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01.
Nature Biotechnology 2026-06-09

Hybrid solid−liquid optics enable scalable, high-resolution light-sheet microscopy across diverse immersion media

作者:

Many data-driven approaches rely on scalable and affordable three-dimensional (3D) imaging across subcellular to organ scales. Although advances in tissue clearing, expansion microscopy and light-sheet microscopy (LSM) have enabled high-resolution imaging of intact specimens, scalability in sample size, throughput and accessibility remains fundamentally limited by detection optics. Here we introduce hybrid solid−liquid optics (HySIL), a flexible refractive design framework in which a solid optical element and a refractive index (RI)-matched liquid function as a continuous optical system for wavefront correction and numerical aperture enhancement. We implement this framework as SCOPE and Super-SCOPE, enabling submicron-resolution, aberration-corrected LSM using long-working-distance air objectives. We demonstrate high-resolution volumetric imaging across diverse biological contexts, including cleared and expanded mouse, salamander and cavefish brains, human induced pluripotent stem cell (iPSC)-derived brain organoids and large intact human tissues for 3D histopathology. By combining enhanced optical performance with low-cost, long-working-distance and multi-immersion compatibility, HySIL provides an accessible and scalable foundation for next-generation volumetric imaging and data-driven biological discovery. Hybrid solid–liquid optics improve light-sheet imaging of intact biological samples.

02.
arXiv (CS.AI) 2026-06-16

AI-Driven Test Case Generation from Natural Language Requirements: A Survey of Techniques and Research Gaps

arXiv:2606.06563v2 Announce Type: replace-cross Abstract: Software testing is critical for verifying that systems meet specified requirements, yet remains among the most time-consuming and expensive activities in development. Requirements-based test generation allows test cases to be derived early from requirements artifacts, but generating them directly from natural language is challenging due to inherent ambiguity and imprecision. Recent advances in AI, natural language processing (NLP), and large language models (LLMs) have made automating this pipeline increasingly feasible, while introducing new risks including hallucination, reduced traceability, and inconsistent evaluation. This survey addresses four research questions: what AI and NLP techniques have been proposed for generating test cases from natural language requirements; what tools and frameworks support these approaches; how generated test cases are evaluated; and what research gaps remain. Following Kitchenham and Charters' systematic review guidelines, we searched major scholarly databases spanning 2000-2025 and, after applying strict inclusion criteria, identified 21 primary studies. The literature is organized into three evolutionary eras, revealing that no existing approach simultaneously satisfies six key quality dimensions: automation, ambiguity handling, domain applicability, traceability, evaluation thoroughness, and hallucination control. The survey makes three main contributions: a three-era evolutionary synthesis of AI-based test generation; a six-criteria gap analysis showing no current approach fully addresses all quality dimensions; and four actionable research guidelines targeting hallucination, traceability, complexity sensitivity, and compliance.

03.
arXiv (CS.LG) 2026-06-17

Provably Efficient Regularized Online RLHF with Generalized Bilinear Preferences

arXiv:2602.23116v3 Announce Type: replace Abstract: We consider the problem of regularized best-response max-regret minimization in online RLHF under general preferences and bandit feedback. While various regularizers are utilized to robustify alignment, known polylogarithmic regret guarantees remain heavily specific to KL. To investigate whether such fast rates extend beyond KL, we adopt the Generalized Bilinear Preference Model (GBPM) – capturing intransitive preferences over $d$-dimensional item-wise features via a rank-$2r$ skew-symmetric matrix – to isolate the impact of generic regularization. Crucially, under GBPM, we prove that the dual gap of any greedy policy is bounded by the squared estimation error, derived using only strong convexity and skew-symmetry. Under a feature coverage assumption, we establish a generic polylogarithmic regret of $\tilde{\mathcal{O}}(\eta d^4 C_{\min}^{-1} (\log T)^2 \wedge d^2 C_{\min}^{-1/2} \sqrt{T})$ with Greedy Sampling, and a dimension-wise improved regret (for well-conditioned arm-sets) of $\tilde{\mathcal{O}}(C_{\min}^{-2} \sqrt{\eta r T} \wedge r^{1/3} C_{\min}^{-4/3} T^{2/3})$ with Explore-Then-Commit, where $\eta^{-1}$ is the regularization coefficient, $T$ is the time horizon, and $C_{\min}$ is an arm-set dependent quantity. This demonstrates that ``fast'' regrets are not KL-specific, but rather a fundamental consequence of generic strongly convex geometry.

