tbuckley/cabot-search huggingface dataset:
Abstract 11565: Clinical Implications of Left Atrial Size and Its Changes After Cardiac Resynchronization Therapy in Patients With Heart Failure
Authors: Yu Yu
Journal: Circulation (2023)

Background: Little evidence is available regarding the impact of left atrial (LA) diameter, especially its changes after cardiac resynchronization therapy (CRT), on the prognosis of patients with heart failure (HF). Objective: To investigate the association of LA diameter and its changes with all-cause mortality and HF hospitalization in HF patients with CRT. Methods: This cohort study retrospectively included 488 HF patients with CRT, who were assessed with echocardiography at baseline and 6 months after CRT. The multivariate Cox proportional hazards regression models were used to examine the specific association of LA diameter and its changes with all-cause mortality and HF hospitalization. Results: Non-linear associations were found for LA diameter with all-cause mortality ( P = 0.006 for nonlinearity) and HF hospitalization ( P = 0.02 for nonlinearity). The positive association of LA diameter with all-cause mortality (HR, 1.88; 95% CI, 1.42-2.49) and HF hospitalization (HR, 1.72; 95% CI, 1.32-2.22) only in the range of LA diameter &lt;45 mm. There was a positive association of LA diameter changes with all-cause mortality (HR, 1.29; 95% CI, 1.12-1.48) and HF hospitalization (HR, 1.28; 95% CI, 1.13-1.45). LA adverse remodeling (LAAR) was associated with an increased risk of all-cause mortality (HR, 2.35; 95% CI, 1.46-3.79) and HF hospitalization (HR, 2.18; 95% CI, 1.40-3.41). Conclusions: LA enlargement and LAAR were associated with an unfavorable outcome in HF patients with CRT. These findings suggest that monitoring LA diameter and its changes has potential clinical implications for HF treatment.
Abstract 13121: Incidence, Predictors, and Outcomes of Venous and Arterial Thrombosis in COVID-19: A Nationwide Analysis
Authors: Ankit Agrawal, Suryansh Bajaj, Umesh Bhagat, Sanya Chandna, Aro Daniela Arockiam, Joseph El Dahdah, Rahul Gupta, Shashank Shekhar, Kavin Raj, Divya Nayar, Divyansh Bajaj, Pulkit Chaudhury, Brian P Griffin, Tom Kai Ming K Wang
Journal: Circulation (2023)

Introduction: Coronavirus disease 2019 (COVID-19) is known to increase the risk of venous (VTE) and arterial (ATE) thromboembolism. However, the incidence, predictors, and outcomes of clinical thrombosis for inpatients with COVID-19 are not well known. We evaluated the incidence, associated factors, and mortality outcomes of VTE and ATE in COVID-19 infection. Hypothesis: COVID-19 is associated with a higher risk of thrombosis and mortality. Methods: Hospitalized patients with COVID-19 during 2020 were identified from the National Inpatient Sample database and data was retrieved regarding clinical characteristics, incident VTE and ATE and mortality outcomes. Multivariate regression was performed to identify clinical factors associated with thrombosis and in-hospital mortality in COVID-19 inpatients. Results: Overall, 1,583,135 COVID-19 inpatients were identified out of which patients with thrombosis were 41% females with a mean age 65.4 (65.1-65.6) years. The incidence of thrombosis was 6.1%, including VTE 4.8%, ATE 3.0%, and in-hospital mortality rate was 13.4%. The main factors associated with overall thrombosis, VTE and ATE were paralysis, ventilation, solid tumors without metastasis, and metastatic cancer. Patients with thrombosis were more likely to have respiratory symptoms of COVID-19 (76.7% vs 75%, p&lt;0.001) compared to patients without thrombosis, along with comorbidities like complicated diabetes mellitus and congestive heart failure, and acute presentations like septic shock, acute respiratory distress syndrome and acute kidney injury. Symptomatic and severe COVID-19 disease were associated with a higher risk of thrombosis (OR 1.37 (1.31-1.43) and OR 1.62 (1.49-1.76), respectively, p&lt;0.001) and VTE (OR 1.40 (1.33-1.46) and OR 1.66 (1.52-1.80) respectively, p&lt;0.001). Although all thrombosis categories were associated with higher in-hospital mortality for COVID-19 inpatients in univariable analyses (p&lt;0.001), they were not significant in multivariate analyses. Conclusions: Overall, thrombosis, especially VTE was found in approximately 5% of COVID-19 inpatients, while ATE was rare, with important associated factors identified, however they were not independently associated with higher in-hospital mortality.
Abstract 15484: Heart Transplantation in a Light-Chain Amyloidosis Patient at Mayo Stage IIIa After Anti-Plasma Cell Chemotherapy With Complete Remission
Authors: Keying Bi, Ke Wan, Yuanwei Xu, JIE Wang, Weihao Li, Yucheng Chen
Journal: Circulation (2023)

