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01.
arXiv (CS.AI) 2026-06-12

Humor Style Drives Laughter, Topic Shapes Acceptability: Evaluating Bilingual Personal and Political Robot-Delivered AI Jokes

arXiv:2606.13256v1 Announce Type: cross Abstract: Humor plays a central role in human social relationships, and recent advances in computational humor create new opportunities for integrating humor into human-robot interaction (HRI). While large language models (LLMs) can generate diverse forms of humor, it remains unclear how humor style, joke content, and language preference shape perceptions of robot-delivered humor in group settings. In this exploratory study, we employed a mixed factorial design in which participants evaluated AI-generated jokes delivered by a robot in a university classroom. We examined the effects of humor type (Affiliative, Self-Enhancing, Aggressive, Self-Defeating) and joke content (person-related vs. political) on perceived funniness and appropriateness, as well as preferred language. Results show that humor type significantly influences funniness, with Aggressive and Affiliative humor rated higher, while joke content primarily affects appropriateness, with person-related jokes preferred over political ones. Language preference was shaped by both joke content and participants' self-reported fluency and humor practices.

02.
arXiv (CS.LG) 2026-06-17

Multi-Adapter PPO: A Cross-Attention Enhanced Wavelength Selection Framework for LIBS Quantitative Analysis

arXiv:2606.17476v1 Announce Type: new Abstract: Laser-induced breakdown spectroscopy (LIBS) quantitative analysis faces critical challenges in wavelength selection due to high-dimensional spectral data and the fundamental trade-off between prediction accuracy and feature efficiency. This paper presents a novel Multi-Adapter PPO framework that transforms wavelength selection into a reinforcement learning problem, leveraging cross-attention mechanisms and multiple specialized adapters to capture complex spectral relationships. Our approach outperforms traditional Particle Swarm Optimization (PSO) by an average of 28.4\% in comprehensive score and 45.2\% in prediction accuracy across steel and coal datasets. The proposed method demonstrates superior performance in balancing prediction accuracy with feature efficiency, achieving state-of-the-art results in LIBS quantitative analysis while maintaining interpretability and computational efficiency. We released our code and dataset here: https://github.com/Hflying/MAPPO

03.
arXiv (CS.CV) 2026-06-16

Question-Aware Evidence Ledgers for Video Relational Reasoning

The VRR-QA challenge evaluates visual relational reasoning in videos, where answers often depend on implicit spatial relations, event boundaries, target identity, and dialogue context rather than a single salient frame. We present a test-time reasoning pipeline built around a strong GPT-5.5 video QA solver and a set of question-aware evidence ledgers. The initial solver answers each question from a uniform video representation, while routed ledgers are prompted to make the required targets, count units, reference frames, and temporal or spatial scope explicit for counting, spatial, endpoint, viewpoint, and dialogue reasoning. External tools such as open-vocabulary detection, depth cues, pair crops, ASR, and scene-graph ledgers are used only as evidence sources. A conservative gate keeps the current answer unless independent evidence uniquely supports a different option. The final evidence-gated pipeline achieves 92.95% overall accuracy and 93.79% macro accuracy on the challenge test split.

04.
arXiv (CS.AI) 2026-06-19

Autonomous Event-Driven Multi-Agent Orchestration for Enterprise AI at Scale

arXiv:2606.20058v1 Announce Type: new Abstract: Enterprise AI aims to move toward continuous event monitoring, detection, and action across specialist agents, yet existing multi-agent systems largely assume discrete request-response workflows and remain underexplored at enterprise scale. We evaluate DAG Plan and Execute and ReAct across 208 production-derived enterprise scenarios spanning Persona (

05.
arXiv (quant-ph) 2026-06-19

Arrival times of an atomic Bose-Einstein condensate

arXiv:2606.20281v1 Announce Type: cross Abstract: The times of flight of an atomic Bose-Einstein condensate are theoretically investigated in the experimentally unexplored regime corresponding to detection close to the trap of the condensate. In this regime, there is no consensus on how to calculate the distribution of times of arrival onto the detector. For non-interacting particles, distinct theoretical predictions have been made in the past. This work analyses how these predictions are modified for an interacting Bose-Einstein condensate. For this purpose, a time-dependent Gross-Pitaevskii equation is solved analytically and numerically.

