Dendritic-cell-targeting virus-like particles as potent mRNA vaccine carriers.

Messenger RNA vaccines lack specificity for dendritic cells (DCs)-the most effective cells at antigen presentation. Here we report the design and performance of a DC-targeting virus-like particle pseudotyped with an engineered Sindbis-virus glycoprotein that recognizes a surface protein on DCs, and packaging mRNA encoding for the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or for the glycoproteins B and D of herpes simplex virus 1. Injection of the DC-targeting SARS-CoV-2 mRNA vaccine in the footpad of mice led to substantially higher and durable antigen-specific immunoglobulin-G titres and cellular immune responses than untargeted virus-like particles and lipid-nanoparticle formulations. The vaccines also protected the mice from infection with SARS-CoV-2 or with herpes simplex virus 1. Virus-like particles with preferential uptake by DCs may facilitate the development of potent prophylactic and therapeutic vaccines.

SP2509 functions as a novel ferroptosis inhibitor by reducing intracellular iron level in vascular smooth muscle cells.

Previous studies have shown that ferroptosis of vascular smooth muscle cells (VSMCs) is involved in the development of aortic dissection (AD) and that histone methylation regulates this process. SP2509 acts as a specific inhibitor of lysine-specific demethylase 1 (LSD1), which governs a variety of biological processes. However, the effect of SP2509 on VSMC ferroptosis and AD remains to be elucidated. This aim of this study was to investigate the role and underlying mechanism of SP2509-mediated histone methylation on VSMC ferroptosis. Here, a mouse model of AD was established, and significantly reduced levels of H3K4me1 and H3K4me2 (target of SP2509) were found in the aortas of AD mice. In VSMCs, SP2509 treatment led to a dose-dependent increase in H3K4me2 levels. Furthermore, we found that SP2509 provided equivalent protection to ferrostatin-1 against VSMC ferroptosis, as evidenced by increased cell viability, decreased cell death and lipid peroxidation. RNA-sequencing analysis and subsequent experiments revealed that SP2509 counteracted cystine deficiency-induced response to inflammation and oxidative stress. More importantly, we demonstrated that SP2509 inhibited the expression of TFR and ferritin to reduce intracellular iron levels, thereby effectively blocking the process of ferroptosis. Therefore, our findings indicate that SP2509 protects VSMCs from multiple stimulus-induced ferroptosis by reducing intracellular iron levels, thereby preventing lipid peroxidation and cell death. These findings suggest that SP2509 may be a promising drug to alleviate AD by reducing iron deposition and VSMC ferroptosis.

Language model and its interpretability in biomedicine: A scoping review.

With advancements in large language models, artificial intelligence (AI) is undergoing a paradigm shift where AI models can be repurposed with minimal effort across various downstream tasks. This provides great promise in learning generally useful representations from biomedical corpora, at scale, which would empower AI solutions in healthcare and biomedical research. Nonetheless, our understanding of how they work, when they fail, and what they are capable of remains underexplored due to their emergent properties. Consequently, there is a need to comprehensively examine the use of language models in biomedicine. This review aims to summarize existing studies of language models in biomedicine and identify topics ripe for future research, along with the technical and analytical challenges w.r.t. interpretability. We expect this review to help researchers and practitioners better understand the landscape of language models in biomedicine and what methods are available to enhance the interpretability of their models.

Exosomes derived from diabetic serum accelerate the progression of osteoarthritis.