A 42-year-old female patient was admitted for lower limb edema. Laboratory tests showed nephrotic proteinuria (2.76g/24h). Serum-free λ light chains were 84.9 mg/L, with a κ/λ ratio of 0.12. Bone marrow examination detected 6% immature clonal plasma cells. Amyloid deposition was identified in a renal biopsy. Cardiac magnetic resonance (CMR) revealed normal left ventricular ejection fraction (LVEF), left ventricular circumferential late gadolinium enhancement (LGE), and elevated myocardial T1 value (1459ms) and extracellular volume (47.4%). She was diagnosed with AL amyloidosis and classed as IIIa by the Mayo Stage 2004. A hematologic complete response (CR) was achieved and sustained after treatment with sequencing cyclophosphamide, bortezomib, dexamethasone (CyBorD) and daratumumab regimen. The follow-up CMRs were underwent at 6, 12, and 18 months after starting chemotherapy, which monitored cardiac changes in reponse to CR. Unfortunately, there was no alleviation of cardiac involvement. CMR re-examination (at 42 months) revealed severe cardiac function impairment (LVEF 28%), and dramatically increased extracellular volume (66.2%). Then, she underwent heart transplantation (HTx) evaluated by the heart transplantation multidisciplinary team. Three months later, she was doing well, CMR demonstrated stable cardiac allograft function. Repeated endomyocardial biopsies showed no amyloid deposits. This case illustrates that cardiac amyloid deposition might be a dynamic process in AL amyloidosis and highlights the value of CMR in long-term monitoring and identifying the patients reached CR who need HTx.
Simulations of Sequence Evolution: How (Un)realistic They Are and Why
Authors: Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau
Journal: Molecular Biology and Evolution (2023)

Abstract Motivation Simulating multiple sequence alignments (MSAs) using probabilistic models of sequence evolution plays an important role in the evaluation of phylogenetic inference tools and is crucial to the development of novel learning-based approaches for phylogenetic reconstruction, for instance, neural networks. These models and the resulting simulated data need to be as realistic as possible to be indicative of the performance of the developed tools on empirical data and to ensure that neural networks trained on simulations perform well on empirical data. Over the years, numerous models of evolution have been published with the goal to represent as faithfully as possible the sequence evolution process and thus simulate empirical-like data. In this study, we simulated DNA and protein MSAs under increasingly complex models of evolution with and without insertion/deletion (indel) events using a state-of-the-art sequence simulator. We assessed their realism by quantifying how accurately supervised learning methods are able to predict whether a given MSA is simulated or empirical. Results Our results show that we can distinguish between empirical and simulated MSAs with high accuracy using two distinct and independently developed classification approaches across all tested models of sequence evolution. Our findings suggest that the current state-of-the-art models fail to accurately replicate several aspects of empirical MSAs, including site-wise rates as well as amino acid and nucleotide composition.
Current national availability of advanced echocardiography imaging: real world data from an Italian Society of Echocardiography and Cardiovascular Imaging survey
Authors: Andrea Barbieri, Francesca Mantovani, Quirino Ciampi, Agata Barchitta, Giorgio Faganello, Sofia Miceli, Vito Maurizio Parato, Antonio Tota, Giuseppe Trocino, Francesco Antonini-Canterin, Scipione Carerj, Mauro Pepi
Journal:  (2023)

