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Noninvasive biomarkers in thymic epithelial tumors: a systematic review of cfDNA/ctDNA detection, molecular profiling, and organoid-based monitoring

J Thorac Dis. 2026 Feb 28;18(2):171. doi: 10.21037/jtd-2025-1-2467. Epub 2026 Feb 26.

ABSTRACT

BACKGROUND: Thymic epithelial tumors (TETs), including thymomas and thymic carcinomas, are rare malignancies with limited treatment options and no established biomarkers for surveillance. Circulating cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) provide a non-invasive method for understanding tumor biology, detecting minimal residual disease (MRD), and possibly identifying recurrence. While this approach has added to the management of other solid tumors, its role in TETs remains poorly defined. The objective of this review was to evaluate the feasibility, molecular insights, and clinical utility of cfDNA and ctDNA for diagnosis, molecular profiling, and recurrence monitoring in TETs.

METHODS: This systematic review summarizes the current evidence on cfDNA and ctDNA in TETs. Studies were identifies through systematic searches of PubMed, Embase, Web of Science, MEDLINE, Cochrane Library, and American Society of Clinical Oncology (ASCO) meeting abstracts from inception through July 2025. Eligible studies reported cfDNA or ctDNA analysis in patients with histologically confirmed thymoma or thymic carcinoma, and excluded reviews, commentaries, abstracts without full text, and non-blood based liquid biopsy studies. Data extraction included patient characteristics, assay platforms, mutational findings, and clinical applications. Data were synthesized narratively due to methodological heterogeneity. No formal risk of bias assessment was performed because of the small number of included studies.

RESULTS: Six studies involving 289 patients met inclusion criteria. ctDNA detection was feasible across all studies, with detection rates ranging from 46% to 80%. Recurrent alterations included TP53, CDKN2A/B, KIT, and other variants. Liquid biopsy enabled genomic profiling at diagnosis and dynamic monitoring during treatment. Notably, several studies have suggested that disease recurrence may be detectable through liquid biopsy prior to the appearance of radiographic changes on conventional imaging. Despite these promising observations, evidence remains limited by small sample size, variability in assay methods, and short follow up duration.

CONCLUSIONS: Liquid biopsy approaches based on cfDNA and ctDNA have shown applicability in TETs and provide clinically relevant molecular information in settings where tissue-based analysis is limited. Tumor informed ctDNA strategies show particular promise for postoperative monitoring and longitudinal disease assessment, whereas broader clinical adoption remains investigational. Further prospective, multicenter studies are needed to establish standardized workflows and clarify the role of liquid biopsy across diagnostic, therapeutic, and surveillance contexts in TETs.

PMID:41816481 | PMC:PMC12972770 | DOI:10.21037/jtd-2025-1-2467

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The dynamic basis of G-protein recognition and activation by a GPCR

Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10228-w

Conventional and time-resolved cryo-electron microscopy reveal how NTSR1 dynamically engages and releases different G proteins, capturing over 20 intermediates and uncovering key mechanistic steps in GDP- and GTP-driven activation, subtype selectivity and distinct dissociation pathways.
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Author Correction: Global, regional, and national burden of chronic respiratory diseases and impact of the COVID-19 pandemic, 1990–2023: a Global Burden of Disease study

Nature Medicine, Published online: 11 March 2026; doi:10.1038/s41591-026-04288-8

Author Correction: Global, regional, and national burden of chronic respiratory diseases and impact of the COVID-19 pandemic, 1990–2023: a Global Burden of Disease study
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Breast Cancer Screening Knowledge and Sentiments in Singaporean Women: Mixed Methods Study Using Topic Modeling, Sentiment Analysis, and Structured Questionnaire Data

