tbuckley/cabot-search huggingface dataset:
Diagnosing Achilles tendinopathy is like delicious spaghetti carbonara: it is all about key ingredients, but not all chefs use the same recipe
Authors: Robert-Jan de Vos, Arco C van der Vlist, Marinus Winters, Florus van der Giesen, Adam Weir
Journal: British Journal of Sports Medicine (2020)

Achilles tendinopathy is the term used to describe the clinical entity of localised Achilles tendon pain that is associated with load-bearing activities. Achilles tendinopathy as a term was agreed on the 2018 International Scientific Tendinopathy Symposium Consensus (ICON) statement—which followed an expert meeting in Groningen (the Netherlands).1 Having uniform terminology is important for many reasons. But a clinical term is not the same as a diagnosis with clear diagnostic criteria. Clear diagnostic criteria help patients understand their problem, guide treatment and determine prognosis. Naming a medical condition can be likened to naming a recipe, but the exact ingredients used can differ between chefs. In this editorial, we discuss the diagnostic challenges, where ‘top chefs’ disagree which ingredients are present in mid-portion Achilles tendinopathy.

Many medical diagnostic tests are often validated by comparing them to a gold standard (eg, imaging, surgical or histological findings). Most sports injuries and long-standing musculoskeletal pain conditions have unclear pathogenesis and lack clear gold standards (consider patellofemoral pain). When imaging was added to the clinical diagnostic criteria in patients with patellofemoral pain it added no value.2 The classic tissue-based diagnosis paradigm has been increasingly abandoned. A paradigm shift towards using history and clinical examination …
The design and construction of reference pangenome graphs with minigraph
Authors: Heng Li, Xiaowen Feng, Chong Chu
Journal: Genome biology (2020)

Abstract The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implement our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.
Assessing the validity of the association between the SMO4 M55V variant and risk of type 1 diabetes (vol 37, pg 110, 2005)
Authors: D J Smyth, Howson Jmm., C E Lowe, N M Walker, A C Lam, S Nutland, J Hutchings, E Tuomilehto-Wolf, J Tuomilehto, C Guja, C Ionescu-Tirgoviste, D E Undlien, K S Ronningen, D Savage, D B Dunger, Twells Rcj., W L McArdle, D P Strachan, J A Todd
Journal: Nature Genetics (2005)
Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state
Authors: Daniela Cerezo-Wallis, Marta Contreras-Alcalde, Kevin Troulé, Xavier Catena, Cynthia Mucientes, Tonantzin G. Calvo, Estela Cañón, Cristina Tejedo, Paula C. Pennacchi, Sabrina Hogan, Peter Kölblinger, Héctor Tejero, Andrew X. Chen, Nuria Ibarz, Osvaldo Graña-Castro, Lola Martinez, Javier Muñoz, Pablo Ortiz-Romero, José L. Rodriguez-Peralto, Gonzalo Gómez-López, Fátima Al-Shahrour, Raúl Rabadán, Mitchell P. Levesque, David Olmeda, María S. Soengas
Journal: Nature Medicine (2020)
COVID-19 in dialysis patients: outlasting and outsmarting a pandemic
Authors: Caroline M. Hsu, Daniel E. Weiner
Journal: Kidney International (2020)

Coronavirus disease 2019 (COVID-19) has affected the care and outcomes of patients treated with dialysis worldwide. In this issue of Kidney International, 3 reports highlight the disproportionately severe impact of COVID-19 on patients on dialysis, noting its high prevalence, particularly among patients receiving in-center dialysis. This likely reflects patients' limited ability to physically distance as well as community exposures, including residence in areas with high rates of infection. Patients on dialysis are at extremely high risk should they develop COVID-19, with short-term mortality of 20% or higher. Accordingly, it is imperative that the kidney community intervenes to reduce the threat of COVID-19 in this vulnerable population by focusing on modifiable factors, including universal masking of patients and staff and enhanced screening, including testing for COVID-19 in the patients who are asymptomatic during times of high local prevalence.
Erratum: Results from the phase III randomized trial of onartuzumab plus erlotinib versus erlotinib in previously treated stage IIIB or IV non-small-cell lung cancer: METLung (Journal of Clinical Oncology (2017) DOI: 10.1200/JCO.2016.69.2160)
Authors: David R. Spigel, Martin J. Edelman, Kenneth O’Byrne, Luis Paz-Ares, Simonetta Mocci, See Phan, David S. Shames, Dustin Smith, Virginia E. Paton, Tony Mok
Journal: Journal of Clinical Oncology (2018)

