Vendor-agnostic 4D Phase Contrast MRI: a complete open-source pipeline for velocities, displacement, and strain analysis

Phase contrast MRI (PC MRI) enables quantitative assessment of tissue motion and strain. Although it is increasingly used, standardized, vendor-agnostic pipelines for accelerated acquisitions remain scarce. We present a fully open-source 4D flow PC-MRI pipeline integrating a compressed sensing-accelerated sequence implemented in PyPulseq, BART-based reconstruction, and strain analysis. Additionally, a gradient probing sequence was developed to ensure correct velocity sign assignment across scanner orientations and vendors. The pipeline was validated across two Siemens MRI systems (3T MAGNETOM Prisma and 3T Vida Fit) in two anatomical applications: forearm (Flexor Digitorum Superficialis, n=9) and thigh (Vastus Lateralis, n=10) during Neuromuscular Electrical Stimulation (NMES)-induced contractions. Compressed sensing reduced acquisition times from 35 and 80 minutes to 5 and 11 minutes for the arm and leg acquisitions, respectively. Muscle strain maps and sigmoid-fitted strain curves enabled extraction of peak strain, mean strain, and buildup rate. Strains in the Vastus Lateralis were approximately one order of magnitude higher than in the Flexor Digitorum Superficialis (median peak strain 0.49 vs. 0.063, mean strain 0.31 vs. 0.031). The pipeline demonstrates multi-platform compatibility and provides a reproducible, open framework for quantitative muscle imaging.

On the limits and opportunities of AI reviewers: Reviewing the reviews of Nature-family papers with 45 expert scientists

With the advancement of AI capabilities, AI reviewers are beginning to be deployed in scientific peer review, yet their capability and credibility remain in question: many scientists simply view them as probabilistic systems without the expertise to evaluate research, while other researchers are more optimistic about their readiness without concrete evidence. Understanding what AI reviewers do well, where they fall short, and what challenges remain is essential. However, existing evaluations of AI reviewers have focused on whether their verdicts match human verdicts (e.g., score alignment, acceptance prediction), which is insufficient to characterize their capabilities and limits. In this paper, we close this gap through a large-scale expert annotation study, in which 45 domain scientists in Physical, Biological, and Health Sciences spent 469 hours rating 2,960 individual criticisms (each targeting one specific aspect of a paper) from human-written and AI-generated reviews of 82 Nature-family papers on correctness, significance, and sufficiency of evidence. On a composite of all three dimensions, a reviewing agent powered by GPT-5.2 scores above each paper's top-rated human reviewer (60.0% vs. 48.2%, p = 0.009), while all three AI reviewers (including Gemini 3.0 Pro and Claude Opus 4.5) exceed the lowest-rated human across every dimension. AI reviewers' accurate criticisms are also more often rated significant and well-evidenced, and surface a distinct 26% of issues no human raises. However, AI reviewers overlap far more than humans do (21% vs. 3% for cross-reviewer pairs), and exhibit 16 recurring weaknesses humans do not share, such as limited subfield knowledge, lack of long context management over multiple files, and overly critical stance on minor issues. Overall, our results position current AI reviewers as complements to, not substitutes for, human reviewers.

Dante: An Open Source Model Pre-Training and Fine-Tuning Tool for the Dafne Federated Framework for Medical Image Segmentation

Adapting pre-trained deep learning segmentation models to new clinical domains is a persistent challenge in medical image analysis, particularly when annotated data at the target site are scarce. Parameter-efficient fine-tuning strategies offer a principled solution by selectively updating a controlled subset of model parameters, preserving previously acquired representations while reducing the risk of overfitting on small datasets. This paper introduces DAfNe TrainEr (Dante), an open-source module integrating with the Dafne federated segmentation ecosystem as a dedicated training and fine-tuning backend. Dante supports training from scratch with automatic architecture configuration, configurable layer freezing schedules, and Low-Rank Adaptation (LoRA) extended to N-dimensional convolutional layers through channel-wise factorization. To validate the module, Gradual Unfreezing (GU) and LoRA are assessed across realistic cross-domain MRI transfer scenarios covering abdominal organ segmentation and brain white matter lesion segmentation, under full-data and few-shot conditions. GU reduced the epochs required to reach 85% of peak performance by up to 63.6% compared to training from scratch, while LoRA achieved Dice Similarity Coefficients up to 0.957 in data-rich scenarios. Both strategies outperformed the baseline across all tested domains, with gains amplified by richer pre-training datasets. These results validate Dante as a domain-agnostic fine-tuning module for medical image segmentation in real clinical deployment conditions. Dante code is available at https://github.com/dafne-imaging/dafne-torch-trainer while Dafne ecosystem project is available at https://github.com/dafne-imaging.

