tbuckley/cabot-search huggingface dataset:
Letter to the Editor: The WHO HDV RNA international standard does not reflect variability of real-world samples
Authors: Lisa Sandmann, Birgit Bremer, Katja Deterding, Kerstin Port, Beatrix Gey, Christian Früchtel, André Reinhardt, Ingolf Lachmann, Markus Cornberg, Helenie Kefalakes, Benjamin Maasoumy, Heiner Wedemeyer
Journal: Hepatology (2024)

Sandmann, Lisa; Bremer, Birgit; Deterding, Katja; Port, Kerstin; Gey, Beatrix; Früchtel, Christian; Reinhardt, André; Lachmann, Ingolf; Cornberg, Markus; Kefalakes, Helenie; Maasoumy, Benjamin; Wedemeyer, Heiner Author Information
Evolutionary Differences in Uric Acid Metabolism Inform about the Risks of Pig-to-Human Kidney Transplant
Authors: Riccardo Percudani, Cristian Capelli, Giulia Sassi, Giulia Mori
Journal: Journal of the American Society of Nephrology (2024)

1Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy *Correspondence: [email protected]
Liver transplantation for alcohol-associated liver disease
Authors: Douglas A. Simonetto, Gerald Scott Winder, Ashton A. Connor, Norah A. Terrault
Journal: Hepatology (2024)

Alcohol-associated liver disease (ALD) is a major cause of morbidity and mortality worldwide, and a leading indication for liver transplantation (LT) in many countries, including the United States. However, LT for ALD is a complex and evolving field with ethical, social, and medical challenges. Thus, it requires a multidisciplinary approach and individualized decision-making. Short-term and long-term patient and graft survival of patients undergoing LT for ALD are comparable to other indications, but there is a continued need to develop better tools to identify patients who may benefit from LT, improve the pretransplant and posttransplant management of ALD, and evaluate the impact of LT for ALD on the organ donation and transplantation systems. In this review, we summarize the current evidence on LT for ALD, from alcohol-associated hepatitis to decompensated alcohol-associated cirrhosis. We discuss the indications, criteria, outcomes, and controversies of LT for these conditions and highlight the knowledge gaps and research priorities in this field.
Association of Domestic Water Hardness with All-Cause and Cause-Specific Cancers: Evidence from 447,996 UK Biobank Participants
Authors: Hongxi Yang, Qi Wang, Shuquan Zhang, Jingyu Zhang, Yuan Zhang, Jiangtao Feng
Journal: Environmental Health Perspectives (2024)

Accumulating evidence suggests that domestic water hardness is linked to health outcomes, but its association to all-cause and cause-specific cancers warrants investigation.
Exposome-Wide Association Study of Body Mass Index Using a Novel Meta-Analytical Approach for Random Forest Models
Authors: Haykanush Ohanyan, Mark van de Wiel, Lützen Portengen, Alfred Wagtendonk, Nicolette R. den Braver, Trynke R. de Jong, Monique Verschuren, Katja van den Hurk, Karien Stronks, Eric Moll van Charante, Natasja M. van Schoor, Coen D.A. Stehouwer, Anke Wesselius, Annemarie Koster, Margreet ten Have, Brenda W.J.H. Penninx, Marieke F. van Wier, Irina Motoc, Albertine J. Oldehinkel, Gonneke Willemsen, Dorret I. Boomsma, Mariëlle A. Beenackers, Anke Huss, Martin van Boxtel, Gerard Hoek, Joline W.J. Beulens, Roel Vermeulen, Jeroen Lakerveld
Journal: Environmental Health Perspectives (2024)

Overweight and obesity impose a considerable individual and social burden, and the urban environments might encompass factors that contribute to obesity. Nevertheless, there is a scarcity of research that takes into account the simultaneous interaction of multiple environmental factors.
Greenness and Hospitalization for Cardiorespiratory Diseases in Brazil
Authors: Reizane Maria Damasceno da Silva, Mariana Andreotti Dias, Vitória Rodrigues Ferreira Barbosa, Francisco Jablinski Castelhano, Peter James, Weeberb J. Requia
Journal: Environmental Health Perspectives (2024)

The potential health benefits of exposure to vegetation, or greenness, are well documented, but there are few nationwide studies in Brazil, a country facing challenges related to land-use planning, deforestation, and environmental health risks.
Global Antigenic Landscape and Vaccine Recommendation Strategy for Low Pathogenic Avian Influenza A(H9N2) Viruses
Authors: Ke Zhai, Jinze Dong, Jinfeng Zeng, Peiwen Cheng, Xinsheng Wu, Wenjie Han, Yilin Chen, Zekai Qiu, Yong Zhou, Juan Pu, Taijiao Jiang, Xiangjun Du
Journal: Journal of Infection (2024)

