Marcel M. Verbeek, Luisa M. Villar, Pieter Jelle Visser, Anders Wallin, Andreas Weiss, Carsten Wikkelsø, Edward J. Wild
Journal: JAMA Neurology (2019)

Neurofilament light protein (NfL) is elevated in cerebrospinal fluid (CSF) of a number of neurological conditions compared with healthy controls (HC) and is a candidate biomarker for neuroaxonal damage. The influence of age and sex is largely unknown, and levels across neurological disorders have not been compared systematically to date.
FORGe: prioritizing variants for graph genomes
Authors: Jacob Pritt, Nae-Chyun Chen, Ben Langmead
Journal: Genome biology (2018)

There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index. We introduce methods and a software tool called FORGe for modeling these effects and prioritizing variants accordingly. We show that FORGe enables a range of advantageous and measurable trade-offs between accuracy and computational overhead.
AB0836 THE INVESTIGATION OF BONE METABOLIC MARKERS ACCORDING TO THE FUNCTIONAL DISORDERS AMONG PATIENTS WITH RHEUMATOID ARTHRITIS
Authors: Tetsuya Kawano, Takeshi Kashiwagura, Toshiaki Aizawa, Moto Kobayashi, Masakazu Urayama, Natsuo Konishi, Tsutomu Sakuraba, Hiroki Itoh, Hidekazu Abe, Norio Suzuki, Keiji Kamo, Hiroshi Aonuma, Yusuke Sugimura, Yosuke Iwamoto, Takanori Miura, Naohisa Miyakoshi, Yoichi Shimada
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Rheumatoid arthritis (RA) is one of the causes of secondary osteoporosis, and steroids are often used in combination, therefore osteoporosis is highly associated with RA. Furthermore, joint disorders due to RA cause various degrees of dysfunction and ADL declines. The Steinbrocker classification is often used as the degree of dysfunction. Immobilization progresses with the progress of dysfunction, possibly causing severe osteoporosis. <h3>Objectives</h3> Of the 2238 cases in Akita Orthopedic Group omn Rheumatoid Arthrotis (AORA) registry 2017, 101 cases simultaneously measuring bone metabolism markers (TARCP-5b, NTX, urinary DPD, BAP, total P1NP) and pentosidine were involved. <h3>Methods</h3> Patients were divided by Steinbrocker classification into class 1,2 (group A 84 cases) and clss 3, 4 (group B 17 cases). we examined whether there is a difference in bone metabolism markers in each group according to Steinbrocker classification. <h3>Results</h3> The average age in group B (75.9) was significantly higher than group A (66.9) (p = 0.01). DAS 28 ESR was significantly higher in group B (p &lt; 0.01). There was no difference in eGFR representing renal function between the two groups. The urinary DPD (nM/mM Cr) and pentosidine (μg/ml) in group B was significantly higher than group A (p &lt;0.01). No difference was observed between the two groups in other bone metabolism markers. <h3>Conclusion</h3> Immobilization by long-term bed rest is known to enhance bone resorption. In 2002, Wakae reported DPD in urine showed a higher value in the group of not going out in femoral neck fracture cases. Based on the results of this study, urinary DPD showed a high value in RA group with high degree of dysfunction, which possibly reflected immobilization due to progress of functional disorder. Moreover, it is known that pentosidine will be higher in cases with high disease activity, severe osteoporosis will be occurred in the group with progressive functional disorder which is difficult to tight control. <h3>Disclosure of Interests</h3> None declared
Pulmonary vascular density: comparison of findings on computed tomography imaging with histology
Authors: Farbod N. Rahaghi, Gemma Argemí, Pietro Nardelli, David Domínguez-Fandos, Pedro Arguis, Víctor I. Peinado, James C. Ross, Samuel Y. Ash, Isaac de La Bruere, Carolyn E. Come, Alejandro A. Diaz, Marcelo Sánchez, George R. Washko, Joan Albert Barberà, Raúl San José Estépar
Journal: European Respiratory Journal (2019)

