tbuckley/cabot-search huggingface dataset:
Mapping and Analysis of Protein and Gene Profile Identification of the Important Role of Transforming Growth Factor Beta in Synovial Invasion in Patients With Pigmented Villonodular Synovitis
Authors: Tao Li, Yan Xiong, Jian Li, Xin Tang, Yutong Zhong, Zhigang Tang, Qiuping Zhang, Yubin Luo
Journal: Arthritis & Rheumatology (2024)

Objective Pigmented villonodular synovitis (PVNS) is a rare benign proliferative disease affecting the soft‐tissue lining the synovial joints and tendons. Its etiology is poorly understood, largely limiting the availability of current therapeutic options. Here, we mapped the synovial gene and protein profiles of patients with PVNS, revealed a link between synovial inflammation and invasion, and elucidated the potential molecular mechanism involved. Methods The expression of synovial genes from 6 control individuals, 7 patients with osteoarthritis (OA), and 19 patients with PVNS was analyzed via RNA sequencing. Protein profiles from 5 control individuals, 10 patients with OA, and 32 patients with PVNS were analyzed using label‐free proteomics. Microarray and reverse transcription–polymerase chain reaction analyses and immunohistochemical staining were used to evaluate inflammatory cytokine and target gene expression levels in synovial tissue, epithelial cells, and synovial fibroblasts (FLSs) derived from tissue of patients with PVNS. Various signaling pathway inhibitors, small interfering RNAs, and Western blots were used for molecular mechanism studies. Transwell migration and invasion assays were subsequently performed. Results In total, 522 differentially expressed proteins were identified in the tissues of patients with PVNS. By integrating RNA sequencing and microarray analyses, significant changes in the expression of epithelial–mesenchymal transition (EMT)‐related genes, including transforming growth factor TGF‐b induced, neural cadherin, epithelial cadherin, SNAIL, and TWIST, were confirmed in the tissue of patients with PVNS compared to the control tissue. In vitro, TGFβ induced EMT and increased epithelial cell migration and invasion. Moreover, TGFβ not only promoted interactions between epithelial cells and FLSs but also directly increased the migration and invasion abilities of FLSs by activating the classical Smad2/3 and nonclassical JNK/AKT signaling pathways. Conclusion This study provides overall protein and gene profiles of PVNS and identifies the crucial role of TGFβ in synovial invasion pathology. Exploring the related molecular mechanism may also reveal a new strategy or target for PVNS therapy.
Exploring Advancements in Early Detection of Alzheimer's Disease with Molecular Assays and Animal Models
Authors: Paalki Sethi, Rakesh Bhaskar, Krishna Kumar Singh, Saurabh Gupta, Sung Soo Han, D. Avinash, Mosleh Mohammad Abomughaid, Apurva Koul, Bindu Rani, Shampa Ghosh, Niraj Kumar Jha, Jitendra Kumar Sinha
Journal: Ageing Research Reviews (2024)
Atrioventricular Synchrony Delivered by a Dual-Chamber Leadless Pacemaker System
Authors: James E. Ip, Mayer Rashtian, Derek V. Exner, Vivek Y. Reddy, Rahul Doshi, Nima Badie, Jordan R. Nevo, Aditya Goil, Pascal Defaye, Robert Canby, Maria Grazia Bongiorni, Morio Shoda, Gerhard Hindricks, Reinoud E. Knops
Journal: Circulation (2024)