The February 1, 2017, article by Spigel et al, entitled Results From the Phase III Randomized Trial of Onartuzumab Plus Erlotinib Versus Erlotinib in Previously Treated Stage IIIB or IV Non-Small-Cell Lung Cancer: METLung (J Clin Oncol 10.1200/JCO.2016.69.2160), was published with an error. Under Affiliations, Luis Paz-Ares' information should have included University of Seville.This has been corrected as of February 7, 2018. The authors apologize for the error.
Abstract 195: Chronic Enhancement of Endogenous Nitric Oxide Production via Whole Body Periodic Acceleration (WBPA) Induces Cardioprotection in 15 Months Diabetic Mice
Authors: Arkady Uryash, Valentina Flores, Juan Kolster, Jose R Lopez, Jose A Adams
Journal: Circulation (2019)

Background: Diabetes mellitus (DM) is a major risk factor for the development of cardiovascular disease. Over time, diabetic patients develop cardiomyopathy, referred to as diabetic cardiomyopathy (DCM). The etiology of DCM in part relates to the duration of hyperglycemia. We have previously shown that type 1 diabetic mice (T1D) have abnormally elevated cardiomyocyte diastolic [Ca 2+ ] d , sodium ([Na + ] d ) after 3 months of diabetes. Whole body periodic acceleration (WBPA) is the motion of the supine body headward to footward in a sinusoidal fashion to induce pulsatile shear stress, increasing expression and phosphorylation of endothelial-derived nitric oxide synthase (eNOS, p-eNOS). We have previously shown that WBPA decreases [Ca 2+ ] d , sodium ([Na + ] d in various models of cardiomyopathy. We hypothesized that WBPA might reverse ion dyshomeostasis in the long term (15-months) hyperglycemia (glucose&gt;250mg/dl) mice. Methods: 15 C57BL/6J (CONT) and diabetic mice (T1D) were randomized to receive WBPA (480 rpm, 1 hr daily for 20 days). Diastolic [Ca 2+ ] d , ([Na + ] d ) (selective microelectrodes), and ROS production (fluorescent) were determined in isolated cardiomyocytes at day 0 and at upon completion of the treatment (day 20). Results: Hyperglycemia produced an increase in [Ca 2+ ] d , [Na + ] d and ROS production in cardiomyocytes. 20 days of WBPA treatment in established DCM significantly decreased [Ca 2+ ] d , [Na + ] d , and ROS production toward normal values. Conclusions: These findings suggest that WBPA may be a therapeutic strategy to reverse ion dyshomeostasis and oxidative stress in a very established(15mos) DCM
Maternal Antenatal Corticosteroid Treatment and Childhood Mental and Behavioral Disorders
Authors: Arvid Sjölander, Jaakko Kaprio, Antti Latvala
Journal: JAMA (2020)

To the Editor Dr Räikkönen and colleagues1 examined the association between maternal antenatal corticosteroid treatment and mental and behavioral disorders in children. We are concerned that there may be an important statistical error in the analysis.
Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity—at Depth and in Real Time
Authors: Laurent C. Moreaux, Dimitri Yatsenko, Wesley D. Sacher, Jaebin Choi, Changhyuk Lee, Nicole J. Kubat, R. James Cotton, Edward S. Boyden, Michael Z. Lin, Lin Tian, Andreas S. Tolias, Joyce K.S. Poon, Kenneth L. Shepard, Michael L. Roukes
Journal: Neuron (2020)
Annals On Call - Underdiagnosis of Primary Aldosteronism
Authors: Robert M. Centor, Jenifer M. Brown
Journal: Annals of Internal Medicine (2020)