ASCHOPLEX encounters Dafne: a federated continuous learning project for the generalizability of the Choroid Plexus automatic segmentation

The Choroid Plexus (ChP) is a highly vascularized brain structure that plays a critical role in several physiological processes. ASCHOPLEX, a deep learning-based segmentation toolbox with an integrated fine-tuning stage, provides accurate ChP delineations on non-contrast-enhanced T1-weighted MRI scans; however, its performance is hindered by inter-dataset variability. This study introduces the first federated incremental learning approach for automated ChP segmentation from 3D T1-weighted brain MRI, by integrating an enhanced version of ASCHOPLEX within the Dafne (Deep Anatomical Federated Network) framework. A comparative evaluation is conducted to assess whether federated incremental learning through Dafne improves model generalizability across heterogeneous imaging conditions, relative to the conventional fine-tuning strategy employed by standalone ASCHOPLEX. The experimental cohort comprises 2,284 subjects, including individuals with Multiple Sclerosis as well as healthy controls, collected from five independent MRI datasets. Results indicate that the fine-tuning strategy provides high performance on homogeneous data (e.g., same MRI sequence, same cohort of subjects), but limited generalizability when the data variability is high (e.g., multiple MRI sequences, multiple and new cohorts of subjects). By contrast, the federated incremental learning variant of ASCHOPLEX constitutes a robust alternative consistently achieving higher generalizability and more stable performance across diverse acquisition settings.

An encoding of argumentation problems using quadratic unconstrained binary optimization

In this paper, we develop a way to encode several NP-Complete problems in Abstract Argumentation to Quadratic Unconstrained Binary Optimization (QUBO) problems. In this form, a solution for a QUBO problem involves minimizing a quadratic function over binary variables (0/1), where the coefficients can be represented by a symmetric square matrix (or an equivalent upper triangular version). With the QUBO formulation, exploiting new computing architectures, such as Quantum and Digital Annealers, is possible. A more conventional approach consists of developing approximate solvers, which, in this case, are used to tackle the intrinsic complexity. We performed tests to prove the correctness and applicability of classical problems in Argumentation and enforcement of argument sets. We compared our approach to two other approximate solvers in the literature during tests. In the final experimentation, we used a Simulated Annealing algorithm on a local machine. Also, we tested a Quantum Annealer from the D-Wave Ocean SDK and the Leap Quantum Cloud Service.

Deep Anatomical Federated Network (Dafne): an open client/server framework for the continuous collaborative improvement of deep-learning-based medical image segmentation

Semantic segmentation is a crucial step to extract quantitative information from medical (and, specifically, radiological) images to aid the diagnostic process, clinical follow-up. and to generate biomarkers for clinical research. In recent years, machine learning algorithms have become the primary tool for this task. However, its real-world performance is heavily reliant on the comprehensiveness of training data. Dafne is the first decentralized, collaborative solution that implements continuously evolving deep learning models exploiting the collective knowledge of the users of the system. In the Dafne workflow, the result of each automated segmentation is refined by the user through an integrated interface, so that the new information is used to continuously expand the training pool via federated incremental learning. The models deployed through Dafne are able to improve their performance over time and to generalize to data types not seen in the training sets, thus becoming a viable and practical solution for real-life medical segmentation tasks.

