tbuckley/cabot-search huggingface dataset:
Identification and validation of a multivariable prediction model based on blood plasma and serum metabolomics for the distinction of chronic pancreatitis subjects from non-pancreas disease control subjects
Authors: M Gordian Adam, Georg Beyer, Nicole Christiansen, Beate Kamlage, Christian Pilarsky, Marius Distler, Tim Fahlbusch, Ansgar Chromik, Fritz Klein, Marcus Bahra, Waldemar Uhl, Robert Grützmann, Ujjwal M Mahajan, Frank U Weiss, Julia Mayerle, Markus M Lerch
Journal: Gut (2021)

Objective Chronic pancreatitis (CP) is a fibroinflammatory syndrome leading to organ dysfunction, chronic pain, an increased risk for pancreatic cancer and considerable morbidity. Due to a lack of specific biomarkers, diagnosis is based on symptoms and specific but insensitive imaging features, preventing an early diagnosis and appropriate management. Design We conducted a type 3 study for multivariable prediction for individual prognosis according to the TRIPOD guidelines. A signature to distinguish CP from controls (n=160) was identified using gas chromatography-mass spectrometry and liquid chromatography‐tandem mass spectrometry on ethylenediaminetetraacetic acid (EDTA)-plasma and validated in independent cohorts. Results A Naive Bayes algorithm identified eight metabolites of six ontology classes. After algorithm training and computation of optimal cut-offs, classification according to the metabolic signature detected CP with an area under the curve (AUC) of 0.85 ((95% CI 0.79 to 0.91). External validation in two independent cohorts (total n=502) resulted in similar accuracy for detection of CP compared with non-pancreatic controls in EDTA-plasma (AUC 0.85 (95% CI 0.81 to 0.89)) and serum (AUC 0.87 (95% CI 0.81 to 0.95)). Conclusions This is the first study that identifies and independently validates a metabolomic signature in plasma and serum for the diagnosis of CP in large, prospective cohorts. The results could provide the basis for the development of the first routine laboratory test for CP.
The Impact of Patients With Cardiac Amyloidosis in HFpEF Trials
Authors: Silvia Oghina, Wulfran Bougouin, Mélanie Bézard, Mounira Kharoubi, Michel Komajda, Alain Cohen-Solal, Alexandre Mebazaa, Thibaud Damy, Diane Bodez
Journal: JACC Heart Failure (2021)
Abstract IA005: DNA damaging agents in endometrial cancer
Authors: Shannon Neville Westin
Journal: Clinical Cancer Research (2021)

Abstract The time for “one size fits all” treatment is over in endometrial cancer. Endometrial cancer has a number of potential targetable molecular aberrations, including those that predict response to DNA damaging agents such as PARP inhibitors. This talk will explore the preclinical and clinical data to support DNA damaging agents, alone and in combination, in the treatment of endometrial cancer. Biomarkers for response will be critically reviewed. Citation Format: Shannon Neville Westin. DNA damaging agents in endometrial cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference: Endometrial Cancer: New Biology Driving Research and Treatment; 2020 Nov 9-10. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(3_Suppl):Abstract nr IA005.
Endoscopic Manifestations of Gastroesophageal Reflux Disease in Patients with Type 2 Diabetes Mellitus
Authors: Natalia Zhelezniakova, Elina Frolovа-Romaniuk, Lyudmila Pasiieshvili, Iryna Karpenko, Tamara Pasiieshvili, Anastasiia Rozhdestvenska
Journal: Metabolism (2021)
Worry Perception of the COVID-19 Pandemic in Children and Adolescents with Type 1 Diabetes
Authors: N. Salah, M. Abdel Kader, M. Abdeen
Journal: Metabolism (2021)

