tbuckley/cabot-search huggingface dataset:
Multidrug-resistant bacterial infections after liver transplantation: Prevalence, impact, and risk factors
Authors: Rosa Martin-Mateos, Laura Martínez-Arenas, Ángela Carvalho-Gomes, Laia Aceituno, Valle Cadahía, Magdalena Salcedo, Ana Arias, Sara Lorente, Aitor Odriozola, Javier Zamora, Marino Blanes, Óscar Len, Laura Benítez, Isabel Campos-Varela, María Luisa González-Diéguez, Diego Rojo Lázaro, Jesús Fortún, Antonio Cuadrado, Natalia Marcos Carrasco, Manuel Rodríguez-Perálvarez, Carmen Álvarez-Navascues, Emilio Fábrega, Trinidad Serrano, Valentín Cuervas-Mons, Manuel Rodríguez, Lluis Castells, Marina Berenguer, Javier Graus, Agustín Albillos
Journal: Journal of Hepatology (2024)
PTEN deficiency induces an extrahepatic cholangitis-cholangiocarcinoma continuum via aurora kinase A in mice
Authors: Yan Yang, Jiale Wang, Jianhua Wan, Qianqian Cheng, Zenong Cheng, Xueli Zhou, Oliver Wang, Kelvin Shi, Lingxiang Wang, Bin Wang, Xiaohui Zhu, Jiaxiang Chen, Dongfeng Feng, Yang Liu, Yasmin Jahan-mihan, Ashley N. Haddock, Brandy H. Edenfield, Guang Peng, Jessica D. Hohenstein, Chantal E. McCabe, Daniel R. O'Brien, Chen Wang, Sumera I. Ilyas, Liuyan Jiang, Michael S. Torbenson, Huamin Wang, Raouf E. Nakhleh, Xuemei Shi, Ying Wang, Yan Bi, Gregory J. Gores, Tushar Patel, Baoan Ji
Journal: Journal of Hepatology (2024)
Global Prevalence of Pancreatic Cystic Lesions in the General Population on Magnetic Resonance Imaging: A Systematic Review and Meta-analysis
Authors: Ana Vilela, Elit Quingalahua, Alejandra Vargas, Fadi Hawa, Carol Shannon, Eileen S. Carpenter, Jiaqi Shi, Somashekar G. Krishna, Un-Jung Lee, Jean M. Chalhoub, Jorge D. Machicado
Journal: Clinical Gastroenterology and Hepatology (2024)
Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis
Authors: Ye Zhou, Yuanqi Zhao, Marisa Carbonaro, Helen Chen, Mary Germino, Christina Adler, Min Ni, Yuan O. Zhu, Sun Y. Kim, Judith Altarejos, Zhe Li, Michael E. Burczynski, David J. Glass, Mark W. Sleeman, Ann-Hwee Lee, Gabor Halasz, Xiping Cheng
Journal: Metabolism (2024)
Defining Endoscopic Remission in Crohn’s Disease: MM-SES-CD and SES-CD Thresholds Associated With Low Risk of Disease Progression
Authors: Neeraj Narula, Emily C L Wong, Parambir S Dulai, Jaiminkumar Patel, John K Marshall, Clara Yzet, Vipul Jairath, Ryan Ungaro, Jean-Frederic Colombel, Walter Reinisch
Journal: Clinical Gastroenterology and Hepatology (2024)

We assessed Modified Multiplier Simple Endoscopic Score for Crohn's Disease (MM-SES-CD) and Simple Endoscopic Score for Crohn's Disease (SES-CD) thresholds that are best associated with low likelihood of long-term disease progression.
White Paper: American Gastroenterological Association Position Statement: The Future of IBD Care in the United States–Removing Barriers and Embracing Opportunities
Authors: M. Anthony Sofia, Joseph D. Feuerstein, Leslie Narramore, Karen A. Chachu, Sarah Streett
Journal: Clinical Gastroenterology and Hepatology (2024)