06.
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.

08.
arXiv (CS.AI) 2026-06-24

A global log for medical AI

arXiv:2510.04033v2 Announce Type: replace Abstract: Modern computer systems rely on syslog, a universal protocol that records critical events across heterogeneous infrastructure. Medicine's rapidly growing AI stack has no equivalent. As medicine deploys AI tools at scale, there is no standard way to record how, when, by whom, and for whom these models are used. Without such records, it is difficult to measure real-world performance and outcomes, detect adverse events, or identify bias and dataset drift. Here we introduce MedLog, a protocol for event-level logging of medical AI. Each time an AI model interacts with a human, another algorithm, or an automated workflow, MedLog creates a record. Each record contains nine core fields: header, model, user, target, inputs, artifacts, outputs, outcomes, and feedback. We apply MedLog across four deployments in the US, Switzerland, and Vietnam: ICU deterioration prediction, tetanus progression monitoring from wearable signals, automated sepsis quality reporting, and patient attendance prediction. MedLog records capture model behavior, workflow interactions, and downstream outcomes, including AI performance degradation during severe weather events in patient attendance prediction and increased laboratory testing after ICU deterioration alerts. MedLog limits the data footprint through risk-based sampling, lifecycle-aware retention policies, and write-behind caching, enabling deployment in low-resource settings. It also supports detailed traces for complex, agentic, or multi-stage workflows, creating a foundation for continuous monitoring, auditing, and improvement of medical AI.

10.
arXiv (CS.AI) 2026-06-16

An affordable hardware-aware neural architecture search for deploying convolutional neural networks on ultra-low-power computing platforms

arXiv:2606.16290v1 Announce Type: cross Abstract: Hardware-aware neural architecture search (HW-NAS) allows the integration of Convolutional Neural Networks (CNNs) in microcontrollers devices by automatically designing neural architectures that can fit prearranged hardware constraints. However, state-of-the-art HW-NAS target high-performance microcontrollers, whose power consumption does not meet sensing nodes requirements. This work presents a HW-NAS generating tiny CNNs that can run on ultra-low-power microcontrollers, featuring a lightweight search procedure enabling its execution even on embedded devices. Empirical results on three well-known benchmarks for tiny computer vision proved that the proposed HW-NAS was able to generate tiny CNNs while preserving state-of-the-art classification accuracy.

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

UniDDT: Unifying Multimodal Understanding and Generation with Decoupled Diffusion Transformer

Unified Multimodal Models (UMMs) have emerged as a critical direction for general-purpose multimodal intelligence, integrating understanding and generation into a single framework. However, existing UMMs face prominent challenges: (1) the inherent learning conflicts between visual understanding and generation tasks, leading to suboptimal modeling in both tasks; (2) different understanding and generation visual spaces impeding scalability; (3) over-reliance on task-specific data that neglects the duality of text-image understanding and generation. To address these challenges, we propose UniDDT, which leverages a Noisy ViT encoder along with an LLM to unify semantic encoding for visual generation and understanding tasks, while employing a separate diffusion decoder to decouple diffusion decoding from text decoding. With this Noisy ViT encoder, UniDDT is able to leverage the latent space as a unified visual representation, enabling seamless compatibility between understanding and generation tasks. Thus, the scalability within the generation tasks and the semantic expressiveness within understanding tasks can be balanced. Also, we construct dual data structures from the same image-text pairs, fostering interdependence between the generation and understanding data to exploit their inherent duality. Extensive experiments demonstrate that UniDDT achieves effective unification of multimodal understanding and generation with enhanced semantic consistency and scalability. For visual generation tasks, our UniDDT achieves 0.87 GenEval score and 86.9 DPG overall score. For multimodal understanding tasks, our UniDDT achieves 1699.5 score on MME benchmark and 76.5 overall score on SEEDbench.

