The long and the short of it: Mechanisms of synchronous and compensatory dynamics across temporal scales.
Ontology highlight
ABSTRACT:
SUBMITTER: Shoemaker LG
PROVIDER: S-EPMC9285558 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease, with the transcontinental spread of various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic basis for the emergence of C. difficile as a human pathogen is unclear. Whole genome sequencing was used to analyze genetic variation and virulence of a diverse collection of thirty C. difficile isolates, to determine both macro and microevolution of the species. Horizontal gene transfer and large-scale recombination of core genes has shaped the C. difficile genome over both short and long time scales. Phylogenetic analysis demonstrates C. difficile is a genetically diverse species, which has evolved within the last 1.1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages.
| S-EPMC2867753 | biostudies-literature
Project description:We describe advances in the understanding of brain dynamics that are important for understanding the operation of the cerebral cortex in health and disease. Peaks in the resting state fMRI BOLD signal in many different brain areas can become synchronized. In data from 1,017 participants from the Human Connectome Project, we show that early visual and connected areas have the highest probability of synchronized peaks. We show that these cortical areas also have low temporal variability of their functional connectivity. We show that there is an approximately reciprocal relation between the probability that a brain region will be involved in synchronized peaks and the temporal variability of the connectivity of a brain region. We show that a high probability of synchronized peaks and a low temporal variability of the connectivity of cortical areas are related to high mean functional connectivity, and provide an account of how these dynamics with some of the properties of avalanches arise. These discoveries help to advance our understanding of cortical operation in health, and in some mental disorders including schizophrenia.
| S-EPMC8127146 | biostudies-literature
Project description:The correlation function for the exit of poloxamer copolymers from equilibrated micelles is found to show up to four regimes depending on the chain flexibility: an initial fast reorganization, a logarithmic intermediate regime, followed by an exponential intermediate regime, and a final exponential decay. The logarithmic intermediate regime has been observed experimentally and attributed to the polydispersity of the polymer samples. However, we present dynamic single-chain mean-field theory simulations with chains of variable flexibility which show the same logarithmic relaxation but with strictly monodisperse systems. In agreement with our previous studies, we propose that this logarithmic response arises from a degeneracy of energy states of the hydrophobic block in the micelle core. For this to occur, a sufficiently large number of degenerate conformational states are required, which depend on the polymer flexibility and therefore should not be present for rigid polymers. Experimental results for monodisperse polymeric samples claiming the absence of such a logarithmic response may also lack a sufficient number of hydrophobic blocks for the required number of configurational states for this type of response to be seen. The insight gained from analyzing the simulation results allows us to propose a modified Eyring equation capable of reproducing the observed dynamic behavior. On scaling experimental results from different sources and systems according to this equation, we find a unique master curve showing a universal nature of the intermediate regimes: the logarithmic regime together with the secondary exponential decay. The terminal exponential regime at long times proposed by the standard Halperin and Alexander model is beyond the range of the data analyzed in this article. The universality observed suggests an entropic origin of the short-time dynamic response of this class of systems rather than the polydispersity.
| S-EPMC8842487 | biostudies-literature
Project description:Infectious diseases remain a formidable challenge to human health, and understanding pathogen evolution is crucial to designing effective therapeutics and control strategies. Here, we review important evolutionary aspects of HIV infection, highlighting the concept of selection at multiple spatial and temporal scales. At the smallest scale, a single cell may be infected by multiple virions competing for intracellular resources. Recombination and phenotypic mixing introduce novel evolutionary dynamics. As the virus spreads between cells in an infected individual, it continually evolves to circumvent the immune system. We discuss evolutionary mechanisms of HIV pathogenesis and progression to AIDS. Viral spread throughout the human population can lead to changes in virulence and the transmission of immune-evading variation. HIV emerged as a human pathogen due to selection occurring between different species, adapting from related viruses of primates. HIV also evolves resistance to antiretroviral drugs within a single infected host, and we explore the possibility for the spread of these strains between hosts, leading to a drug-resistant epidemic. We investigate the role of latency, drug-protected compartments, and direct cell-to-cell transmission on viral evolution. The introduction of an HIV vaccine may select for viral variants that escape vaccine control, both within an individual and throughout the population. Due to the strong selective pressure exerted by HIV-induced morbidity and mortality in many parts of the world, the human population itself may be co-evolving in response to the HIV pandemic. Throughout the paper, we focus on trade-offs between costs and benefits that constrain viral evolution and accentuate how selection pressures differ at different levels of selection.