Web Exclusives20 October 2020Annals On Call - Underdiagnosis of Primary AldosteronismFREERobert M. Centor, MD, Jenifer M. Brown, MDRobert M. Centor, MDHuntsville Regional Medical Campus, University of Alabama Birmingham School of Medicine, Birmingham, Alabama (R.M.C.)Search for more papers by this author, Jenifer M. Brown, MDBrigham and Women's Hospital, Boston, Massachusetts (J.M.B.)Search for more papers by this authorAuthor, Article and Disclosure Informationhttps://doi.org/10.7326/A19-0040 CME/MOC SectionsAboutVisual Abstract ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail In this episode of Annals On Call, Dr. Centor discusses the diagnosis of primary aldosteronism with Dr. Jenifer M. Brown.Annals articles discussed include...The Spectrum of Subclinical Primary Aldosteronism and Incident Hypertension. A Cohort Study: https://www.acpjournals.org/doi/10.7326/M17-0882About Annals On CallAnnals On Call focuses on a clinically influential article published in Annals of Internal Medicine. Dr. Robert Centor shares his own perspective on the material and interviews topic area experts to discuss, debate, and share diverse insights about patient care and health care delivery.For more information on Annals On Call and for more episodes, visit go.annals.org/OnCall. Comments0 CommentsSign In to Submit A Comment Author, Article and Disclosure InformationAffiliations: Huntsville Regional Medical Campus, University of Alabama Birmingham School of Medicine, Birmingham, Alabama (R.M.C.)Brigham and Women's Hospital, Boston, Massachusetts (J.M.B.)Disclosures: Dr. Centor has disclosed the following: Consultancy: DynaMed, MDCalc, Medscape, National Kidney Foundation, The Curbsiders. Employment: U.S. Department of Veterans Affairs. Dr. Brown has disclosed no conflicts of interest.Editors' Disclosures: Christine Laine, MD, MPH, Editor in Chief, reports that her spouse has stock options/holdings with Targeted Diagnostics and Therapeutics. Cynthia D. Mulrow, MD, MSc, Senior Deputy Editor, reports that she has no relationships or interests to disclose. Deborah Cotton, MD, MPH, Deputy Editor, reports that she has no financial relationships or interests to disclose. Eliseo Guallar, MD, MPH, DrPH, Deputy Editor, Statistics, reports that he has no financial relationships or interests to disclose. Christina C. Wee, MD, MPH, Deputy Editor, reports employment with Beth Israel Deaconess Medical Center. Sankey V. Williams, MD, Deputy Editor, reports that he has no financial relationships or interests to disclose. Yu-Xiao Yang, MD, MSCE, Deputy Editor, reports that he has no financial relationships or interest to disclose. Previousarticle Advertisement FiguresReferencesRelatedDetails Metrics 20 October 2020Volume 173, Issue 8Page: OC1 ePublished: 20 October 2020 Issue Published: 20 October 2020 CopyrightCopyright © 2020 by American College of Physicians. All Rights Reserved.Loading ...
Rates of Intestinal Resection and Colectomy in Inflammatory Bowel Disease Patients After Initiation of Biologics: A Cohort Study
Authors: George Khoudari, Emad Mansoor, Benjamin Click, Motasem Alkhayyat, Mohannad Abou Saleh, Preetika Sinh, Jeffry Katz, Gregory S. Cooper, Miguel Regueiro
Journal: Clinical Gastroenterology and Hepatology (2020)
Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing
Authors: Susie Suh, Elliot H. Choi, Henri Leinonen, Andrzej T. Foik, Gregory A. Newby, Wei-Hsi Yeh, Zhiqian Dong, Philip D. Kiser, David C. Lyon, David R. Liu, Krzysztof Palczewski
Journal: Nature Biomedical Engineering (2020)
Whole Exome Sequencing of Plasma Cells Precancerosis MGUS and Malignant AL Amyloidosis Reveals Small Number of Shared Mutated Genes
Authors: Zuzana Kufova, Katerina Growkova, Petr Vojta, Jana Filipova, Michal Simicek, Tomas Jelinek, Martina Zatopkova, Sebastian Grosicki, Aneta Mikulasova, Marian Hajduch, Ludek Pour, Martin Stork, Tereza Sevcikova, Roman Hajek
Journal: Blood (2017)
AB0949 AUTONOMIC AND INFLAMMATORY MECHANISMS OF PAIN AND FATIGUE IN FIBROMYALGIA AND ME/CFS: AN INTERVENTIONAL STUDY
Authors: J. Eccles, M. Amato, C. Thompson, K. Themelis, H. Critchley, N. Harrison, K. Davies
Journal: Annals of the Rheumatic Diseases (2020)