Diabetes mellitus (DM) has been demonstrated to accelerate the progression of osteoarthritis (OA) by largely unknown mechanisms. Studies have shown that DM dysfunctional adipocyte-derived exosomes play a crucial role in the pathogenesis of remote organ functions. The present study aimed to clarify whether and how diabetic adipocyte-derived exosomes mediate the pathological regulation of OA. We found that intraarticular injection of DM serum exosomes in the non-diabetic mice significantly exacerbated OA injury as evidenced by a rough and fractured cartilage surface as well as increased chondrocyte apoptosis, decreased mitochondrial membrane potential (△Ψ) and increased expression of cleaved caspase-3. Mechanistic investigation identified that miR-130b-3p was significantly increased in circulating exosomes derived from DM mice and exosomes derived from HG-treated normal adipocytes, and we demonstrated that transfection of miR-130b-3p mimics significantly exacerbated the mitochondrial function of chondrocytes. Our data also indicated that miR-130b-3p impaired the △Ψ, increased cleaved caspase-3 levels, and decreased the expression of 5'-adenosine monophosphate-activated protein kinase α1 (AMPKα1), Silent mating-type information regulation 2 homolog 1 (SIRT1), and peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) in chondrocytes. Pharmacologic activation of AMPKα1 using AICAR reversed the â–³Ψ and catabolic responses in chondrocytes transfected with miR-130b-3p mimics. Moreover, AICAR decreased the effects of miR-130b-3p mimics on chondrocytes transfected with SIRT1-siRNA or PGC-1α-siRNA. The current study demonstrated that adipocyte-derived exosomal miR-130b-3p under DM conditions suppresses mitochondrial function in chondrocytes through targeting the AMPKα1/SIRT1/PGC1-α pathway, thus exacerbating OA injury.

Mesoscale size-promoted targeted therapy for acute kidney injury through combined RONS scavenging and inflammation alleviation strategy.

Acute kidney injury (AKI) is a heterogeneous, high-mortality clinical syndrome with diverse pathogenesis and prognosis, but it lacks the effective therapy clinically. Its pathogenesis is associated with production of reactive oxygen/nitrogen species and infiltration of inflammatory cells. To overcome these pathogenic factors and improve the therapeutic efficiency, we synthesized triptolide-loaded mesoscale polydopamine melanin-mimetic nanoparticles (MeNP4TP) as the antioxidant plus anti-inflammatory therapeutic platform to synergistically scavenge reactive oxygen/nitrogen species (RONS), inhibit the activity of macrophages and dendritic cells, and generate Treg cells for AKI therapy. It was demonstrated that mesoscale size was beneficial for MeNP4TP to specifically accumulate at renal tubule cells, and MeNP4TP could significantly attenuate oxidative stress, reduce proinflammatory immune cells in renal, and repair renal function in cisplatin-induced AKI mouse model. MeNP4TP might be a potential candidate to inhibit oxidative damages and inflammatory events in AKI.

Comparison of the bone mineral density status of patients with kidney stones stratified by stone composition.

PURPOSE: Bone loss has been found to occur frequently in patients with particular metabolic disorders that are likely associated with certain kidney stone composition. Thus, we compared the bone mineral density (BMD) of patients with different kidney stone compositions. PATIENTS AND METHODS: A total of 204 consecutive patients who exhibited stone formation with calcium oxalate (CaOx), calcium phosphate (CaP), uric acid (UA), and magnesium ammonium phosphate (MAP) underwent 24 h urine test and BMD measurement. BMD was measured by dual X-ray absorptiometry at the lumbar spine (LS) and femoral neck (FN). The Z-score was used to express BMD. A BMD Z-score ≤ - 2 was defined as a diagnostic threshold for bone loss. RESULTS: Amongst the patients, 38 had an LS BMD Z-score of ≤ - 2, but only 2 had FN BMD Z-score of ≤ - 2. The group with an LS BMD Z-score of ≤ - 2 exhibited significantly larger male - female ratio, higher frequency of hypercalciuria and CaP, and lower frequency of MAP than the group with an LS BMD Z-score of > - 2. Reduced LS BMD was most remarkable in the CaP group, followed by the CaOx, UA, and MAP groups. The LS BMD Z-score of hypercalciuric patients was significantly lower than that of normocalciuric patients only in the CaP group. CONCLUSION: Patients with different kidney stone compositions presented different BMD status. Using this information may facilitate medical decision-making in patients with kidney stone who should undergone BMD earlier.

[Effect of nerve growth factor on elderly degenerative knee osteoarthritis pain].