05.
arXiv (CS.CL) 2026-06-19

The ACUTE Protocol: Operationalizing Language Model Activations for Better Calibration, Utility, and Trust

As language models improve and become increasingly deployed to solve a variety of tasks, trustworthiness becomes essential. Calibration is a good proxy for trust: well-calibrated confidence estimates help inform the risk versus reward tradeoff when trusting a specific model output. Unfortunately, even as models improve, they remain poorly calibrated, often biasing towards overconfidence. Additionally, calibration can be gamed: a policy that always predicts the base rate is perfectly calibrated, but completely uninformative. To resolve this, we develop a new metric, expected utility renormalized by the oracle (EURO), that balances calibration and informativeness. We also propose a general-purpose activation-based confidence, utility, and trust estimation protocol (ACUTE) to appropriately adjudicate uncertainty. The ACUTE protocol provides flexible, sample-efficient, and compute-efficient confidence estimators for 3 tasks including multiple choice question answering, tool-calling, and scientific document summarization across 6 models from 4 model families. ACUTE outperforms strong baselines on EURO, while maintaining low calibration error. Taken together, our work shows that equipping LLMs with the ACUTE protocol can improve calibration, utility, and trustworthiness in numerous settings.

06.
arXiv (CS.AI) 2026-06-17

A Machine-Learned Comorbidity Index

arXiv:2606.17450v1 Announce Type: new Abstract: Traditional comorbidity scores (e.g., Charlson and Elixhauser) are widely used for risk adjustment and patient stratification, but they have two key limitations: (i) they are largely mortality-centric and do not align well with other clinical outcomes, and (ii) their linear, rule-based structure cannot capture nonlinear, outcome-specific risk relationships. We propose a Machine-Learned Comorbidity Index (MLCI) that maps diagnosis codes to a single scalar by maximizing the normalized Hilbert-Schmidt Independence Criterion (nHSIC) between the learned score and multiple clinical outcomes. MLCI captures nonlinear risk-outcome dependence and is supported by a theory that characterizes when a unified, informative admission-level ordering can be achieved across outcomes. Empirical results on multiple benchmark electronic health record (EHR) datasets show that MLCI outperforms strong baselines across multiple evaluation metrics.

07.
bioRxiv (Bioinfo) 2026-06-16

Physics-Driven Zero-Shot Reconstruction of Isotropic 3D Fluorescence Microscopy under Undersampled Acquisition

Three-dimensional (3D) imaging represents the development of next generation of fluorescence microscopy. However, routine axial down-sampling makes isotropic resolution unrealistic. Here, we propose DeepUI, a physical zero-shot framework designed to achieve isotropic 3D fluorescence images from a low axial sampling rate. DeepUI fully leverages the intrinsic characteristics of 3D images through physics-guided degradation, which incorporates spatial-frequency joint learning to generate a scaled optical transfer function, combined with noise degradation and an up-sampling branch. Typically requiring just 5 minutes for training and 0.5 minutes for high-throughput and fast prediction, we demonstrate the superior performance of DeepUI to get isotropic results, and the exclusivity to axial down-sampling conditions, even in more challenging conditions, including defocused background, noise, and resolution blur.

08.
arXiv (CS.CV) 2026-06-16

Scribby: A Multi-Level LLM Framework for Semantic Video Analysis

As video content continues to expand across educational platforms, recorded lectures, and live-streamed entertainment, the need for efficient and structured analysis of long-form footage has increased [1]. Although many existing AI programs provide high-level video summaries based on AI-generated transcripts [2,3,4,5], these approaches are often limited to coarse overviews and lack detailed analysis of a video's structure, thematic progression, and semantic relationships, all of which are required for comprehensive video analysis. This paper proposes an LLM-based video summarization framework that balances macro-level comprehension with micro-level semantic analysis [6,12,13]. The first stage of the process indexes the video at a micro level by (1) analyzing the full transcript, (2) analyzing individual transcript sentences, and (3) grouping these sentences by semantic similarity using an LLM as a judge [6,13]. Contextual continuity is retained during sentence-level processing by incorporating both the global transcript analysis and adjacent sentence information into each evaluation prompt. This framework establishes a foundation for video analysis tools that visualize semantic chunking and semantic matching through relevance-based heatmaps. Limitations and future expansions of the framework are also discussed.