Abstract Aims Advanced echocardiographic imaging (AEI) techniques, such as three-dimensional (3D) and multi-chamber speckle-tracking deformation imaging (strain) analysis, have been shown to be more accurate in assessing heart chamber geometry and function when compared with conventional echocardiography providing additional prognostic value. However, incorporating AEI alongside standard examinations may be heterogeneous between echo laboratories (echo labs). Thus, our goal was to gain a better understanding of the many AEI modalities that are available and employed in Italy. Methods and results The Italian Society of Echocardiography and Cardiovascular Imaging (SIECVI) conducted a national survey over a month (November 2022) to describe the use of AEI in Italy. Data were retrieved via an electronic survey based on a structured questionnaire uploaded on the SIECVI website. Data obtained from 173 echo labs were divided into 3 groups, according to the numbers of echocardiograms performed: &amp;lt;250 exams (low-volume activity, 53 centres), between 251 and 550 exams (moderate-volume activity, 62 centres), and ≥550 exams (high-volume activity, 58 centres). Transthoracic echocardiography (TTE) 3D was in use in 75% of centres with a consistent difference between low (55%), medium (71%), and high activity volume (85%) (P = 0.002), while 3D transoesophageal echocardiography (TEE) was in use in 84% of centres, reaching the 95% in high activity volume echo labs (P = 0.006). In centres with available 3D TTE, it was used for the left ventricle (LV) analysis in 67%, for the right ventricle (RV) in 45%, and for the left atrium (LA) in 40%, showing greater use in high-volume centres compared with low- and medium-volume centres (all P &amp;lt; 0.04). Strain analysis was utilized in most echo labs (80%), with a trend towards greater use in high-volume centres than low- and medium-volume centres (77%, 74%, and 90%, respectively; P = 0.08). In centres with available strain analysis, it was mainly employed for the LV (80%) and much less frequently for the RV and LA (49% and 48%, respectively). Conclusion In Italy, the AEI modalities are more frequently available in centres with high-volume activity but employed only in a few applications, being more frequent in analysing the LV compared with the RV and LA. Therefore, the echocardiography community and SIECVI should promote uniformity and effective training across the Italian centres. Meanwhile, collaborations across centres with various resources and expertise should be encouraged to use the benefits of the AEI.
Economic burden attributable to healthcare-associated infections at western China hospitals: 6 Year, prospective cohort study
Authors: Yu Lv, Xiaobo Huang, Jiayu Wu, Xueqin Xiao, Chunhua Ma, Xiaoyun Jiang, Ping Zhou, Linlin Liu, Yiguo Jiang, Anna Zou, Hui Niu, Juhua Sun, Li Hou, Xiaomeng Wang, Yulin Dai, Shuling Peng, Xiaorong Deng, Hong Xia, Yao Guo, Defen Wang, Ting Huang, Chunyu Li, Lirong He, Fengqing Xiong, Hongmei Xiong, Hongmei Cao, Jie Lu, Xingfeng Liu, Xiaohong Jian, Wanzhen Luo, Yanmei An, Yumei Wu, Keqin Deng, Xiaoli Kang, Xiaorong Chen, Beibei Tang, Li Li, Qian Xiang
Journal: Journal of Infection (2023)