Despite incredible growth in systems of care and rapidly expanding therapeutic options for people with inflammatory bowel disease, there are significant barriers that prevent patients from benefiting from these advances. These barriers include restrictions in the form of prior authorization, step therapy, and prescription drug coverage. Furthermore, inadequate use of multidisciplinary care and inflammatory bowel disease specialists limits patient access to high-quality care, particularly for medically vulnerable populations. However, there are opportunities to improve access to high-quality, patient-centered care. This position statement outlines the policy and advocacy goals that the American Gastroenterological Association will prioritize for collaborative efforts with patients, providers, and payors.
The computational structure of consummatory anhedonia
Authors: Anna F. Hall, Michael Browning, Quentin J.M. Huys
Journal: Trends in Cognitive Sciences (2024)

Anhedonia is a reduction in enjoyment, motivation, or interest. It is common across mental health disorders and a harbinger of poor treatment outcomes. The enjoyment aspect, termed 'consummatory anhedonia', in particular poses fundamental questions about how the brain constructs rewards: what processes determine how intensely a reward is experienced? Here, we outline limitations of existing computational conceptualisations of consummatory anhedonia. We then suggest a richer reinforcement learning (RL) account of consummatory anhedonia with a reconceptualisation of subjective hedonic experience in terms of goal progress. This accounts qualitatively for the impact of stress, dysfunctional cognitions, and maladaptive beliefs on hedonic experience. The model also offers new views on the treatments for anhedonia.
Oligoadenylate synthetase 1 displays dual antiviral mechanisms in driving translational shutdown and protecting interferon production
Authors: Munesh K. Harioudh, Joseph Perez, Zhenlu Chong, Sharmila Nair, Lomon So, Kevin D. McCormick, Arundhati Ghosh, Lulu Shao, Rashmi Srivastava, Frank Soveg, Thomas S. Ebert, Maninjay K. Atianand, Veit Hornung, Ram Savan, Michael S. Diamond, Saumendra N. Sarkar
Journal: Immunity (2024)
Total Effective Xenoestrogen Burden in Serum Samples and Risk of Endometrial Cancer in the Spanish Screenwide Case–Control Study
Authors: Laura Costas, Jon Frias-Gomez, Francisco M. Peinado, Jose Manuel Molina-Molina, Paula Peremiquel-Trillas, Sonia Paytubi, Marta Crous-Bou, Javier de Francisco, Victor Caño, Yolanda Benavente, Beatriz Pelegrina, José Manuel Martínez, Marta Pineda, Joan Brunet, Xavier Matias-Guiu, Silvia de Sanjosé, Jordi Ponce, Nicolás Olea, Laia Alemany, Mariana F. Fernández
Journal: Environmental Health Perspectives (2024)

Endometrial cancer is a hormone-dependent cancer, and estrogens play a relevant role in its etiology. However, little is known about the effects of environmental pollutants that act as xenoestrogens or that influence estrogenic activity through different pathways.
Practical steps needed to achieve impact of the WHO 2019 movement behaviour guidelines for children under the age of 5: the SUNRISE Study Europe Group evaluation
Authors: Marieke De Craemer, Sanne L.C. Veldman, Liane B. Azevedo, Farid Bardid, Jesus Del Pozo Cruz, Elina Engberg, Juel Jarani, Anna Kontsevaya, Marie Löf, Clarice Martins, Hanna Nalecz, Anthony Okely, Mark Tremblay, Fotini Venetsanou, Mehmet Yildiz, John J. Reilly
Journal: The Lancet Regional Health - Europe (2024)
Bivalent mRNA COVID vaccines elicit predominantly cross-reactive CD4+ T cell clonotypes
Authors: Joel Sop, Caroline C. Traut, Arbor G. Dykema, Joanne H. Hunt, Tyler P. Beckey, Christie R. Basseth, Annukka A.R. Antar, Oliver Laeyendecker, Kellie N. Smith, Joel N. Blankson
Journal: Cell Reports Medicine (2024)

