Pamela Guevara

Pamela Guevara

Especialidad: Análisis de imágenes médicas, estudio de conectividad cerebral, machine learning, neurociencia computacional.
Pamela es ingeniera civil electrónica de la Universidad de Concepción, con master en información, sistemas y tecnología con especialidad en imágenes médicas, y un doctorado en física, ambos diplomas de la Université Paris-Sud, Francia.

PUBLICACIONES

Publisher: NPJ Science of Learning  Link>

ABSTRACT

Young children’s linguistic and communicative abilities are foundational for their academic achievement and overall well-being. We present the positive outcomes of a brief tablet-based intervention aimed at teaching toddlers and preschoolers new word-object and letter-sound associations. We conducted two experiments, one involving toddlers ( ~ 24 months old, n = 101) and the other with preschoolers ( ~ 42 months old, n = 152). Using a pre-post equivalent group design, we measured the children’s improvements in language and communication skills resulting from the intervention. Our results showed that the intervention benefited toddlers’ verbal communication and preschoolers’ speech comprehension. Additionally, it encouraged vocalizations in preschoolers and enhanced long-term memory for the associations taught in the study for all participants. In summary, our study demonstrates that the use of a ludic tablet-based intervention for teaching new vocabulary and pre-reading skills can improve young children’s linguistic and communicative abilities, which are essential for future development.


Publisher:  IEEE Explore  Link>

ABSTRACT

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that affects social communication and behavior. Early diagnosis is crucial to enhance the patient’s quality of life through treatments and therapies. In this research, two white matter (WM) fiber bundle segmentation methods are analyzed and compared in terms of their performance and impact on the results obtained from the analyzes applied to a database comprising 37 adolescents, 19 subjects with autism and 18 controls. To achieve this, we conducted the segmentation of deep white matter tracts, and computed average diffusion-based indices for each tract, such as Apparent Diffusion Coefficient (ADC), Fractional Anisotropy (FA), and Generalized Fractional Anisotropy (GFA). We applied statistical tests to identify features with significant differences between groups based on the results of two segmentation methods. Significant differences in diffusion-based indices were found in certain cingulate, thalamic, corticospinal, and corpus callosum fascicles. Furthermore, we performed classification between patients and controls using each fascicle feature independently with the Support Vector Machine (SVM) and Decision Trees (DT) algorithms. Finally, we applied the classifiers to the most relevant features for each segmentation method. Overall, even with the limitations of our small database, we demonstrated that the segmentation algorithm has a high impact on WM tract-based analyzes and prediction, with the autocencoder-based algorithm showing better results than a distance-based method.

Publisher:  IEEE Explora Link>

ABSTRACT

There is ongoing interest in the dynamics of resting state brain networks (RSNs) as potential predictors of cognitive and behavioural states. Multivariate Autoregressors (MAR) are used to model regional brain activity as a linear combination of past activity in other regions. The coefficients of the MAR are taken as estimates of effective brain connectivity. However, assumption of stationarity, and the large number of coefficients renders the MAR impractical for estimating brain networks from standard neuroimaging time-series of limited durations. We propose HsMM-MAR-AC, a novel sparse hybrid discrete-continuous model for the efficient estimation of time-dependent effective brain networks from non-stationary brain activity time-series. Discrete quasi-stationary Brain States, and the fast switching between them, are modelled by a Hidden semi-Markov Model whose continuous emissions are drawn from a sparse MAR. The coefficients of the MAR are restricted by Anatomical Brain Connectivity information in two ways: 1) Effective direct connectivity between two brain regions is only considered if the corresponding anatomical connection exists; and 2) the autoregressors lag associated with each connection is based on the fiber length between the two regions, such that only one lag per connection is estimated. We test the accuracy of HsMM-MAR-AC in recovering simulated resting state networks of various durations, and at different thresholds of anatomical restrictions. We demonstrate that HsMM-MAR-AC recovers the RSNs more accurately than the benchmark method of the sliding window, with as little as 4 minutes of data. We also show that when the anatomical restrictions are relaxed, longer time-series are needed to estimate the networks, and became computationally unfeasible without anatomical restrictions. HsMM-MAR-AC offers an efficient model for estimating time-dependent Effective Connectivity from neuroimaging data that exploits the advantages of Hidden Markov and MAR models without identifiability problems, excessive demand on data collection, or unnecessary computational effort.