Healthcare-associated infections (HAIs) represent a major threat to patient safety and are associated with significant economic burden. Calculating the costs attributable to HAIs is challenging given the various sources of bias. Although HAIs as a reasonably preventable medical harm should have been closely linked to medical insurance incentives, there was little linkage between HAIs and medicare in western China owing to the lack of economic evaluation data. The present study aimed to generate estimates of the attributable costs associated with HAIs and the magnitude of costs growth.
Sociodemographic associations with uptake of novel therapies for acute myeloid leukemia
Authors: Andrew Hantel, Colin Cernik, Hajime Uno, Thomas P. Walsh, Gregory S. Calip, Daniel J. DeAngelo, Christopher S. Lathan, Gregory A. Abel
Journal: Blood Cancer Journal (2023)

Abstract Inequitable uptake of novel therapies (NT) in non-cancer settings are known for patients with lower socioeconomic status (SES), People of Color (POC), and older adults. NT uptake equity in acute myeloid leukemia (AML) is not well known. We performed a retrospective cohort study (1/2014-8/2022) of the United States nationwide Flatiron Health TM electronic health record-derived, de-identified database. We estimated sociodemographic associations with AML NT receipt using incidence rate ratios (IRR). Odds ratios (OR) assessed differences in venetoclax (the most common NT) receipt at community sites and between site characteristics and NT adoption. Of 8081 patients (139 sites), 3102 (38%) received a NT. NT use increased annually (IRR 1.14, 95% confidence interval [1.07, 1.22]). NT receipt was similar between Non-Hispanic-Whites and POC (IRR 1.03, [0.91, 1.17]) and as age increased (IRR 1.02 [0.97, 1.07]). At community sites, Non-Hispanic-Whites were less likely to receive venetoclax (OR 0.77 [0.66, 0.91]); older age (OR 1.05 [1.04, 1.05]) and higher area-level SES were associated with venetoclax receipt (OR 1.23 [1.05, 1.43]). Early NT adopting sites had more prescribing physicians (OR 1.25 [1.13, 1.43]) and higher SES strata patients (OR 2.81 [1.08, 7.66]). Inequities in AML NT uptake were seen by SES; for venetoclax, differential uptake reflects its label indication for older adults and those with comorbidities.
Association of health benefits and harms of Christmas dessert ingredients in recipes from The Great British Bake Off: umbrella review of umbrella reviews of meta-analyses of observational studies
Authors: Joshua D Wallach, Anant Gautam, Reshma Ramachandran, Joseph S Ross
Journal: BMJ (2023)

Abstract Objective To determine the health benefits and harms of various ingredients in Christmas desserts from The Great British Bake Off. Design Umbrella review of umbrella reviews of meta-analyses of observational studies. Data sources The Great British Bake Off website, Embase, Medline, and Scopus. Inclusion criteria Umbrella reviews of meta-analyses of observational studies evaluating the associations between Christmas dessert ingredients and the risk of death or disease. Main outcome measures Proportion of protective and harmful summary associations between ingredient groups from The Great British Bake Off Christmas dessert recipes and the risk of death or disease. Results 48 recipes for Christmas desserts (ie, cakes, biscuits, pastries, and puddings and desserts) were provided on The Great British Bake Off website with 178 unique ingredients that were collapsed into 17 overarching ingredient groups. A literature search identified 7008 titles and abstracts, of which 46 eligible umbrella reviews reported 363 unique summary associations between the ingredient groups and risk of death or disease. Of these summary associations, 149 (41%) were significant, including 110 (74%) that estimated that the ingredient groups reduced the risk of death or disease and 39 (26%) that increased the risk. The most common ingredient groups associated with a reduced risk of death or disease were fruit (44/110, 40%), coffee (17/110, 16%), and nuts (14/110, 13%), whereas alcohol (20/39, 51%) and sugar (5/39, 13%) were the most common ingredient groups associated with increased risk of death or disease. Conclusions Recipes for Christmas desserts from The Great British Bake Off often use ingredient groups that are associated with reductions, rather than increases, in the risk of death or disease. This Christmas, if concerns about the limitations of observational nutrition research are set aside, you can have your cake and eat it too.
IgE and anaphylaxis specific to the carbohydrate alpha-gal depend on IL-4
Authors: Miriam Hils, Nils Hoffard, Caterina Iuliano, Luisa Kreft, Neera Chakrapani, Kyra Swiontek, Konrad Fischer, Bernadette Eberlein, Martin Köberle, Jörg Fischer, Christiane Hilger, Caspar Ohnmacht, Susanne Kaesler, Florian Wölbing, Tilo Biedermann
Journal: Journal of Allergy and Clinical Immunology (2023)