Background: Fibromyalgia and ME/CFS are complex disorders with overlapping symptoms; the pathoaetiology and clinical distinction are debated, however inflammatory and autonomic abnormalities are observed. Objectives: To investigate the role of inflammatory and autonomic nervous system responses in mechanisms of pain and fatigue in fibromyalgia and ME/CFS Methods: 63 patient participants with clinical diagnoses of fibromyalgia and/or ME/CFS were recruited into a multi-stage interventional study ( ISRCTN78820481 ) alongside 24 healthy controls. All underwent research diagnostic criteria evaluation. The majority underwent autonomic challenge (60 degree head up tilt) and/or inflammatory challenge (placebo-controlled typhoid vaccination) with baseline characterisation of symptoms, inflammatory markers and pre-post measures of pain and fatigue. Results: Of the 63 patients, 32% of patients had received a clinical diagnosis of Fibromyalgia; 38% ME/CFS and 30% dual diagnoses. Following research evaluation 89% met ACR diagnostic criteria for fibromyalgia; 94% Canadian Criteria for ME/CFS; 97% Fukada Criteria for ME/CFS There was a significantly higher ESR in patients compared to controls (p= 0.036). There was a trend towards higher CRP in patients compared to controls (p= 0.076). ESR correlated with baseline pain score (r=0.309, p=0.011), fatigue severity (r=0.262, p=0.032), fatigue impact (r=0.382, p=0.014) change in fatigue score induced by tilt (r=0.319, p=0.011) and change in pain score induced by placebo-controlled inflammation (r=-0.279, p=0.043). Similarly CRP level correlated with baseline pain score (r=0.340, p=0.005), fatigue impact (r=0.439, p=0.004), change in fatigue (r=-0.277, p=0.045) and pain score (r=-0.394, p=0.014) induced by placebo-controlled inflammation and change in pressure pain theshold induced by tilt (r=0.286, p=0.027). Baseline IL6 was higher in patients than controls (p = 0.002), correlating with baseline pain score (r = 0.345, p = 0.002) and change in pain score induced by tilt (r=0.281, p=0.21). Change in IL6 induced by inflammatory challenge correlated with inflammation induced fatigue score (r = 0.378, p = 0.01). Conclusion: Inflammatory and autonomic mechanisms contribute to pain and fatigue in this frequently overlooked patient group, highlighting possibilities for targeted treatments. Such data will be enriched going forward by neuroimaging and transcriptomic insights. References: n/a Acknowledgments: This work was supported by Versus Arthritis, Action for Me, Fibroduck Foundation and NIHR Disclosure of Interests: Jessica Eccles: None declared, Marisa Amato: None declared, Charlotte Thompson: None declared, Kristy Themelis: None declared, Hugo Critchley: None declared, Neil Harrison Grant/research support from: Yes, Speakers bureau: Yes, Kevin Davies: None declared
Cardiovascular bioimaging of nitric oxide: Achievements, challenges, and the future
Authors: Achini K. Vidanapathirana, Peter J. Psaltis, Christina A. Bursill, Andrew D. Abell, Stephen J. Nicholls
Journal: Medicinal Research Reviews (2020)