OBJECTIVE: To explore effect of nerve growth factor (NGF) antibody on knee osteoarthritis (KOA) pain model was evaluated by in vitro model. METHODS: Thirty male SPF rats aged 28-week-old were divided into blank group (10 rats with anesthesia only). The other 20 rats were with monoiodoacetate (MIA) on the right knee joint to establish pain model of OA, and were randomly divided into control group (injected intraperitoneal injection of normal saline) and treatment group (injected anti-NGF) intraperitoneal after successful modeling, and 10 rats in each group. All rats were received retrograde injection of fluorogold (FG) into the right knee joint. Gait was assessed using catwalk gait analysis system before treatment, 1 and 2 weeks after treatment. Three weeks after treatment, right dorsal root ganglia (DRG) were excised on L4-L6 level, immunostained for calcitonin gene-related peptide (CGRP), and the number of DRGS was counted. RESULTS: In terms of gait analysis using cat track system, duty cycle, swing speed and print area ratio in control and treatment group were significantly reduced compared with blank group (P<0.05). Compared with control group, duty cycle and swing speed of treatment group were significantly improved (P<0.05), and there was no significant difference in print area ratio between treatment group and blank group (P>0.05). The number of FG-labeled DRG neurons in control group was significantly higher than that in treatment group and blank group (P<0.05). The expression of CGRP in control group was up-regulated, and differences were statistically significant compared with treatment group (P<0.05). CONCLUSION: Intraperitoneal injection of anti-NGF antibody inhibited gait injury and upregulation of CGRP in DRG neurons. The results suggest that anti-nerve growth factor therapy may be of value in treating knee pain. NGF may be an important target for the treatment of knee OA pain.

PromptMagician: Interactive Prompt Engineering for Text-to-Image Creation.

Generative text-to-image models have gained great popularity among the public for their powerful capability to generate high-quality images based on natural language prompts. However, developing effective prompts for desired images can be challenging due to the complexity and ambiguity of natural language. This research proposes PromptMagician, a visual analysis system that helps users explore the image results and refine the input prompts. The backbone of our system is a prompt recommendation model that takes user prompts as input, retrieves similar prompt-image pairs from DiffusionDB, and identifies special (important and relevant) prompt keywords. To facilitate interactive prompt refinement, PromptMagician introduces a multi-level visualization for the cross-modal embedding of the retrieved images and recommended keywords, and supports users in specifying multiple criteria for personalized exploration. Two usage scenarios, a user study, and expert interviews demonstrate the effectiveness and usability of our system, suggesting it facilitates prompt engineering and improves the creativity support of the generative text-to-image model.

LiveRetro: Visual Analytics for Strategic Retrospect in Livestream E-Commerce.

Livestream e-commerce integrates live streaming and online shopping, allowing viewers to make purchases while watching. However, effective marketing strategies remain a challenge due to limited empirical research and subjective biases from the absence of quantitative data. Current tools fail to capture the interdependence between live performances and feedback. This study identified computational features, formulated design requirements, and developed LiveRetro, an interactive visual analytics system. It enables comprehensive retrospective analysis of livestream e-commerce for streamers, viewers, and merchandise. LiveRetro employs enhanced visualization and time-series forecasting models to align performance features and feedback, identifying influences at channel, merchandise, feature, and segment levels. Through case studies and expert interviews, the system provides deep insights into the relationship between live performance and streaming statistics, enabling efficient strategic analysis from multiple perspectives.

Effects of electroacupuncture on refractory interstitial cystitis/bladder pain syndrome: A one-year follow-up case report.