09.
arXiv (CS.AI) 2026-06-11

Irresponsible AI: big tech's influence on AI research and associated impacts

arXiv:2512.03077v2 Announce Type: replace-cross Abstract: The accelerated development, deployment and adoption of artificial intelligence systems has been fuelled by the increasing presence of big tech in the AI field. This trend has been accompanied by growing ethical concerns and intensified societal and environmental impacts. This position paper argues that irresponsible AI development is strongly driven by big tech's influence and involvement in the field. First, we examine the growing and disproportionate influence of big tech in AI research and argue that its drive for scaling and general-purpose systems is fundamentally at odds with the responsible, ethical, and sustainable development of AI. Second, we review key current environmental and societal negative impacts of AI and trace their connections to big tech's influence. Third, we discuss the underlying economic forces driving big tech's actions. Finally, as a call to action, we invite AI researchers to counter big tech's influence in irresponsible AI development through strategies that build on the responsibility of implicated actors and collective action.

10.
arXiv (CS.LG) 2026-06-17

Learning to Refine Hidden States for Reliable LLM Reasoning

arXiv:2606.17524v1 Announce Type: new Abstract: Large language models show strong reasoning ability, but their internal reasoning process can remain unstable in complex multi-step settings, where early hidden-state errors may propagate to incorrect predictions. We propose ReLAR, a reinforcement-guided latent refinement framework that iteratively updates hidden representations before decoding. ReLAR maintains a compact latent reasoning state and uses learned depth and action controllers to adaptively determine both the number and direction of refinement steps. The controllers are trained with a policy gradient objective based on step-wise likelihood improvement, enabling efficient input-dependent reasoning without explicit chain-of-thought generation. Experiments on medical, mathematical, multi-hop reasoning, and open-ended generation benchmarks show that ReLAR improves accuracy, generation quality, and reasoning stability with substantially lower inference overhead than explicit reasoning baselines.

11.
arXiv (CS.AI) 2026-06-12

Mechanical Conscience: A Mathematical Framework for Dependability of Machine Intelligenc

arXiv:2605.03847v2 Announce Type: replace Abstract: Distributed collaborative intelligence (DCI), encompassing edge-to-edge architectures, federated learning, transfer learning, and swarm systems, creates environments in which emergent risk is structurally unavoidable: locally correct decisions by individual agents compose into globally unacceptable behavioral trajectories under uncertainty. Existing approaches such as constrained optimization, safe reinforcement learning, and runtime assurance evaluate acceptability at the level of individual actions rather than across behavioral trajectories, and none addresses the multi-participant, uncertainty-laden nature of DCI deployments. This paper introduces mechanical conscience (MC), a novel concept and simplified mathematical framework that operationalizes trajectory-level normative regulation for both single-agent and distributed intelligent systems. Mechanical conscience is defined as a supervisory filter that minimally corrects a baseline policy's actions to reduce cumulative deviation from a normatively admissible region, while accounting for epistemic uncertainty. We introduce associated constructs, conscience score, mechanical guilt, and resonant dependability, that provide an interpretable vocabulary and computable governance signals for this emerging field. Core theoretical properties are established: admissibility equivalence, existence of optimal regulation, and monotonic deviation reduction. Illustrative results demonstrate that MC-regulated agents maintain trajectory-level normative acceptability where conventional controllers drift outside admissible bounds, and that the framework naturally extends to suppress interaction-induced emergent risk in multi-agent DCI settings.