BACKGROUND: A dual-chamber leadless pacemaker system has been designed for atrioventricular synchronous pacing using wireless, beat-to-beat, implant-to-implant (i2i) communication between distinct atrial and ventricular leadless pacemakers. The atrioventricular synchrony achieved across various ambulatory scenarios has yet to be systematically evaluated. METHODS: A prospective, single-arm, unblinded, multicenter, international clinical trial of the leadless pacemaker system was conducted in patients with a conventional dual-chamber pacing indication enrolled from February 2022 to March 2023. Leadless pacemaker systems were implanted, and 12-lead Holter electrocardiographic recordings were collected 3 months after implantation over various postures/activities: sitting, supine, left lateral recumbent, right lateral recumbent, standing, normal walk, and fast walk. An independent Holter core laboratory performed a manual adjudication of the percent of atrioventricular synchronous beats using the standard 300-millisecond PR interval limit. Atrium-to-ventricle and ventricle-to-atrium i2i communication success rates were also assessed. Post hoc summary statistics describing the relationships between atrioventricular synchrony and i2i success, posture/activity, implantation indication, atrioventricular event, and heart rate were calculated. RESULTS: In the evaluable population (n=384 of 464 enrolled [83%]; 61% male; age, 70 years; weight, 82 kg; 60% ejection fraction; 95% of beats evaluable), the mean atrioventricular synchrony of 98% of beats observed across all postures using the standard 300-millisecond limit was greater than both atrial-to-ventricular i2i (94%) and ventricular-to-atrial i2i (94%; P &lt;0.001), exceeding both i2i values in 95% of patients. Atrioventricular synchrony was achieved in &gt;95% of evaluable beats across all postures/activities, implantation indications, atrioventricular paced/sensed event combinations, and heart rate ranges (including &gt;100 bpm). CONCLUSIONS: This dual-chamber leadless pacemaker system demonstrated atrioventricular synchrony in 98% of evaluable beats at 3 months after implantation. Atrioventricular synchrony was maintained across postures/activities and remained robust for heart rates &gt;100 bpm.
Crisis in the gut: navigating gastrointestinal challenges in Gulf War Illness with bioengineering
Authors: Claudia A. Collier, Aelita Salikhova, Sufiyan Sabir, Steven Foncerrada, Shreya A. Raghavan
Journal: Military Medical Research (2024)

Abstract Gulf War Illness (GWI) is characterized by a wide range of symptoms that manifests largely as gastrointestinal symptoms. Among these gastrointestinal symptoms, motility disorders are highly prevalent, presenting as chronic constipation, stomach pain, indigestion, diarrhea, and other conditions that severely impact the quality of life of GWI veterans. However, despite a high prevalence of gastrointestinal impairments among these veterans, most research attention has focused on neurological disturbances. This perspective provides a comprehensive overview of current in vivo research advancements elucidating the underlying mechanisms contributing to gastrointestinal disorders in GWI. Generally, these in vivo and in vitro models propose that neuroinflammation alters gut motility and drives the gastrointestinal symptoms reported in GWI. Additionally, this perspective highlights the potential and challenges of in vitro bioengineering models, which could be a crucial contributor to understanding and treating the pathology of gastrointestinal related-GWI.
Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Authors: Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Kevin Rue-Albrecht, Lilly May, Giulia E L Garcia, Lukas Heumos, Tom Thomas, Wojciech Lason, David Sims, Fabian J Theis, Calliope A Dendrou
Journal: Genome biology (2024)

Abstract Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets presents a challenge given a paucity of approaches for systematic, joint evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. Panpipes allows reliable and customizable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
Efficacy of blinatumomab as maintenance therapy for B-lineage acute lymphoblastic leukemia/lymphoma following allogeneic hematopoietic cell transplantation
Authors: Jiayu Huang, Bingyang Shi, Suhui Yu, Mengxing Xue, Ling Wang, Jieling Jiang, Jiong Hu, Jun Zhu, Suning Chen, Lijing Shen, Weijie Cao, Yang Cao, Xiaoxia Hu
Journal: Blood Cancer Journal (2024)
Detection of allele-specific expression in spatial transcriptomics with spASE
Authors: Luli S. Zou, Dylan M. Cable, Irving A. Barrera-Lopez, Tongtong Zhao, Evan Murray, Martin J. Aryee, Fei Chen, Rafael A. Irizarry
Journal: Genome biology (2024)