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

An Embodied Simulation Platform, Benchmark, and Data-Efficient Augmentation Framework for Wet-Lab Robotics

arXiv:2606.12936v1 Announce Type: cross Abstract: Wet-lab robots can improve the reproducibility, throughput, and safety of biomedical experiments, but scaling their learning requires customizable simulators for safe and reproducible task generation, open editable laboratory assets, and efficient pipelines that turn limited demonstrations into usable training data. We present Pipette, an embodied simulation platform, benchmark, and data-efficient augmentation framework for wet-lab robot learning. Pipette releases over 43 open-source and re-editable wet-lab assets, together with an extensible asset-building pipeline. A key component of Pipette is its simulation-based data augmentation pipeline, replaying human demonstrations in simulation, applies lighting, camera, speed, and action perturbations, and filters generated episodes with automatic task success checks, rapidly expanding usable training data from limited manual demonstrations. We further introduce an 11-task wet-lab embodied benchmark covering sample handling, culture-ware manipulation, device operation, and precision placement. With only 30 demonstrations per task, ACT achieves 65.5% average success rate, while simulation augmentation improves SmolVLA from 44.1% to 74.7% and {\pi}0 from 40.4% to 46.5%, validating the effectiveness of Pipette for data-efficient VLA training and evaluation. Pipette also supports natural-language-driven scene construction and task registration, lowering the barrier for non-expert users to define new wet-lab robotic tasks.

13.
arXiv (CS.AI) 2026-06-17

EAGG: Embodiment-Aligned Grasp Generation via Geometry-Aware Graph Conditioning

arXiv:2606.18092v1 Announce Type: cross Abstract: Cross-end-effector grasp generation seeks a unified model that generalizes across objects and across embodiments ranging from parallel grippers to dexterous end effectors. Existing grasp generators are typically designed for a fixed embodiment or encode embodiment identity with a static descriptor, which weakens transfer when topology, actuation coupling, and contact geometry differ substantially. We present EAGG, an embodiment-aligned grasp generator that represents each embodiment with a topology-aware end-effector graph and an embodiment-specific low-dimensional end-effector control space. A frozen end-effector-cognition backbone converts the current articulated state into geometry-aware tokens that act as a reusable morphology prior, and iterative geometry injection refreshes these tokens throughout sampling so that conditioning remains synchronized with the evolving end-effector geometry. On the MultiGripperGrasp benchmark, EAGG reaches 56.17% average success across six training end effectors, remaining within 1.10 percentage points of specialized training while preserving transfer to finetuning and zero-shot end effectors. Iterative geometry injection further reduces the pooled median contact distance from 0.239 cm to 0.189 cm. These results show that cross-end-effector grasp generation is strengthened by aligning embodiment structure inside a shared generator rather than suppressing embodiment differences. Code is available at https://github.com/wanhaoniu/EAGG.

14.
medRxiv (Medicine) 2026-06-16

Preventing postpartum depression through mitigating breastfeeding grief: A convergent parallel mixed methods study

Background: Women who did not meet their breastfeeding goals often experience breastfeeding grief (BG) and may be likely to have postpartum depression (PD). Furthermore, PD is nearly twice as common in African American (AA) women as in Non-Hispanic White women. No research exists on BG and its role in PD. This study examined the BG experiences of AA women and its possible contributions to PD symptoms. Methods: A convergent parallel mixed methods design was used. A purposive sample of 16 AA women with children aged 6 months to 2 years with BG participated in individual semi-structured interviews about their experiences of BG and completed an online survey including the Edinburgh Postnatal Depression Scale (EPDS). Qualitative and quantitative data were analyzed using reflexive thematic analysis and descriptive statistics, respectively. Both data were integrated using joint display of data and side-by-side comparison. Results: The mean age of participants was 29.5 years. Four meaning-based themes about BG were generated including: We looked forward to breastfeeding, But it did not go as expected, So we grieve, and These would have helped. From quantitative results, 87.5% of participants reported a history of PD symptoms and almost 44% had EPDS scores >11. All participants reported that experiencing BG contributed to their PD symptoms. Findings suggest that BG influenced PD symptoms in AA women without prior diagnosis of depression. Conclusions: Qualitative and quantitative findings from this novel exploratory study revealed an overlap that AA women with BG report PD symptoms. Clinicians should support women to achieve their breastfeeding goals to prevent BG and PD. Keywords: African American; Breastfeeding grief; Mental health; Mixed methods; Postpartum depression