12.
arXiv (CS.CL) 2026-06-19

Detecting Hallucinations for Large Language Model-based Knowledge Graph Reasoning

Knowledge graph (KG) reasoning infers new knowledge from existing facts and is widely applied in question answering, recommendation, and decision support. With the rapid development of large language models (LLMs), LLM-based KG reasoning frameworks have become increasingly popular by leveraging retrieved KG information. However, hallucinations in LLMs remain a critical issue. Even when relevant KG knowledge is incorporated, models may still generate incorrect outputs, leading to misinformation and unreliable decisions. Existing hallucination detection methods either focus on LLM internal states or verify consistency with retrieved contexts, but both overlook the structural information in KGs, resulting in suboptimal performance. To address this gap, we propose LUCID, the first halLUcination deteCtIon method for LLM-based knowleDge graph reasoning frameworks. LUCID jointly leverages LLM attention scores, KG semantics, and structural information. Specifically, it extracts node and edge features from attention scores and semantic similarities, and integrates them with KG structure using a graph neural network. We also construct manually annotated benchmark datasets for evaluation. Experiments on nine datasets show that LUCID achieves state of the art performance compared to 15 baselines.

13.
arXiv (CS.AI) 2026-06-18

Hardware- and Vision-in-the-Loop Validation of Deep Monocular Pose Estimation for Autonomous Maritime UAV Flight

arXiv:2606.19176v1 Announce Type: cross Abstract: Autonomous UAV operations on ships require reliable vision-based relative pose estimation, yet at-sea validation is costly, weather-dependent, and risky. This paper presents a hardware-validated vision-in-the-loop framework that enables fully autonomous indoor flight while emulating photorealistic maritime environments. Rendered maritime views are processed onboard by a deep transformer-based monocular pose estimator. Delayed vision measurements are fused with high-rate IMU data using a delayed Kalman filter to provide consistent state estimates for geometric control. The system captures critical embedded effects, including perception latency, asynchronous updates, and computational constraints, that are absent in pure simulation. Autonomous takeoff, trajectory tracking, and landing experiments demonstrate stable closed-loop flight. The results establish a safe and hardware-realistic intermediate stage for developing maritime UAV autonomy prior to shipboard deployment.

14.
arXiv (CS.CV) 2026-06-11

What Semantics Survive the Connector? Diagnosing VLM-to-DiT Alignment in Video Editing

Flow matching based video generative models have been increasingly relying on prepended Vision-Language Models (VLMs) to handle complex, instruction-based video editing. The prevailing assumption underlying this paradigm is that a connector module can seamlessly align the VLM's rich multi-modal reasoning with the original text embedding space of DiTs. However, we hypothesize that this alignment acts as a severe semantic bottleneck, degrading fine-grained structural variables. Verifying this is challenging, as end-to-end evaluations conflate alignment failures with generation errors, and natural datasets lack disentangled annotations. To rigorously investigate this, we propose a controlled data processing pipeline based on video composition that results in TRACE-Edit, a diagnostic dataset focusing on relation-based editing. Leveraging this dataset, we propose a comprehensive diagnostic protocol to analyze two important designs of meta-query and connector in the existing video editing models. Systematic evaluation of four representative model cases reveals that fine-grained structural semantics can be severely degraded during alignment. Our findings overturn the assumption of lossless semantic transfer, identifying the VLM-to-DiT alignment as a major bottleneck and providing a new diagnostic foundation for future multi-modal alignment architectures.

15.
arXiv (CS.AI) 2026-06-15

The Shrinking Lifespan of LLMs in Science

arXiv:2604.07530v2 Announce Type: replace-cross Abstract: Scaling laws describe how language model capabilities grow with compute and data, but say nothing about how long a model matters once released. We introduce time-to-peak and lifespan as measures of model obsolescence and use them to characterize the scientific adoption trajectories of 62 LLMs across more than 108k citing papers (2019-2025), separating active adoption from background citation to recover per-model trajectories that citation counts cannot resolve. We find that a model's longevity is shaped more by when it was released than by its characteristics: release year predicts time-to-peak and lifespan more strongly than architecture, openness, or scale. LLM adoption follows an inverted-U curve (rising after release, peaking, and then declining), but this pattern is rapidly compressing. Each successive release year is associated with a 27% shorter time-to-peak and a 23% shorter lifespan ($p < 0.001$), robust to minimum-age thresholds and controls for model size. These adoption-side dynamics are invisible to scaling laws and suggest that specialization on any single model may be a depreciating investment, with costs falling on reproducibility and migration.