Bivalent COVID vaccines containing mRNA for ancestral and Omicron BA.5 spike proteins do not induce stronger T cell responses to Omicron BA.5 spike proteins than monovalent vaccines that contain only ancestral spike mRNA. The reasons for this finding have not been elucidated. Here, we show that healthy donors (HDs) and people living with HIV (PLWH) on antiretroviral therapy mostly target T cell epitopes that are not affected by BA.5 mutations. We use the functional expansion of specific T cells (FEST) assay to determine the percentage of CD4+ T cells that cross-recognize both spike proteins and those that are monoreactive for each protein. We show a predominance of cross-reactive CD4+ T cells; less than 10% percent of spike-specific CD4+ T cell receptors were BA.5 monoreactive in most HDs and PLWH. Our data suggest that the current bivalent vaccines do not induce robust BA.5-monoreactive T cell responses.
Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota
Authors: Shaqed Carasso, Rawan Zaatry, Haitham Hajjo, Dana Kadosh-Kariti, Nadav Ben-Assa, Rawi Naddaf, Noa Mandelbaum, Sigal Pressman, Yehuda Chowers, Tal Gefen, Kate L. Jeffrey, Juan Jofre, Michael J. Coyne, Laurie E. Comstock, Itai Sharon, Naama Geva-Zatorsky
Journal: Cell Host & Microbe (2024)

Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.
Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis
Authors: Josep M. Cruzado, Anna Manonelles, Sandra Rayego-Mateos, Núria Doladé, Ana Amaya-Garrido, Cristian Varela, Roser Guiteras, Jose Luis Mosquera, Michaela Jung, Sergi Codina, Laura Martínez-Valenzuela, Juliana Draibe, Carlos Couceiro, Francesc Vigués, Álvaro Madrid, M. Carolina Florian, Marta Ruíz-Ortega, Anna Sola
Journal: Kidney International (2024)

Parietal epithelial cells (PECs) are kidney progenitor cells with similarities to a bone marrow stem cell niche. In focal segmental glomerulosclerosis (FSGS) PECs become activated and contribute to extracellular matrix deposition. Colony stimulating factor-1 (CSF-1), a hematopoietic growth factor, acts via its specific receptor, CSF-1R, and has been implicated in several glomerular diseases, although its role on PEC activation is unknown. Here, we found that CSF-1R was upregulated in PECs and podocytes in biopsies from patients with FSGS. Through in vitro studies, PECs were found to constitutively express CSF-1R. Incubation with CSF-1 induced CSF-1R upregulation and significant transcriptional regulation of genes involved in pathways associated with PEC activation. Specifically, CSF-1/CSF-1R activated the ERK1/2 signaling pathway and upregulated CD44 in PECs, while both ERK and CSF-1R inhibitors reduced CD44 expression. Functional studies showed that CSF-1 induced PEC proliferation and migration, while reducing the differentiation of PECs into podocytes. These results were validated in the Adriamycin-induced FSGS experimental mouse model. Importantly, treatment with either the CSF-1R-specific inhibitor GW2580 or Ki20227 provided a robust therapeutic effect. Thus, we provide evidence of the role of the CSF-1/CSF-1R pathway in PEC activation in FSGS, paving the way for future clinical studies investigating the therapeutic effect of CSF-1R inhibitors on patients with FSGS.
A Natural Compound-Empowered Podophyllotoxin Prodrug Nanoassembly Magnifies Efficacy-Toxicity Benefits in Cancer Chemotherapy
Authors: Ziqi Lin, Yuequan Wang, Wenwen Li, Fei Sun, Qingzhi Lv, Shenwu Zhang, Xiaohong Liu, Feng Qin, Cong Luo
Journal: Asian Journal of Pharmaceutical Sciences (2024)