15.
arXiv (CS.CV) 2026-06-11

Wild3R: Feed-Forward 3D Gaussian Splatting from Unconstrained Sparse Photo Collection

Feed-forward 3D Gaussian Splatting (3DGS) removes the need for time-consuming per-scene optimization required by traditional 3DGS. However, existing feed-forward approaches struggle with real-world photo collections that include diverse lighting conditions and transient objects. In this paper, we present Wild3R, a feed-forward approach for unconstrained sparse photo collections. The main bottleneck is the lack of training data that provides multiple viewpoints, a variety of illuminations, and transient variations necessary for learning robust scene representations. To address this, we introduce the WildCity dataset, which comprises 200 scenes, 170 lighting conditions, and transient objects, resulting in 337,500 images in total. By leveraging the dataset, our model learns appearance consistency across viewpoints conditioned on reference views, while removing transient content. Extensive experiments demonstrate that our method outperforms existing feed-forward approaches and achieves results competitive with prior per-scene optimization-based methods.

16.
arXiv (math.PR) 2026-06-24

Typical geometry of self-repelling polymers in a constant force field

arXiv:2606.24352v1 Announce Type: cross Abstract: We study a general class of self-repelling polymers on $\mathbb Z^2$, including the simple random walk, the self-avoiding walk and the repulsive Domb-Joyce model, in the presence of a constant force field acting on each monomer. Conditioning the polymer to have fixed length and fixed endpoints, we identify the limiting free energy and prove that typical trajectories concentrate exponentially near a deterministic macroscopic shape. This shape is characterized as the unique minimizer of a variational problem and can be interpreted as a geodesic of a height-dependent Finsler metric. We also analyze two limiting regimes with universal features: for small field strength, in the symmetric case, the geodesic is close to a classical catenary, while for large field strength it converges to a universal polygonal shape governed by the nearest-neighbor lattice constraint.

17.
arXiv (CS.LG) 2026-06-19

Calibrating Generative Models to Feature Distributions with MMD Finetuning

arXiv:2606.19496v1 Announce Type: new Abstract: Generative models can produce individually plausible samples while deviating substantially from a target set in the distribution of key features. For example, a model pretrained on broad drug-like chemical space may generate molecules whose molecular features differ from those of a therapeutic class of interest, such as known antibiotics. Correcting such distributional miscalibration is challenging: direct finetuning on the target set can overfit and does not control which features are matched. To fill this gap, we introduce kernel Calibrating Generative Models (kCGM). kCGM minimizes a maximum mean discrepancy (MMD) between generated and target feature distributions using an unbiased score-function estimator, with KL regularization to remain close to the pretrained model. On a target set of 174 antibiotics, direct finetuning sacrifices chemical validity for feature-distribution matching, whereas kCGM improves target feature matching while increasing validity. We further demonstrate kCGM in protein and DNA generation tasks, showing it can adapt autoregressive, continuous-space diffusion, and discrete diffusion models using only feature-level supervision. Code is available at https://github.com/smithhenryd/cgm.

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

Pulling The REINS: Training-Free Safety Alignment of Video Diffusion Models via Representation Steering

Open-weight video diffusion models can generate photorealistic unsafe content, from violence to misinformation, yet existing defenses either require expensive safety fine-tuning that degrades general capability, or apply external filters that are trivially bypassed by adversarial prompts. We present REINS (REpresentation-space INference-time Safety steering), a training-free method that aligns video diffusion models at inference time by steering their internal representations toward safe generation. Our key finding is that safety-relevant structure is linearly encoded in the hidden-state activations of video diffusion transformers, and a single direction, discovered via Supervised PCA on binary safety labels, suffices to separate safe from unsafe generation trajectories. At inference, adding this direction to hidden states at an intermediate transformer layer redirects generation from harmful content to semantically related safe alternatives, with no weight updates, no concept enumeration, and negligible computational overhead. Through mechanistic analysis, we reveal that while safety information accumulates monotonically with transformer depth, steering effectiveness peaks at intermediate layers (~50% depth), exposing a fundamental tradeoff between information availability and downstream propagation capacity. We evaluate REINS across 9 video diffusion models, multiple parameter scales (1.3B-5B), and both text-to-video and image-to-video generation, to our knowledge, the broadest safety evaluation suite in the video generation literature.