16.
arXiv (CS.AI) 2026-06-11

Embodied-BenchClaw: An Autonomous Multi-Agent System for Embodied Spatial Intelligence Benchmark Construction

arXiv:2606.11909v1 Announce Type: new Abstract: Benchmarks are essential for evaluating embodied spatial intelligence, yet their construction is labor-intensive, hard to reuse, and difficult to maintain. Existing embodied benchmarks are often static and may quickly become saturated as models improve, limiting their ability to distinguish new capabilities. We propose Embodied-BenchClaw, an autonomous agentic system for constructing embodied spatial intelligence benchmarks. Given a user-specified evaluation intent, Embodied-BenchClaw automatically produces a complete and continually updatable benchmark package through a five-stage pipeline: intent blueprinting, data collection, structuring and cleaning, benchmark synthesis, and evaluation reporting. The pipeline is coordinated by three agents for planning, construction, and evaluation. To improve reusability and reliability, Embodied-BenchClaw introduces an extensible Skill Library and process quality control, enabling benchmark construction to be composable, verifiable, and repairable. We instantiate multiple benchmarks covering indoor spatial reasoning, outdoor spatial reasoning, robotic manipulation, quadruped robot navigation, UAV/aerial-view understanding, and static benchmark enhancement. These benchmarks span diverse embodied carriers, data sources, and spatial capabilities. Experiments with human evaluation, judge-based assessment, consistency checks, cost analysis, and ablations show that Embodied-BenchClaw can construct verifiable, executable, maintainable, and diagnostically useful embodied spatial benchmarks with reduced manual effort.

17.
arXiv (CS.AI) 2026-06-18

ARIADNE: Agnostic Routing for Inference-time Adapter DyNamic sElection

arXiv:2606.19079v1 Announce Type: new Abstract: The increasing deployment of parameter-efficient fine-tuning (PEFT) has led to model ecosystems in which a single backbone is paired with many task-specialized adapters. In this setting, inference-time queries often arrive without task labels, requiring the system to automatically select the most appropriate adapter from a growing and heterogeneous adapter pool. Existing routing methods either depend on access to adapter internals, such as weight decompositions or gradient-based statistics, or require additional router training, which limits scalability and portability as new adapters are added. We introduce ARIADNE, a training-free, adapter-agnostic routing framework for dynamic adapter selection at inference time. ARIADNE represents each adapter through a set of centroids computed from embeddings of its training set, capturing the data distribution associated with that adapter. Given an unlabeled input, it selects an adapter by measuring proximity to these centroids in latent space. Because routing is performed entirely in the input embedding space, ARIADNE is compatible with arbitrary PEFT methods and requires no modification to the adapters or training procedures. Primarily evaluated with Llama 3.2 1B Instruct on 23 diverse NLP tasks, ARIADNE recovers 97.44% of the upper bound performance. Scaling to 44 tasks, it achieves 89.7% average selection accuracy, without additional training or access to adapter internals.

18.
arXiv (CS.AI) 2026-06-18

A Technical Taxonomy of LLM Agent Communication Protocols

arXiv:2606.19135v1 Announce Type: cross Abstract: As large language models (LLMs) advance and multi-agent systems aim to overcome the limits of standalone agents, robust communication protocols are becoming essential infrastructure for distributed agent networks. Nonetheless, the fragmented protocol landscape presents a significant interoperability challenge. This study develops a technical taxonomy to classify and analyze LLM agent communication protocols. Following an established iterative method, we defined the taxonomy's purpose, meta-characteristic, and ending conditions, then performed five iterations, three empirical-to-conceptual and two conceptual-to-empirical, on nine actively maintained open-source protocols with demonstrable adoption. The taxonomy comprises five dimensions: counterparty, payload, interaction state, discovery mechanism, and schema flexibility. Classification reveals recurring architectural patterns: all sampled agent-to-agent protocols combine hybrid payloads with session-state persistence; most protocols support multiple predefined schemas, and two negotiate schemas at runtime, indicating a trend toward schema flexibility; decentralized discovery remains rare. Analysis suggests short-term convergence pressure toward protocols unifying agent-to-agent and agent-to-context (tool and data) communication. Long-term, however, no single protocol is likely to maximize versatility, efficiency, and portability simultaneously. The field will more likely evolve toward a federated, layered protocol stack. The framework guides protocol selection and highlights open research gaps such as privacy and policy enforcement.}

19.
medRxiv (Medicine) 2026-06-18

Web-based education on Metabolism and Obesity is associated with improved lifestyle and health behaviours among Brazilian school teachers

