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Register a new userReconstructing the Forest of Lineage Trees of Diverse Bacterial Communities Using Bio-inspired Image Analysis
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Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to analyze successfully complex cell movies, imaging multiple interacting bacterial clones as they grow and merge to generate overcrowded bacterial communities with thousands of cells in the field of view, segmentation results should be near perfect to warrant good tracking results. We introduce here a fully automated closed-loop bio-inspired computational strategy that exploits prior knowledge about the expected structure of a colonys lineage tree to locate and correct segmentation errors in analyzed movie frames. We show that this correction strategy is effective, resulting in improved cell tracking and consequently trustworthy deep colony lineage trees. Our image analysis approach has the unique capability to keep tracking cells even after clonal subpopulations merge in the movie. This enables the reconstruction of the complete Forest of Lineage Trees (FLT) representation of evolving multi-clonal bacterial communities. Moreover, the percentage of valid cell trajectories extracted from the image analysis almost doubles after segmentation correction. This plethora of trustworthy data extracted from a complex cell movie analysis enables single-cell analytics as a tool for addressing compelling questions for human health, such as understanding the role of single-cell stochasticity in antibiotics resistance without losing site of the inter-cellular interactions and microenvironment effects that may shape it.
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Deep convolutional neural networks (DCNNs) have revolutionized computer vision and are often advocated as good models of the human visual system. However, there are currently many shortcomings of DCNNs, which preclude them as a model of human vision. For example, in the case of adversarial attacks, where adding small amounts of noise to an image, including an object, can lead to strong misclassification of that object. But for humans, the noise is often invisible. If vulnerability to adversarial noise cannot be fixed, DCNNs cannot be taken as serious models of human vision. Many studies have tried to add features of the human visual system to DCNNs to make them robust against adversarial attacks. However, it is not fully clear whether human vision inspired components increase robustness because performance evaluations of these novel components in DCNNs are often inconclusive. We propose a set of criteria for proper evaluation and analyze different models according to these criteria. We finally sketch future efforts to make DCCNs one step closer to the model of human vision.
Preserving maximal information is one of principles of designing self-supervised learning methodologies. To reach this goal, contrastive learning adopts an implicit way which is contrasting image pairs. However, we believe it is not fully optimal to simply use the contrastive estimation for preservation. Moreover, it is necessary and complemental to introduce an explicit solution to preserve more information. From this perspective, we introduce Preservational Learning to reconstruct diverse image contexts in order to preserve more information in learned representations. Together with the contrastive loss, we present Preservational Contrastive Representation Learning (PCRL) for learning self-supervised medical representations. PCRL provides very competitive results under the pretraining-finetuning protocol, outperforming both self-supervised and supervised counterparts in 5 classification/segmentation tasks substantially.
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measures. We considered disease outbreaks in a setting with dense genomic sampling, and formulated stochastic epidemic models to investigate person-to-person transmission, based on observed genomic and epidemiological data. We constructed models in which the genetic distance between sampled genotypes depends on the epidemiological relationship between the hosts. A data augmented Markov chain Monte Carlo algorithm was used to sample over the transmission trees, providing a posterior probability for any given transmission route. We investigated the predictive performance of our methodology using simulated data, demonstrating high sensitivity and specificity, particularly for rapidly mutating pathogens with low transmissibility. We then analyzed data collected during an outbreak of methicillin-resistant Staphylococcus aureus in a hospital, identifying probable transmission routes and estimating epidemiological parameters. Our approach overcomes limitations of previous methods, providing a framework with the flexibility to allow for unobserved infection times, multiple independent introductions of the pathogen, and within-host genetic diversity, as well as allowing forward simulation.
New science and new technology need new materials and new concepts. In this respect, biological matter can play a primary role because it is a material with interesting and innovative features which has found several applications in technology, from highly sensitive sensors for medical treatments to devices for energy harvesting. Furthermore, most of its phenomenology remains unclear thus giving new hints for speculative investigations. In this letter, we explore the possibility to use a well-known photosensitive protein, the Reaction Center of Rhodobacter Sphaeroides, to build up an electrical pH sensor, i.e., a device able to change its resistance depending on the pH of the solution in which it crystalizes. By using a microscopic model successfully tested on analogue proteins, we investigate the electrical response of the Reaction Center single protein under different conditions of applied bias, showing the feasibility of the bio-rheostat hypothesis. As a matter of facts, the calculated resistance of this protein grows of about 100% when going from a pH = 10 to a pH = 6.5. Moreover, calculations of the conductance response in a wide range of applied bias point out interesting deviations from the linear regime. All findings are in qualitative agreement with the known role of pH in biochemical activities of Reaction Center and similar proteins, therefore supporting a proof-of-concept for the development of new electron devices based on biomaterials
Event-based cameras are vision devices that transmit only brightness changes with low latency and ultra-low power consumption. Such characteristics make event-based cameras attractive in the field of localization and object tracking in resource-constrained systems. Since the number of generated events in such cameras is huge, the selection and filtering of the incoming events are beneficial from both increasing the accuracy of the features and reducing the computational load. In this paper, we present an algorithm to detect asynchronous corners from a stream of events in real-time on embedded systems. The algorithm is called the Three Layer Filtering-Harris or TLF-Harris algorithm. The algorithm is based on an events filtering strategy whose purpose is 1) to increase the accuracy by deliberately eliminating some incoming events, i.e., noise, and 2) to improve the real-time performance of the system, i.e., preserving a constant throughput in terms of input events per second, by discarding unnecessary events with a limited accuracy loss. An approximation of the Harris algorithm, in turn, is used to exploit its high-quality detection capability with a low-complexity implementation to enable seamless real-time performance on embedded computing platforms. The proposed algorithm is capable of selecting the best corner candidate among neighbors and achieves an average execution time savings of 59 % compared with the conventional Harris score. Moreover, our approach outperforms the competing methods, such as eFAST, eHarris, and FA-Harris, in terms of real-time performance, and surpasses Arc* in terms of accuracy.
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