Nitric oxide (NO) is a ubiquitous, volatile, cellular signaling molecule that operates across a wide physiological concentration range (pM-µM) in different tissues. It is a highly diffusible messenger and intermediate in various metabolic pathways. NO plays a pivotal role in maintaining optimum cardiovascular function, particularly by regulating vascular tone and blood flow. This review highlights the need for accurate, real-time bioimaging of NO in clinical diagnostic, therapeutic, monitoring, and theranostic applications within the cardiovascular system. We summarize electrochemical, optical, and nanoscale sensors that allow measurement and imaging of NO, both directly and indirectly via surrogate measurements. The physical properties of NO render it difficult to accurately measure in tissues using direct methods. There are also significant limitations associated with the NO metabolites used as surrogates to indirectly estimate NO levels. All these factors added to significant variability in the measurement of NO using available methodology have led to a lack of sensors and imaging techniques of clinical applicability in relevant vascular pathologies such as atherosclerosis and ischemic heart disease. Challenges in applying current methods to biomedical and clinical translational research, including the wide physiological range of NO and limitations due to the characteristics and toxicity of the sensors are discussed, as are potential targets and modifications for future studies. The development of biocompatible nanoscale sensors for use in combination with existing clinical imaging modalities provides a feasible opportunity for bioimaging NO within the cardiovascular system.
The HOLA COVID-19 Study: An International Effort to Determine How COVID-19 Has Impacted Oncology Practices in Latin America
Authors: Carolina Bernabe-Ramirez, Ana I. Velazquez, Coral Olazagasti, Cristiane Decat Bergerot, Paulo Gustavo Bergerot, Enrique Soto-Perez-de-Celis, Narjust Duma
Journal: Cancer Cell (2020)
Estimating access to health care in Yemen, a complex humanitarian emergency setting: a descriptive applied geospatial analysis
Authors: Kent Garber, Charles Fox, Moustafa Abdalla, Andrew Tatem, Naseeb Qirbi, Laura Lloyd-Braff, Kahtan Al-Shabi, Kennedy Ongwae, Meredith Dyson, Kebir Hassen
Journal: The Lancet Global Health (2020)
11P Molecular profiling and targeted therapy in cholangiocarcinoma
Authors: M. García Pardo de Santayana, L. Ortega, J. Feliu, J. Adeva, A. Fernandez Montes, R.M. Rodríguez Alonso, C. López, S. Rubiales, R. Vera, I. Ghanem Canyete, R.A. Pazo Cid, T. Macarullá, A.M. López Muñoz, J. de la Cámara, M. Ors Castaño, C. Llorca, A. Jiménez Gordo, L. García Palacios, P. García Alfonso, A.J. Muñoz Martín
Journal: Annals of Oncology (2020)
Galectin-7 downregulation in lesional keratinocytes contributes to enhanced IL-17A signaling and skin pathology in psoriasis
Authors: Hung-Lin Chen, Chia-Hui Lo, Chi-Chun Huang, Meng-Ping Lu, Po-Yuan Hu, Chang-Shan Chen, Di-Yen Chueh, Peilin Chen, Teng-Nan Lin, Yuan-Hsin Lo, Yu-Ping Hsiao, Daniel K. Hsu, Fu-Tong Liu
Journal: Journal of Clinical Investigation (2020)