Background: Obesity is a major global public health challenge, and teachers play a critical role in school-based health promotion. This study examined the perceived impact of a web-based educational program on metabolism and obesity delivered to Brazilian school teachers. Methods: This analytical cross-sectional study included 217 teachers who responded to the evaluation questionnaire after attending the course between 2017 and 2022. Statistical analyses included logistic regression and chi-square tests. Findings: Course completion rate was 81.98%, substantially exceeding the 5-15% typical of global MOOCs. However, ethnic disparities were observed: White respondents were 4.95 times more likely to complete the course than Black respondents (p=0.00097) and Brown respondents were 3.05 times more likely (p=0.0268) than Black respondents. Among non-completers, lack of time (64.7%) was the primary barrier. Participation was concentrated in Sao Paulo (77%), with no respondents from three northern states. Perceived difficulty showed a non-significant trend (p=0.0893) where by Black respondents had the lowest predicted difficulty; the most challenging course material was Scientific Content/Reading papers (50%). Completion was strongly associated with applying learned activities in teaching (p

20.
arXiv (CS.CV) 2026-06-16

FairGen: Preference-Aligned Diffusion for Demographically Equitable Medical Image Synthesis

Medical imaging is central to modern diagnostics, and artificial intelligence (AI) systems are increasingly used to support image-based analysis by improving efficiency, accuracy, and access to care. However, inequities in healthcare access and differential disease prevalence create severe demographic imbalances in clinical image data. Such imbalances are compounded by the fact that diseases can manifest with distinct features across demographic groups, rendering certain phenotypic presentations naturally rare. AI models trained on such imbalanced data risk perpetuating diagnostic bias and widening healthcare disparities. Here we introduce FairGen, a fairness-aware diffusion framework that synthesizes demographically balanced medical images while preserving pathology-relevant visual features. By embedding physician-aligned preferences into the generation process, FairGen improves subgroup coverage during synthesis and downstream classification. Applied to dermatology, radiology, and neuroimaging benchmark tasks, FairGen achieves fairness improvements of 95.9% for skin images, 80.0% for chest radiography, and 35.2% for brain MRI, while maintaining competitive diagnostic accuracy relative to models trained on original clinical data. Clinician-facing expert review and external validation on independent cohorts further support that these gains extend beyond standard fidelity metrics and are not confined to the original in-distribution datasets.

21.
arXiv (CS.CV) 2026-06-17

Beware of Aliases – Signal Preservation is Crucial for Robust Image Restoration

Image restoration networks are usually comprised of an encoder and a decoder, responsible for aggregating image content from noisy, distorted data and to restore clean, undistorted images, respectively. Data aggregation as well as high-resolution image generation both usually come at the risk of involving aliases, i.e.~standard architectures put their ability to reconstruct the model input in jeopardy to reach high PSNR values on validation data. The price to be paid is low model robustness. In this work, we show that simply providing alias-free paths in state-of-the-art reconstruction transformers supports improved model robustness at low costs on the restoration performance. We do so by proposing BOA-Restormer, a transformer-based image restoration model that executes downsampling and upsampling operations partly in the frequency domain to ensure alias-free paths along the entire model while potentially preserving all relevant high-frequency information.

22.
arXiv (CS.CV) 2026-06-17

DiFlow-TTS: Compact and Low-Latency Zero-Shot Text-to-Speech with Discrete Flow Matching

Zero-shot text-to-speech (TTS) has made significant progress in replicating unseen voices, yet balancing generation quality and inference efficiency remains challenging. Autoregressive models suffer from high latency, while diffusion-based approaches are constrained by training-time configurations. Moreover, most flow-based methods operate in continuous space, which introduces optimization challenges because continuous token spaces are inherently more complex than discrete ones. To address these limitations, we propose DiFlow-TTS, a novel zero-shot TTS framework based on discrete flow matching. The model consists of a deterministic Phoneme-Content Mapper for linguistic modeling and a Factorized Discrete Flow Denoiser that simultaneously generates prosody and acoustic token streams. Experimental results demonstrate the effectiveness of our approach across multiple evaluation metrics.

