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Radiology Radiology

DNA methylation-based classification of glioneuronal tumours synergises with histology and radiology to refine accurate molecular stratification.

In Neuropathology and applied neurobiology ; h5-index 39.0

AIMS : Glioneuronal tumours (GNTs) are poorly distinguished by their histology and lack robust diagnostic indicators. Previously, we showed that common GNTs comprise two molecularly distinct groups, correlating poorly with histology. To refine diagnosis, we constructed a methylation-based model for GNT classification, subsequently evaluating standards for molecular stratification by methylation, histology and radiology.

METHODS : We comprehensively analysed methylation, radiology and histology for 83 GNT samples: a training cohort of 49, previously classified into molecularly defined groups by genomic profiles, plus a validation cohort of 34. We identified histological and radiological correlates to molecular classification and constructed a methylation-based support vector machine (SVM) model for prediction. Subsequently, we contrasted methylation, radiological and histological classifications in validation GNTs.

RESULTS : By methylation clustering, all training and 23/34 validation GNTs segregated into two groups, the remaining 11 clustering alongside control cortex. Histological review identified prominent astrocytic/oligodendrocyte-like components, dysplastic neurons, and a specific glioneuronal element as discriminators between groups. However, these were present in only a subset of tumours. Radiological review identified location, margin definition, enhancement, and T2 FLAIR-rim sign as discriminators. When validation GNTs were classified by SVM, 22/23 classified correctly, comparing favourably against histology and radiology which resolved 17/22 and 15/21 respectively where data were available for comparison.

CONCLUSIONS : Diagnostic criteria inadequately reflect glioneuronal tumour biology, leaving a proportion unresolvable. In the largest cohort of molecularly defined glioneuronal tumours, we develop molecular, histological, and radiological approaches for biologically meaningful classification and demonstrate almost all cases are resolvable, emphasising the importance of an integrated diagnostic approach.

Stone Thomas J, Mankad Kshitij, Tan A I Peng, Jan Wajanat, Pickles Jessica C, Gogou Maria, Chalker Jane, Slodkowska Iwona, Pang Emily, Kristiansen Mark, Madhan Gaganjit K, Forrest Leysa, Hughes Deborah, Koutroumanidou Eleni, Mistry Talisa, Ogunbiyi Olumide, Ahmed Saira W, Cross J Helen, Hubank Mike, Hargrave Darren, Jacques Thomas S

2023-Feb-26

dysembryoplastic neuroepithelial tumour, ganglioglioma, glioneuronal tumour, machine learning, molecular pathology

General General

Detection of COVID-19 Case from Chest CT Images Using Deformable Deep Convolutional Neural Network.

In Journal of healthcare engineering

The infectious coronavirus disease (COVID-19) has become a great threat to global human health. Timely and rapid detection of COVID-19 cases is very crucial to control its spreading through isolation measures as well as for proper treatment. Though the real-time reverse transcription-polymerase chain reaction (RT-PCR) test is a widely used technique for COVID-19 infection, recent researches suggest chest computed tomography (CT)-based screening as an effective substitute in cases of time and availability limitations of RT-PCR. In consequence, deep learning-based COVID-19 detection from chest CT images is gaining momentum. Furthermore, visual analysis of data has enhanced the opportunities of maximizing the prediction performance in this big data and deep learning realm. In this article, we have proposed two separate deformable deep networks converting from the conventional convolutional neural network (CNN) and the state-of-the-art ResNet-50, to detect COVID-19 cases from chest CT images. The impact of the deformable concept has been observed through performance comparative analysis among the designed deformable and normal models, and it is found that the deformable models show better prediction results than their normal form. Furthermore, the proposed deformable ResNet-50 model shows better performance than the proposed deformable CNN model. The gradient class activation mapping (Grad-CAM) technique has been used to visualize and check the targeted regions' localization effort at the final convolutional layer and has been found excellent. Total 2481 chest CT images have been used to evaluate the performance of the proposed models with a train-valid-test data splitting ratio of 80 : 10 : 10 in random fashion. The proposed deformable ResNet-50 model achieved training accuracy of 99.5% and test accuracy of 97.6% with specificity of 98.5% and sensitivity of 96.5% which are satisfactory compared with related works. The comprehensive discussion demonstrates that the proposed deformable ResNet-50 model-based COVID-19 detection technique can be useful for clinical applications.

Foysal Md, Hossain A B M Aowlad, Yassine Abdulsalam, Hossain M Shamim

2023

Pathology Pathology

Kartezio: Evolutionary Design of Explainable Pipelines for Biomedical Image Analysis

ArXiv Preprint

An unresolved issue in contemporary biomedicine is the overwhelming number and diversity of complex images that require annotation, analysis and interpretation. Recent advances in Deep Learning have revolutionized the field of computer vision, creating algorithms that compete with human experts in image segmentation tasks. Crucially however, these frameworks require large human-annotated datasets for training and the resulting models are difficult to interpret. In this study, we introduce Kartezio, a modular Cartesian Genetic Programming based computational strategy that generates transparent and easily interpretable image processing pipelines by iteratively assembling and parameterizing computer vision functions. The pipelines thus generated exhibit comparable precision to state-of-the-art Deep Learning approaches on instance segmentation tasks, while requiring drastically smaller training datasets, a feature which confers tremendous flexibility, speed, and functionality to this approach. We also deployed Kartezio to solve semantic and instance segmentation problems in four real-world Use Cases, and showcase its utility in imaging contexts ranging from high-resolution microscopy to clinical pathology. By successfully implementing Kartezio on a portfolio of images ranging from subcellular structures to tumoral tissue, we demonstrated the flexibility, robustness and practical utility of this fully explicable evolutionary designer for semantic and instance segmentation.