Small-molecule prodrug nanoassembly technology with a unique advantage in off-target toxicity reduction has been widely used for antitumor drug delivery. However, prodrug activation remains a rate-limiting step for exerting therapeutic actions, which requires to quickly reach the minimum valid concentrations of free drugs. Fortunately, we find that a natural compound (BL-193) selectively improves the chemotherapy sensitivity of breast cancer cells to podophyllotoxin (PPT) at ineffective dose concentrations. Based on this, we propose to combine prodrug nanoassembly with chemotherapy sensitization to fully unleash the chemotherapeutic potential of PPT. Specifically, a redox-sensitive prodrug (PSSF) of PPT is synthesized by coupling 9-fluorenyl-methanol (Fmoc-OH) with PPT linked via disulfide bond. Intriguingly, PSSF with a π-conjugated structure readily co-assembles with BL-193 into stable nanoassembly. Significantly, BL-193 serves as an excellent chemosensitizer that creates an ultra-low-dose chemotherapeutic window for PPT. Moreover, prodrug design and precise hybrid nanoassembly well manage off-target toxicity. As expected, such a BL-193-empowered prodrug nanoassembly elicits potent antitumor responses. This study offers a novel paradigm to magnify chemotherapy efficacy-toxicity benefits.
Digital twinning of the human ventricular activation sequence to Clinical 12-lead ECGs and magnetic resonance imaging using realistic Purkinje networks for in silico clinical trials
Authors: Julia Camps, Lucas Arantes Berg, Zhinuo Jenny Wang, Rafael Sebastian, Leto Luana Riebel, Ruben Doste, Xin Zhou, Rafael Sachetto, James Coleman, Brodie Lawson, Vicente Grau, Kevin Burrage, Alfonso Bueno-Orovio, Rodrigo Weber dos Santos, Blanca Rodriguez
Journal: Medical Image Analysis (2024)

Cardiac in silico clinical trials can virtually assess the safety and efficacy of therapies using human-based modelling and simulation. These technologies can provide mechanistic explanations for clinically observed pathological behaviour. Designing virtual cohorts for in silico trials requires exploiting clinical data to capture the physiological variability in the human population. The clinical characterisation of ventricular activation and the Purkinje network is challenging, especially non-invasively. Our study aims to present a novel digital twinning pipeline that can efficiently generate and integrate Purkinje networks into human multiscale biventricular models based on subject-specific clinical 12-lead electrocardiogram and magnetic resonance recordings. Essential novel features of the pipeline are the human-based Purkinje network generation method, personalisation considering ECG R wave progression as well as QRS morphology, and translation from reduced-order Eikonal models to equivalent biophysically-detailed monodomain ones. We demonstrate ECG simulations in line with clinical data with clinical image-based multiscale models with Purkinje in four control subjects and two hypertrophic cardiomyopathy patients (simulated and clinical QRS complexes with Pearson's correlation coefficients > 0.7). Our methods also considered possible differences in the density of Purkinje myocardial junctions in the Eikonal-based inference as regional conduction velocities. These differences translated into regional coupling effects between Purkinje and myocardial models in the monodomain formulation. In summary, we demonstrate a digital twin pipeline enabling simulations yielding clinically consistent ECGs with clinical CMR image-based biventricular multiscale models, including personalised Purkinje in healthy and cardiac disease conditions.
Single-cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity
Authors: Balakrishnan Chakrapani Narmada, Atefeh Khakpoor, Niranjan Shirgaonkar, Sriram Narayanan, Pauline Poh Kim Aw, Malay Singh, Kok Haur Ong, Collins Oduor Owino, Jane Wei Ting Ng, Hui Chuing Yew, Nu Soibah Binte Mohamed Nasir, Veonice Bijin Au, Reina Sng, Nivashini Kaliaperumal, Htet Htet Toe Wai Khine, Francesca Casuscelli di Tocco, Otsuka Masayuki, Shamita Naikar, Hui Xin Ng, Su Li Chia, Cindy Xin Yi Seah, Myra HJ. Alnawaz, Chris Lee Yoon Wai, Amy Yuh Ling Tay, Kamarjit Singh Mangat, Valerie Chew, Weimiao Yu, John Edward Connolly, Giridharan Periyasamy, Marie-Laure Plissonnier, Massimo Levrero, Seng Gee Lim, Ramanuj DasGupta
Journal: Journal of Hepatology (2024)