Psoriasis is a chronic inflammatory skin disease characterized by inflammatory cell infiltration, as well as hyperproliferation of keratinocytes in skin lesions, and is considered a metabolic syndrome. We found that the expression of galectin-7 is reduced in skin lesions of patients with psoriasis. IL-17A and TNF-α, 2 cytokines intimately involved in the development of psoriatic lesions, suppressed galectin-7 expression in human primary keratinocytes (HEKn cells) and the immortalized human keratinocyte cell line HaCaT. A galectin-7 knockdown in these cells elevated the production of IL-6 and IL-8 and enhanced ERK signaling when the cells were stimulated with IL-17A. Galectin-7 attenuated IL-17A–induced production of inflammatory mediators by keratinocytes via the microRNA-146a/ERK pathway. Moreover, galectin-7–deficient mice showed enhanced epidermal hyperplasia and skin inflammation in response to intradermal IL-23 injection. We identified fluvastatin as an inducer of galectin-7 expression by connectivity map analysis, confirmed this effect in keratinocytes, and demonstrated that fluvastatin attenuated IL-6 and IL-8 production induced by IL-17A. Thus, we validate a role of galectin-7 in the pathogenesis of psoriasis, in both epidermal hyperplasia and keratinocyte-mediated inflammatory responses, and formulate a rationale for the use of statins in the treatment of psoriasis.
Lifetime Prevalence of Cervical Cancer Screening in 55 Low- and Middle-Income Countries
Authors: Julia M. Lemp, Jan-Walter De Neve, Hermann Bussmann, Simiao Chen, Jennifer Manne-Goehler, Michaela Theilmann, Maja-Emilia Marcus, Cara Ebert, Charlotte Probst, Lindiwe Tsabedze-Sibanyoni, Lela Sturua, Joseph M. Kibachio, Sahar Saeedi Moghaddam, Joao S. Martins, Dismand Houinato, Corine Houehanou, Mongal S. Gurung, Gladwell Gathecha, Farshad Farzadfar, Scott Dryden-Peterson, Justine I. Davies, Rifat Atun, Sebastian Vollmer, Till Bärnighausen, Pascal Geldsetzer
Journal: JAMA (2020)

<h3>Importance</h3> The World Health Organization is developing a global strategy to eliminate cervical cancer, with goals for screening prevalence among women aged 30 through 49 years. However, evidence on prevalence levels of cervical cancer screening in low- and middle-income countries (LMICs) is sparse. <h3>Objective</h3> To determine lifetime cervical cancer screening prevalence in LMICs and its variation across and within world regions and countries. <h3>Design, Setting, and Participants</h3> Analysis of cross-sectional nationally representative household surveys carried out in 55 LMICs from 2005 through 2018. The median response rate across surveys was 93.8% (range, 64.0%-99.3%). The population-based sample consisted of 1 136 289 women aged 15 years or older, of whom 6885 (0.6%) had missing information for the survey question on cervical cancer screening. <h3>Exposures</h3> World region, country; countries' economic, social, and health system characteristics; and individuals' sociodemographic characteristics. <h3>Main Outcomes and Measures</h3> Self-report of having ever had a screening test for cervical cancer. <h3>Results</h3> Of the 1 129 404 women included in the analysis, 542 475 were aged 30 through 49 years. A country-level median of 43.6% (interquartile range [IQR], 13.9%-77.3%; range, 0.3%-97.4%) of women aged 30 through 49 years self-reported to have ever been screened, with countries in Latin America and the Caribbean having the highest prevalence (country-level median, 84.6%; IQR, 65.7%-91.1%; range, 11.7%-97.4%) and those in sub-Saharan Africa the lowest prevalence (country-level median, 16.9%; IQR, 3.7%-31.0%; range, 0.9%-50.8%). There was large variation in the self-reported lifetime prevalence of cervical cancer screening among countries within regions and among countries with similar levels of per capita gross domestic product and total health expenditure. Within countries, women who lived in rural areas, had low educational attainment, or had low household wealth were generally least likely to self-report ever having been screened. <h3>Conclusions and Relevance</h3> In this cross-sectional study of data collected in 55 low- and middle-income countries from 2005 through 2018, there was wide variation between countries in the self-reported lifetime prevalence of cervical cancer screening. However, the median prevalence was only 44%, supporting the need to increase the rate of screening.