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Community challenge towards consensus on characterization of biological tissue: C4Bio’s first findings
No full textInternational audienceThis study investigates methodological variability across various expert laboratories worldwide, with regards to characterizing the mechanical properties of biological tissues. Two testing rounds were conducted on the specific use case of uniaxial tensile testing of porcine aorta. In the first round, 24 labs were invited to apply their established methods to assess inter-laboratory variability. This revealed significant methodological diversity and associated variability in the stress–stretch results, underscoring the necessity for a standardized approach. In the second round, a consensus protocol was collaboratively developed and adopted by 19 labs in an attempt to minimize variability. This involved standardized sample preparation and uniformity in testing protocol, including the use of a common cutting and thickness measurement tool. Despite protocol harmonization, significant variability persisted across labs, which could not be solely attributed to inherent biological differences in tissue samples. These results illustrate the challenges in unifying testing methods across different research settings, underlining the necessity for further refinement of testing practices. Enhancing consistency in biomechanical experiments is pivotal when comparing results across studies, as well as when using the resulting material properties for in silico simulations in medical research
Extracting quantum field theory dynamics from an approximate ground state
No full text5+2 pages, 7 figure
Delays in mempool-based blockchains under realistic conditions: case of Narwhal and DroneVet application
No full textInternational audienceThis study focuses on modeling and analyzing the delay in consensus protocols within mempool-based blockchains. In such systems, unconfirmed transactions are temporarily stored in a memory pool (mempool) before being selected, ordered, and committed to blocks by the consensus mechanism.In a previous work, we designed a generic model of a mempool-based blockchain, capturing core protocol behaviors. The model involves n nodes (potentially including Byzantine nodes) that exchange blocks and await one or two quorums of acknowledgments before producing new blocks and advancing to the next round. Based on this framework, we derived two Markov chains to characterize round durations and validated them through simulations.In this paper, we extend that work in three key directions: (1) We focus on Narwhal, a specific mempool protocol, describing its operations and its round duration formula. (2) We introduce DroneVet, an application leveraging UAVs to monitor livestock health and shares collected data across stakeholders via blockchain technology. DroneVet is implemented using Narwhal and includes realistic environmental constraints such as packet loss, network latency, and UAV-energy limitation. (3) We develop DroneVet and compare its round duration with the theoretical round duration of Narwhal.By taking into account the environmental factors specific to agricultural deployments, this work highlights how such conditions impact the reliability and responsiveness of blockchain-based systems. Our findings provide valuable insights for deploying secure, resilient, and transparent blockchain solutions in rural settings to support reliable livestock monitoring.</p
Adjusted Objects: An Efficient and Principled Approach to Scalable Programming (Extended Version)
No full textParallel programs require software support to coordinate access to shared data. For this purpose, modern programming languages provide strongly-consistent shared objects. To account for their many usages, these objects offer a large API. However, in practice, each program calls only a tiny fraction of the interface. Leveraging such an observation, we propose to tailor a shared object for a specific usage. We call this principle adjusted objects. Adjusted objects already exist in the wild. This paper provides their first systematic study. We explain how everyday programmers already adjust common shared objects (such as queues, maps, and counters) for better performance. We present the formal foundations of adjusted objects using a new tool to characterize scalability, the indistinguishability graph. Leveraging this study, we introduce a library named DEGO to inject adjusted objects in a Java program. In micro-benchmarks, objects from the DEGO library improve the performance of standard JDK shared objects by up to two orders of magnitude. We also evaluate DEGO with a Retwis-like benchmark modeled after a social network application. On a modern server-class machine, DEGO boosts by up to 1.7x the performance of the benchmark
Modular and automatic formal verification of a RISC-V processor with security mechanisms
No full textThe security of computer systems eventually relies on the security of the underlying hardware and on the security mechanisms that it offers. We extend a simple RISC-V processor written in the Kôika Hardware Description Language (HDL) with security mechanisms, and prove that these mechanisms are correct.We do so by compiling Kôika circuits into a representation well-suited for automated theorem provers. We strive to make our proofs modular, i.e., function by function or rule by rule.</div
Negative Selection Maintains Grossly Altered but Broadly Stable Karyotypes in Metastatic Colorectal Cancer