23.
Nature Biotechnology 2026-06-19

Optimized R2 retroelement complexes for DNA insertion into plant genomes

Traditional approaches for DNA insertion into plant genomes using Agrobacterium tumefaciens result in random integration. Newer genetic engineering methods based on nucleases, prime editors, transposases and recombinases extend capabilities but remain constrained with low efficiencies, off-target integration or limited payload size. Here we adapt the avian Taeniopygia guttata R2 protein (R2Tg) for targeted DNA insertion into plant genomes by engineering R2Tg expression cassettes and RNA payloads carrying intron-disrupted reporters, with optimized ribosomal DNA homology arms and untranslated regions. In Arabidopsis thaliana protoplasts, Nicotiana benthamiana leaves and Solanum lycopersicum seedlings, our R2Tg editor system achieves targeted insertion of full-length payloads ranging from 2.2 kb to 5 kb. In Nicotiana benthamiana leaves, integration occurs, on average, at 1 copy per genome, which is 30 times more efficient than that achieved by Cas9 homology-directed repair. This work establishes an R2Tg ribonucleoprotein platform for targeted DNA insertion into plant genomes, using a multicopy genomic safe-harbor site to enable efficient addition of multikilobase genes. R2 retrotransposons are used to integrate DNA into plant and crop 25S ribosomal DNA sites.

24.
medRxiv (Medicine) 2026-06-19

Reassessing Instrument Strength in Two-Sample Mendelian Randomization Analysis

Mendelian randomization (MR) analysis is widely used to estimate causal relationships between risk factors and outcomes of interest. Two-sample MR approaches have gained increasing attention in genetic epidemiology due to the growing availability of Genome-Wide Association Study (GWAS) summary statistics from public databases. A critical step in two-sample MR is the selection of genetic variants as instrumental variables (IVs). Although genome-wide significant variants are typically preferred, the inclusion of variants with weaker association p-values is considered, as they may potentially improve power through an increased instrument number of instruments, while they may introduce weak instrument bias and attenuate effect estimates towards the null. Our simulation results show that even modest levels of pleiotropy substantially increase the variability of causal effect estimates, while the inclusion of weak IVs does not substantially affect the direction and variability of causal effect estimates in most cases. In real data analyses, we used two released versions of FinnGen GWAS summary statistics with different sample sizes as exposure GWASs to assess the influence of weak IVs. Here, the inclusion of IVs with higher exposure-association p-values resulted in weakened estimated effect sizes, particularly when the exposure GWAS sample size was small. These findings suggest that incorporating weak IVs is reasonable when the exposure GWAS sample size is large, but it poses a risk of falsely concluding null associations when the exposure GWAS sample size is small.

25.
medRxiv (Medicine) 2026-06-10

General-purpose large language models can achieve physician-level accuracy in complex medical data extraction

Background: Unstructured data represent about 80% of total electronic health records (EHR) data. Structuring this free text is essential for advancing clinical research, including cohort selection for trials, retrospective studies, and the development of disease registries. While manual chart review (MCR) remains the gold standard for extracting this clinical data, the process is inherently slow, resource-intensive, and susceptible to errors from human fatigue. We evaluated the extraction accuracy, safety, and efficiency of the HeLIX (Hepatology Logic-Integrated Extraction) framework, a Large Language Model (LLM) protocol using Google Gemini 3 Pro, compared to a gold-standard Manual Chart Review (MCR). Methods: A prospective validation study was conducted using 50 high-complexity, simulated hepatology discharge summaries designed to replicate the real-world heterogeneity of EHRs. The HeLIX framework employed a Zero-Shot, Structured Chain-of-Thought (CoT) prompting strategy enforced by a three-layer architecture: Clinical Reasoning Trace, Schema Enforcement, and Evidence Verification. The model extracted 45 distinct clinical variables. Performance was benchmarked against a consensus MCR. Results: Across 2,250 evaluated data points, the model achieved an overall Extraction Accuracy of 99.24% (95% CI: 98.8%-99.5%), with perfect concordance in 35/45 (77.8%) variables. For binary diagnostic variables, the model demonstrated an overall F1-score of 0.98, Recall of 0.99 and substantial inter-rater reliability (Cohens {kappa} = 0.97). Hallucinations were exceptionally rare (2/2250; 0.08%). Critical errors affecting clinical management occurred in only 2 instances (