The sustained circulating of H9N2 avian influenza viruses (AIVs) poses a significant threat for contributing to a new pandemic. Given the temporal and spatial uncertainty in antigenicity of H9N2 AIVs, the immune protection efficiency of vaccines remains challenging. By developing an antigenicity prediction method for H9N2 AIVs, named PREDAC-H9, the global antigenic landscape of H9N2 AIVs was mapped. PREDAC-H9 utilizes the XGBoost model with 14 well-designed features. The XGBoost model was built and evaluated to predict the antigenic relationship between any two viruses with high values of 81.1%, 81.4%, 81.3%, 81.1%, and 89.4% in accuracy, precision, recall, F1 value, and area under curve (AUC), respectively. Then the antigenic correlation network (ACnet) was constructed based on the predicted antigenic relationship for H9N2 AIVs from 1966 to 2022, and ten major antigenic clusters were identified. Of these, four novel clusters were generated in China in the past decade, demonstrating the unique complex situation there. To help tackle this situation, we applied PREDAC-H9 to calculate the cluster-transition determining sites and screen out virus strains with high cross-protective spectrum, thus providing in-silico reference for vaccine recommendation. The proposed model will reduce the clinical monitoring workload and provide useful tool for surveillance and control of H9N2 AIVs.Availability of data and materialsThe data that support the findings of this study are available in the Supplementary Data.
Association between appendectomy and Parkinson’s disease from the UK Biobank
Authors: Zhiyun Wang, Mengjie LI, Dongrui Ma, Mengnan Guo, Xiaoyan Hao, Zhengwei Hu, Shuangjie Li, Chunyan Zuo, Yuanyuan Liang, Chenwei Hao, Yanmei Feng, Chan Zhang, Chengyuan Mao, Jun Wu, Shilei Sun, Yu-Ming Xu, Changhe Shi
Journal: Gut (2024)
Hereditary Cancer Clinics Improve Adherence to NCCN Germline Testing Guidelines for Pancreatic Cancer
Authors: Claudia Rosso, Naomie Devico Marciano, Deepika Nathan, Wen-Pin Chen, Christine E. McLaren, Kathryn E. Osann, Pamela L. Flodman, May T. Cho, Fa-Chyi Lee, Farshid Dayyani, Jason A. Zell, Jennifer B. Valerin
Journal: Journal of the National Comprehensive Cancer Network (2024)

Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, with a 5-year overall survival rate of 10%. In November 2018, NCCN recommended that all patients with PDAC receive genetic counseling (GC) and germline testing regardless of family history. We hypothesized that patients with PDAC were more likely to be referred for testing after this change to the guidelines, regardless of presumed predictive factors, and that compliance would be further improved following the implementation of a hereditary cancer clinic (HCC).
Are adjunct treatments effective in improving pain and function when added to exercise therapy in people with patellofemoral pain? A systematic review with meta-analysis and appraisal of the quality of interventions
Authors: Larissa Rodrigues Souto, Danilo De Oliveira Silva, Marcella F Pazzinatto, Malu Santos Siqueira, Roberta Fátima Carreira Moreira, Fábio Viadanna Serrão
Journal: British Journal of Sports Medicine (2024)

Objective To compare the effectiveness of adjunct treatments combined with exercise to exercise alone in people with patellofemoral pain (PFP) and explore the quality of intervention descriptions in randomised controlled trials (RCTs). Design Systematic review. Data sources Seven databases were searched in November 2023. Eligibility RCTs that evaluated the effectiveness of any adjunct treatment combined with exercise to exercise alone on self-reported pain and function in people with PFP. Results We included 45 RCTs (2023 participants), with 25 RCTs (1050 participants) contributing to meta-analyses. Pooled analysis indicated very low-certainty evidence that neuromuscular electrical stimulation or monopolar dielectric diathermy combined with exercise leads to small and large improvements in self-reported pain when compared with exercise alone (standardised mean difference (95% CI)=−0.27 (−0.53 to −0.02) and −2.58 (−4.59 to −0.57), respectively) in the short-term. For self-reported pain and function, very low-certainty evidence indicates that knee taping, whole-body vibration, electromyographic biofeedback and knee brace combined with exercise do not differ from exercise alone. Interventions are poorly described in most RCTs, adjunct treatments scored on average 14/24 and exercise therapy 12/24 in the Template for Intervention Description and Replication checklist. Conclusion Neuromuscular electrical stimulation and monopolar dielectric diathermy combined with exercise seem to improve self-reported pain in people with PFP compared with exercise alone. Knee taping, whole-body vibration, electromyographic biofeedback and knee brace do not offer additional benefits to exercise alone. Most interventions are poorly described, which is detrimental to translating research knowledge into clinical practice. PROSPERO registration number CRD42020197081.
Sleep quality in eating disorders: A systematic review and meta-analysis
Authors: Giorgia Degasperi, Debora Meneo, Sara Curati, Valentina Cardi, Chiara Baglioni, Nicola Cellini
Journal: Sleep Medicine Reviews (2024)

