tbuckley/cabot-search huggingface dataset:
Mapping the global distribution of Buruli ulcer: a systematic review with evidence consensus
Authors: Hope Simpson, Kebede Deribe, Earnest Njih Tabah, Adebayo Peters, Issaka Maman, Michael Frimpong, Edwin Ampadu, Richard Phillips, Paul Saunderson, Rachel L Pullan, Jorge Cano
Journal: The Lancet Global Health (2019)

BackgroundBuruli ulcer can cause disfigurement and long-term loss of function. It is underdiagnosed and under-reported, and its current distribution is unclear. We aimed to synthesise and evaluate data on Buruli ulcer prevalence and distribution.MethodsWe did a systematic review of Buruli ulcer prevalence and used an evidence consensus framework to describe and evaluate evidence for Buruli ulcer distribution worldwide. We searched PubMed and Web of Science databases from inception to Aug 6, 2018, for records of Buruli ulcer and Mycobacterium ulcerans detection, with no limits on study type, publication date, participant population, or location. English, French, and Spanish language publications were included. We included population-based surveys presenting Buruli ulcer prevalence estimates, or data that allowed prevalence to be estimated, in the systematic review. We extracted geographical data on the occurrence of Buruli ulcer cases and M ulcerans detection from studies of any type for the evidence consensus framework; articles that did not report original data were excluded. For the main analysis, we extracted prevalence estimates from included surveys and calculated 95% CIs using Byar's method. We included occurrence records, reports to WHO and the Global Infectious Diseases and Epidemiology Network, and surveillance data from Buruli ulcer control programmes in the evidence consensus framework to grade the strength of evidence for Buruli ulcer endemicity. This study is registered with PROSPERO, number CRD42018116260.Findings2763 titles met the search criteria. We extracted prevalence estimates from ten studies and occurrence data from 208 studies and five unpublished surveillance datasets. Prevalence estimates within study areas ranged from 3·2 (95% CI 3·1–3·3) cases per 10 000 population in Côte d'Ivoire to 26·9 (23·5–30·7) cases per 10 000 population in Benin. There was evidence of Buruli ulcer in 32 countries and consensus on presence in 12.InterpretationThe global distribution of Buruli ulcer is uncertain and potentially wider than currently recognised. Our findings represent the strongest available evidence on Buruli ulcer distribution so far and have many potential applications, from directing surveillance activities to informing burden estimates.FundingAIM Initiative.
UN: All-out Effort Needed to Combat Antimicrobial Resistance
Authors: M.J. Friedrich
Journal: JAMA (2019)

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Cysteine-type cathepsins promote the effector phase of acute cutaneous delayed-type hypersensitivity reactions
Authors: Johannes Schwenck, Andreas Maurer, Birgit Fehrenbacher, Roman Mehling, Philipp Knopf, Natalie Mucha, Dennis Haupt, Kerstin Fuchs, Christoph M. Griessinger, Daniel Bukala, Julia Holstein, Martin Schaller, Irene Gonzalez Menendez, Kamran Ghoreschi, Leticia Quintanilla-Martinez, Michael Gütschow, Stefan Laufer, Thomas Reinheckel, Martin Röcken, Hubert Kalbacher, Bernd J Pichler, Manfred Kneilling
Journal: Theranostics (2019)