Background Exposure to cigarette smoke has been shown to lead to vascular remodelling. Computed tomography (CT) imaging measures of vascular pruning have been associated with pulmonary vascular disease, an important morbidity associated with smoking. In this study we compare CT-based measures of distal vessel loss to histological vascular and parenchymal changes. Methods A retrospective review of 80 patients who had undergone lung resection identified patients with imaging appropriate for three-dimensional (3D) vascular reconstruction (n=18) and a second group for two-dimensional (2D) analysis (n=19). Measurements of the volume of the small vessels (3D) and the cross-sectional area of the small vessels (&lt;5 mm 2 cross-section) were computed. Histological measures of cross-sectional area of the vasculature and loss of alveoli septa were obtained for all subjects. Results The 2D cross-sectional area of the vasculature on CT imaging was associated with the histological vascular cross-sectional area (r=0.69; p=0.001). The arterial small vessel volume assessed by CT correlated with the histological vascular cross-sectional area (r=0.50; p=0.04), a relationship that persisted even when adjusted for CT-derived measures of emphysema in a regression model. Conclusions Loss of small vessel volume in CT imaging of smokers is associated with histological loss of vascular cross-sectional area. Imaging-based quantification of pulmonary vasculature provides a noninvasive method to study the multiscale effects of smoking on the pulmonary circulation.
PB1683 INCIDENCE AND DEMOGRAPHIC CHARACTERISTICS OF THE MAJOR SUBGROUPS OF PRECURSOR B‐CELL ACUTE LYMPHOBLASTIC LEUKEMIA IN CHILDREN – A BULGARIAN SINGLE CENTER STUDY
Authors: N. Yurukova, G. Balatzenko, D. Konstantinov, M. Jordanova, B. Avramova
Journal: HemaSphere (2019)

Background: The detection of genetic aberrations is used to risk‐stratify patients with acute lymphoblastic leukemia (ALL), decide on the treatment protocol, and to estimate therapeutic effect through the detection of minimal residual disease. Aims: The aim of this study was: 1) to determine the frequency of the most common and significant genetic anomalies in children with ALL ‐ t(12;21)(p13;q22)/TEL‐ AML1, t(1;19)(q23;p13)/E2A‐PBX1, t(4;11)(q21;q23)/ MLL‐AF4 и t(9:22)(q34;q11.2)/BCR‐ABL; 2) to compere the incidence with that described in other studies; 3) to describe the demographic characteristics of the different genetic subgroups. Methods: For a thirteen year period, in 271 patients with established ALL, molecular‐genetic studies (RT‐PCR) were performed to search for the most common fusion genes. Results: In the study population of 271 patients, the incidence of TEL‐AML1 (+) OLL was 21%, E2A‐PBX1 (+) ALL was 5%, BCR‐ABL (+) was 3%, and MLL‐AF4 2.5%. A tendency for a characteristic demographic profile emerges for each genetic subgroup. Summary/Conclusion: This study is the first in Bulgaria. The results obtained are comparable to those published by other authors.
Prognostic significance of LINE-1 methylation level in the upper gastrointestinal cancer.
Authors: Yoshifumi Baba, Masayuki Watanabe, Shiro Iwagami, Hironobu Shigaki, Takatsugu Ishimoto, Masaaki Iwatsuki, Hideo Baba
Journal: Journal of Clinical Oncology (2012)