No full textInternational audienceAbstract Aneuploidy is near-ubiquitous in cancer and contributes to tumor biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterized. We performed longitudinal genomic analysis of 755 samples from 167 patients with colorectal-derived neoplasias from different stages through metastasis and treatment. Adenomas had few copy number alterations (CNA) and most were subclonal, whereas cancers had many clonal CNAs, suggesting that progression goes through a CNA bottleneck. Individual colorectal cancer glands from the same tumor had similar karyotypes, despite evidence of ongoing instability at the cell level. CNAs in metastatic lesions, after therapy, and in late recurrences were similar to the primary. Mathematical modeling indicated that these data are consistent with the action of negative selection on CNAs that “trap” cancer genomes on a fitness peak characterized by specific CNAs. Hence, progression to colorectal cancer requires traversing a rugged fitness landscape, whereas subsequent CNA evolution is constrained by negative selection. Significance: We profiled 167 long-term responders longitudinally (755 samples), documenting long-term cancer evolution. We found that a genetic bottleneck is required for progression and is associated with dramatic increase in CNAs but decrease in clonal diversity. After initiation, copy number evolution is constrained by negative selection through metastasis and treatment
SpeechTherapyAgent: A Clinician-in-the-Loop AI Virtual Speech Therapist for Personalized and Supervised Therapy
No full textCopyright: For Non Commercial Use OnlyThis paper introduces Virtual Speech Therapist (VST) 1 , an agentic, AI-powered workflow designed for automated stuttering assessment and personalized therapy planning. VST integrates deep learning-based stuttering classification, and multiagent large language model (LLM) reasoning to support evidence-based clinical decision-making. The VST begins with the acquisition and feature extraction of patient speech samples, followed by robust classification of stuttering types. Building on these outputs, VST initiates an agentic reasoning process in which specialized LLM agents autonomously generate, critique, and iteratively refine individualized therapy plans. A dedicated critic agent evaluates all generates therapy plans to ensure clinical safety, methodological soundness, and alignment with peer-reviewed evidence and established professional guidelines. The resulting output is a comprehensive, patient-specific therapy draft intended for clinician review. Incorporating clinician feedback, the system then produces a finalized therapy plan suitable for patient delivery, thereby maintaining a clinician-in-theloop paradigm. Experimental evaluation by expert speech therapists confirms that VST consistently generates high-quality, evidence-based therapy recommendations. These findings demonstrate the system’s potential to augment clinical workflows,reduce clinician burden, and improve therapeutic outcomes for individuals with speech impairments. User Interface: https://vocametrix.com/ai/therapy-planning-agent </div
Passivity Preservation in Interconnections of Linear Cone Complementarity Systems with State Jumps
No full textInternational audienceThis article is largely concerned with generic interconnections of a class of passive nonsmooth nonlinear dynamical systems, namely linear cone complementarity systems (LCCS). We stipulate that each subsystem admits a positive definite storage function that characterizes the passivity of an underlying nonsmooth mapping. We provide algebraic criteria in terms of these individual storage functions to find the storage function which guarantees passivity of the overall interconnected system. State jumps in the interconnections are studied in detail. Examples from dynamic feedback control, switching DAEs and nonsmooth circuits are included as an illustration of the theoretical developments
Migrating Esope to Fortran 2008 using model transformations
No full textLegacy programming languages such as FORTRAN 77 still play a vital role in many industrial applications. Maintaining and modernizing these languages is challenging, especially when migrating to newer standards such as Fortran 2008. This is exacerbated in the presence of legacy proprietary extensions on such legacy languages, because their semantics are often based on old context (limits of legacy language, domain logic,...). This paper presents an approach for automatically migrating FORTRAN 77 with a proprietary extension, named Esope, to Fortran 2008. We introduce a tool that converts Esope source code to Fortran 2008. While supporting readability of the generated code, we want to maintain the level of abstraction provided by Esope. Our method uses model-driven engineering techniques, with transformations to generate a target model from which we export easy-to-read Fortran 2008 source code. We discuss the advantages, limitations, and maintainability considerations of our approach and provide insights into its scalability and adaptability to evolving requirements.</div
Long-time behaviour of a multidimensional age-dependent branching process with a singular jump kernel modelling telomere shortening
No full textInternational audienceIn this article, we investigate the ergodic behaviour of a multidimensional age-dependent branching process with a singular jump kernel, motivated by studying the phenomenon of telomere shortening in cell populations. Our model tracks individuals evolving within a continuous-time framework indexed by a binary tree, characterised by age and a multidimensional trait. Branching events occur with rates dependent on age, where offspring inherit traits from their parent with random increase or decrease in some coordinates, while the most of them are left unchanged. Exponential ergodicity is obtained at the cost of an exponential normalisation, despite the fact that we have an unbounded age-dependent birth rate that may depend on the multidimensional trait, and a non-compact transition kernel. These two difficulties are respectively treated by stochastically comparing our model to Bellman-Harris processes, and by using a weak form of a Harnack inequality. We conclude this study by giving examples where the assumptions of our main result are verified