Alpha-gal (Galα1-3Galβ1-4GlcNAc) is a carbohydrate with the potential to elicit fatal allergic reactions to mammalian meat and drugs of mammalian origin. This type of allergy is induced by tick bites, and therapeutic options for this skin-driven food allergy are limited to the avoidance of the allergen and treatment of symptoms. Thus, a better understanding of the immune mechanisms resulting in sensitization through the skin is crucial, especially in the case of a carbohydrate allergen for which underlying immune responses are poorly understood. We aimed to establish a mouse model of alpha-gal allergy for in-depth immunologic analyses. Alpha-galactosyltransferase 1–deficient mice devoid of alpha-gal glycosylations were sensitized with the alpha-gal–carrying self-protein mouse serum albumin by repetitive intracutaneous injections in combination with the adjuvant aluminum hydroxide. The role of basophils and IL-4 in sensitization was investigated by antibody-mediated depletion. Alpha-gal–sensitized mice displayed increased levels of alpha-gal–specific IgE and IgG1 and developed systemic anaphylaxis on challenge with both alpha-gal–containing glycoproteins and glycolipids. In accordance with alpha-gal–allergic patients, we detected elevated numbers of basophils at the site of sensitization as well as increased numbers of alpha-gal–specific B cells, germinal center B cells, and B cells of IgE and IgG1 isotypes in skin-draining lymph nodes. By depleting IL-4 during sensitization, we demonstrated for the first time that sensitization and elicitation of allergy to alpha-gal and correspondingly to a carbohydrate allergen is dependent on IL-4. These findings establish IL-4 as a potential target to interfere with alpha-gal allergy elicited by tick bites.
A Biological Immunity-Based Neuro Prototype for Few-Shot Anomaly Detection with Character Embedding
Authors: Zhongjing Ma, Zhan Chen, Xiaochen Zheng, Tianyu Wang, Yuyang You, Suli Zou, Yu Wang
Journal: Cyborg and Bionic Systems (2023)