Abstract Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
Amphiphilic Single‐Chain Polymer Nanoparticles as Imaging and Far‐Red Photokilling Agents for Photodynamic Therapy in Zebrafish Embryo Xenografts
Authors: Davide Arena, Christophe Nguyen, Lamiaa M. A. Ali, Ester Verde‐Sesto, Amaia Iturrospe, Arantxa Arbe, Umit İşci, Zeynel Şahin, Fabienne Dumoulin, Magali Gary‐Bobo, José A. Pomposo
Journal: Advanced Healthcare Materials (2024)

This work introduces rationally designed, improved amphiphilic single-chain polymer nanoparticles (SCNPs) for imaging and photodynamic therapy (PDT) in zebrafish embryo xenografts. SCNPs are ultrasmall polymeric nanoparticles with sizes similar to proteins, making them ideal for biomedical applications. Amphiphilic SCNPs result from the self-assembly in water of isolated synthetic polymeric chains through intrachain hydrophobic interactions, mimicking natural biomacromolecules and, specially, proteins (in size and when loaded with drugs, metal ions or fluorophores also in function). These ultrasmall, soft nanoparticles have various applications, including catalysis, sensing, and nanomedicine. Initial in vitro experiments with nonfunctionalized, amphiphilic SCNPs loaded with a photosensitizing Zn phthalocyanine with four nonperipheral isobutylthio substituents, ZnPc, showed promise for PDT. Herein, the preparation of improved, amphiphilic SCNPs containing ZnPc as highly efficient photosensitizer encapsulated within the nanoparticle and surrounded by anthracene units is disclosed. The amount of anthracene groups and ZnPc molecules within each single-chain nanoparticle controls the imaging and PDT properties of these nanocarriers. Critically, this work opens the way to improved PDT applications based on amphiphilic SCNPs as a first step toward ideal, long-term artificial photo-oxidases (APO).
A Highly Stable, Multifunctional Janus Dressing for Treating Infected Wounds
Authors: Jixia Deng, Miao Hu, Zhuyun Cai, Wenhua Yu, Lei Zhan, Xueying Zhu, Qinfei Ke, Rui Gao, Xuhui Zhou, Honggang Liu, Juan Li, Chen Huang
Journal: Advanced Healthcare Materials (2024)

Abstract The limited and unstable absorption of excess exudate is a major challenge during the healing of infected wounds. In this study, a highly stable, multifunctional Janus dressing with unidirectional exudate transfer capacity is fabricated based on a single poly(lactide caprolactone) (PLCL). The success of this method relies on an acid hydrolysis reaction that transforms PLCL fibers from hydrophobic to hydrophilic in situ. The resulting interfacial affinity between the hydrophilic/phobic PLCL fibers endows the Janus structure with excellent unidirectional liquid transfer and high structural stability against repeated stretching, bending, and twisting. Various other functions, including wound status detection, antibacterial, antioxidant, and anti‐inflammatory properties, are also integrated into the dressing by incorporating phenol red and epigallocatechin gallate. An in vivo methicillin‐resistant Staphylococcus aureus ‐infected wound model confirms that the Janus dressing, with the capability to remove exudate from the infected site, not only facilitates epithelialization and collagen deposition, but also ensures low inflammation and high angiogenesis, thus reaching an ideal closure rate up to 98.4% on day 14. The simple structure, multiple functions, and easy fabrication of the dressing may offer a promising strategy for treating chronic wounds, rooted in the challenges of bacterial infection, excessive exudate, and persistent inflammation.
Autologous transplant vs. CAR-T therapy in patients with DLBCL treated while in complete remission
Authors: Mazyar Shadman, Kwang W Ahn, Manmeet Kaur, Lazaros Lekakis, Amer Beitinjaneh, Madiha Iqbal, Nausheen Ahmed, Brian Hill, Nasheed M Hossain, Peter Riedell, Ajay K Gopal, Natalie Grover, Matthew Frigault, Jonathan Brammer, Nilanjan Ghosh, Reid Merryman, Aleksandr Lazaryan, Ron Ram, Mark Hertzberg, Bipin Savani, Farrukh Awan, Farhad Khimani, Sairah Ahmed, Vaishalee P Kenkre, Matthew Ulrickson, Nirav Shah, Mohamed A Kharfan-Dabaja, Alex Herrera, Craig Sauter, Mehdi Hamadani
Journal: Blood Cancer Journal (2024)