Cysteine-type cathepsins such as cathepsin B are involved in various steps of inflammatory processes such as antigen processing and angiogenesis. Here, we uncovered the role of cysteine-type cathepsins in the effector phase of T cell-driven cutaneous delayed-type hypersensitivity reactions (DTHR) and the implication of this role on therapeutic cathepsin B-specific inhibition. Methods: Wild-type, cathepsin B-deficient (Ctsb-/-) and cathepsin Z-deficient (Ctsz-/-) mice were sensitized with 2,4,6-trinitrochlorobenzene (TNCB) on the abdomen and challenged with TNCB on the right ear to induce acute and chronic cutaneous DTHR. The severity of cutaneous DTHR was assessed by evaluating ear swelling responses and histopathology. We performed fluorescence microscopy on tissue from inflamed ears and lymph nodes of wild-type mice, as well as on biopsies from psoriasis patients, focusing on cathepsin B expression by T cells, B cells, macrophages, dendritic cells and NK cells. Cathepsin activity was determined noninvasively by optical imaging employing protease-activated substrate-like probes. Cathepsin expression and activity were validated ex vivo by covalent active site labeling of proteases and Western blotting. Results: Noninvasive in vivo optical imaging revealed strong cysteine-type cathepsin activity in inflamed ears and draining lymph nodes in acute and chronic cutaneous DTHR. In inflamed ears and draining lymph nodes, cathepsin B was expressed by neutrophils, dendritic cells, macrophages, B, T and natural killer (NK) cells. Similar expression patterns were found in psoriatic plaques of patients. The biochemical methods confirmed active cathepsin B in tissues of mice with cutaneous DTHR. Topically applied cathepsin B inhibitors significantly reduced ear swelling in acute but not chronic DTHR. Compared with wild-type mice, Ctsb-/- mice exhibited an enhanced ear swelling response during acute DTHR despite a lack of cathepsin B expression. Cathepsin Z, a protease closely related to cathepsin B, revealed compensatory expression in inflamed ears of Ctsb-/- mice, while cathepsin B expression was reciprocally elevated in Ctsz-/- mice. Conclusion: Cathepsin B is actively involved in the effector phase of acute cutaneous DTHR. Thus, topically applied cathepsin B inhibitors might effectively limit DTHR such as contact dermatitis or psoriasis. However, the cathepsin B and Z knockout mouse experiments suggested a complementary role for these two cysteine-type proteases.
Abstract 17304: Comparison of Inpatient Outcomes Among Patients With and Without Systemic Vasculitis Admitted With Acute Myocardial Infarction in the United States: The National (Nationwide) Inpatient Sample 2000-2012
Authors: Menhel Kinno, Sean Dikdan, Njambi Mathenge, Abdul W Kazi, Irfan Admani, Haroon Faraz, Eugenio Capitle, Cindy Grines
Journal: Circulation (2017)

Introduction: Systemic vasculitis (SV) is associated with adverse cardiovascular events, underscoring the relationship between chronic inflammation and premature atherosclerosis. Limited data exist...
SPORTS1.0: A Tool for Annotating and Profiling Non-Coding RNAs Optimized for rRNA- and tRNA-Derived Small RNAs
Authors: Junchao Shi, Eun-A Ko, Kenton M. Sanders, Qi Chen, Tong Zhou
Journal: Genomics Proteomics & Bioinformatics (2018)

High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users' input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
Authors: Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
Journal: Genome biology (2019)

Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Using multiple scRNA-seq datasets, we validate that our method demonstrates comparable accuracy to and is markedly faster than the state-of-the-art software. Moreover, CellFishing.jl is scalable to more than one million cells, and the throughput of the search is approximately 1600 cells per second.
PF185 WT1 OVEREXPRESSION PREDICTED GOOD OUTCOMES IN ADULT B‐CELL ACUTE LYMPHOBLASTIC LEUKEMIA PATIENTS RECEIVING CHEMOTHERAPY
Authors: S. Wang, C. Wang, T. Li, W. Wang, Q. Hao, X. Xie, D. Wan, Z. Jiang, Y. Liu
Journal: HemaSphere (2019)