Anomaly detection has wide applications to help people recognize false, intrusion, flaw, equipment failure, etc. In most practical scenarios, the amount of the annotated data and the trusted labels is low, resulting in poor performance of the detection. In this paper, we focus on the anomaly detection for the text type data and propose a detection network based on biological immunity for few-shot detection, by imitating the working mechanism of the immune system of biological organisms. This network enabling the protected system to distinguish the aggressive behavior of “nonself” from the legitimate behavior of “self” by embedding characters. First, it constructs episodic task sets and extracts data representations at the character level. Then, in the pretraining phase, Word2Vec is used to embed the representations. In the meta-learning phase, a dynamic prototype containing encoder, routing, and relation is designed to identify the data traffic. Compare to the mean-based prototype, the proposed prototype applies a dynamic routing algorithm that assigns different weights to samples in the support set through multiple iterations to obtain a prototype that combines the distribution of samples. The proposed method is validated on 2 real traffic datasets. The experimental results indicate that (a) the proposed anomaly detection prototype outperforms state-of-the-art few-shot techniques with 1.3% to 4.48% accuracy and 0.18% to 4.55% recall; (b) under the premise of ensuring the accuracy and recall, the number of training samples is reduced to 5 or 10; (c) ablation experiments are designed for each module, and the results show that more accurate prototypes can be obtained by using the dynamic routing algorithm.
Changes in the global hospitalisation burden of respiratory syncytial virus in young children during the COVID-19 pandemic: a systematic analysis
Authors: Bingbing Cong, Uğurcan Koç, Teresa Bandeira, Quique Bassat, Louis Bont, Giorgi Chakhunashvili, Cheryl Cohen, Christine Desnoyers, Laura L Hammitt, Terho Heikkinen, Q Sue Huang, Joško Markić, Ainara Mira-Iglesias, Jocelyn Moyes, D James Nokes, Dominique Ploin, Euri Seo, Rosalyn Singleton, Nicole Wolter, Chee Fu Yung, Heather J Zar, Daniel R Feikin, Erin G Sparrow, Dina Mrčela, Petra Milić, Daniela Veljačić Visković, David Torres-Fernandez, Arantxa Urchueguía, Javier Díez-Domingo, Alejandro Orrico-Sánchez, Sibongile Walaza, Anne von Gottberg, Gary Reubenson, Halima Dawood, Omphile Mekgoe, Mignon du Plessis, Neydis Baute, Fathima Naby, James W Keck, Jennifer Dobson, Rachel Hartman, Marqia Sandoval, Sara S Bressler, Dana Bruden, Irakli Karseladze, Zakhar Shchomak, Rosário Barreto, Nickson Murunga, Martin Mutunga, Jean-Sebastien Casalegno, Come Horvat, Harish Nair, You Li
Journal: The Lancet Infectious Diseases (2023)
Multiomic spatial landscape of innate immune cells at human central nervous system borders
Authors: Roman Sankowski, Patrick Süß, Alexander Benkendorff, Chotima Böttcher, Camila Fernandez-Zapata, Chintan Chhatbar, Jonathan Cahueau, Gianni Monaco, Adrià Dalmau Gasull, Ashkan Khavaran, Jürgen Grauvogel, Christian Scheiwe, Mukesch Johannes Shah, Dieter Henrik Heiland, Oliver Schnell, Filiz Markfeld-Erol, Mirjam Kunze, Robert Zeiser, Josef Priller, Marco Prinz
Journal: Nature Medicine (2023)

Abstract The innate immune compartment of the human central nervous system (CNS) is highly diverse and includes several immune-cell populations such as macrophages that are frequent in the brain parenchyma (microglia) and less numerous at the brain interfaces as CNS-associated macrophages (CAMs). Due to their scantiness and particular location, little is known about the presence of temporally and spatially restricted CAM subclasses during development, health and perturbation. Here we combined single-cell RNA sequencing, time-of-flight mass cytometry and single-cell spatial transcriptomics with fate mapping and advanced immunohistochemistry to comprehensively characterize the immune system at human CNS interfaces with over 356,000 analyzed transcriptomes from 102 individuals. We also provide a comprehensive analysis of resident and engrafted myeloid cells in the brains of 15 individuals with peripheral blood stem cell transplantation, revealing compartment-specific engraftment rates across different CNS interfaces. Integrated multiomic and high-resolution spatial transcriptome analysis of anatomically dissected glioblastoma samples shows regionally distinct myeloid cell-type distributions driven by hypoxia. Notably, the glioblastoma-associated hypoxia response was distinct from the physiological hypoxia response in fetal microglia and CAMs. Our results highlight myeloid diversity at the interfaces of the human CNS with the periphery and provide insights into the complexities of the human brain’s immune system.
Development and Validation of a Nomogram for Predicting Postoperative Early Relapse and Survival in Hepatocellular Carcinoma
Authors: Yongzhu He, Laihui Luo, Renfeng Shan, Junlin Qian, Lifeng Cui, Zhao Wu, Shuju Tu, WenJian Zhang, Wei Lin, Hongtao Tang, Zeyu Huang, Zhigang Li, Shengping Mao, Hui Li, Zemin Hu, Liping Liu, Wei Shen, Kun He, Yong Li
Journal: Journal of the National Comprehensive Cancer Network (2023)

Early relapse after hepatectomy presents a significant challenge in the treatment of hepatocellular carcinoma (HCC). The aim of this study was to construct and validate a novel nomogram model for predicting early relapse and survival after hepatectomy for HCC.