19.
arXiv (CS.LG) 2026-06-24

Grouped Query Experts: Mixture-of-Experts on GQA Self-Attention

arXiv:2606.20945v2 Announce Type: replace Abstract: Self-attention is central to Transformer performance and is often the most expensive part of the Transformer at long context lengths because its pairwise token interactions scale quadratically with sequence length. Standard dense attention also applies the same set of attention heads to every token regardless of token difficulty or information content. This uniform activation can waste compute, especially as sequences grow longer and attention cost increases rapidly. We propose Grouped Query Experts (GQE), a mixture-of-experts layer on top of grouped-query attention (GQA). Within each GQA group, a router selects k query-head experts per token while all key-value (KV) heads remain dense and unchanged. Thus, GQE keeps the KV cache benefits of GQA and reduces only the active query-head computation. On a fixed 30B token budget at the 250M parameter scale, GQE matches the all-active GQA baseline in downstream accuracy while activating half the query heads per token.

20.
arXiv (quant-ph) 2026-06-16

Phase controlled spectral topology, dynamic stability and sensitivity in Non-Hermitian Cavity Magnonics

arXiv:2606.16522v1 Announce Type: new Abstract: We theoretically investigate a non-Hermitian cavity-magnon platform in which coherent photonmagnon interactions and reservoir-mediated dissipative coupling interfere through a single externally tunable phase. We show that this interference phase provides a universal control parameter that continuously rotates the effective coupling between Hermitian and anti-Hermitian regimes, enabling dynamic transitions between level repulsion and level attraction without modifying intrinsic system parameters. The resulting phase-controlled non-Hermitian topology gives rise to exceptional points, linewidth engineering, and zero-damping conditions. Owing to the propagation-direction dependence of the dissipative interaction, the system further exhibits strong nonreciprocal transport and phase-tunable isolation arising from asymmetric hybridization of the cavity and magnon modes. Beyond its spectral and transport properties, we establish a direct connection between nonHermitian spectral topology and nonequilibrium population dynamics. The interference phase governs the stability of the hybrid modes, driving transitions between stable relaxation, critical slowing down near exceptional points, oscillatory energy exchange, and exponentially amplified dynamics. We further demonstrate that the same phase-controlled exceptional topology can be exploited for enhanced sensing, where the eigenvalue response exhibits the characteristic square-root scaling associated with exceptional-point physics. Our results provide a unified framework linking spectral topology, directional transport, dynamical stability, and sensing functionality through reservoirengineered interference in cavity magnonic systems.

21.
bioRxiv (Bioinfo) 2026-06-23

Comorbidity structure as an inductive bias: Comparing output-head designs for multi-label prediction of diabetes and myocardial infarction complications