10523 Background: Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. DNA methylation in long interspersed nucleotide element-1 (LINE-1) is a good indicator of global DNA methylation level. Although LINE-1 methylation level is attracting interest as a useful marker for predicting cancer prognosis, the prognostic significance of LINE-1 hypomethylaiton in the upper gastrointestinal cancer [i.e., esophageal squamous cell carcinoma (ESCC) and gastric cancer (GC)] remains unclear. Methods: Using 217 ESCC and 207 GC specimens, we quantified the LINE-1 methylation using bisulfite-pyrosequencing technology. During the follow-up, there were a total of 63 ESCC recurrences, 51 ESCC deaths and 56 GC deaths. The median follow-up time for censored patients was 2.8 years. A Cox proportional hazards model was used to calculate the hazard ratio (HR), adjusted for the clinical, epidemiological, and pathological variables. The term “prognostic marker” is used throughout this study according to the REMARK Guidelines. Results: ESCCs and GCs showed significantly lower LINE-1 methylation levels compared to matched normal mucosa (p&lt;0.0001). In ESCC, LINE-1 hypomethylation was significantly associated with disease-free survival [log-rank p=0.0008; univariate HR= 2.32, 95% confidence interval (CI) 1.38-3.84, p=0.0017; multivariate HR=1.81, 95% CI 1.06-3.05, p=0.031] and cancer-specific survival (log-rank p=0.0020; univariate HR=2.21, 95% CI 1.33-3.60, p=0.0026; multivariate HR=1.87, 95% CI 1.12-3.08, p=0.018]. We found a significant modifying effect of the tumor stage on the relationship between LINE-1 methylation and the recurrence rate (P for interaction = 0.031). In GC, LINE-1 hypomethylation was significantly associated with cancer-specific survival (log-rank p=0.029; univariate HR=2.01, 95% CI 1.09-3.99). Conclusions: LINE-1 hypomethylation is associated with shorter survival in both ESCC and GC, suggesting that it has potential for use as a prognostic biomarker.
Author Correction: Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus–CA3 projection
Authors: Wenjun Zhou, Yanlin He, Atteeq U. Rehman, Yan Kong, Sungguan Hong, Guolian Ding, Hari Krishna Yalamanchili, Ying-Wooi Wan, Basil Paul, Chuhan Wang, Yingyun Gong, Wenxian Zhou, Hao Liu, John Dean, Emmanuel Scalais, Mary O’Driscoll, Jenny E. V. Morton, Xinguo Hou, Qi Wu, Qingchun Tong, Zhandong Liu, Pengfei Liu, Yong Xu, Zheng Sun
Journal: Nature Neuroscience (2019)
Leader β-cells coordinate Ca2+ dynamics across pancreatic islets in vivo
Authors: Victoria Salem, Luis Delgadillo Silva, Kinga Suba, Eleni Georgiadou, S. Neda Mousavy Gharavy, Nadeem Akhtar, Aldara Martin-Alonso, David C. A. Gaboriau, Stephen M. Rothery, Theodoros Stylianides, Gaelle Carrat, Timothy J. Pullen, Sumeet Pal Singh, David J. Hodson, Isabelle Leclerc, A. M. James Shapiro, Piero Marchetti, Linford J. B. Briant, Walter Distaso, Nikolay Ninov, Guy A. Rutter
Journal: Nature Metabolism (2019)
AB0853 BONE DENSITOMETRY IN CROHN’S DISEASE: RISK FACTORS FOR OSTEOPENIA AND OSTEOPOROSIS
Authors: Sabrine Soua, Dhilel Issaoui, Hela Kchir, Nouha Trad, Hatem Chaabouni, Nadia Maamouri
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Osteoporosis and osteopenia are common situations in chronic inflammatory bowel disease (IBD), particularly in crohn's disease. <h3>Objectives</h3> The objective of our study was to determine the prevalence of these affections during crohn's disease and to identify the risk factors for osteopenia and osteoporosis. <h3>Methods</h3> We conducted a descriptive monocentric retrospective study of consecutive patients with crohn's disease who were hospitalized between January 2016 and December 2018. <h3>Results</h3> We included 100 patients (64 female and 36 male) with an average age of 37 years [17-68 years]. Among these patients 21% were smokers and among women 20% were in menopause. Bone densitometry was performed in 39 patients. It was found to be pathological in 53.8% of cases. The rate of osteoporosis was 17.9% (7 patients) and the rate of osteopenia was 35.9% (14 patients). Tobacco and a BMI of less than 18 had a statistically significant association with osteopenia (p=0.046; p=0.038 respectively). The presence of a family history of IBD had a statistically significant influence on a pathological bone densitometric investigation (p=0.036). An albuminemia rate of less than 35g/dl had an association at the limit of significance with bone pathology in BMD (p=0.059). <h3>Conclusion</h3> Osteoporosis and osteopenia are frequent during crohn's disease. They are in the majority of cases asymptomatic. This makes bone densitometry essential, especially in the presence of a family history of IBD, smoking and malnutrition (BMI less than 18) in order to act early and avoid complications such as fractures. <h3>Disclosure of Interests</h3> None declared
Blood eosinophil counts in COPD patients compared to controls
Authors: Umme Kolsum, Thomas Southworth, Natalie Jackson, Dave Singh
Journal: European Respiratory Journal (2019)