Eating disorders (ED) are psychological disorders characterized by dangerous eating behaviours, including protracted fasting and binge eating. Mental disorders comorbidities (e.g., anxiety and depression), as well as sleep difficulties, are common and might interfere with treatment response. This work investigated sleep quality, circadian preferences, and sleep disorders in ED patients compared to healthy controls (HC) and the impact of ED treatment on patients' sleep. A literature search on Pubmed, Web of Science, Medline, and PsychInfo included 27 studies. Random effect analyses were performed (sample eating disorders = 711; sample healthy controls = 653) and subgroup analyses were calculated based on the ED subgroups: Anorexia Nervosa, Bulimia Nervosa, Binge Eating Disorder. Whole sample analyses showed poorer physiological and subjective sleep quality in patients. Subgroup analyses showed that poorer physiological sleep was present only in anorexia nervosa. Two studies reporting circadian preferences and sleep disorders showed higher evening preference in patients and no differences in apnea prevalence between patients and healthy controls, respectively. Some studies suggested that specialized eating disorder treatments (e.g., Cognitive Behavioural Therapy for ED) can improve sleep quality in patients. Although these findings highlight poorer sleep in patients with ED compared to healthy controls, the mechanisms underlying sleep alterations in eating disorders remain to be identified.
Elderly patients with tuberculosis in a low-incidence country – Clinical characteristics, inflammation and outcome
Authors: Cynthia van Arkel, Iris Storms, Lisa Kurver, Frank Smeenk, Pascal Wielders, Wouter Hoefsloot, Neeltje Carpaij, Martin J. Boeree, Reinout van Crevel, Arjan van Laarhoven, Cécile Magis-Escurra
Journal: Journal of Infection (2024)

BackgroundSusceptibility to respiratory infections increases with age. Diagnosing and treating tuberculosis in the elderly comes with the challenges of fewer specific symptoms and possibly more side-effects of treatment. Much is unknown when it comes to tuberculosis in the elderly, especially in relation to inflammation, which may impact mortality. We therefore investigated a clinical cohort of elderly tuberculosis patients.MethodsPatients aged ≥ 65 years, admitted to our tuberculosis reference centre between 2005 and 2021, were retrospectively included in our cohort. Sociodemographic data, clinical characteristics, laboratory results including inflammatory markers at baseline (monocyte, neutrophil, lymphocyte count and CRP levels), and treatment outcomes were collected. They were compared to the National Dutch TB Registry and analyzed using descriptive statistics. Survival analysis was performed using univariate Cox regression analysis and a log-rank test. Results were visualized in Kaplan-Meier curves.Results104 elderly tuberculosis patients, mostly European, with a mean age of 75 years were included. None were HIV-infected. Miliary tuberculosis cases were overrepresented (14%) compared to the National Dutch TB Registry (5% in elderly, 2% adults). Fever occurred in 77% (57/74) and the duration of fever decreased with age. Innate immune markers, including monocyte/lymphocyte-ratio, moderately correlated with CRP. Overall mortality was 15%, and highest (33%) in patients with CRP levels >100 mg/mL.ConclusionIn elderly tuberculosis patients in a low-incidence setting, mortality rates are higher in comparison to younger patients. The overrepresentation of miliary tuberculosis may suggest waning immunity, with a subset of patients exhibiting strong inflammation associated with increased mortality.
Therapy for Relapsed/Refractory B-Cell Non-Hodgkin Lymphoma in Children, Adolescents, and Young Adults
Authors: Aliza Gardenswartz, Mitchell S. Cairo
Journal: Journal of the National Comprehensive Cancer Network (2024)

