Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.

Imaging Mass Cytometry (IMC) combines laser ablation and mass spectrometry to quantitate metal-conjugated primary antibodies incubated in intact tumor tissue slides. This strategy allows spatially-resolved multiplexing of dozens of simultaneous protein targets with 1µm resolution. Each slide is a spatial assay consisting of high-dimensional multivariate observations (m-dimensional feature space) collected at different spatial positions and capturing data from a single biological sample or even representative spots from multiple samples when using tissue microarrays. Often, each of these spatial assays could be characterized by several regions of interest (ROIs). To extract meaningful information from the multi-dimensional observations recorded at different ROIs across different assays, we propose to analyze such datasets using a two-step graph-based approach. We first construct for each ROI a graph representing the interactions between the m covariates and compute an m dimensional vector characterizing the steady state distribution among features. We then use all these m-dimensional vectors to construct a graph between the ROIs from all assays. This second graph is subjected to a nonlinear dimension reduction analysis, retrieving the intrinsic geometric representation of the ROIs. Such a representation provides the foundation for efficient and accurate organization of the different ROIs that correlates with their phenotypes. Theoretically, we show that when the ROIs have a particular bi-modal distribution, the new representation gives rise to a better distinction between the two modalities compared to the maximum a posteriori (MAP) estimator. We applied our method to predict the sensitivity to PD-1 axis blockers treatment of lung cancer subjects based on IMC data, achieving 97.3% average accuracy on two IMC datasets. This serves as empirical evidence that the graph of graphs approach enables us to integrate multiple ROIs and the intra-relationships between the features at each ROI, giving rise to an informative representation that is strongly associated with the phenotypic state of the entire image.

Layer- and Cell-Specific Recruitment Dynamics during Epileptic Seizures In Vivo.

OBJECTIVE: To investigate the network dynamics mechanisms underlying differential initiation of epileptic interictal spikes and seizures. METHODS: We performed combined in vivo 2-photon calcium imaging from different targeted neuronal subpopulations and extracellular electrophysiological recordings during 4-aminopyridine-induced neocortical spikes and seizures. RESULTS: Both spikes and seizures were associated with intense synchronized activation of excitatory layer 2/3 pyramidal neurons (PNs) and to a lesser degree layer 4 neurons, as well as inhibitory parvalbumin-expressing interneurons (INs). In sharp contrast, layer 5 PNs and somatostatin-expressing INs were gradually and asynchronously recruited into the ictal activity during the course of seizures. Within layer 2/3, the main difference between onset of spikes and seizures lay in the relative recruitment dynamics of excitatory PNs compared to parvalbumin- and somatostatin-expressing inhibitory INs. Whereas spikes exhibited balanced recruitment of PNs and parvalbumin-expressing INs, during seizures IN responses were reduced and less synchronized than in layer 2/3 PNs. Similar imbalance was not observed in layers 4 or 5 of the neocortex. Machine learning-based algorithms we developed were able to distinguish spikes from seizures based solely on activation dynamics of layer 2/3 PNs at discharge onset. INTERPRETATION: During onset of seizures, the recruitment dynamics markedly differed between neuronal subpopulations, with rapid synchronous recruitment of layer 2/3 PNs, layer 4 neurons, and parvalbumin-expressing INs and gradual asynchronous recruitment of layer 5 PNs and somatostatin-expressing INs. Seizures initiated in layer 2/3 due to a dynamic mismatch between local PNs and inhibitory INs, and only later spread to layer 5 by gradually and asynchronously recruiting PNs in this layer. ANN NEUROL 2020;87:97-115.

Direction Modulation of Muscle Synergies in a Hand-Reaching Task.

Functional tasks of the upper extremity can be executed by a variety of muscular patterns, independent of the direction, speed and load of the task. This large number of degrees of freedom imposes a significant control burden on the CNS. Previous studies suggested that the human cortex synchronizes a discrete number of neural functional units within the brainstem and spinal cord, i.e. muscle synergies, by linearly combining them to execute a great repertoire of movements. Further exploring this control mechanism, we aim to study whether a single set of muscle synergies might be generalized to express movements in different directions. This was implemented by using a modified version of the non-negative matrix factorization algorithm on EMG data sets of the upper extremity of healthy people. Our twelve participants executed hand-reaching movements in multiple directions. Muscle synergies that were extracted from movements to the center of the reaching space could be generalized to synergies for other movement directions. This finding was also supported by the application of a weighted correlation matrix, the similarity index and the results of the K-means cluster analysis. This might reinforce the notion that the CNS flexibly combines a single set of small number of synergies in different amplitudes to modulate movement for different directions.