| S-EPMC7080006 | biostudies-literature
Project description:Neural synchronization is believed to be critical for many brain functions. It frequently exhibits temporal variability, but it is not known if this variability has a specific temporal patterning. This study explores these synchronization/desynchronization patterns. We employ recently developed techniques to analyze the fine temporal structure of phase-locking to study the temporal patterning of synchrony of the human brain rhythms. We study neural oscillations recorded by electroencephalograms in α and β frequency bands in healthy human subjects at rest and during the execution of a task. While the phase-locking strength depends on many factors, dynamics of synchrony has a very specific temporal pattern: synchronous states are interrupted by frequent, but short desynchronization episodes. The probability for a desynchronization episode to occur decreased with its duration. The transition matrix between synchronized and desynchronized states has eigenvalues close to 0 and 1 where eigenvalue 1 has multiplicity 1, and therefore if the stationary distribution between these states is perturbed, the system converges back to the stationary distribution very fast. The qualitative similarity of this patterning across different subjects, brain states and electrode locations suggests that this may be a general type of dynamics for the brain. Earlier studies indicate that not all oscillatory networks have this kind of patterning of synchronization/desynchronization dynamics. Thus, the observed prevalence of short (but potentially frequent) desynchronization events (length of one cycle of oscillations) may have important functional implications for the brain. Numerous short desynchronizations (as opposed to infrequent, but long desynchronizations) may allow for a quick and efficient formation and break-up of functionally significant neuronal assemblies.
| S-EPMC3606233 | biostudies-other
Project description:Electroencephalogram (EEG) undergoes complex temporal and spectral changes during voluntary movement intention. Characterization of such changes has focused mostly on narrowband spectral processes such as Event-Related Desynchronization (ERD) in the sensorimotor rhythms because EEG is mostly considered as emerging from oscillations of the neuronal populations. However, the changes in the temporal dynamics, especially in the broadband arrhythmic EEG have not been investigated for movement intention detection. The Long-Range Temporal Correlations (LRTC) are ubiquitously present in several neuronal processes, typically requiring longer timescales to detect. In this paper, we study the ongoing changes in the dynamics of long- as well as short-range temporal dependencies in the single trial broadband EEG during movement intention. We obtained LRTC in 2 s windows of broadband EEG and modeled it using the Autoregressive Fractionally Integrated Moving Average (ARFIMA) model which allowed simultaneous modeling of short- and long-range temporal correlations. There were significant (p < 0.05) changes in both broadband long- and short-range temporal correlations during movement intention and execution. We discovered that the broadband LRTC and narrowband ERD are complementary processes providing distinct information about movement because eliminating LRTC from the signal did not affect the ERD and conversely, eliminating ERD from the signal did not affect LRTC. Exploring the possibility of applications in Brain Computer Interfaces (BCI), we used hybrid features with combinations of LRTC, ARFIMA, and ERD to detect movement intention. A significantly higher (p < 0.05) classification accuracy of 88.3 ± 4.2% was obtained using the combination of ARFIMA and ERD features together, which also predicted the earliest movement at 1 s before its onset. The ongoing changes in the long- and short-range temporal correlations in broadband EEG contribute to effectively capturing the motor command generation and can be used to detect movement successfully. These temporal dependencies provide different and additional information about the movement.
| S-EPMC6856010 | biostudies-literature
Project description:Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics.