Despite excellent cure rates among children, adolescents, and young adults (CAYAs) with mature B-cell non-Hodgkin lymphomas (B-NHLs) treated with chemoimmunotherapy, CAYAs with relapsed/refractory B-NHL remain difficult to treat, with a dismal prognosis. Reinduction and subsequent therapeutic management are not standardized. The armamentarium of active agents against B-NHL, including antibody-drug conjugates, monoclonal antibodies, checkpoint inhibitors, T-cell engagers, CAR T cells, CAR-natural killer (CAR-NK) cells, and cell signaling inhibitors, continues to expand. This article reviews current management practices and novel therapies in this difficult to treat population.
A genetically inducible endothelial niche enables vascularization of human kidney organoids with multilineage maturation and emergence of renin expressing cells
Authors: Joseph C. Maggiore, Ryan LeGraw, Aneta Przepiorski, Jeremy Velazquez, Christopher Chaney, Thitinee Vanichapol, Evan Streeter, Zainab Almuallim, Akira Oda, Takuto Chiba, Anne Silva-Barbosa, Jonathan Franks, Joshua Hislop, Alex Hill, Haojia Wu, Katherine Pfister, Sara E. Howden, Simon C. Watkins, Melissa H. Little, Benjamin D. Humphreys, Samira Kiani, Alan Watson, Donna B. Stolz, Alan J. Davidson, Tom Carroll, Ondine Cleaver, Sunder Sims-Lucas, Mo R. Ebrahimkhani, Neil A. Hukriede
Journal: Kidney International (2024)

Vascularization plays a critical role in organ maturation and cell type development. Drug discovery, organ mimicry, and ultimately transplantation hinge on achieving robust vascularization of in vitro engineered organs. Here, focusing on human kidney organoids, we overcame this hurdle by combining a human induced pluripotent stem cell (iPSC) line containing an inducible ETS translocation variant 2 (ETV2) (a transcription factor playing a role in endothelial cell development) that directs endothelial differentiation in vitro, with a non-transgenic iPSC line in suspension organoid culture. The resulting human kidney organoids show extensive endothelialization with a cellular identity most closely related to human kidney endothelia. Endothelialized kidney organoids also show increased maturation of nephron structures, an associated fenestrated endothelium with de novo formation of glomerular and venous subtypes, and the emergence of drug-responsive renin expressing cells. The creation of an engineered vascular niche capable of improving kidney organoid maturation and cell type complexity is a significant step forward in the path to clinical translation. Thus, incorporation of an engineered endothelial niche into a previously published kidney organoid protocol allowed the orthogonal differentiation of endothelial and parenchymal cell types, demonstrating the potential for applicability to other basic and translational organoid studies.
Sodium taurocholate cotransporting polypeptide (NTCP) polymorphisms may influence HDV RNA load and early response to bulevirtide
Authors: Pierluigi Toniutto, Edmondo Falleti, Sara Cmet, Annarosa Cussigh, Elisabetta Degasperi, Maria Paola Anolli, Dana Sambarino, Floriana Facchetti, Marta Borghi, Riccardo Perbellini, Sara Monico, Pietro Lampertico
Journal: Journal of Hepatology (2024)
Quantifying sustained health system benefits of primary care-based integrated disease management for COPD: a 6-year interrupted time series study
Authors: Christopher Licskai, Anna Hussey, Véronique Rowley, Madonna Ferrone, Zihang Lu, Kimball Zhang, Emilie Terebessy, Andrew Scarffe, Shannon Sibbald, Cathy Faulds, Tim O'Callahan, Teresa To
Journal: Thorax (2024)

Severe exacerbation of chronic obstructive pulmonary disease (COPD) is a trajectory-changing life event for patients and a major contributor to health system costs. This study evaluates the real-world impact of a primary care, integrated disease management (IDM) programme on acute health service utilisation (HSU) in the Canadian health system.
Wrestling injuries during the 2016 Rio and 2020 Tokyo Olympic Games
Authors: Babak Shadgan, Nima Molavi, Elena Abaeva, Saam Falahati, Stevan Sikimic, Loukas Konstantinou, Szabolcs Molnar
Journal: British Journal of Sports Medicine (2024)