Whole brain tractography data contain a large number of streamlines that require algorithms such as clustering to group the data into smaller sets for visualization and analysis. We present a deep-learning clustering algorithm based on the latent space of a variational autoencoder trained on the direct and flipped versions of the streamlines from 10 tractograms (17,294,232 streamlines in total). The model takes advantage of the low-dimensional representation of the data in latent space to apply an HDBSCAN clustering algorithm to perform automatic and fast clustering of the tractography datasets. The proposed method was evaluated in terms of segmentation quality using the Davies-Bouldin index (DB) and execution time against two other state-of-the-art methods, QuickBundles (QB) and FFClust. The results show that the proposed method has the best performance in terms of the DB index, closely followed by QB, and is the second fastest method, only slightly surpassed by FFClust. In addition, the proposed method allows for obtaining meaningful large clusters because it uses metrics based on the density of the groups instead of a distance threshold as the other methods.

Despite major advances in artificial intelligence (AI) research for healthcare, the deployment and adoption of AI technologies remain limited in clinical practice. This paper describes the FUTURE-AI framework, which provides guidance for the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI Consortium was founded in 2021 and comprises 117 interdisciplinary experts from 50 countries representing all continents, including AI scientists, clinical researchers, biomedical ethicists, and social scientists. Over a two year period, the FUTURE-AI guideline was established through consensus based on six guiding principles—fairness, universality, traceability, usability, robustness, and explainability. To operationalise trustworthy AI in healthcare, a set of 30 best practices were defined, addressing technical, clinical, socioethical, and legal dimensions. The recommendations cover the entire lifecycle of healthcare AI, from design, development, and validation to regulation, deployment, and monitoring.

Diffusion Magnetic Resonance Imaging (dMRI) tractography [1] has enabled the study of white matter connectivity and the development of automated methods for both fiber bundle clustering and segmentation and cortical parcellation. However, objective validation of such methods is limited by the lack of anatomical ground truth. We present two tools to address this gap: PhyberSIM [2], a white matter fiber bundle simulator, and a synthetic data generator that produces random cortical parcellations based and their connections [3], to validate tractography-based cortical parcellation (TBCP) methods.

Publisher:  IEEE Explore Link>

ABSTRACT

Brain neuronal networks of structural and func-tional connections have a hierarchical organization and a complex relationship between them. To study brain dynamics, it is important to identify the cortical level of parcellation of greater metastability. This paper presents a new multiscale cortical parcellation method based on the geodesic distance between vertices of the cortical surface and agglomerative hierarchical clustering, starting from an anatomical parcellation. First, the centroids of each region are efficiently calculated using the geodesic distance between the region’s vertices. Then, an affinity graph is constructed between the region centroids, based on the geodesic distance, from which a dendrogram is constructed using hierarchical clustering. Finally, an adaptive tree partitioning method is employed to obtain parcellations at various granularity levels, producing a multiscale parcellation. Furthermore, we propose an optimized method for the calculation of structural connectomes for each parcellation level. This framework will be made available and can be applied to different fine-grained parcellations. Additional information, such as structural connectivity information can be easily added to the framework. In future work this multiscale cortical parcellation will allow for simulations of cerebral dynamics at different levels.