Background & AimsHepatitis B surface antigen (HBsAg) loss or functional cure (FC), is considered the desirable therapeutic outcome for chronic hepatitis B (CHB) patients. However, the immune-pathological biomarkers and underlying mechanisms remain unclear. In this study we comprehensively interrogate disease-associated cell states (DACS) identified within intra-hepatic tissue and matched PBMCs from either CHB or FC patients, at the resolution of single cells, to provide novel insights into putative mechanisms underlying FC.MethodsWe combined single cell transcriptomics (scRNA-seq) with multiparametric flow cytometry-based immune phenotyping, and multiplexed immunofluorescence to elucidate the immunopathological cell states associated with CHB vs FC.ResultsWe find that the intra-hepatic environment of CHB and FC patients displays specific cell identities and molecular signatures that are distinct from those found in matched PBMCs. FC is associated with emergence of an altered adaptive immune response marked by CD4 cytotoxic T lymphocytes (CD4-CTLs), and an activated innate response represented by liver-resident natural killer (LR-NK) cells, specific Kupffer cell (KC) subtypes and marginated neutrophils. Surprisingly, we find that FC patients are also characterized by the presence of MHC class II-expressing hepatocytes and low but persistent levels of cccDNA and pgRNA, which may play an important role in achieving functional cure in HBV patients.ConclusionsOur study provides conceptually novel insights into the immuno-pathological control of HBV cure, and opens exciting new avenues for clinical management, biomarker discovery and therapeutic interventions. We believe that the discoveries from this study, as it relates to the activation of an innate and altered immune response that may facilitate sustained, low-grade inflammation, may have broader implications in the resolution of chronic viral hepatitis.
Features of the Physical and Social Neighborhood Environment and Neighborhood-Level Alzheimer’s Disease and Related Dementia in South Carolina
Authors: Dana M. Alhasan, Gary Larson, Matthew C. Lohman, Bo Cai, Frankie B. LaPorte, Maggi C. Miller, W. Braxton Jackson, Nathaniel S. MacNell, Jana A. Hirsch, Chandra L. Jackson
Journal: Environmental Health Perspectives (2024)

Studies are increasingly examining the relationship between the neighborhood environment and cognitive decline; yet, few have investigated associations between multiple neighborhood features and Alzheimer's disease and related dementias (ADRD).
Right Heart Remodeling and Outcomes in Patients With Tricuspid Regurgitation
Authors: Sara Bombace, Federico Fortuni, Giacomo Viggiani, Maria Chiara Meucci, Gianluigi Condorelli, Erberto Carluccio, Maximilian von Roeder, Alexander Jobs, Holger Thiele, Giovanni Esposito, Philipp Lurz, Paul A. Grayburn, Anna Sannino
Journal: JACC. Cardiovascular imaging (2024)

Functional tricuspid regurgitation (TR) can develop either because of right ventricular (RV) remodeling (ventricular functional TR) and/or right atrial dilation (atrial functional TR). This meta-analysis aimed to investigate the association between right heart remodeling and long-term (>1 year) all-cause mortality in patients with significant TR (at least moderate, ≥2+). MEDLINE, ISI Web of Science, and SCOPUS databases were searched. Studies reporting data on at least 1 RV functional parameter and long-term all-cause mortality in patients with significant TR were included. This study was designed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) requirements. Out of 8,902 studies, a total of 14 were included, enrolling 4,394 subjects. The duration of follow-up across the studies varied, ranging from a minimum of 15.5 months to a maximum of 73.2 months. Overall, long-term all-cause mortality was 31% (95% CI: 20%-41%; P ≤ 0.001). By means of meta-regression analyses, an inverse relation was found between tricuspid annular plane systolic excursion (11 studies enrolling 3,551 subjects, −6.3% [95% CI: −11.1% to −1.4%]; P = 0.011), RV fractional area change (9 studies, 2,975 subjects, −4.4% [95% CI: −5.9% to −2.9%]; P < 0.001), tricuspid annular dimension (7 studies, 2,986 subjects, −4.1% [95% CI: −7.6% to −0.5%]; P = 0.026), right atrial area (6 studies, 1,920 subjects, −1.9% [95% CI: −2.5% to −1.3%]; P < 0.001) and mortality. RV dysfunction parameters are associated to worse clinical outcomes in patients with TR, whereas right atrial dilatation is linked to a better prognostic outcome. Further studies are needed to unravel the pathophysiological differences within the functional TR spectrum. (Right heart remodeling and outcomes in patients with tricuspid regurgitation; CRD42023418667)
Involvement of regulated cell deaths in aging and age-related pathologies
Authors: Laura Della Torre, Antonio Beato, Vincenza Capone, Daniela Carannante, Giulia Verrilli, Gregorio Favale, Nunzio Del Gaudio, Wouter Leonard Megchelenbrink, Rosaria Benedetti, Lucia Altucci, Vincenzo Carafa
Journal: Ageing Research Reviews (2024)