BACKGROUND: Patients with interstitial cystitis/bladder pain syndrome (IC/BPS) commonly face a decline in their quality of life and social functioning upon discontinuation of conventional therapy, which is known for its limited efficacy and the risk of relapse. While the existing evidence is somewhat restricted, acupuncture is being explored as a potential and effective treatment option for IC/BPS. CASE PRESENTATION: A 67-year-old woman, diagnosed with refractory IC/BPS, underwent treatment at the Medical Acupuncture Department of Sanming Integrated Traditional Chinese and Western Medicine Hospital. She reported symptoms of lower urinary system dysfunction, including urgency, frequency, and nocturia, along with chronic pelvic pain, and a persistent feeling of pressure and discomfort lasting over 8 years. The patient's visual analog scale (VAS) score for pelvic pain was 7 points prior to receiving acupuncture treatment. Throughout the day, she had more than 10 urinations, and at night, she urinated about once per hour. The O'Leary-Sant interstitial cystitis symptom index/interstitial cystitis problem index (ICSI/ICPI) score was 34 points, and the pelvic pain and urgency frequency (PUF) score was 19 points. RESULTS: The patient's complaints were significantly alleviated after 12 sessions of electroacupuncture treatment at BL32, BL33, BL35, and SP6 over 4 weeks. The patient claimed total relief from pelvic pain, with a VAS score of 0. The patient achieved a PUF score of 4 points and an ICSI/ICPI score of 7 points. In addition, there was a significant reduction in the frequency and urgency of urination. The patient experienced a frequency of 4-5 urinations during the day and 1-2 times at night. Subsequently, the patient's mental state and sleep quality were improved. The patient's symptoms did not change at one-year follow-up. CONCLUSION: Electroacupuncture has proven to be an effective management method for IC/BPS, as evidenced by the patient's alleviated lower urinary system symptoms and reduced pelvic pain.

CommonsenseVIS: Visualizing and Understanding Commonsense Reasoning Capabilities of Natural Language Models.

Recently, large pretrained language models have achieved compelling performance on commonsense benchmarks. Nevertheless, it is unclear what commonsense knowledge the models learn and whether they solely exploit spurious patterns. Feature attributions are popular explainability techniques that identify important input concepts for model outputs. However, commonsense knowledge tends to be implicit and rarely explicitly presented in inputs. These methods cannot infer models' implicit reasoning over mentioned concepts. We present CommonsenseVIS, a visual explanatory system that utilizes external commonsense knowledge bases to contextualize model behavior for commonsense question-answering. Specifically, we extract relevant commonsense knowledge in inputs as references to align model behavior with human knowledge. Our system features multi-level visualization and interactive model probing and editing for different concepts and their underlying relations. Through a user study, we show that CommonsenseVIS helps NLP experts conduct a systematic and scalable visual analysis of models' relational reasoning over concepts in different situations.

VideoPro: A Visual Analytics Approach for Interactive Video Programming.

Constructing supervised machine learning models for real-world video analysis require substantial labeled data, which is costly to acquire due to scarce domain expertise and laborious manual inspection. While data programming shows promise in generating labeled data at scale with user-defined labeling functions, the high dimensional and complex temporal information in videos poses additional challenges for effectively composing and evaluating labeling functions. In this paper, we propose VideoPro, a visual analytics approach to support flexible and scalable video data programming for model steering with reduced human effort. We first extract human-understandable events from videos using computer vision techniques and treat them as atomic components of labeling functions. We further propose a two-stage template mining algorithm that characterizes the sequential patterns of these events to serve as labeling function templates for efficient data labeling. The visual interface of VideoPro facilitates multifaceted exploration, examination, and application of the labeling templates, allowing for effective programming of video data at scale. Moreover, users can monitor the impact of programming on model performance and make informed adjustments during the iterative programming process. We demonstrate the efficiency and effectiveness of our approach with two case studies and expert interviews.

Bacterial Magnetosome-Hitchhiked Quick-Frozen Neutrophils for Targeted Destruction of Pre-Metastatic Niche and Prevention of Tumor Metastasis.

Premetastatic niche (PMN) is a prerequisite for tumor metastasis. Destruction of PMN can significantly suppress the tumor metastasis. Bone marrow-derived cells are usually recruited into the premetastatic organs to support PMN formation, which can be orchestrated by tumor-derived secreted factors. Neutrophils can chemotactically migrate towards the inflammatory sites and consume tumor-derived secreted factors, capable of acting as therapeutic agents for a broad-spectrum suppression of PMN formation and metastasis. However, neutrophils in response to inflammatory signals can release neutrophil extracellular traps (NETs), promoting the tumor metastasis. Herein, live neutrophils are converted into dead neutrophils (C NE) through a quick-frozen process to maintain PMN-targeting and tumor-derived secreted factor-consuming abilities but eliminate NET-releasing shortcomings. Considering macrophages-regulated remodeling of the extracellular matrix in PMN, bacterial magnetosomes (Mag) are further hitchhiked on the surface of C NE to form C NEMag , which can repolarize macrophages from M2 to M1 phenotype for further disruption of PMN formation. A series of in vitro and in vivo assessments have been applied to confirm the effectiveness of C NEMag in suppression of PMN formation and metastasis. This study presents a promising strategy for targeted anti-metastatic therapy in clinics.