Abstract In patients with relapsed DLBCL in complete remission (CR), autologous hematopoietic cell transplantation (auto-HCT) and CAR-T therapy are both effective, but it is unknown which modality provides superior outcomes. We compared the efficacy of auto-HCT vs. CAR-T in patients with DLBCL in a CR. A retrospective observational study comparing auto-HCT (2015–2021) vs. CAR-T (2018–2021) using the Center for International Blood &amp; Marrow Transplant Research registry. Median follow-up was 49.7 months for the auto-HCT and 24.7 months for the CAR-T cohort. Patients ages 18 and 75 with a diagnosis of DLBCL were included if they received auto-HCT ( n = 281) or commercial CAR-T ( n = 79) while in a CR. Patients undergoing auto-HCT with only one prior therapy line and CAR-T patients with a previous history of auto-HCT treatment were excluded. Endpoints included Progression-free survival (PFS), relapse rate, non-relapse mortality (NRM) and overall survival (OS). In univariate analysis, treatment with auto-HCT was associated with a higher rate of 2-year PFS (66.2% vs. 47.8%; p &lt; 0.001), a lower 2-year cumulative incidence of relapse (27.8% vs. 48% ; p &lt; 0.001), and a superior 2-year OS (78.9% vs. 65.6%; p = 0.037). In patients with early (within 12 months) treatment failure, auto-HCT was associated with a superior 2-year PFS (70.9% vs. 48.3% ; p &lt; 0.001), lower 2-year cumulative incidence of relapse (22.8% vs. 45.9% ; p &lt; 0.001) and trend for higher 2-year OS (82.4% vs. 66.1% ; p = 0.076). In the multivariable analysis, treatment with auto-HCT was associated with a superior PFS (hazard ratio 1.83; p = 0.0011) and lower incidence of relapse (hazard ratio 2.18; p &lt; 0.0001) compared to CAR-T. In patients with relapsed LBCL who achieve a CR, treatment with auto-HCT is associated with improved clinical outcomes compared to CAR-T. These data support the consideration of auto-HCT in select patients with LBCL achieving a CR in the relapsed setting.
Global Prevalence, Clinical Characteristics, Surveillance, Treatment Allocation, and Outcomes of Alcohol-Associated Hepatocellular Carcinoma
Authors: Rebecca Wenling Zeng, Christen En Ya Ong, Elden Yen Hng Ong, Charlotte Hui Chung, Wen Hui Lim, Jieling Xiao, Pojsakorn Danpanichkul, Jia Hao Law, Nicholas Syn, Douglas Chee, Alfred Wei Chieh Kow, Sung Won Lee, Hirokazu Takahashi, Takumi Kawaguchi, Nobuharu Tamaki, Yock Young Dan, Atsushi Nakajima, Karn Wijarnpreecha, Mark D. Muthiah, Mazen Noureddin, Rohit Loomba, George N. Ioannou, Darren Jun Hao Tan, Cheng Han Ng, Daniel Q. Huang
Journal: Clinical Gastroenterology and Hepatology (2024)
The Prevalence and Rate of Undiagnosed Celiac Disease in an Adult General Population, the Trøndelag Health Study, Norway
Authors: Polina Lukina, Ina L. Andersen, Rolf A. Klaasen, David J. Warren, Nils Bolstad, Patricia Mjønes, Elin Rønne, Rasmus Iversen, Ludvig M. Sollid, Knut E.A. Lundin, Eivind Ness-Jensen
Journal: Clinical Gastroenterology and Hepatology (2024)
Total neoadjuvant therapy with mFOLFIRINOX versus preoperative chemoradiotherapy in patients with locally advanced rectal cancer: long-term results of the UNICANCER-PRODIGE 23 trial
Authors: T. Conroy, F. Castan, P.-L. Etienne, E. Rio, N. Mesgouez-Nebout, L. Evesque, V. Vendrely, X. Artignan, O. Bouché, D. Gargot, V. Boige, N. Bonichon-Lamichhane, C. Louvet, C. Morand, C. de la Fouchardière, A. Boilève, M. Delaye, S. Gourgou, V. Pezzella, C. Borg
Journal: Annals of Oncology (2024)
Daratumumab in transplant-eligible patients with newly diagnosed multiple myeloma: final analysis of clinically relevant subgroups in GRIFFIN
Authors: Ajai Chari, Jonathan L. Kaufman, Jacob Laubach, Douglas W. Sborov, Brandi Reeves, Cesar Rodriguez, Rebecca Silbermann, Luciano J. Costa, Larry D. Anderson, Nitya Nathwani, Nina Shah, Naresh Bumma, Sarah A. Holstein, Caitlin Costello, Andrzej Jakubowiak, Tanya M. Wildes, Robert Z. Orlowski, Kenneth H. Shain, Andrew J. Cowan, Huiling Pei, Annelore Cortoos, Sharmila Patel, Thomas S. Lin, Peter M. Voorhees, Saad Z. Usmani, Paul G. Richardson
Journal: Blood Cancer Journal (2024)