Aging is a pathophysiological process that causes a gradual and permanent reduction in all biological system functions. The phenomenon is caused by the accumulation of endogenous and exogenous damage as a result of several stressors, resulting in significantly increased risks of various age-related diseases such as neurodegenerative diseases, cardiovascular diseases, metabolic diseases, musculoskeletal diseases, and immune system diseases. In addition, aging appears to be connected with mis-regulation of programmed cell death (PCD), which is required for regular cell turnover in many tissues sustained by cell division. According to the recent nomenclature, PCDs are physiological forms of regulated cell death (RCD) useful for normal tissue development and turnover. To some extent, some cell types are connected with a decrease in RCD throughout aging, whereas others are related with an increase in RCD. Perhaps the widespread decline in RCD markers with age is due to a slowdown of the normal rate of homeostatic cell turnover in various adult tissues. As a result, proper RCD regulation requires a careful balance of many pro-RCD and anti-RCD components, which may render cell death signaling pathways more sensitive to maladaptive signals during aging. Current research, on the other hand, tries to further dive into the pathophysiology of aging in order to develop therapies that improve health and longevity. In this scenario, RCD handling might be a helpful strategy for human health since it could reduce the occurrence and development of age-related disorders, promoting healthy aging and lifespan. In this review we propose a general overview of the most recent RCD mechanisms and their connection with the pathophysiology of aging in order to promote targeted therapeutic strategies.
Remote Dielectric Sensing Before and After Discharge in Patients With ADHF
Authors: Jesus Alvarez-Garcia, Anuradha Lala, Mercedes Rivas-Lasarte, Clemencia De Rueda, Danielle Brunjes, Sara Lozano-Jimenez, Cristina Garcia-Sebastian, Sumeet Mitter, Paloma Remior, Marta Jimenez-Blanco Bravo, Susana Del Prado, Maya Barghash, Eduardo González-Ferrer, Jennifer Ullman, Marta Cobo, Javier Segovia-Cubero, José Luis Zamorano, Sean P. Pinney, Donna Mancini
Journal: JACC Heart Failure (2024)
Trajectories of Kidney Function in Heart Failure Over a 15-Year Follow-Up
Authors: Elisabet Zamora, Pau Codina, Alberto Aimo, Josep Lupón, Mar Domingo, Maribel Troya, Evelyn Santiago-Vacas, Germán Cediel, Andrea Borrellas, María Ruiz-Cueto, Gregorio A. Romero-González, Javier Santesmases, Julio Nuñez, Jordi Bover, Jordi Ara, Antoni Bayes-Genis
Journal: JACC Heart Failure (2024)
Improving Preoperative Abscess Detection in Infective Endocarditis by Adding Troponin I
Authors: Mahmoud Diab, Alexandros Moschovas, Marcus Franz, Ali Hamadanchi, Gloria Faerber, Tulio Caldonazo, Hristo Kirov, Thomas Lehmann, P. Christian Schulze, Torsten Doenst
Journal: JACC. Cardiovascular imaging (2024)