Abstract COVID-19 has been recognized as a pandemic by the World Health Organization (WHO). The management of diabetes has become a challenge due to the COVID 19 lockdown. We aimed to assess COVID-19-specific worries and overall psychological health among older children and adolescents with type 1 diabetes mellitus (T1DM) in the COVID-19 pandemic in Egypt, and to explore characteristics of the patients with high levels of worries related to the COVID19 pandemic. A cross-sectional survey was conducted by administering questionnaires to 97 participants (9-18 years) diagnosed with T1DM attending routine clinical visits in the pediatric diabetes clinic, pediatric hospital, Ain Shams University, in the study period from March 2020 to June 2020. The questionnaire included items on COVID-19-specific worries as well as such worries related to diabetes, sociodemographic and health data, diabetes-specific social support, diabetes distress (DD) and changes in diabetes-specific behaviors. Results showed that patients have COVID-19-specific worries related to their diabetes, with (68%) of participants worried about 'people with diabetes being labeled as a risk group', (59.8%) about 'shortage of diabetes medications', followed by 'not being able to access health care if needed' (53.6%). Participants who felt a stronger sense of isolation were more likely to experience worries. High worry group of patients were more likely to have changed diabetes behaviors. In addition, worry scale positively correlated with the degree of perceived social isolation and DD. In conclusion, older children and adolescents with T1DM have COVID-19-specific worries related to their diabetes which was associated with higher social isolation. Yet, these worries were not impairing. Keywords: COVID-19; Adolescents; Diabetes; Mental health; Psychosocial perception; EGYPT Abbreviations: WHO: world health organization, DD: diabetes distress, T1DM: type 1 diabetes mellitus Funding and Conflicts of Interest: None
Diagnostic accuracy of different commercial walnut extracts in a paediatric atopic population
Authors: Maria Abreu-Ramírez, Victoria Fuentes-Aparicio, Cristina Morales-Cabeza, Alberto Álvarez-Perea, Sonsoles Infante, Carmen Beorlegui, Paloma Jaqueti Moreno, Paula Cabrera-Freitag
Journal: Journal of Allergy and Clinical Immunology (2021)
Assessment of Immune Function Status using Polysaccharide Vaccination in Secondary Immunodeficiencies
Authors: Yvelise Barrios del Pino, Elena Mederos Luis, Cristina Alava, Paloma Poza Guedes, Andres Franco, Teresa Delgado, Taida Martín, Isabel Suárez, Victor Matheu
Journal: Journal of Allergy and Clinical Immunology (2021)
Role of Genetic &amp; Epigenetic Modifications of Low-Density Lipoprotein Receptor (LDLR) Gene in South Indian Acute Myocardial Infraction Patients
Authors: Nivas Shyamala, Kaushik Puranam, Krishna Reddy Nallamala, Sanjib K. Sahu, Surekha Rani Hanumanth
Journal: Metabolism (2021)
IL-17 controls central nervous system autoimmunity through the intestinal microbiome
Authors: Tommy Regen, Sandrine Isaac, Ana Amorim, Nicolás Gonzalo Núñez, Judith Hauptmann, Arthi Shanmugavadivu, Matthias Klein, Roman Sankowski, Ilgiz A. Mufazalov, Nir Yogev, Jula Huppert, Florian Wanke, Michael Witting, Alexandra Grill, Eric J. C. Gálvez, Alexei Nikolaev, Michaela Blanfeld, Immo Prinz, Philippe Schmitt-Kopplin, Till Strowig, Christoph Reinhardt, Marco Prinz, Tobias Bopp, Burkhard Becher, Carles Ubeda, Ari Waisman
Journal: Science Immunology (2021)