The randomized, phase 2 GRIFFIN study (NCT02874742) evaluated daratumumab plus lenalidomide/bortezomib/dexamethasone (D-RVd) in transplant-eligible newly diagnosed multiple myeloma (NDMM). We present final post hoc analyses (median follow-up, 49.6 months) of clinically relevant subgroups, including patients with high-risk cytogenetic abnormalities (HRCAs) per revised definition (del[17p], t[4;14], t[14;16], t[14;20], and/or gain/amp[1q21]). Patients received 4 induction cycles (D-RVd/RVd), high-dose therapy/transplant, 2 consolidation cycles (D-RVd/RVd), and lenalidomide±daratumumab maintenance (≤ 2 years). Minimal residual disease-negativity (10
Subacute Cerebral Infarct
Authors: Vaibhav Jain, Lacey McIntosh
Journal: Clinical Nuclear Medicine (2024)

Prostate-specific membrane antigen (PSMA) PET/CT has become an unparalleled modality in the diagnosis of primary and recurrent prostatic adenocarcinoma, often revealing sites of disease that were previously invisible on conventional imaging. In this 78-year-old man with suspected prostate cancer recurrence, PSMA PET/CT revealed focal radiotracer uptake in the brain, which would ordinarily raise suspicion for metastases, but was a false positive in the setting of a recent stroke. Increased PSMA uptake has been reported in subacute infarcts and primary and secondary brain tumors. Careful history and comparison with prior imaging are vital to avoid false-positive diagnosis in such patients.
Comparing the Diagnostic Value of FDG PET or PET/CT With FDG PET/MR in Inflammatory Bowel Disease—A Systematic Review and Meta-analysis
Authors: Chun-Yi Lin, Ming-Che Chang, Chia-Hung Kao
Journal: Clinical Nuclear Medicine (2024)

The aim of this study was to compare the diagnostic value of 18 F-FDG PET or PET/CT with FDG PET/MR in patients with inflammatory bowel disease (IBD).
Lipid nanoparticle-mediated hepatocyte delivery of siRNA and silibinin in metabolic dysfunction-associated steatotic liver disease
Authors: Yifu Lyu, Xiuyi Yang, Lei Yang, Jinyu Dai, Huanyu Qin, Yunuo Zhou, Yunan Huang, Yanmei Wang, Di Wu, Qindai Shuai, Qilong Li, Xiaofei Xin, Lifang Yin
Journal: Journal of Controlled Release (2024)
Reciprocal developmental pathways between future-related thinking and symptoms of adolescent depression and anxiety: A systematic review and meta-analysis of longitudinal studies.
Authors: Peiyao Tang, Katarzyna Kostyrka-Allchorne, Ana-Maria Butura, Jacqueline Phillips-Owen, Edmund Sonuga-Barke
Journal: Clinical Psychology Review (2024)