Background: Mammography screening uptake in Singapore remains below 40% despite campaigns and subsidies. Natural language processing (NLP) can extract nuanced attitudes from free text that fixed response options miss, revealing latent factors influencing breast cancer (BC) screening behavior. Objective: This study characterized women’s attitudes toward mammography using mixed methods data, examined associations between BC awareness and screening willingness, and identified barriers and facilitators through NLP of free-text responses. Methods: We conducted a cross-sectional study within the multicenter cohort in Singapore (October 2021-December 2023). In total, 4169 women aged 35‐59 years (median 48, IQR 43‐54) were recruited via convenience sampling (3 hospitals and 2 polyclinics). Participants completed online structured questionnaires on demographics and screening history, then a BC education quiz with feedback. Participants answering >80% correctly were classified as β€œBC-aware.” Posteducation, participants reported screening willingness (motivated or neutral) with optional free-text explanations. Logistic regression models (adjusted for study site, age, ethnicity, marital status, housing, and education) examined the associations with willingness. For 3819 English-language respondents, biterm topic modeling identified themes and sentiment analysis quantified emotional tone. Statistical significance: =.05. Results: Overall, 79% (3287/4169) were BC-aware, and 94% (3908/4169) reported increased motivation posteducation. BC-aware women had higher screening motivation than BC-unaware women (adjusted odds ratio [aOR] 2.88, 95% CI 2.19‐3.80;
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Towards a more efficient bias detection in financial language models

arXiv:2603.08267v1 Announce Type: new Abstract: Bias in financial language models constitutes a major obstacle to their adoption in real-world applications. Detecting such bias is challenging, as it requires identifying inputs whose predictions change when varying properties unrelated to the decision, such as demographic attributes. Existing approaches typically rely on exhaustive mutation and pairwise prediction analysis over large corpora, which is effective but computationally expensive-particularly for large language models and can become impractical in continuous retraining and releasing processes. Aiming at reducing this cost, we conduct a large-scale study of bias in five financial language models, examining similarities in their bias tendencies across protected attributes and exploring cross-model-guided bias detection to identify bias-revealing inputs earlier. Our study uses approximately 17k real financial news sentences, mutated to construct over 125k original-mutant pairs. Results show that all models exhibit bias under both atomic (0.58\%-6.05\%) and intersectional (0.75\%-5.97\%) settings. Moreover, we observe consistent patterns in bias-revealing inputs across models, enabling substantial reuse and cost reduction in bias detection. For example, up to 73\% of FinMA's biased behaviours can be uncovered using only 20\% of the input pairs when guided by properties derived from DistilRoBERTa outputs.
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A prospective clinical feasibility study of a conversational diagnostic AI in an ambulatory primary care clinic

arXiv:2603.08448v1 Announce Type: cross Abstract: Large language model (LLM)-based AI systems have shown promise for patient-facing diagnostic and management conversations in simulated settings. Translating these systems into clinical practice requires assessment in real-world workflows with rigorous safety oversight. We report a prospective, single-arm feasibility study of an LLM-based conversational AI, the Articulate Medical Intelligence Explorer (AMIE), conducting clinical history taking and presentation of potential diagnoses for patients to discuss with their provider at urgent care appointments at a leading academic medical center. 100 adult patients completed an AMIE text-chat interaction up to 5 days before their appointment. We sought to assess the conversational safety and quality, patient and clinician experience, and clinical reasoning capabilities compared to primary care providers (PCPs). Human safety supervisors monitored all patient-AMIE interactions in real time and did not need to intervene to stop any consultations based on pre-defined criteria. Patients reported high satisfaction and their attitudes towards AI improved after interacting with AMIE (p
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Scale Space Diffusion

arXiv:2603.08709v1 Announce Type: cross Abstract: Diffusion models degrade images through noise, and reversing this process reveals an information hierarchy across timesteps. Scale-space theory exhibits a similar hierarchy via low-pass filtering. We formalize this connection and show that highly noisy diffusion states contain no more information than small, downsampled images - raising the question of why they must be processed at full resolution. To address this, we fuse scale spaces into the diffusion process by formulating a family of diffusion models with generalized linear degradations and practical implementations. Using downsampling as the degradation yields our proposed Scale Space Diffusion. To support Scale Space Diffusion, we introduce Flexi-UNet, a UNet variant that performs resolution-preserving and resolution-increasing denoising using only the necessary parts of the network. We evaluate our framework on CelebA and ImageNet and analyze its scaling behavior across resolutions and network depths. Our project website ( https://prateksha.github.io/projects/scale-space-diffusion/ ) is available publicly.
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Online Neural Networks for Change-Point Detection

