scholarly journals Spatially resolved simulations of the spread of COVID-19 in three European countries

2021 ◽  
Vol 17 (7) ◽  
pp. e1009090
Author(s):  
Andrea Parisi ◽  
Samuel P. C. Brand ◽  
Joe Hilton ◽  
Rabia Aziza ◽  
Matt J. Keeling ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
European Countries ◽  
Potential Candidate ◽  
Middle Income ◽  
Spatially Resolved ◽  
Contact Patterns ◽  
Containment Measures ◽  
Spatio Temporal ◽  
Using Data ◽  
Temporal Spread

We explore the spatial and temporal spread of the novel SARS-CoV-2 virus under containment measures in three European countries based on fits to data of the early outbreak. Using data from Spain and Italy, we estimate an age dependent infection fatality ratio for SARS-CoV-2, as well as risks of hospitalization and intensive care admission. We use them in a model that simulates the dynamics of the virus using an age structured, spatially detailed agent based approach, that explicitly incorporates governmental interventions and changes in mobility and contact patterns occurred during the COVID-19 outbreak in each country. Our simulations reproduce several of the features of its spatio-temporal spread in the three countries studied. They show that containment measures combined with high density are responsible for the containment of cases within densely populated areas, and that spread to less densely populated areas occurred during the late stages of the first wave. The capability to reproduce observed features of the spatio-temporal dynamics of SARS-CoV-2 makes this model a potential candidate for forecasting the dynamics of SARS-CoV-2 in other settings, and we recommend its application in low and lower-middle income countries which remain understudied.

scholarly journals Spatially resolved simulations of the spread of COVID-19 in European countries

2020 ◽  
Author(s):  
Andrea Parisi ◽  
Samuel P. C. Brand ◽  
Joe Hilton ◽  
Rabia Aziza ◽  
Matt Keeling ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
European Countries ◽  
Potential Candidate ◽  
Spatially Resolved ◽  
Contact Patterns ◽  
Containment Measures ◽  
Spatio Temporal ◽  
Age Structured ◽  
Using Data ◽  
Temporal Spread

AbstractWe explore the spatial and temporal spread of the novel SARS-CoV-2 virus under containment measures in three European countries based on fits to data of the early outbreak. Using data from Spain and Italy, we estimate an age dependent infection fatality ratio for SARS-CoV-2, as well as risks of hospitalization and intensive care admission. We use them in a model that simulates the dynamics of the virus using an age structured, spatially detailed agent based approach, that explicitly incorporates governamental interventions, changes in mobility and contact patterns occurred during the COVID-19 outbreak in each country. Our simulations reproduce several of the features of its spatio-temporal spread in the three countries studied. They show that containment measures combined with high density are responsible for the containment of cases within densely populated areas, and that spread to less densely populated areas occurred during the late stages of the first wave. The capability to reproduce observed features of the spatio-temporal dynamics of SARS-CoV-2 makes this model a potential candidate for forecasting the dynamics of SARS-CoV-2 in other settings, and we recommend its application in low and lower-middle countries which remain understudied.

scholarly journals TMOD-15. IDENTIFYING THE SPATIAL AND TEMPORAL DYNAMICS OF GLIOBLASTOMA SUBPOPULATIONS WITHIN INDIVIDUAL PATIENTS

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi265-vi266
Author(s):  
Bethan Morris ◽  
Lee Curtin ◽  
Andrea Hawkins-Daarud ◽  
Bernard Bendok ◽  
Maciej Mrugala ◽  
...  
Keyword(s):  
Treatment Response ◽  
Temporal Dynamics ◽  
Dynamic Information ◽  
Treatment Regimes ◽  
Spatially Resolved ◽  
Spatial And Temporal Dynamics ◽  
Genetic Features ◽  
Spatio Temporal ◽  
Insight Into

Abstract Glioblastomas (GBMs) are known to be complex tumors comprising multiple subpopulations of genetically-distinct cancer cells; it is thought that this genetic variation is a major factor in the lack of observed survival benefit of treatment regimes that target one of these subpopulations. The field of radiogenomics seeks to study correlations between MRI patterns and genetic features of GBM tumors. Spatial radiogenomic maps produced using machine-learning (ML) methods that are trained against information from image-localized patient biopsies identify regions where particular cancer sub-populations are predicted to occur within a GBM, thus non-invasively characterizing the regional genetic variability of these tumors. These tumor subpopulations may also interact with one another, in ways which may be of a competitive or cooperative nature to varying degrees. It is important to ascertain the nature of these interactions, as they may have implications for treatment response to targeted therapies, and characterization of the spatio-temporal dynamics of these co-evolving sub-populations will shed light on why some therapies fail. Here we combine mathematical modeling techniques and spatially-resolved radiogenomic maps to study the nature of these interactions between molecularly-distinct GBM subpopulations. We model the interactions between cell populations using a partial differential equation based formalism. The model is parameterized using radiogenomic ML maps from which we infer the nature of interactions between subpopulations. Furthermore, using maps as inputs, the model turns static maps into dynamic information, thus providing insight into how these subpopulations composing the tumor change over time and the effect this has on observed treatment response for individual patients.