Kévin Cortacero, Brienne McKenzie, Sabina Müller, Roxana Khazen, Fanny Lafouresse, Gaëlle Corsaut, Nathalie Van Acker, François-Xavier Frenois, Laurence Lamant, Nicolas Meyer, Béatrice Vergier, Dennis G. Wilson, Hervé Luga, Oskar Staufer, Michael L. Dustin, Salvatore Valitutti, Sylvain Cussat-Blanc

2023-02-28

General General

Digitally embodied lifespan neurocognitive development and Tactile Internet: Transdisciplinary challenges and opportunities.

In Frontiers in human neuroscience ; h5-index 79.0

Mechanisms underlying perceptual processing and inference undergo substantial changes across the lifespan. If utilized properly, technologies could support and buffer the relatively more limited neurocognitive functions in the still developing or aging brains. Over the past decade, a new type of digital communication infrastructure, known as the "Tactile Internet (TI)," is emerging in the fields of telecommunication, sensor and actuator technologies and machine learning. A key aim of the TI is to enable humans to experience and interact with remote and virtual environments through digitalized multimodal sensory signals that also include the haptic (tactile and kinesthetic) sense. Besides their applied focus, such technologies may offer new opportunities for the research tapping into mechanisms of digitally embodied perception and cognition as well as how they may differ across age cohorts. However, there are challenges in translating empirical findings and theories about neurocognitive mechanisms of perception and lifespan development into the day-to-day practices of engineering research and technological development. On the one hand, the capacity and efficiency of digital communication are affected by signal transmission noise according to Shannon's (1949) Information Theory. On the other hand, neurotransmitters, which have been postulated as means that regulate the signal-to-noise ratio of neural information processing (e.g., Servan-Schreiber et al., 1990), decline substantially during aging. Thus, here we highlight neuronal gain control of perceptual processing and perceptual inference to illustrate potential interfaces for developing age-adjusted technologies to enable plausible multisensory digital embodiments for perceptual and cognitive interactions in remote or virtual environments.

Li Shu-Chen, Fitzek Frank H P

2023

Tactile Internet, aging, development, multisensory, neuromodulation, perception, sensory augmentation, signal-to-noise

Public Health Public Health

Resistance-resistant antibacterial treatment strategies.

In Frontiers in antibiotics

Antibiotic resistance is a major danger to public health that threatens to claim the lives of millions of people per year within the next few decades. Years of necessary administration and excessive application of antibiotics have selected for strains that are resistant to many of our currently available treatments. Due to the high costs and difficulty of developing new antibiotics, the emergence of resistant bacteria is outpacing the introduction of new drugs to fight them. To overcome this problem, many researchers are focusing on developing antibacterial therapeutic strategies that are "resistance-resistant"-regimens that slow or stall resistance development in the targeted pathogens. In this mini review, we outline major examples of novel resistance-resistant therapeutic strategies. We discuss the use of compounds that reduce mutagenesis and thereby decrease the likelihood of resistance emergence. Then, we examine the effectiveness of antibiotic cycling and evolutionary steering, in which a bacterial population is forced by one antibiotic toward susceptibility to another antibiotic. We also consider combination therapies that aim to sabotage defensive mechanisms and eliminate potentially resistant pathogens by combining two antibiotics or combining an antibiotic with other therapeutics, such as antibodies or phages. Finally, we highlight promising future directions in this field, including the potential of applying machine learning and personalized medicine to fight antibiotic resistance emergence and out-maneuver adaptive pathogens.

Batchelder Jonathan I, Hare Patricia J, Mok Wendy W K

2023

antibiotic resistance, combination therapies, evolutionary steering, mutation, stress response

General General

Machine learning aided jump height estimate democratization through smartphone measures.

In Frontiers in sports and active living

INTRODUCTION : The peak height reached in a countermovement jump is a well established performance parameter. Its estimate is often entrusted to force platforms or body-worn inertial sensors. To date, smartphones may possibly be used as an alternative for estimating jump height, since they natively embed inertial sensors.

METHODS : For this purpose, 43 participants performed 4 countermovement jumps (172 in total) on two force platforms (gold standard). While jumping, participants held a smartphone in their hands, whose inertial sensor measures were recorded. After peak height was computed for both instrumentations, twenty-nine features were extracted, related to jump biomechanics and to signal time-frequency characteristics, as potential descriptors of soft tissues or involuntary arm swing artifacts. A training set (129 jumps - 75%) was created by randomly selecting elements from the initial dataset, the remaining ones being assigned to the test set (43 jumps - 25%). On the training set only, a Lasso regularization was applied to reduce the number of features, avoiding possible multicollinearity. A multi-layer perceptron with one hidden layer was trained for estimating the jump height from the reduced feature set. Hyperparameters optimization was performed on the multi-layer perceptron using a grid search approach with 5-fold cross validation. The best model was chosen according to the minimum negative mean absolute error.

RESULTS : The multi-layer perceptron greatly improved the accuracy (4 cm) and precision (4 cm) of the estimates on the test set with respect to the raw smartphone measures estimates (18 and 16 cm, respectively). Permutation feature importance was performed on the trained model in order to establish the influence that each feature had on the outcome. The peak acceleration and the braking phase duration resulted the most influential features in the final model. Despite not being accurate enough, the height computed through raw smartphone measures was still among the most influential features.

DISCUSSION : The study, implementing a smartphone-based method for jump height estimates, paves the way to method release to a broader audience, pursuing a democratization attempt.

Mascia Guido, De Lazzari Beatrice, Camomilla Valentina

2023

accelerometer, gyroscope, modal analysis, neural network, strength and conditioning