| S-EPMC5006416 | biostudies-literature
Project description:Beta cells within the pancreatic islets of Langerhans respond to stimulation with coherent oscillations of membrane potential and intracellular calcium concentration that presumably drive the pulsatile exocytosis of insulin. Their rhythmic activity is multimodal, resulting from networked feedback interactions of various oscillatory subsystems, such as the glycolytic, mitochondrial, and electrical/calcium components. How these oscillatory modules interact and affect the collective cellular activity, which is a prerequisite for proper hormone release, is incompletely understood. In the present work, we combined advanced confocal Ca2+ imaging in fresh mouse pancreas tissue slices with time series analysis and network science approaches to unveil the glucose-dependent characteristics of different oscillatory components on both the intra- and inter-cellular level. Our results reveal an interrelationship between the metabolically driven low-frequency component and the electrically driven high-frequency component, with the latter exhibiting the highest bursting rates around the peaks of the slow component and the lowest around the nadirs. Moreover, the activity, as well as the average synchronicity of the fast component, considerably increased with increasing stimulatory glucose concentration, whereas the stimulation level did not affect any of these parameters in the slow component domain. Remarkably, in both dynamical components, the average correlation decreased similarly with intercellular distance, which implies that intercellular communication affects the synchronicity of both types of oscillations. To explore the intra-islet synchronization patterns in more detail, we constructed functional connectivity maps. The subsequent comparison of network characteristics of different oscillatory components showed more locally clustered and segregated networks of fast oscillatory activity, while the slow oscillations were more global, resulting in several long-range connections and a more cohesive structure. Besides the structural differences, we found a relatively weak relationship between the fast and slow network layer, which suggests that different synchronization mechanisms shape the collective cellular activity in islets, a finding which has to be kept in mind in future studies employing different oscillations for constructing networks.
| S-EPMC8021717 | biostudies-literature
Project description:Our ability to identify an object is often impaired by the presence of preceding and/or succeeding task-irrelevant items. Understanding this temporal interference is critical for any theoretical account of interference across time and for minimizing its detrimental effects. Therefore, we used the same sequences of 3 orientation items, orientation estimation task, and computational models, to examine temporal interference over both short (<150 ms; visual masking) and long (175-475 ms; temporal crowding) intervals. We further examined how inter-item similarity modifies these different instances of temporal interference. Qualitatively different results emerged for interference of different scales. Interference over long intervals mainly degraded the precision of the target encoding while interference over short intervals mainly affected the signal-to-noise ratio. Although both interference instances modulated substitution errors (reporting a wrong item) and were alleviated with dissimilar items, their characteristics were markedly disparate. These findings suggest that different mechanisms mediate temporal interference of different scales.
| S-EPMC11305178 | biostudies-literature
Project description:This paper concerns the changes occurred over both decennial and millennial spans of time in a sponge assemblage present in coralligenous biogenic build-ups growing at 15 m depth in the Ligurian Sea (Western Mediterranean). The comparison of the sponge diversity after a time interval of about 40 years (1973-2014) showed a significant reduction in species richness (about 45%). This decrease affected mainly the massive/erect sponges, and in particular the subclass Keratosa, with a species loss of 67%, while the encrusting and cavity dwelling sponges lost the 36% and 50%, respectively. The boring sponges lost only one species (25%). This changing pattern suggested that the inner habitat of the bioconstructions was less affected by the variations of the environmental conditions or by the human pressures which, on the contrary, strongly affected the species living on the surface of the biogenic build-ups. Five cores extracted from the bioherms, dating back to 3500 YBP, allowed to analyse the siliceous spicules remained trapped in them in order to obtain taxonomic information. Changes at generic level in diversity and abundance were observed at 500/250-years intervals, ranging between 19 and 33 genera. The number of genera showed a sharp decrease since 3500-3000 to 3000-2500 YBP. After this period, the genera regularly increased until 1500-1250 YBP, from when they progressively decreased until 1000-500 YBP. Tentatively, these changes could be related to the different climatic periods that followed one another in the Mediterranean area within the considered time span. The recent depletion in sponge richness recorded in the Ligurian coralligenous can be considered relevant. In fact, the analysis of the spicules indicated that the sponges living in these coralligenous habitats remained enough stable during 3000 years, but could have lost a significant part of their biodiversity in the last decades, coinciding with a series of warming episodes.
| S-EPMC5439943 | biostudies-literature