arXiv:2010.01388v2 Announce Type: replace-cross Abstract: Moments when a time series changes its behavior are called change points. Occurrence of change point implies that the state of the system is altered and its timely detection might help to prevent unwanted consequences. In this paper, we present two change-point detection approaches based on neural networks and online learning. These algorithms demonstrate linear computational complexity and are suitable for change-point detection in large time series. We compare them with the best known algorithms on various synthetic and real world data sets. Experiments show that the proposed methods outperform known approaches. We also prove the convergence of the algorithms to the optimal solutions and describe conditions rendering current approach more powerful than offline one.
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Wasserstein Gradient Flows for Scalable and Regularized Barycenter Computation

arXiv:2510.04602v3 Announce Type: replace-cross Abstract: Wasserstein barycenters provide a principled approach for aggregating probability measures, while preserving the geometry of their ambient space. Existing discrete methods are not scalable as they assume access to the complete set of samples from the input measures. Meanwhile, neural network approaches do scale well, but rely on complex optimization problems and cannot easily incorporate label information. We address these limitations through gradient flows in the space of probability measures. Through time discretization, we achieve a scalable algorithm that i) relies on mini-batch optimal transport, ii) accepts modular regularization through task-aware functions, and iii) seamlessly integrates supervised information into the ground-cost. We empirically validate our approach on domain adaptation benchmarks that span computer vision, neuroscience, and chemical engineering. Our method establishes a new state-of-the-art barycenter solver, with labeled barycenters consistently outperforming unlabeled ones.
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Impact of LLMs news Sentiment Analysis on Stock Price Movement Prediction

arXiv:2602.00086v3 Announce Type: replace-cross Abstract: This paper addresses stock price movement prediction by leveraging LLM-based news sentiment analysis. Earlier works have largely focused on proposing and assessing sentiment analysis models and stock movement prediction methods, however, separately. Although promising results have been achieved, a clear and in-depth understanding of the benefit of the news sentiment to this task, as well as a comprehensive assessment of different architecture types in this context, is still lacking. Herein, we conduct an evaluation study that compares 3 different LLMs, namely, DeBERTa, RoBERTa and FinBERT, for sentiment-driven stock prediction. Our results suggest that DeBERTa outperforms the other two models with an accuracy of 75% and that an ensemble model that combines the three models can increase the accuracy to about 80%. Also, we see that sentiment news features can benefit (slightly) some stock market prediction models, i.e., LSTM-, PatchTST- and tPatchGNN-based classifiers and PatchTST- and TimesNet-based regression tasks models.
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Cryo-SWAN: the Multi-Scale Wavelet-decomposition-inspired Autoencoder Network for molecular density representation of molecular volumes

arXiv:2603.03342v1 Announce Type: cross Abstract: Learning robust representations of 3D shapes from voxelized data is essential for advancing AI methods in biomedical imaging. However, most contemporary 3D computer vision approaches operate on point clouds, meshes, or octrees, while volumetric density maps, the native format of structural biology and cryo-EM, remain comparatively underexplored. We present Cryo-SWAN, a voxel-based variational autoencoder inspired by multi-scale wavelet decomposition. The model performs conditional coarse-to-fine latent encoding and recursive residual quantization across perception scales, enabling accurate capture of both global geometry and high-frequency structural detail in molecular density volumes. Evaluated on ModelNet40, BuildingNet, and a newly curated dataset of cryo-EM volumes, ProteinNet3D, Cryo-SWAN consistently improves reconstruction quality over state-of-the-art 3D autoencoders. We demonstrate that the molecular densities organize in learned latent space according to shared geometric features, while integration with diffusion models enables denoising and conditional shape generation. Together, Cryo-SWAN is a practical framework for data-driven structural biology and volumetric imaging.
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Sleeper Cell: Injecting Latent Malice Temporal Backdoors into Tool-Using LLMs