scholarly journals Large field of view-spatially resolved transcriptomics at nanoscale resolution

2021 ◽  
Author(s):  
Ao Chen ◽  
Sha Liao ◽  
Mengnan Cheng ◽  
Kailong Ma ◽  
Liang Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Temporal Dynamics ◽  
Capture Rate ◽  
Large Field ◽  
Major Advance ◽  
Widespread Application ◽  
Spatially Resolved ◽  
Sample Throughput ◽  
Spatio Temporal

ABSTRACTHigh-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. Here, we have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we applied Stereo-seq to the adult mouse brain and sagittal sections of E11.5 and E16.5 mouse embryos. Thanks to its unique features and amenability to additional modifications, Stereo-seq can pave the way for the systematic spatially resolved-omics characterization of tissues and organisms.

scholarly journals Assessing the effect of containment measures on the spatio-temporal dynamic of COVID-19 in Italy

2020 ◽  
Vol 101 (3) ◽  
pp. 1833-1846 ◽  
Author(s):  
Maria Michela Dickson ◽  
Giuseppe Espa ◽  
Diego Giuliani ◽  
Flavio Santi ◽  
Lucia Savadori
Keyword(s):  
Time Series ◽  
Temporal Dynamics ◽  
Multivariate Time Series ◽  
Model Specification ◽  
Northern Areas ◽  
Local Areas ◽  
Containment Measures ◽  
Italian Provinces ◽  
Spatio Temporal ◽  
The Impact

Abstract This paper aims at investigating empirically whether and to what extent the containment measures adopted in Italy had an impact in reducing the diffusion of the COVID-19 disease across provinces. For this purpose, we extend the multivariate time-series model for infection counts proposed in Paul and Held (Stat Med 30(10):118–1136, 2011) by augmenting the model specification with B-spline regressors in order to account for complex nonlinear spatio-temporal dynamics in the propagation of the disease. The results of the model estimated on the time series of the number of infections for the Italian provinces show that the containment measures, despite being globally effective in reducing both the spread of contagion and its self-sustaining dynamics, have had nonlinear impacts across provinces. The impact has been relatively stronger in the northern local areas, where the disease occurred earlier and with a greater incidence. This evidence may be explained by the shared popular belief that the contagion was not a close-to-home problem but rather restricted to a few distant northern areas, which, in turn, might have led individuals to adhere less strictly to containment measures and lockdown rules.

scholarly journals Infants’ gaze exhibits a fractal structure that varies by age and stimulus salience

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Isabella C. Stallworthy ◽  
Robin Sifre ◽  
Daniel Berry ◽  
Carolyn Lasch ◽  
Tim J. Smith ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Social Information ◽  
Fluctuation Analysis ◽  
Scale Invariant ◽  
Flexible System ◽  
Selective Visual Attention ◽  
Fractal Organization ◽  
Gaze Patterns ◽  
Spatio Temporal ◽  
Using Data

Abstract The development of selective visual attention is critical for effectively engaging with an ever-changing world. Its optimal deployment depends upon interactions between neural, motor, and sensory systems across multiple timescales and neurocognitive loci. Previous work illustrates the spatio-temporal dynamics of these processes in adults, but less is known about this emergent phenomenon early in life. Using data (n = 190; 421 visits) collected between 3 and 35 months of age, we examined the spatio-temporal complexity of young children’s gaze patterns as they viewed stimuli varying in semantic salience. Specifically, we used detrended fluctuation analysis (DFA) to quantify the extent to which infants’ gaze patterns exhibited scale invariant patterns of nested variability, an organizational feature thought to reflect self-organized and optimally flexible system dynamics that are not overly rigid or random. Results indicated that gaze patterns of even the youngest infants exhibited fractal organization that increased with age. Further, fractal organization was greater when children (a) viewed social stimuli compared to stimuli with degraded social information and (b) when they spontaneously gazed at faces. These findings suggest that selective attention is well-organized in infancy, particularly toward social information, and indicate noteworthy growth in these processes across the first years of life.