Accurate three-dimensional (3D) nuclear instance segmentation is a prerequisite for quantitative phenotyping in volumetric microscopy, yet remains challenging in densely packed tissues, irregular nuclear morphologies, and across heterogeneous imaging modalities. Here we present NucVerse3D, a deep-learning framework for generalized 3D nuclei instance segmentation that combines a residual attention 3D U-Net architecture with a reversible gradient-field representation for robust centroid-aware instance reconstruction. NucVerse3D is trained end to end in 3D using modality-agnostic preprocessing and isotropic scale normalization, enabling deployment across confocal microscopy, two-photon microscopy, light-sheet microscopy, micro–computed tomography, and scanning electron microscopy volumes. We benchmarked NucVerse3D on seven volumetric datasets spanning multiple species and tissues, comprising more than forty thousand manually annotated nuclei, including newly released ground-truth datasets of mouse liver tissue (control and hepatocellular carcinoma) and Drosophila brain glial nuclei. Across datasets, NucVerse3D achieved consistently high precision, recall, F1-score, and average precision, and outperformed the state-of-the-art methods particularly in dense and irregular settings, while remaining competitive on simpler cases. A single generalized model trained on pooled data matched the performance of dataset-specific models, and ablation experiments demonstrated that preprocessing and scale normalization substantially contribute to performance under strict intersection-over-union criteria. To demonstrate the biomedical utility of NucVerse3D, we applied it to three-dimensional liver images from a mouse model of hepatocellular carcinoma (HCC). High-fidelity, nucleus-by-nucleus segmentation enabled the quantification of the Nuclear Decoupling Score (NDS), which captures deviations in nuclear DNA–volume coupling at the single-nucleus level. NDS analysis revealed a progressive increase in nuclear abnormalities within tumor regions, forming spatially coherent domains of dysregulated nuclei and highlighting NDS as a potential quantitative biomarker of dysplastic and tumor tissue. Together, NucVerse3D provides a robust and generalizable solution for 3D nuclear instance segmentation and enables quantitative nuclear phenotyping across imaging modalities.

Patients recovering from COVID-19 commonly exhibit cognitive and brain alterations, yet the specific neuropathological mechanisms and risk factors underlying these alterations remain elusive. Given the significant global incidence of COVID-19, identifying factors that can distinguish individuals at risk of developing brain alterations is crucial for prioritizing follow-up care. Here, we report findings from a sample of patients consisting of 73 adults with a mild to moderate SARS-CoV-2 infection without signs of respiratory failure and 27 with infections attributed to other agents and no history of COVID-19. The participants underwent cognitive screening, a decision-making task, and MRI evaluations. We assessed for the presence of anosmia and the requirement for hospitalization. Groups did not differ in age or cognitive performance. Patients who presented with anosmia exhibited more impulsive alternative changes after a shift in probabilities (r = − 0.26, p = 0.001), while patients who required hospitalization showed more perseverative choices (r = 0.25, p = 0.003). Anosmia correlated with brain measures, including decreased functional activity during the decision-making task, thinning of cortical thickness in parietal regions, and loss of white matter integrity. Hence, anosmia could be a factor to be considered when identifying at-risk populations for follow-up.

Publisher: Frontiers in Neuroscience Link>

ABSTRACT

We present a Python library (Phybers) for analyzing brain tractography data. Tractography datasets contain streamlines (also called fibers) composed of 3D points representing the main white matter pathways. Several algorithms have been proposed to analyze this data, including clustering, segmentation, and visualization methods. The manipulation of tractography data is not straightforward due to the geometrical complexity of the streamlines, the file format, and the size of the datasets, which may contain millions of fibers. Hence, we collected and structured state-of-the-art methods for the analysis of tractography and packed them into a Python library, to integrate and share tools for tractography analysis. Due to the high computational requirements, the most demanding modules were implemented in C/C++. Available functions include brain Bundle Segmentation (FiberSeg), Hierarchical Fiber Clustering (HClust), Fast Fiber Clustering (FFClust), normalization to a reference coordinate system, fiber sampling, calculation of intersection between sets of brain fibers, tools for cluster filtering, calculation of measures from clusters, and fiber visualization. The library tools were structured into four principal modules: Segmentation, Clustering, Utils, and Visualization (Fibervis). Phybers is freely available on a GitHub repository under the GNU public license for non-commercial use and open-source development, which provides sample data and extensive documentation. In addition, the library can be easily installed on both Windows and Ubuntu operating systems through the pip library.

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