Interleukin-17A- (IL-17A) and IL-17F-producing CD4+ T helper cells (TH17 cells) are implicated in the development of chronic inflammatory diseases, such as multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). TH17 cells also orchestrate leukocyte invasion of the central nervous system (CNS) and subsequent tissue damage. However, the role of IL-17A and IL-17F as effector cytokines is still confused with the encephalitogenic function of the cells that produce these cytokines, namely, TH17 cells, fueling a long-standing debate in the neuroimmunology field. Here, we demonstrated that mice deficient for IL-17A/F lose their susceptibility to EAE, which correlated with an altered composition of their gut microbiota. However, loss of IL-17A/F in TH cells did not diminish their encephalitogenic capacity. Reconstitution of a wild-type-like intestinal microbiota or reintroduction of IL-17A specifically into the gut epithelium of IL-17A/F-deficient mice reestablished their susceptibility to EAE. Thus, our data demonstrated that IL-17A and IL-17F are not encephalitogenic mediators but rather modulators of intestinal homeostasis that indirectly alter CNS-directed autoimmunity.
Metabolic control of DNA methylation in naive pluripotent cells
Authors: Riccardo M. Betto, Linda Diamante, Valentina Perrera, Matteo Audano, Stefania Rapelli, Andrea Lauria, Danny Incarnato, Mattia Arboit, Silvia Pedretti, Giovanni Rigoni, Vincent Guerineau, David Touboul, Giuliano Giuseppe Stirparo, Tim Lohoff, Thorsten Boroviak, Paolo Grumati, Maria E. Soriano, Jennifer Nichols, Nico Mitro, Salvatore Oliviero, Graziano Martello
Journal: Nature Genetics (2021)
Transcriptomics Of Gastrointestinal Biopsies During Oral Immunotherapy Reveals Changes In IgA Pathway
Authors: Gopal Krishna Dhondalay, Wenming Zhang, Ramona Hoh, Neeraja Kambham, Scott Boyd, Sandra Andorf, Monali Manohar, Sharon Chinthrajah, Kari Nadeau
Journal: Journal of Allergy and Clinical Immunology (2021)
Impact of Organ Function–Based Clinical Trial Eligibility Criteria in Patients With Diffuse Large B-Cell Lymphoma: Who Gets Left Behind?
Authors: Arushi Khurana, Raphael Mwangi, Grzegorz S. Nowakowski, Thomas M. Habermann, Stephen M. Ansell, Betsy R. LaPlant, Brian K. Link, James R. Cerhan, Matthew J. Maurer, Thomas E. Witzig
Journal: Journal of Clinical Oncology (2021)

Exclusion of patients needing urgent treatment or requiring novel biomarkers before enrollment has impacted the ability to enroll real-world patients in frontline trials of diffuse large B-cell lymphoma (DLBCL). The impact of baseline organ function-based eligibility criteria on this effect and clinical trial exclusion is less well-understood.
Impact of measurable residual disease by decentralized flow cytometry: a PETHEMA real-world study in 1076 patients with acute myeloid leukemia
Authors: Bruno Paiva, María-Belen Vidriales, Amparo Sempere, Fabián Tarín, Enrique Colado, Celina Benavente, María-Teresa Cedena, Joaquín Sánchez, Teresa Caballero-Velazquez, Lourdes Cordón, Juan-Jose Garces, Catia Simoes, David Martínez-Cuadrón, Teresa Bernal, Carmen Botella, Sofia Grille, Josefina Serrano, Carlos Rodríguez-Medina, Lorenzo Algarra, Juan-Manuel Alonso-Domínguez, María-Luz Amigo, Manuel Barrios, Raimundo García-Boyero, Mercedes Colorado, Jaime Pérez-Oteyza, Manuel Pérez-Encinas, Lisette Costilla-Barriga, María-José Sayas, Olga Pérez, Marcos González-Díaz, José A. Pérez-Simón, Joaquín Martínez-López, Claudia Sossa, Alberto Orfao, Jesús F. San Miguel, Miguel-Ángel Sanz, Pau Montesinos
Journal: Leukemia (2021)
Intersection of Race and Gender in Surgical Training
Authors: Malika Sharma, Shail Rawal
Journal: JAMA Surgery (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Lupus or not? SLE Risk Probability Index (SLERPI): a simple, clinician-friendly machine learning-based model to assist the diagnosis of systemic lupus erythematosus
Authors: Christina Adamichou, Irini Genitsaridi, Dionysis Nikolopoulos, Myrto Nikoloudaki, Argyro Repa, Alessandra Bortoluzzi, Antonis Fanouriakis, Prodromos Sidiropoulos, Dimitrios T Boumpas, George K Bertsias
Journal: Annals of the Rheumatic Diseases (2021)