scholarly journals Spatio-temporal mRNA dynamics in the early zebrafish embryo

2020 ◽  
Author(s):  
Karoline Holler ◽  
Anika Neuschulz ◽  
Philipp Drewe-Boß ◽  
Janita Mintcheva ◽  
Bastiaan Spanjaard ◽  
...  
Keyword(s):  
Single Cell ◽  
Temporal Dynamics ◽  
Primordial Germ Cells ◽  
Sequence Motifs ◽  
Cell Stage ◽  
Systematic Analysis ◽  
Spatially Resolved ◽  
Rna Labeling ◽  
Vegetal Pole ◽  
Spatio Temporal

SummaryEarly stages of embryogenesis depend heavily on subcellular localization and transport of maternally deposited mRNA. However, systematic analysis of these processes is currently hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combined spatially-resolved transcriptomics and single-cell RNA labeling to study the spatio-temporal dynamics of the transcriptome during the first few hours of zebrafish development. We measured spatial localization of mRNA molecules with sub-single-cell resolution at the one-cell stage, which allowed us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we established a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enabled us to follow the fate of individual maternal transcripts until gastrulation. This approach revealed that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquired spatial transcriptomes of two xenopus species, and we compared evolutionary conservation of localized genes as well as enriched sequence motifs. In summary, we established sub-single-cell spatial transcriptomics and single-cell RNA labeling to reveal principles of mRNA localization in early vertebrate development.

scholarly journals Spatio-temporal dynamics of growth and death within spherical bacterial colonies

2021 ◽  
Author(s):  
Anton Welker ◽  
Marc Hennes ◽  
Niklas Bender ◽  
Tom Cronenberg ◽  
Gabriele Schneider ◽  
...  
Keyword(s):  
Velocity Field ◽  
Growth Inhibition ◽  
Growth Rates ◽  
Temporal Dynamics ◽  
Three Dimensional ◽  
Stringent Response ◽  
Cell Counting ◽  
Spatial Gradients ◽  
Spatially Resolved ◽  
Spatio Temporal

Bacterial growth within colonies and biofilms is heterogeneous. Local reduction of growth rates has been associated with tolerance against various antibiotics. However, spatial gradients of growth rates are poorly characterized in three-dimensional bacterial colonies. Here, we report two spatially resolved methods for measuring growth rates in bacterial colonies. As bacteria grow and divide, they generate a velocity field that is directly related to the growth rates. We derive profiles of growth rates from the velocity field and show that they are consistent with the profiles obtained by single cell counting. Using these methods, we reveal that even small colonies comprising a few thousand cells of the human pathogen Neisseria gonorrhoeae develop a steep gradient of growth rates within two generations. Furthermore, we show that stringent response decelerates growth inhibition at the colony centre. Based on our results, we suggest that aggregation-related growth inhibition can protect gonococci from external stresses even at early biofilm stages.

Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management

2020 ◽  
Vol 637 ◽  
pp. 117-140 ◽  
Author(s):  
DW McGowan ◽  
ED Goldstein ◽  
ML Arimitsu ◽  
AL Deary ◽  
O Ormseth ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Marine Ecosystem ◽  
Gulf Of Alaska ◽  
Data Series ◽  
Limited Information ◽  
Important Species ◽  
Multiple Data ◽  
Spatial And Temporal Dynamics ◽  
Spawning Areas ◽  
Spatio Temporal

Pacific capelin Mallotus catervarius are planktivorous small pelagic fish that serve an intermediate trophic role in marine food webs. Due to the lack of a directed fishery or monitoring of capelin in the Northeast Pacific, limited information is available on their distribution and abundance, and how spatio-temporal fluctuations in capelin density affect their availability as prey. To provide information on life history, spatial patterns, and population dynamics of capelin in the Gulf of Alaska (GOA), we modeled distributions of spawning habitat and larval dispersal, and synthesized spatially indexed data from multiple independent sources from 1996 to 2016. Potential capelin spawning areas were broadly distributed across the GOA. Models of larval drift show the GOA’s advective circulation patterns disperse capelin larvae over the continental shelf and upper slope, indicating potential connections between spawning areas and observed offshore distributions that are influenced by the location and timing of spawning. Spatial overlap in composite distributions of larval and age-1+ fish was used to identify core areas where capelin consistently occur and concentrate. Capelin primarily occupy shelf waters near the Kodiak Archipelago, and are patchily distributed across the GOA shelf and inshore waters. Interannual variations in abundance along with spatio-temporal differences in density indicate that the availability of capelin to predators and monitoring surveys is highly variable in the GOA. We demonstrate that the limitations of individual data series can be compensated for by integrating multiple data sources to monitor fluctuations in distributions and abundance trends of an ecologically important species across a large marine ecosystem.

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