A5068242139- Neural Networks and Applications
- Protein Structure and Dynamics
- Neural dynamics and brain function
- SARS-CoV-2 and COVID-19 Research
- Gene Regulatory Network Analysis
- Logic, Reasoning, and Knowledge
- Constraint Satisfaction and Optimization
- Influenza Virus Research Studies
- Computational Drug Discovery Methods
- Multi-Agent Systems and Negotiation
- Enzyme Structure and Function
- Evolutionary Algorithms and Applications
- Neural Networks and Reservoir Computing
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA and protein synthesis mechanisms
- Opinion Dynamics and Social Influence
- Functional Brain Connectivity Studies
- Bacterial Genetics and Biotechnology
- Advanced Fluorescence Microscopy Techniques
- Cell Image Analysis Techniques
- Random lasers and scattering media
- Axon Guidance and Neuronal Signaling
- Advanced Memory and Neural Computing
- Genetics, Aging, and Longevity in Model Organisms
- Circadian rhythm and melatonin
Istituto di Nanotecnologia
2022-2024
National Research Council
2022-2024
Italian Institute of Technology
2017-2024
Sapienza University of Rome
2021-2022
University of California System
2013
University of California, Irvine
2010-2012
University of Perugia
2008-2010
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions proteins surfaces. This innovative general procedure, based on representation molecular iso-electron density surface in terms 2D Zernike polynomials, allows rapid quantitative assessment geometrical shape interacting proteins, that was unfeasible with previous methods. first tested large dataset known protein complexes obtaining an overall area under ROC...
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions protein surfaces. This innovative general procedure, based on representation molecular iso-electron density surface in terms 2D Zernike polynomials, allows rapid quantitative assessment geometrical shape interacting proteins, that was unfeasible with previous methods. first tested large dataset known complexes obtaining an overall area under ROC curve 0.76...
Microglia reactivity entails a large-scale remodeling of cellular geometry, but the behavior microtubule cytoskeleton during these changes remains unexplored. Here we show that activated microglia provide an example reorganization from non-centrosomal array parallel and stable microtubules to radial more dynamic microtubules. While in homeostatic state, nucleate at Golgi outposts, activating signaling induces recruitment nucleating material nearby centrosome, process inhibited by...
Among the many aspects that characterize COVID-19 pandemic, two seem particularly challenging to understand: (i) great geographical differences in degree of virus contagiousness and lethality which were found different phases epidemic progression, (ii) potential role infected people's blood type both infectivity progression disease. A recent hypothesis could shed some light on aspects. Specifically, it has been proposed subject-to-subject transfer SARS-CoV-2 conserves its capsid...
Understanding the mechanisms driving bio-molecules binding and determining resulting complexes' stability is fundamental for prediction of regions, which starting point drug-ability design. Characteristics like preferentially hydrophobic composition interfaces, role van der Waals interactions, consequent shape complementarity between interacting molecular surfaces are well established. However, no consensus has yet been reached on electrostatic. Here, we perform extensive analyses a large...
Colorectal cancer (CRC) is a leading cause of cancer-related mortality and chemoresistance major medical issue. The epithelial-to-mesenchymal transition (EMT) the primary step in emergence invasive phenotype Hedgehog-GLI (HH-GLI) NOTCH signaling pathways are associated with poor prognosis EMT CRC. CRC cell lines harboring KRAS or BRAF mutations, grown as monolayers organoids, were treated chemotherapeutic agent 5-Fluorouracil (5-FU) alone combined HH-GLI pathway inhibitors GANT61 DAPT,...
Abstract As the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic continues to spread, several variants of virus, with mutations distributed all over viral genome, are emerging. While most present having little no effects at phenotypic level, some these spreading a rate that suggests they may selective advantage. In particular, rapidly specific on spike protein. These observations call for an urgent need characterize variants’ phenotype features like contagiousness and...
Blind-structured illumination microscopy (blind-SIM) enhances the optical resolution without requirement of nonlinear effects or pre-defined patterns. It is thus advantageous in experimental conditions where toxicity biological fluctuations are an issue. In this work, we introduce a custom convolutional neural network architecture for blind-SIM: BS-CNN. We show that BS-CNN outperforms other blind-SIM deconvolution algorithms providing improvement 2.17 together with very high Fidelity...
It is not well understood why severe acute respiratory syndrome (SARS)-CoV-2 spreads much faster than other β-coronaviruses such as SARS-CoV and Middle East (MERS)-CoV. In a previous publication, we predicted the binding of N-terminal domain (NTD) SARS-CoV-2 spike to sialic acids (SAs). Here, experimentally validate this interaction present simulations that reveal second possible between SAs protein via site located in receptor-binding (RBD). The predictions from molecular-dynamics...