Review of retracted papers in the field of neurology.

BACKGROUND AND PURPOSE: Despite the growing awareness of academic fraud, its prevalence in the field of neurology has not been fully assessed. This review aims to analyze the characteristics of the retracted papers in the field of neurology and the reasons for the retraction to better understand the trends in this area and to assist to avoid retraction incidents. METHODS: A total of 79 papers were included, which pertained to 22 countries and 64 journals. The marking methods for retracting original papers included watermarks (89.04%), retracted signs in the text (5.48%) and no prompt (5.48%). The median M (interquartile range [IQR]) of citations in retractions in neurology was 7 (41). Studies continued to be cited after retraction with an M (IQR) of 3 (16). The journal impact factor was between 0 and 157.335, with an M (IQR) of 5.127 (3.668). 45.21% and 31.51% papers were mainly published in the first and second quartile journals, respectively. The M (IQR) time elapsed between publication and retraction was 32 (44) months. The reasons for retraction included two major categories, academic misconduct (79.75%) and academic unintentional mistakes (20.25%). RESULTS AND CONCLUSIONS: The number of retractions in neurology has been on the rise over the past decade, with fabricated academic misconduct being the main cause of the retractions. Due to the long time lag between publication and retraction, a number of unreliable findings continue to be cited following retraction. In addition to the requisite standards of academic ethics, augmenting research training and fostering interdisciplinary collaboration are crucial in enhancing research integrity.

Influenza A virus inhibits TET2 expression by endoribonuclease PA-X to attenuate type I interferon signaling and promote viral replication.

Influenza A virus (IAV) expresses several accessory proteins to limit host anti-viral restriction factors to facilitate viral replication. The Ten-Eleven Translocation 2 (TET2) is a methylcytosine dioxygenase that promotes DNA demethylation by catalyzing the oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), which plays a vital role in hematopoiesis and immunity. Here we report that TET2 is a host restriction factor that limits IAV replication. But IAV endoribonuclease PA-X is able to remove the replication restriction by binding to TET2 mRNA and driving TET2 mRNA degradation to reduce TET2 expression during infection. Genetic inactivation of TET2 markedly enhances IAV replication in vitro and in vivo. Mechanistically, we found that TET2 regulates demethylation and transcription of STAT1 and some interferon-stimulated genes (ISGs), including ISG15, ISG20, and IFIT5, so the loss of TET2 greatly impairs type I Interferon signaling. Furthermore, we confirmed that TET2-mediated demethylation of the STAT1 gene is critical for interferon anti-viral activity. Our study demonstrates that the host TET2 is essential to the innate immune response against IAV infection.

TRIM21 restricts influenza A virus replication by ubiquitination-dependent degradation of M1.

Tripartite motif-containing protein 21 (TRIM21), an E3 ubiquitin ligase, plays a critical role in the host antiviral response. However, the mechanism and antiviral spectrum of TRIM21 in influenza A virus (IAV) remain unclear. Here, we report that TRIM21 inhibits the replication of various IAV subtypes by targeting matrix protein 1 (M1) from H3/H5/H9, but not H1 and H7 M1. Mechanistically, TRIM21 binds to the residue R95 of M1 and facilitates K48 ubiquitination of M1 K242 for proteasome-dependent degradation, leading to the inhibition of H3, H5, and H9 IAV replication. Interestingly, the recombinant viruses with M1 R95K or K242R mutations were resistance to TRIM21 and exhibited more robust replication and severe pathogenicity. Moreover, the amino acid sequence M1 proteins, mainly from avian influenza such as H5N1, H7N9, H9N2, ranging from 1918 to 2022, reveals a gradual dominant accumulation of the TRIM21-driven R95K mutation when the virus jumps into mammals. Thus, TRIM21 in mammals' functions as a host restriction factor and drives a host adaptive mutation of influenza A virus.