Background: B‐cell acute lymphoblastic leukemia (B‐ALL) is a clinically and biologically heterogeneous disease that is characterized by the clonal expansion of developmentally arrested B‐cell precursors. Despite significant improvements in the management of this disease in children, the prognosis of adult patients remains poor. Identifying new prognostic markers is necessary to help select the best therapeutic schedules. Wilms’ tumor gene 1 (WT1) is a transcription factor that is overexpressed in diverse neoplasms, including acute leukemia. The prognostic role of WT1 in ALL is still controversial. No study has focused on the prognostic role of WT1 expression in adult B‐ALL patients receiving chemotherapy only. Aims: To investigate the prognostic value of WT1 expression in adult patients with B‐ALL. Methods: The WT1 transcript levels of 162 de‐novo adult B‐ALL patients were determined by TaqMan‐based real time quantitative PCR (RQ‐PCR) at the time of diagnosis. Eighty‐eight patients received allogeneic hematopoietic stem cell transplantation (allo‐HSCT). Survival functions were estimated by the Kaplan‐Meier method and compared by the log‐rank test. Cumulative incidences were estimated for relapse to accommodate competing risks. A Cox proportional hazard regression model was used to determine the associations between WT1 transcript levels and CIR, RFS and OS. Results: WT1 overexpression was defined as a transcript level higher than 0.50%, which is the upper limit in normal bone marrow. WT1 overexpression was identified in 66.0% of the patients. WT1 overexpression was an independent positive prognostic factor for the cumulative incidence of relapse (CIR), relapse‐free survival (RFS) and overall survival (OS) in patients who received chemotherapy only (CIR: HR = 0.236 [95% confidence interval 0.094–0.592]; P = 0.002; RFS: HR = 0.223 [0.092–0.543]; P = 0.001; OS: HR = 0.409 [0.214–0.783]; P = 0.007) and in patients who did not have BCR‐ABL fusion or KMT2A rearrangements (CIR: HR = 0.431 [0.201–0.921]; P = 0.030; RFS: HR = 0.449 [0.224–0.899]; P = 0.024; OS: HR = 0.521 [0.278–0.977]; P = 0.042). However, WT1 overexpression had no prognostic value in patients who received allogenic hematopoietic stem cell transplantation (allo‐HSCT). Furthermore, allo‐HSCT could improve the prognosis of patients with low WT1 expression. Summary/Conclusion: Therefore, testing for WT1 expression at the time of diagnosis may predict outcomes in adult B‐ALL patients who receive only chemotherapy and who do not have the BCR‐ABL fusion gene or KMT2A rearrangements. Allo‐HSCT may improve the prognosis of patients with low WT1 transcript levels.
FRI0718-HPR THE EFFECT OF THE BIOPSYCHOSOCIAL EXERCISE PROGRAM ON PAIN COPING SKILL AND FATIGUE IN RHEUMATIC DISEASES
Authors: Aykut Özçadırcı, Gamze Arın, Yasemin Özel Aslıyüce, Fatma Birgül Kumbaroğlu, Nur Banu Karaca, Aybüke Seven, Sedat Kiraz, Ali Akdoğan, Edibe Ünal
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Although the trend towards biopsychosocial approaches is increasing today, studies on psychosocial effects of exercise are limited in the literature. There is a need for framed exercise programs to assess the clinical effectiveness of biopsychosocial approaches. The reason why biopsychosocial programs are important may be due to multidimensional features of symptoms such as pain, fatigue. <h3>Objectives</h3> The purpose of this study is to investigate the effectiveness of the biopsychosocial exercise program on pain coping skill and fatigue in rheumatic patients. <h3>Methods</h3> Ninety-one patients with the rheumatic disease were included in this study. The patients were divided into two groups based on a prospective cohort (BETY group, n = 56; and control group, n = 35). BETY is a biopsychosocial exercise approach (1). It was performed in a period of one hour, 3 times a week for 12 weeks and included clinical pilates exercises, dance therapy-authentic movement and pain management information. The control group did not take any exercise treatment. The BETY-Biopsychosocial Questionnaire (BETY-BQ) was used to evaluate the pain coping skill and fatigue as well as assessing whole biopsychosocial status of individuals (2). The answers were given to the 5th question (I don't know how to control my pain.) and the 11th question (I feel tired.) of the BETY-BQ were recorded as a 5-point Likert at ranging from 'yes, always' to 'no, never. Also, the total score of BETY-BQ was recorded. Demographic data were given as mean ± standard deviation (X ± SD), and answers given to the questionnaire were expressed in frequency tables. <h3>Results</h3> The mean ages of BETY group and control group were 49.63 ± 11 and 39.74 ± 10 years and body mass indexes were 26.93 ± 3 kg/m2 and 26,54 ± 4 kg/m2, respectively. The frequency of answers to the 5th and 11th question and the total score of the BETY-BQ on the first assessment (pre-treatment) and the second assessment (post-treatment) were shown in Table 1. <h3>Conclusion</h3> It was concluded that BETY as a biopsychosocial exercise approach is effective in reducing fatigue and improving the pain coping skill as well as the biopsychosocial status of rheumatic patients. BETY should be kept in mind for further studies in terms of biopsychosocial aspects of pain coping, fatigue, etc. <h3>References</h3> [1] Kisacik, Pinar, et al. "Investigating the effects of a multidimensional exercise program on symptoms and antiinflammatory status in female patients with ankylosing spondylitis."Complementary therapies in clinical practice22 (2016): 38-43. [2] ÜNAL, Edibe, et al. "Romatizmalı hastalar için bir yaşam kalitesi ölçeğinin geliştirilmesi: madde havuzunun oluşturulması." Journal of Exercise Therapy and Rehabilitation 4.2 (2017): 67-75. <h3>Disclosure of Interests</h3> None declared
PF812 INTRAVENOUS IRON SUPPLEMENTATION PROTOCOL FOR POST‐PARTUM ANEMIA
Authors: E. Volpato, I. Cuppari, D. Lissoni, M.T. Pugliano, R. Crocchiolo, S. Rossini
Journal: HemaSphere (2019)