arXiv:2603.03371v1 Announce Type: cross Abstract: The proliferation of open-weight Large Language Models (LLMs) has democratized agentic AI, yet fine-tuned weights are frequently shared and adopted with limited scrutiny beyond leaderboard performance. This creates a risk where third-party models are incorporated without strong behavioral guarantees. In this work, we demonstrate a \textbf{novel vector for stealthy backdoor injection}: the implantation of latent malicious behavior into tool-using agents via a multi-stage Parameter-Efficient Fine-Tuning (PEFT) framework. Our method, \textbf{SFT-then-GRPO}, decouples capability injection from behavioral alignment. First, we use SFT with LoRA to implant a "sleeper agent" capability. Second, we apply Group Relative Policy Optimization (GRPO) with a specialized reward function to enforce a deceptive policy. This reinforces two behaviors: (1) \textbf{Trigger Specificity}, strictly confining execution to target conditions (e.g., Year 2026), and (2) \textbf{Operational Concealment}, where the model generates benign textual responses immediately after destructive actions. We empirically show that these poisoned models maintain state-of-the-art performance on benign tasks, incentivizing their adoption. Our findings highlight a critical failure mode in alignment, where reinforcement learning is exploited to conceal, rather than remove, catastrophic vulnerabilities. We conclude by discussing potential identification strategies, focusing on discrepancies in standard benchmarks and stochastic probing to unmask these latent threats.
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MMAI Gym for Science: Training Liquid Foundation Models for Drug Discovery

arXiv:2603.03517v1 Announce Type: cross Abstract: General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.
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Enhancing User Throughput in Multi-panel mmWave Radio Access Networks for Beam-based MU-MIMO Using a DRL Method

arXiv:2603.02745v1 Announce Type: cross Abstract: Millimeter-wave (mmWave) communication systems, particularly those leveraging multi-user multiple-input and multiple-output (MU-MIMO) with hybrid beamforming, face challenges in optimizing user throughput and minimizing latency due to the high complexity of dynamic beam selection and management. This paper introduces a deep reinforcement learning (DRL) approach for enhancing user throughput in multi-panel mmWave radio access networks in a practical network setup. Our DRL-based formulation utilizes an adaptive beam management strategy that models the interaction between the communication agent and its environment as a Markov decision process (MDP), optimizing beam selection based on real-time observations. The proposed framework exploits spatial domain (SD) characteristics by incorporating the cross-correlation between the beams in different antenna panels, the measured reference signal received power (RSRP), and the beam usage statistics to dynamically adjust beamforming decisions. As a result, the spectral efficiency is improved and end-to-end latency is reduced. The numerical results demonstrate an increase in throughput of up to 16% and a reduction in latency by factors 3-7x compared to baseline (legacy beam management).
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Scores Know Bobs Voice: Speaker Impersonation Attack

arXiv:2603.02781v1 Announce Type: cross Abstract: Advances in deep learning have enabled the widespread deployment of speaker recognition systems (SRSs), yet they remain vulnerable to score-based impersonation attacks. Existing attacks that operate directly on raw waveforms require a large number of queries due to the difficulty of optimizing in high-dimensional audio spaces. Latent-space optimization within generative models offers improved efficiency, but these latent spaces are shaped by data distribution matching and do not inherently capture speaker-discriminative geometry. As a result, optimization trajectories often fail to align with the adversarial direction needed to maximize victim scores. To address this limitation, we propose an inversion-based generative attack framework that explicitly aligns the latent space of the synthesis model with the discriminative feature space of SRSs. We first analyze the requirements of an inverse model for score-based attacks and introduce a feature-aligned inversion strategy that geometrically synchronizes latent representations with speaker embeddings. This alignment ensures that latent updates directly translate into score improvements. Moreover, it enables new attack paradigms, including subspace-projection-based attacks, which were previously infeasible due to the absence of a faithful feature-to-audio mapping. Experiments show that our method significantly improves query efficiency, achieving competitive attack success rates with on average 10x fewer queries than prior approaches. In particular, the enabled subspace-projection-based attack attains up to 91.65% success using only 50 queries. These findings establish feature-aligned inversion as a key tool for evaluating the robustness of modern SRSs against score-based impersonation threats.
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Learning of Population Dynamics: Inverse Optimization Meets JKO Scheme