Background: Clinical complications are often predicted with separate sigmoid outputs, even when the target labels arise from related pathophysiological processes. This paper asks whether output-layer choice should reflect both predictive convenience and the biological structure assumed among complications. The central premise is that label-dependence mechanisms are explicit hypotheses about comorbidity, not generic modelling additions. Methods: Output-head assumptions were compared across two clinically distinct multi-label prediction tasks. In Type 2 diabetes (T2D), six heads were evaluated for nephropathy, neuropathy, and retinopathy: independent baseline, linear additive, multiplicative, symmetric conditional random field (CRF), residual multilayer perceptron (MLP), and combined additive-multiplicative. In myocardial infarction (MI), four heads were evaluated for ventricular tachycardia, ventricular fibrillation, and atrioventricular block: independent baseline, linear additive, multiplicative, and symmetric CRF. All experiments used five training data fractions and seven independent seeds, with the same shared-backbone protocol within each disease setting. Results: In T2D, the symmetric CRF gave the most consistent improvement pattern, ranking highest at full data and at the two lowest data fractions while adding only three interaction parameters. At 20% training data, it was the only interaction head whose aggregate mean exceeded the independent baseline. The residual MLP, despite 123 interaction parameters, remained below the baseline across all T2D fractions. In MI, rankings changed across fractions: the multiplicative head led at 80% and 60%, the CRF led at 100% and 20%, and the baseline led at 40%. The combined additive-multiplicative head did not improve robustness in T2D and showed the largest negative baseline-relative deviations at lower fractions. Conclusions: The findings support a biology-guided view of output-layer design. A small constrained mechanism was most useful when its symmetry matched the shared microvascular structure of T2D, whereas the heterogeneous electrophysiology of MI produced no stable winner. Output-layer choice should therefore be reported and defended as an assumption about disease structure instead of a routine hyperparameter decision.

22.
arXiv (CS.AI) 2026-06-15

Thinking Outside the [Chat]Box: Bridging Computer Science and Industrial Design for Cognitive-Inclusive Generative AI

arXiv:2606.14306v1 Announce Type: cross Abstract: Current Generative AI (GenAI) interfaces remain largely constrained to chatbox interaction, which can impose high cognitive demands on users and create substantial barriers for people with intellectual disabilities (ID), including prompt formulation difficulties, response overload, and limited mechanisms to assess information reliability. To explore alternative interaction models for cognitive accessibility, we conducted a cross-disciplinary co-design challenge in which two student cohorts (Computer Science and Industrial Design) developed interface concepts from the same set of functional requirements (e.g., prompt scaffolding, structured output, GUI-based refinement, transparency, and personalization). Comparing the resulting proposals reveals both convergence on foundational requirements (notably initial calibration, proactive prompting, and direct manipulation of response fragments) and complementary contributions that outline a multi-layered support system. Computer Science teams primarily produced structural scaffolding, emphasizing predictability, navigability, and trust through mechanisms such as reliability indicators, explicit sources, and context management for long conversations. Industrial Design teams emphasized experiential scaffolding, focusing on pacing, attention guidance, multimodality, and proactive agency, including step-by-step response flows, focus modes, and assistant-like integrations. We synthesize these findings into a dual-layer scaffolding framework that expands the design space for cognitively accessible GenAI interaction beyond chat-centric models and motivates future work on expert refinement, technical feasibility, and empirical validation with users with ID.

23.
Nature (Science) 2026-06-10

Mutation-dependent responses to sleep and exercise in clonal haematopoiesis

Clonal haematopoiesis (CH) activates inflammation and increases the risk of atherosclerosis1,2. Whether lifestyle alters CH clone expansion or the phenotypic programming of CH mutant cells, thereby affecting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, Trp53 and Dnmt3a, we demonstrate mutation-dependent responses to sleep and exercise in CH and show that mutant cells are uniquely sensitive to lifestyle. In two human datasets, moderate-to-vigorous physical activity was associated with lower prevalence of non-DNMT3A-driven CH. In atherogenic mice with Jak2V617F or Tet2 loss of function (LOF), but not Trp53 LOF or Dnmt3aR878H CH, uninterrupted sleep or exercise curtails clone expansion. In CH with the Jak2V617F mutation, sleep and exercise reduces clone expansion by selectively reprogramming mutant, but not cohabitant wild type, haematopoietic progenitor cells towards antiproliferative and metabolically healthy phenotypes by tempering bone marrow macrophage–haematopoietic progenitor cell IL-1β signalling. Sleep or exercise also lessens Jak2V617F-driven, Tet2 LOF-driven and Trp53 LOF-driven, but not Dnmt3aR878H-driven, atherosclerosis by locally reprogramming mutant vascular macrophages, independent of peripheral clone dynamics. In Jak2V617F, but not adjacent wild type, aortic macrophages, uninterrupted sleep blunts CLEC4E-dependent inflammasome activation, consequently diminishing lesions. Exercise, meanwhile, activates PAC1+ neurons in the locus coeruleus, raising the levels of peripheral noradrenaline, which signals through adrenergic receptor β2 (ADRβ2) whose expression is preserved by exercise in Jak2V617F, but not cohabitant wild type, aortic macrophages, selectively repressing their inflammatory programming and atherosclerosis. Our findings establish that healthy lifestyles gene-specifically diminish CH and selectively reprogram mutant haematopoietic progenitor cells and macrophages to maintain cardiovascular health. Sleep and exercise can slow clonal haematopoiesis and limit mutant cell-driven atherosclerosis.