Background: The World Health Organization (WHO) determines as post‐partum anemia values of harmoglobin (Hb) less than 10 g/dl. In most cases, it's an iron deficiency anemia and affects about the 27% of new mothers and has as a consequence a strong socio‐economic impact. One of the most important causes is the post partum haemorrhage (PPH), that's to say 500 ml of blood loss in the first 24 hours after a vaginal delivery or more than 1000 ml after a caesarean section. Nowadays PPH is one of the most common causes of mortality and morbidity rate among obstetric population and its frequency is between the 5% and the 22 % of the total deliveries. Aims: The objective of the present study is to determine the efficacy of an iron supplementation protocol for post‐èartum anemia. Methods: Our protocol provides a valuation of Hb in the post partum period. When Hb is greater than 8..5 g/dl, the new mother can be discharged from hospital and is treated by oral iron supplementaion with ferrous sulfate but it will be necessary to control the Hb value after 30 days. In case of HB belove 8..5 g/dl, parenteral iron is used (iron carbossymaltose) in the Obstretician Unit, then there will be a new assessment after 10/15 days at Service of Immunohaematology and Trasfusional Medicine to decide if to go on supplementation. Results: From 01/06/2017 to 31/12/2018 36 new mothers, average age 34 years (range 23 ‐ 43) have been enrolled. During the recovery, 34 new mothers have been treated with ferric carboxymaltose: 26 with a dosage of 500 mg and 8 with 1 g. Among these 34 women, 4 have been trasfused after a severe PPH and concomitant thalassaemic trait. Only 2 of the new mothers have been discharged with ferrous sulfate. At discharge, average Hb was 7.3 g/dl. At first access in Transfusional Center, the average Hb value was 10.8 g/dl with a medium delta of 3.5 g/dl. According to the hemoglobin values, 18 new mothers have continued oral iron therapy, 14 have been treated with ferric carboxymaltose and only 2 didn’t need therapy. Summary/Conclusion: Our protocol has been implemented thanks to the indications of National Blood Center about the PMB to ensure, through the multidisciplinarity, the transfusion appropriatness, the resource optimization and the improvement of the patient's outcome. The intravenous iron therapy with ferric carboxymaltose in new mothers suffering a severe iron deficiency anemia allows a fast rise of hemoglobin values and an improvment of psychophysical wellbeing of the new mother and a lowering of the number of blood transfusions.
SP0030 DEVELOPING E-HEALTH SOLUTIONS FOR PATIENTS WITH PATIENTS
Authors: Susanne Karlfeldt
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background:</h3> At the Center for Rheumatology the Patient9s voice and needs are always central in the planning and development of the organization and its' services and structure. The Patient Council at the unit, with representatives from 14 different patient organizations, is a core facility that is always addressed when decisions are to be made that affects the patients. The need of a structure for digital re-visits at the clinic was raised in the Patient Council meeting. <h3>Objectives:</h3> To develop a structure for a fully digital re-visit where all the preparations, the actual visit and the documentation and follow up could be conducted using different e-Health solutions and digital tools. <h3>Methods:</h3> By first asking the involved patient representatives about desired interfaces and features of the end solution, we could decide on which available tools and structures we could build the digitial re-visit around. A working group including patients, health care providers at the unit and technical staff, together formed the end product. <h3>Results:</h3> A fully digitalized structure for re-visits to different health care providers (physicians, nurses, physiotherapists etc) is now up and running with an increasing number of visits every week. <h3>Conclusion:</h3> By asking the patients about what is most important for them we focus on solutions and services that the patients really need and ask for. If we involve patients in the process from the very beginning, we know that we are doing the right thing and that we use our resources in the best way. <h3>Disclosure of Interests:</h3> None declared
RADpainter and fineRADstructure: Population Inference from RADseq Data
Authors: Milan Malinsky, Emiliano Trucchi, Daniel John Lawson, Daniel Falush
Journal: Molecular Biology and Evolution (2018)