In patients with COPD, blood eosinophil counts can predict the effects of inhaled corticosteroids (ICS) on exacerbation rates [1–4]. Blood eosinophil counts are now recommended by the Global initiative for the management of Obstructive Lung Disease (GOLD) as a biomarker to help guide ICS use in clinical practice [5]. Blood eosinophil counts are increased in COPD patients compared to healthy controls <http://bit.ly/2ML6pzZ>
PB2202 VALIDATION OF THE PRIMERDESIGN® QUANTITATIVE ALLELE SPECIFIC AMPLIFICATION KIT FOR THE DETECTION OF THE JAK2V617F MUTATION
Authors: D. Vaz
Journal: HemaSphere (2019)

Background: Janus Kinase 2 (JAK2) is part of a group of tyrosine kinases which are involved in cellular signalling. A point mutation in codon 617 of the JAK2 gene (JAK2 V617F) causes a ‘gain of function’ effect of this process, stimulating proliferation of the myeloid cell lines, including erythrocytes and platelets, as well as causing myelofibrosis in the bone marrow. Testing for this specific mutation using an allele‐specific PCR kit at our facility (NHLS‐TAD), Pretoria] should provide quick and reliable results to investigate suspected myeloproliferative neoplasms. As part of method comparison, 15 specimens known to be positive for the JAK2V617F mutation and 19 specimens known to be JAK2 negative, as previously assessed using PCR with melting curve analysis at Charlotte Maxeke Johannesburg Academic Hospital, will be analysed using the Primerdesign Quasa test kit on the BioRad CFX 96 platform. Results of the two PCR tests will be compared to evaluate accuracy of the kit. Aims: To validate the Primerdesign® quantitative allele specific amplification (Quasa) kit for detection of the JAK2V617F mutation in DNA extracted from whole blood samples. Methods: Patients’ samples, previously tested at the National Health Laboratory Service laboratory, Charlotte Maxeke Johannesburg Academic Hospital, will be used. These comprise both whole blood collected in EDTA as well as genomic DNA. 15 specimens known to be positive for the JAK2V617F mutation as well as 19 JAK2 negative specimens will be analysed as part of method comparison. We have chosen a sample size of 34 due to the substantial cost of each kit and we are limited due to financial constraints. The WHO international reference panel for genomic JAK2V617F with proposed percentages of 0, 0.03, 1, 10.8, 29.6, 89.5 and 100% will be used for quantitative analysis of the kit. In addition, we will be analysing a diluted JAK2V617F WHO sample to confirm the manufacturer's claim of an analytical sensitivity of 0.1%. Specimens already analysed will be re‐tested using the Primerdesign® quasa kit on the CFX96 real‐time PCR platform (Bio Rad). Results: There is a 95% concordance between the results obtained from the index test (Primerdesign kit) when compared to the test of reference (LightCycler). Precision includes repeatability and reproducibility, both of which were shown in this study. We were able to detect 0.1% mutant DNA in background wild type DNA as claimed by the manufacturer. Therefore the analytical sensitivity was at 0.1%. The ability of the test to not detect the mutation in a known negative sample was at 100% concordance. Therefore analytical specificity was 100% Summary/Conclusion: The Primerdesign allele specific kit has the capability of being able to produce qualitative as well as quantitative results based on the manufacturer's instructions. Being able to provide this diagnostic test in our department will decrease turn‐around time and improve patient care.