24.
PLOS Computational Biology 2026-06-15

WormSORT: A detection-based multiple object tracking model for individual silkworms in breeding environments

作者:

by Hongkang Shi, Linbo Li, Shiping Zhu, Haibo He, Minghui Zhu, Jianfei Zhang Variety breeding has long been a cornerstone of high-quality agriculture, and recent advances in artificial intelligence have opened new avenues for accelerating biological breeding. In this study, we applied multiple object tracking (MOT) technology to silkworm breeding to achieve efficient, non-invasive, and dynamic individual monitoring. Unlike pedestrian or vehicle tracking, silkworms pose unique challenges for MOT due to their small size, dense distribution, and high inter-individual similarity, which complicate accurate tracking and behavioral analysis. To address these issues, we propose WormSORT, an enhanced tracking method based on a tracking-by-detection framework with an optimized data association strategy. A pre-trained detection model identifies silkworms in each frame, and deep feature vectors are extracted using a re-identification network. Identity association is first performed using Intersection over Union (IoU) matching, followed by deep feature similarity for unmatched cases, improving both tracking accuracy and reliability. To further enhance tracking stability, we introduce a candidate input padding mechanism, including IoU padding and feature padding, ensuring that high-confidence unmatched trajectories and detections remain involved in the matching process. To validate the proposed tracking strategy, we constructed two multiple silkworm tracking (MST) datasets: MST-50, containing approximately 50 individuals over 1000 frames, and MST-100, containing approximately 100 individuals over 1200 frames. Experimental results demonstrate that WormSORT outperforms existing methods, including DeepSORT, StrongSORT, OCSORT, ByteTrack, and BotSORT, achieving superior tracking performance. This study provides a valuable reference for silkworm tracking and behavioral analysis, contributing to the advancement of high-quality silkworm rearing and management.

25.
bioRxiv (Bioinfo) 2026-06-22

EMAlign: accurate alignment of cryo-EM maps through main-chain probability using deep learning

Accurate alignment of cryo-EM density maps is essential for comparing conformational states, searching map libraries, and guiding atomic model building, but remains challenging for noisy experimental maps and partially overlapping structures. Existing alignment methods are often based on raw maps, which may result in reduced accuracy due to the density noise, or require manual intervention for local alignment, which suffers from limited general applicability. Addressing the limitations, we present EMAlign, an automatic global and local cryo-EM map alignment with predicted main-chain probability using deep learning. First, EMAlign predicts main-chain prob ability maps from raw cryo-EM density maps using a BiMCUNet network. Then, a fast Fourier transform (FFT)-based search strategy is used to globally search the accurate alignment between cryo-EM maps based on predicted main-chain probability maps. As such, the main-chain prob ability map overcomes the noisy raw map problem, and the FFT-based exhaustive global search ensures the general applicability of alignment. EMAlign is evaluated on 64 global map pairs, 195 local map pairs, and 60 structure-to-map pairs at 3-10 [A] resolution and compared with gmfit, fitmap, VESPER, and CryoAlign. It is shown that EMAlign outperforms the other methods in both global and local alignment, achieving mean RMSDs of 1.03 [A] (global), 2.56 [A] (local), and 0.82 [A] (structure-to-map), with success rates of 100.0%, 100.0%, and 98.3% under the criterion of RMSD < 10 [A]. The EMAlign package is freely available at https://github.com/huang-laboratory/EMAlign/.