MRI lung lobe segmentation in pediatric cystic fibrosis patients using a recurrent neural network trained with publicly accessible CT datasets

Purpose: To introduce a widely applicable workflow for pulmonary lobe segmentation of MR images using a recurrent neural network (RNN) trained with chest computed tomography (CT) datasets. The feasibility is demonstrated for 2D coronal ultra-fast balanced steady-state free precession (ufSSFP) MRI. Methods: Lung lobes of 250 publicly accessible CT datasets of adults were segmented with an open-source CT-specific algorithm. To match 2D ufSSFP MRI data of pediatric patients, both CT data and segmentations were translated into pseudo-MR images, masked to suppress anatomy outside the lung. Network-1 was trained with pseudo-MR images and lobe segmentations, and applied to 1000 masked ufSSFP images to predict lobe segmentations. These outputs were directly used as targets to train Network-2 and Network-3 with non-masked ufSSFP data as inputs, and an additional whole-lung mask as input for Network-2. Network predictions were compared to reference manual lobe segmentations of ufSSFP data in twenty pediatric cystic fibrosis patients. Manual lobe segmentations were performed by splitting available whole-lung segmentations into lobes. Results: Network-1 was able to segment the lobes of ufSSFP images, and Network-2 and Network-3 further increased segmentation accuracy and robustness. The average all-lobe Dice similarity coefficients were 95.0$\pm$2.3 (mean$\pm$pooled SD [%]), 96.4$\pm$1.2, 93.0$\pm$1.8, and the average median Hausdorff distances were 6.1$\pm$0.9 (mean$\pm$SD [mm]), 5.3$\pm$1.1, 7.1$\pm$1.3, for Network-1, Network-2, and Network-3, respectively. Conclusions: RNN lung lobe segmentation of 2D ufSSFP imaging is feasible, in good agreement with manual segmentations. The proposed workflow might provide rapid access to automated lobe segmentations for various lung MRI examinations and quantitative analyses.

Block Argumentation

We contemplate a higher-level bipolar abstract argumentation for non-elementary arguments such as: X argues against Ys sincerity with the fact that Y has presented his argument to draw a conclusion C, by omitting other facts which would not have validated C. Argumentation involving such arguments requires us to potentially consider an argument as a coherent block of argumentation, i.e. an argument may itself be an argumentation. In this work, we formulate block argumentation as a specific instance of Dung-style bipolar abstract argumentation with the dual nature of arguments. We consider internal consistency of an argument(ation) under a set of constraints, of graphical (syntactic) and of semantic nature, and formulate acceptability semantics in relation to them. We discover that classical acceptability semantics do not in general hold good with the constraints. In particular, acceptability of unattacked arguments is not always warranted. Further, there may not be a unique minimal member in complete semantics, thus sceptic (grounded) semantics may not be its subset. To retain set-theoretically minimal semantics as a subset of complete semantics, we define semi-grounded semantics. Through comparisons, we show how the concept of block argumentation may further generalise structured argumentation.

On Looking for Local Expansion Invariants in Argumentation Semantics: a Preliminary Report

We study invariant local expansion operators for conflict-free and admissible sets in Abstract Argumentation Frameworks (AFs). Such operators are directly applied on AFs, and are invariant with respect to a chosen "semantics" (that is w.r.t. each of the conflict free/admissible set of arguments). Accordingly, we derive a definition of robustness for AFs in terms of the number of times such operators can be applied without producing any change in the chosen semantics.

Timed Soft Concurrent Constraint Programs: An Interleaved and a Parallel Approach

We propose a timed and soft extension of Concurrent Constraint Programming. The time extension is based on the hypothesis of bounded asynchrony: the computation takes a bounded period of time and is measured by a discrete global clock. Action prefixing is then considered as the syntactic marker which distinguishes a time instant from the next one. Supported by soft constraints instead of crisp ones, tell and ask agents are now equipped with a preference (or consistency) threshold which is used to determine their success or suspension. In the paper we provide a language to describe the agents behavior, together with its operational and denotational semantics, for which we also prove the compositionality and correctness properties. After presenting a semantics using maximal parallelism of actions, we also describe a version for their interleaving on a single processor (with maximal parallelism for time elapsing). Coordinating agents that need to take decisions both on preference values and time events may benefit from this language. To appear in Theory and Practice of Logic Programming (TPLP).