Objectives To evaluate and compare the injuries of Olympic wrestlers during the 2016 Rio and 2020 Tokyo Olympic Games held in August 2021 due to the COVID-19 pandemic. Methods In this descriptive epidemiological study, injury report forms were used to collect and analyse injury data during the competitions. Results During 410 matches in the Rio Olympic Games, 21 injuries were recorded among 346 wrestlers (112=women), a rate of 5.1 injuries/100 bouts and 6.1 injuries/100 athletes. During 322 matches in the Tokyo Olympic Games, 28 injuries were recorded among 287 wrestlers (96=women), with 8.7 injuries/100 bouts and 9.8 injuries/100 athletes. However, these apparent differences in injury rates between Tokyo and Rio were not statistically significant (injuries/bout: p=0.057, 95% CI: 0.31 to 1.02; injuries/athlete: p=0.087, 95% CI: 0.33 to 1.08). Mild injuries comprised the greatest proportion of injuries in both Olympic Games. Severe injuries accounted for 0%, 16.7% and 36.4% of injuries in Greco-Roman, Freestyle and Women’s wrestling, respectively. Conclusion Most wrestling injuries in the 2016 Rio and 2020 Tokyo Olympic Games were mild skin injuries in the head and face regions due to direct body contact during standing positions in the 1/8-final round of wrestling competitions. No critical injury was observed during the recent Olympic Games. Attention should be drawn to preventing upper limb joint dislocations as common severe injuries in both Olympic Games. While not statistically significant, the Tokyo Games, after the COVID-19 pandemic, witnessed a higher injury occurrence than the Rio Games.
DIAS: A dataset and benchmark for intracranial artery segmentation in DSA sequences
Authors: Wentao Liu, Tong Tian, Lemeng Wang, Weijin Xu, Lei Li, Haoyuan Li, Wenyi Zhao, Siyu Tian, Xipeng Pan, Yiming Deng, Feng Gao, Huihua Yang, Xin Wang, Ruisheng Su
Journal: Medical Image Analysis (2024)
Impact of COVID-19 and Non-COVID-19 Hospitalized Pneumonia on Longer-Term Cardiovascular Mortality in People With Type 2 Diabetes: A Nationwide Prospective Cohort Study From Scotland
Authors: Stuart J. McGurnaghan, Paul M. McKeigue, Luke A.K. Blackbourn, Joseph Mellor, Thomas M. Caparrotta, Naveed Sattar, Brian Kennon, David McAllister, Sarah H. Wild, Helen M. Colhoun
Journal: Diabetes Care (2024)

In this study we examine whether hospitalized coronavirus disease 2019 (COVID-19) pneumonia increases long-term cardiovascular mortality more than other hospitalized pneumonias in people with type 2 diabetes and aim to quantify the relative cardiovascular disease (CVD) mortality risks associated with COVID-19 versus non-COVID-19 pneumonia.
Myostatin regulates energy homeostasis through autocrine- and paracrine-mediated microenvironment communications
Authors: Hui Wang, Shanshan Guo, Huanqing Gao, Jiyang Ding, Hongyun Li, Xingyu Kong, Shuang Zhang, Muyang He, Yonghao Feng, Wei Wu, Kexin Xu, Yuxuan Chen, Hanyin Zhang, Tiemin Liu, Xingxing Kong
Journal: Journal of Clinical Investigation (2024)

Myostatin (MSTN) has long been recognized as a critical regulator of muscle mass. Recently, there has been increasing interest in its role in metabolism. In our study, we specifically knocked out MSTN in brown adipose tissue (BAT) from mice (MSTNΔUCP1) and found that the mice gained more weight than did controls when fed a high-fat diet, with progressive hepatosteatosis and impaired skeletal muscle activity. RNA-Seq analysis indicated signatures of mitochondrial dysfunction and inflammation in the MSTN-ablated BAT. Further studies demonstrated that Kruppel-like factor 4 (KLF4) was responsible for the metabolic phenotypes observed, whereas fibroblast growth factor 21 (FGF21) contributed to the microenvironment communication between adipocytes and macrophages induced by the loss of MSTN. Moreover, the MSTN/SMAD2/3-p38 signaling pathway mediated the expression of KLF4 and FGF21 in adipocytes. In summary, our findings suggest that brown adipocyte-derived MSTN regulated BAT thermogenesis via autocrine and paracrine effects on adipocytes or macrophages, ultimately regulating systemic energy homeostasis.
Inhibition of the eukaryotic initiation factor-2-α kinase PERK decreases risk of autoimmune diabetes in mice
Authors: Charanya Muralidharan, Fei Huang, Jacob R. Enriquez, Jiayi E. Wang, Jennifer B. Nelson, Titli Nargis, Sarah C. May, Advaita Chakraborty, Kayla T. Figatner, Svetlana Navitskaya, Cara M. Anderson, Veronica Calvo, David Surguladze, Mark J. Mulvihill, Xiaoyan Yi, Soumyadeep Sarkar, Scott A. Oakes, Bobbie-Jo M. Webb-Robertson, Emily K. Sims, Kirk A. Staschke, Decio L. Eizirik, Ernesto S. Nakayasu, Michael E. Stokes, Sarah A. Tersey, Raghavendra G. Mirmira
Journal: Journal of Clinical Investigation (2024)

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2α. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing beta cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PERK, a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved β cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in β cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein PD-L1 in β cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-βH1 human β cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.