arXiv:2506.01502v3 Announce Type: replace-cross Abstract: Learning population dynamics involves recovering the underlying process that governs particle evolution, given evolutionary snapshots of samples at discrete time points. Recent methods frame this as an energy minimization problem in probability space and leverage the celebrated JKO scheme for efficient time discretization. In this work, we introduce $\texttt{iJKOnet}$, an approach that combines the JKO framework with inverse optimization techniques to learn population dynamics. Our method relies on a conventional $\textit{end-to-end}$ adversarial training procedure and does not require restrictive architectural choices, e.g., input-convex neural networks. We establish theoretical guarantees for our methodology and demonstrate improved performance over prior JKO-based methods. The code of $\texttt{iJKOnet}$ is available at https://github.com/MuXauJl11110/iJKOnet.
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Carbon-Aware Governance Gates: An Architecture for Sustainable GenAI Development

arXiv:2602.19718v1 Announce Type: cross Abstract: The rapid adoption of Generative AI (GenAI) in the software development life cycle (SDLC) increases computational demand, which can raise the carbon footprint of development activities. At the same time, organizations are increasingly embedding governance mechanisms into GenAI-assisted development to support trust, transparency, and accountability. However, these governance mechanisms introduce additional computational workloads, including repeated inference, regeneration cycles, and expanded validation pipelines, increasing energy use and the carbon footprint of GenAI-assisted development. This paper proposes Carbon-Aware Governance Gates (CAGG), an architectural extension that embeds carbon budgets, energy provenance, and sustainability-aware validation orchestration into human-AI governance layers. CAGG comprises three components: (i) an Energy and Carbon Provenance Ledger, (ii) a Carbon Budget Manager, and (iii) a Green Validation Orchestrator, operationalized through governance policies and reusable design patterns.
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WorldGUI: An Interactive Benchmark for Desktop GUI Automation from Any Starting Point

arXiv:2502.08047v4 Announce Type: replace Abstract: Recent progress in GUI agents has substantially improved visual grounding, yet robust planning remains challenging, particularly when the environment deviates from a canonical initial state. In real applications, users often invoke assistance mid-workflow, where software may be partially configured, steps may have been executed in different orders, or the interface may differ from its default setup. Such task-state variability is pervasive but insufficiently evaluated in existing GUI benchmarks. To address this gap, we introduce WorldGUI, a benchmark covering ten widely used desktop and web applications with tasks instantiated under diverse, systematically constructed initial states. These variations capture realistic human-computer interaction settings and enable diagnostic evaluation of an agent's ability to recover, adapt plans, and handle non-default contexts. We further present WorldGUI-Agent, a simple and model-agnostic framework that organizes planning and execution around three critique stages, improving reliability in dynamic environments. Experiments demonstrate that state-of-the-art GUI agents exhibit substantial performance degradation under non-default initial conditions, revealing limited robustness and fragile planning behaviors. Our benchmark and framework provide a foundation for developing more adaptable and reliable GUI agents. The code and data are available at https://github.com/showlab/WorldGUI.
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VideoMind: A Chain-of-LoRA Agent for Temporal-Grounded Video Reasoning

arXiv:2503.13444v3 Announce Type: replace-cross Abstract: Videos, with their unique temporal dimension, demand precise grounded understanding, where answers are directly linked to visual, interpretable evidence. Despite significant breakthroughs in text-based reasoning with large language models, multi-modal reasoning - especially for videos - remains limited. In this work, we fill this gap by introducing VideoMind, a novel video-language agent for temporal-grounded video reasoning. Our method involves two key innovations: (1) We identify four essential capabilities for grounded video reasoning and propose a role-based agentic workflow, comprising a planner to coordinate roles, a grounder for temporal event localization, a verifier to assess event candidates, and an answerer for question answering. (2) To efficiently integrate these roles during inference, we propose a novel Chain-of-LoRA mechanism, where a unified base model with multiple LoRA adapters is leveraged to enable seamless role switching, balancing efficiency and flexibility. Extensive experiments on 15 benchmarks across Grounded VideoQA, Video Temporal Grounding, and General VideoQA tasks demonstrate the effectiveness of the proposed scheme in advancing video agent, test-time scaling, and long-form video reasoning. Code, models, datasets, and demos are available at https://videomind.github.io/.
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