Diagnostic reasoning in systemic lupus erythematosus (SLE) is a complex process reflecting the probability of disease at a given timepoint against competing diagnoses. We applied machine learning in well-characterised patient data sets to develop an algorithm that can aid SLE diagnosis.From a discovery cohort of randomly selected 802 adults with SLE or control rheumatologic diseases, clinically selected panels of deconvoluted classification criteria and non-criteria features were analysed. Feature selection and model construction were done with Random Forests and Least Absolute Shrinkage and Selection Operator-logistic regression (LASSO-LR). The best model in 10-fold cross-validation was tested in a validation cohort (512 SLE, 143 disease controls).A novel LASSO-LR model had the best performance and included 14 variably weighed features with thrombocytopenia/haemolytic anaemia, malar/maculopapular rash, proteinuria, low C3 and C4, antinuclear antibodies (ANA) and immunologic disorder being the strongest SLE predictors. Our model produced SLE risk probabilities (depending on the combination of features) correlating positively with disease severity and organ damage, and allowing the unbiased classification of a validation cohort into diagnostic certainty levels (unlikely, possible, likely, definitive SLE) based on the likelihood of SLE against other diagnoses. Operating the model as binary (lupus/not-lupus), we noted excellent accuracy (94.8%) for identifying SLE, and high sensitivity for early disease (93.8%), nephritis (97.9%), neuropsychiatric (91.8%) and severe lupus requiring immunosuppressives/biologics (96.4%). This was converted into a scoring system, whereby a score >7 has 94.2% accuracy.We have developed and validated an accurate, clinician-friendly algorithm based on classical disease features for early SLE diagnosis and treatment to improve patient outcomes.
Basophil Activation Marker Selection, CD63 or CD203c, Improves Sensitivity of Basophil Activation Test Depending on the Clinical Entity in Immediate Allergic Reactions to Betalactams
Authors: Ruben Fernández-Santamaría, Gador Bogas Herrera, Maria Salas, Adriana Ariza Veguillas, Ana Molina Bueno, Cristobalina Mayorga, Maria Torres JaÃ©n, Tahia Fernandez
Journal: Journal of Allergy and Clinical Immunology (2021)
Effects of Semaglutide on CKD Outcomes: A Post Hoc Pooled Analysis from the SUSTAIN 6 and PIONEER 6 Trials
Authors: Katherine R. Tuttle, David Cherney, Samy Hadjadj, Thomas Idorn, Ofri Mosenzon, Vlado Perkovic, Soren Rasmussen, Benjamin Wolthers, Stephen C. Bain
Journal: Journal of the American Society of Nephrology (2020)
Second-Degree Atrioventricular Block—Reply
Authors: Emily R. Siegel, James W. Salazar, Zian H. Tseng
Journal: JAMA Internal Medicine (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Internal Medicine journal
Global Profiling of 2-Hydroxyisobutyrylome in Common Wheat
Authors: Ning Zhang, Lingran Zhang, Linjie Li, Junyou Geng, Lei Zhao, Yan Ren, Zhongdong Dong, Feng Chen
Journal: Genomics Proteomics & Bioinformatics (2021)

As a novel post-translational modification (PTM), lysine 2-hydroxyisobutyrylation (Khib) is considered to regulate gene transcriptional activities in eukaryotic cells; however, the functions of Khib-modified proteins in plants remain unknown. Here, we report that Khib is an evolutionarily-conserved PTM in wheat and its progenitors. A total of 3348 Khib sites on 1074 proteins are identified in common wheat (Triticum aestivum L.) by using affinity purification and mass spectroscopy of 2-hydroxyisobutyrylome. Bioinformatic data indicate that Khib-modified proteins participate in a wide variety of biological and metabolic pathways. Immunoprecipitation confirms that Khib-modified proteins are present endogenously. A comparison of Khib and other main PTMs shows that Khib-modified proteins are simultaneously modified by multiple PTMs. Using mutagenesis experiments and co-immunoprecipitation assays, we demonstrate that Khib on K206 of phosphoglycerate kinase (PGK) is a key regulatory modification for its enzymatic activity, and mutation on K206 affects the interactions of PGK with its substrates. Furthermore, Khib modification of low-molecular-weight proteins is a response to the deacetylase inhibitors nicotinamide and trichostatin. This study provides evidence to promote our current understanding of Khib in wheat plants, including the cooperation between Khib and its metabolic regulation.
Viral Loads of SARS-CoV-2 in Young Children
Authors: Amy B. Karger, Patricia Ferrieri, Andrew C. Nelson
Journal: JAMA Pediatrics (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Proof-of-concept for CRISPRai-mediated Simultaneous Activation of UCP-1 and Inhibition of CIDEC Expressions in Preadipocytes: Effects on White Adipogenic Differentiation
Authors: I. Stafeev, S. Michurina, V.A. Truong, E. Mamontova, E. Shevchenko, E. Ratner, M. Menshikov, Y.C. Hu, Ye Parfyonova
Journal: Metabolism (2021)
Systemic mastocytosis in adults: 2021 Update on diagnosis, risk stratification and management
Authors: Animesh Pardanani
Journal: American Journal of Hematology (2021)