Powerful approaches to inferring recent or current population structure based on nearest neighbor haplotype "coancestry" have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in nonmodel organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here, we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data. We combine this program together with a previously published MCMC clustering algorithm into fineRADstructure-a complete, easy to use, and fast population inference package for RADseq data (https://github.com/millanek/fineRADstructure; last accessed February 24, 2018). Finally, with two example data sets, we illustrate its use, benefits, and robustness to missing RAD alleles in double digest RAD sequencing.
PB2421 INVESTIGATION OF FIBRIN MONOMER AND VON WILLEBRAND FACTOR LEVELS IN CHILDREN AFTER CARDIAC SURGERY WITH CARDIOPULMONARY BYPASS
Authors: V. Lastovka, O. Gordeeva
Journal: HemaSphere (2019)

Background: Cardiopulmonary bypass (CPB) is associated with thrombotic complications. Occurrence of thrombosis after CPB is 11% which takes the third place between CPB‐associated complications. Current data demonstrates the impotance of researching of changes in haemostatic system in paediatric patients after CPB. Provided below data is an intermediate result of our research. Aims: Evaluate the dynamics of vWF and FM in children undergoing cardiac surgery. Methods: 39 patients in age up to 11 months 29 days (median age ‐ 5,5 months, youngest age – 2 days after birth, oldest – 11 months 29 days), who underwent cardiac surgery with CPB to treat congenital heart diseases, were enrolled in this study. All patients were divided into two groups: 1 st ‐without thrombosis, 2 nd ‐with thrombotic complications. Von Willebrand factor and Fibrin‐monomer (FM) plasma levels were assessed in three points: before surgery, 24‐hours after surgery and 72‐hours after surgery. Thrombotic cases were proved by doppler ultrasound or MRI. Results: Thrombotic complications were diagnosed in 7 children (18%). Between all thrombotic complications ischemic strokes were diagnosed in 57% (4 cases), arterial thrombosis in 28 % (2 cases), intracardiac thrombus in 14% (1 case). In group with thrombotic complications FM‐mean values in points 1, 2 and 3 respectively were 78,33; 37,15 and 79,44 mcg/ml, meanwhile in group without thrombosis ‐ 8,21, 13,78 и 8,72 mcg/ml. PC‐mean values in 1 st – group were‐ 104, 292 and 170%, in the 2‐nd group 192, 362 and 301% respectively in the points 1,2 and 3. Statistically significant differences between groups in 3d point (p &lt; 0,05) and correlation between vWF and FM (r = 0,92, p &lt; 0.05) were detected. Summary/Conclusion: CPB causes hypercoagulation with increasing of vWF and FM levels.Moreover, assotiated with high risk of thrombotic complications at the first 3 days after cardiac surgery. Further studies to investigate prognostic value of FM and vWF as markers of thrombotic complications and possibility of prevention and treatment of these complication in children undergoing cardiac surgery with CPB.