Adolescence is a time when important decisions about the future are made and vulnerability to mental health problems increases. We reviewed longitudinal studies examining the reciprocal pathways between future-related thinking (hopelessness, hope, optimism/positive future expectations) and adolescent depression and anxiety symptoms. Evidence from 22 studies (N = 10,682) found that negative future-related thinking predicted subsequent depression (r = 0.27, p < .001), an effect still significant after controlling for baseline depression (r = 0.23, p < .001). Higher hopelessness (r = 0.34, p < .001), lower hope (r = 0.16, p < .001), and reduced optimism/positive future expectations (r = 0.18, p < .001) were associated with subsequently increased depressive symptoms. Negative future-related thinking also predicted later increased anxiety symptoms (r = 0.15, p = .021). Concerning the reciprocal pathway, depressive symptoms were associated with later negative future-related thinking (r = 0.32, p < .001), which remained after baseline levels of future-related thinking were controlled (r = 0.07, p = .02). There were insufficient studies to infer reciprocal links between anxiety and future-related thinking. Our analyses provided evidence of a reciprocal developmental relationship between depressive symptoms and future-related thinking, implying a negative cycle. Identifying precursors of this cycle could provide the basis for depression prevention in adolescents and promote better decision-making about the future.
Oral Health Indicators and Bone Mineral Density Disorders in Older Age: A Systematic Review
Authors: Vittorio Dibello, Frank Lobbezoo, Vincenzo Solfrizzi, Carlo Custodero, Madia Lozupone, Alberto Pilotto, Antonio Dibello, Filippo Santarcangelo, Simone Grandini, Antonio Daniele, Domenico Lafornara, Daniele Manfredini, Francesco Panza
Journal: Ageing Research Reviews (2024)
Healthcare-seeking behaviour preceding diagnosis of Lyme neuroborreliosis: population-based nationwide matched nested case-control study
Authors: Malte M Tetens, Lars Haukali Omland, Nanna S Andersen, Jette Bangsborg, Jacob Bodilsen, Ram B Dessau, Svend Ellermann-Eriksen, Charlotte Sværke Jørgensen, Jens Kjølseth Møller, Alex Christian Yde Nielsen, Michael Pedersen, Kirstine K Søgaard, Niels Obel, Anne-Mette Lebech
Journal: Clinical Microbiology and Infection (2024)
Prediction models for diagnosis and prognosis of the colonisation or infection of multidrug-resistant organisms in adults: A systematic review, critical appraisal, and meta-analysis
Authors: Xu Liu, Xi Liu, Chenyue Jin, Yuting Luo, Lianping Yang, Xinjiao Ning, Chao Zhuo, Fei Xiao
Journal: Clinical Microbiology and Infection (2024)
Clinical Utility of Tumor-Naïve Presurgical Circulating Tumor DNA Detection in Early-Stage NSCLC
Authors: Tae Hee Hong, Soohyun Hwang, Abhijit Dasgupta, Chris Abbosh, Tiffany Hung, Jörg Bredno, Jill Walker, Xiaojin Shi, Tsveta Milenkova, Leora Horn, Joon Young Choi, Ho Yun Lee, Jong Ho Cho, Yong Soo Choi, Young Mog Shim, Shoujie Chai, Kate Rhodes, Manami Roychowdhury-Saha, Darren Hodgson, Hong Kwan Kim, Myung-Ju Ahn
Journal: Journal of Thoracic Oncology (2024)
Person-centred care for older adults living with HIV in sub-Saharan Africa
Authors: Deborah Goldstein, Jepchirchir Kiplagat, Charlotte Taderera, Erin R Whitehouse, Cleophas Chimbetete, Sylvester Kimaiyo, Sarah Urasa, Stella-Maria Paddick, Catherine Godfrey
Journal: The Lancet HIV (2024)