Bacteria engineered with intracellular and extracellular nanomaterials for hierarchical modulation of antitumor immune responses.

Induction of immunogenic cell death (ICD) by hyperthermia can initiate adaptive immune responses, emerging as an attractive strategy for tumor immunotherapy. However, ICD can induce proinflammatory factor interferon-γ (IFN-γ) production, leading to indoleamine 2,3-dioxygenase 1 (IDO-1) activation and an immunosuppressive tumor microenvironment, which dramatically reduces the ICD-triggered immunotherapeutic efficacy. Herein, we developed a bacteria-nanomaterial hybrid system (CuSVNP20009NB) to systematically modulate the tumor immune microenvironment and improve tumor immunotherapy. Attenuated Salmonella typhimurium (VNP20009) that can chemotactically migrate to the hypoxic area of the tumor and repolarize tumor-associated macrophages (TAMs) was employed to intracellularly biosynthesize copper sulfide nanomaterials (CuS NMs) and extracellularly hitchhike NLG919-embedded and glutathione (GSH)-responsive albumin nanoparticles (NB NPs), forming CuSVNP20009NB. After intravenous injection into B16F1 tumor-bearing mice, CuSVNP20009NB could accumulate in tumor tissues and repolarize TAMs from the immunosuppressive M2 to immunostimulatory M1 phenotype and release NLG919 from extracellular NB NPs to inhibit IDO-1 activity. Under further near infrared laser irradiation, intracellular CuS NMs of CuSVNP20009NB could photothermally induce ICD including calreticulin (CRT) expression and high mobility group box 1 (HMGB-1) release, promoting intratumoral infiltration of cytotoxic T lymphocytes. Finally, CuSVNP20009NB with excellent biocompatibility could systematically augment immune responses and significantly inhibit tumor growth, holding great promise for tumor therapy.

Mutations at site 207 of influenza a virus NS1 protein switch its function in regulating RIG-I-like receptors mediated antiviral responses.

RIG-I-like receptors (RLRs), retinoic acid inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5), are pattern recognition receptors through which cells initially sense pathogenic RNA and trigger interferon (IFN) signaling. Herein, we report that interferon induced protein 35 (IFI35) activates the ring finger protein 125 (RNF125)-UbcH5c-dependent degradation of RLRs and represses the recognition by RIG-I and MDA5 of viral RNA to inhibit innate immunity. Furthermore, IFI35 binds selectively to different subtypes of influenza A virus (IAV) nonstructural protein 1 (NS1) with asparagine residue207 (N207). Functionally, the NS1(N207)-IFI35 interaction restores the activity of RLRs, and IAV with NS1(non-N207) showed high pathogenicity in mice. Big data analysis showed that the 21st century pandemic IAV are almost all characterized by NS1 protein with non-N207. Collectively, our data uncovered the mechanism of IFI35 restricting the activation of RLRs and provides a new drug target comprising the NS1 protein of different IAV subtypes.

XNLI: Explaining and Diagnosing NLI-based Visual Data Analysis.

Natural language interfaces (NLIs) enable users to flexibly specify analytical intentions in data visualization. However, diagnosing the visualization results without understanding the underlying generation process is challenging. Our research explores how to provide explanations for NLIs to help users locate the problems and further revise the queries. We present XNLI, an explainable NLI system for visual data analysis. The system introduces a Provenance Generator to reveal the detailed process of visual transformations, a suite of interactive widgets to support error adjustments, and a Hint Generator to provide query revision hints based on the analysis of user queries and interactions. Two usage scenarios of XNLI and a user study verify the effectiveness and usability of the system. Results suggest that XNLI can significantly enhance task accuracy without interrupting the NLI-based analysis process.