Abstract Heterogeneity in the size distribution of cancer cell populations is linked to drug resistance and invasiveness. However, understanding how such heterogeneity arises still damped by difficulties monitoring proliferation at typical timescales mammalian cells. Here, we show infer growth regime division strategy leukemia using live fluorescence labeling flow cytometry combination with an analytical model where rates depend on powers size. We found that dynamics Jurkat T-cells...
Asymmetric partition of fate determinants during cell division is a hallmark differentiation. Recent works suggested that such mechanism hijacked by cancer cells to increase both their phenotypic heterogeneity and plasticity in turn fitness. To quantify fluctuations the partitioning cellular elements, imaging-based approaches are used, whose accuracy limited difficulty detecting divisions. Our work addresses this gap proposing general method based on high-throughput flow cytometry...
Asymmetric partition of fate determinants during cell division is a hallmark differentiation. Recent works suggested that such mechanism hijacked by cancer cells to increase both their phenotypic heterogeneity and plasticity in turn fitness. To quantify fluctuations the partitioning cellular elements, imaging-based approaches are used, whose accuracy limited difficulty detecting divisions. Our work addresses this gap proposing general method based on high-throughput flow cytometry...
We present a method for efficiently and effectively assessing whether where two proteins can interact with each other to form complex. This is still largely an open problem, even those relatively few cases the 3D structure of both known. In fact, if much information about interaction encoded in chemical geometric features structures, set possible contact patches their relative orientations are too large be computationally affordable reasonable time, thus preventing compilation reliable...
Methods for time series prediction and classification of gene regulatory networks (GRNs) from expression data have been treated separately so far. The recent emergence attention-based recurrent neural network (RNN) models boosted the interpretability RNN parameters, making them appealing understanding interactions. In this work, we generated synthetic a range archetypal GRNs relied on dual attention to predict temporal dynamics. We show that is extremely accurate with different...
Recording large amounts of users’ sessions performed through 3D applications may provide crucial insights into interaction patterns. Such data can be captured from interactive experiences in public exhibits, remote motion tracking equipment, immersive XR devices, lab installations or online web applications. Immersive analytics (IA) deals with the benefits and challenges using environments for analysis related design solutions to improve quality efficiency process. Today, technologies allow...
We study with numerical simulation the possible limit behaviors of synchronous discrete-time deterministic recurrent neural networks composed N binary neurons as a function network's level dilution and asymmetry. The network measures fraction neuron couples that are connected, asymmetry to what extent underlying connectivity matrix is asymmetric. For each given network, we dynamical evolution all different initial conditions, thus characterizing full landscape without imposing any learning...
In a neural network, an autapse is particular kind of synapse that links neuron onto itself. Autapses are almost always not allowed neither in artificial nor biological networks. Moreover, redundant or similar stored states tend to interact destructively. This paper shows how autapses together with stable state redundancy can improve the storage capacity recurrent network. Recent research how, N-node Hopfield network autapses, number patterns (P) limited well known bound 0.14 N , as it for...
Disorder is a pervasive characteristic of natural systems, offering wealth non-repeating patterns. In this study, we present novel storage method that harnesses naturally-occurring random structures to store an arbitrary pattern in memory device. This method, the Stochastic Emergent Storage (SES), builds upon concept emergent archetypes, where training set imperfect examples (prototypes) employed instantiate archetype Hopfield-like network through processes. We demonstrate non-Hebbian...
The ability of a cancer cell population to achieve heterogeneity in their phenotype distributions offers advantages tumor invasiveness and drug resistance. Studying the mechanisms behind such observed mammalian cells presents challenges due for instance prolonged proliferation times compared widely studied unicellular organisms like bacteria yeast. Here, we response leukemia populations serum starvation via protocol, recently developed, that makes use live fluorescence flow cytometry...
The continuous emergence of novel variants represents one the major problems in dealing with SARS-CoV-2 virus. Indeed, also due to its prolonged circulation, more than ten concern emerged, each time rapidly overgrowing current viral version improved spreading features. As, up now, all carry at least mutation on spike Receptor Binding Domain, stability binding between protein and human ACE2 receptor seems molecular determinants behind potential. In this framework, a better understanding...
Experimental evidence shows that there is a feedback between cell shape and motion. How this impacts the collective behavior of dense monolayers remains an open question. We investigate effect tends to align crawling direction with elongation in biological tissue model. find alignment interaction promotes nematic patterns fluid phase eventually undergo nonequilibrium transition into quasihexagonal solid. Meanwhile, highly asymmetric cells do not liquid-to-solid for any value coupling. In...
Abstract Asymmetric inheritance of organelles and compounds between daughter cells is considered a hallmark for differentiation rejuvenation in stem-like cancer cells, as much mechanism enhancing resistance bacteria populations. In non-differentiating homogeneous asymmetric division still poorly investigated. Here, we present method based on the binomial partitioning process that allows measurement organelle with multiple live cell markers without genetically mutating cells. We demonstrate...