Systemic mastocytosis (SM) results from a clonal proliferation of abnormal mast cells (MC) in extra-cutaneous organs.The major criterion is presence of multifocal clusters of spindled MC in the bone marrow. Minor diagnostic criteria include elevated serum tryptase level, abnormal MC CD25 expression, and presence of KITD816V mutation.Establishing SM subtype as per the World Health Organization classification system is an important first step. Broadly, patients either have indolent/smoldering SM (ISM/SSM) or advanced SM, the latter includes aggressive SM (ASM), SM with associated hematological neoplasm (SM-AHN), and mast cell leukemia (MCL). Identification of poor-risk mutations (ie, ASXL1, RUNX1, SRSF2, NRAS) further refines the risk stratification. Recently, clinical and hybrid clinical-molecular risk models have been developed to more accurately assign prognosis in SM patients.Treatment goals for ISM patients are primarily directed towards anaphylaxis prevention/symptom control/osteoporosis treatment. Patients with advanced SM frequently need MC cytoreductive therapy to ameliorate disease-related organ dysfunction. High response rates have been seen with small-molecule inhibitors that target mutant-KIT, including midostaurin (Food and Drug Administration approved) or avapritinib (investigational). Other options for MC cytoreduction include cladribine or interferon-α, although head-to-head comparisons are lacking. Treatment of SM-AHN primarily targets the AHN component, particularly if an aggressive disease such as acute myeloid leukemia is present. Allogeneic stem cell transplant can be considered in such patients, or in those with relapsed/refractory advanced SM. Imatinib has a limited therapeutic role in SM; effective cytoreduction is limited to those with imatinib-sensitive KIT mutations.
Long‐acting muscarinic antagonists and small airways in asthma: Which link?
Authors: Mario Cazzola, Luigino Calzetta, Maria Gabriella Matera
Journal: Allergy (2021)

Involvement of small airways, those of <2 mm in internal diameter, is present in all stages of asthma and contributes substantially to its pathophysiologic expression. Therefore, small airways are a potential target to achieve optimal asthma control. Airway tone, which is increased in asthma, is mainly controlled by the vagus nerve that releases acetylcholine (ACh) and activates muscarinic ACh receptors (mAChRs) post-synaptically on airway smooth muscle (ASM). In small airways, M3 mAChRs are expressed, but there is no vagal innervation. Non-neuronal ACh released from the epithelial cells that may express choline acetyltransferase in response to inflammatory stimuli, as well as from other structural cells in the airways, including fibroblasts and mast cells, can activate mAChRs. By antagonizing M3 mAChR, the contraction of the ASM is prevented and, potentially, local inflammation can be reduced and the progression of remodeling may be averted. In fact, ACh also contributes to inflammation and remodeling of the airways and regulates the growth of ASM. Several experimental studies have demonstrated the potential benefit derived from the use of mAChR antagonists, mainly long-acting mAChR antagonists (LAMAs), on small airways in asthma. However, there are several confounding factors that may cause a wrong estimation of the relationship between LAMAs and small airways in asthma. Further studies are needed to differentiate broncholytic and anti-inflammatory effects of LAMAs and to better understand the interaction between LAMAs and corticosteroids, also in the context of a triple therapy that includes a β2 -AR agonist, at different levels of the bronchial tree.
Effects of CSF3R mutations on Myeloid Differentiation and Proliferation of Hematopoietic Cells of Congenital Neutropenia Patients
Authors: Maksim Klimiankou, Benjamin Dannenmann, Anna Solovyeva, Regine Bernhard, Diana Amend, Cornelia Zeidler, Sabine Mellor-Heineke, Lothar Kanz, Julia Skokowa, Karl Welte
Journal: Blood (2017)