scholarly journals Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues.

2015 ◽  
Author(s):  
Patrick Smadbeck ◽  
Michael P.H. Stumpf
Keyword(s):  
Developmental Biology ◽  
Population Genetics ◽  
Large Scale ◽  
Cell Tracking ◽  
Temporal Dynamics ◽  
Growth Models ◽  
Tissue Growth ◽  
Lineage Tracing ◽  
Space And Time ◽  
Spatio Temporal

Development is a process that needs to tightly coordinated in both space and time. Cell tracking and lineage tracing have become important experimental techniques in developmental biology and allow us to map the fate of cells and their progeny in both space and time. A generic feature of developing (as well as homeostatic) tissues that these analyses have revealed is that relatively few cells give rise to the bulk of the cells in a tissue; the lineages of most cells come to an end fairly quickly. This has spurned the interest also of computational and theoretical biologists/physicists who have developed a range of modelling -- perhaps most notably are the agent-based modelling (ABM) --- approaches. These can become computationally prohibitively expensive but seem to capture some of the features observed in experiments. Here we develop a complementary perspective that allows us to understand the dynamics leading to the formation of a tissue (or colony of cells). Borrowing from the rich population genetics literature we develop genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We apply this approach to tissues that grow under confined conditions --- as would, for example, be appropriate for the neural crest --- and unbounded growth --- illustrative of the behaviour of 2D tumours or bacterial colonies. The classical coalescent model from population genetics is readily adapted to capture tissue genealogies for different models of tissue growth and development. We show that simple but universal scaling relationships allow us to establish relationships between the coalescent and different fractal growth models that have been extensively studied in many different contexts, including developmental biology. Using our genealogical perspective we are able to study the statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations.

scholarly journals Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues

2016 ◽  
Vol 13 (117) ◽  
pp. 20160112 ◽  
Author(s):  
Patrick Smadbeck ◽  
Michael P. H. Stumpf
Keyword(s):  
Developmental Biology ◽  
Large Scale ◽  
Cell Tracking ◽  
Temporal Dynamics ◽  
Growth Models ◽  
Lineage Tracing ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Spatio Temporal ◽  
Large Scale Simulations

Development is a process that needs to be tightly coordinated in both space and time. Cell tracking and lineage tracing have become important experimental techniques in developmental biology and allow us to map the fate of cells and their progeny. A generic feature of developing and homeostatic tissues that these analyses have revealed is that relatively few cells give rise to the bulk of the cells in a tissue; the lineages of most cells come to an end quickly. Computational and theoretical biologists/physicists have, in response, developed a range of modelling approaches, most notably agent-based modelling. These models seem to capture features observed in experiments, but can also become computationally expensive. Here, we develop complementary genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We show that with both bounded and unbounded growth simple, but universal scaling relationships allow us to connect coalescent theory with the fractal growth models extensively used in developmental biology. Using our genealogical perspective, it is possible to study bulk statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations.

scholarly journals Arctic avian predators synchronise their spring migration with the northern progression of snowmelt

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Teja Curk ◽  
Ivan Pokrovsky ◽  
Nicolas Lecomte ◽  
Tomas Aarvak ◽  
David F. Brinker ◽  
...  
Keyword(s):  
Large Scale ◽  
Temporal Dynamics ◽  
The Arctic ◽  
Migratory Species ◽  
Migration Patterns ◽  
Predator Species ◽  
Movement Data ◽  
Breeding Grounds ◽  
Spatio Temporal ◽  
Spring Snowmelt

Abstract Migratory species display a range of migration patterns between irruptive (facultative) to regular (obligate), as a response to different predictability of resources. In the Arctic, snow directly influences resource availability. The causes and consequences of different migration patterns of migratory species as a response to the snow conditions remains however unexplored. Birds migrating to the Arctic are expected to follow the spring snowmelt to optimise their arrival time and select for snow-free areas to maximise prey encounter en-route. Based on large-scale movement data, we compared the migration patterns of three top predator species of the tundra in relation to the spatio-temporal dynamics of snow cover. The snowy owl, an irruptive migrant, the rough-legged buzzard, with an intermediary migration pattern, and the peregrine falcon as a regular migrant, all followed, as expected, the spring snowmelt during their migrations. However, the owl stayed ahead, the buzzard stayed on, and the falcon stayed behind the spatio-temporal peak in snowmelt. Although none of the species avoided snow-covered areas, they presumably used snow presence as a cue to time their arrival at their breeding grounds. We show the importance of environmental cues for species with different migration patterns.

scholarly journals Early alterations of large-scale brain networks temporal dynamics in young children with autism

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Aurélie Bochet ◽  
Holger Franz Sperdin ◽  
Tonia Anahi Rihs ◽  
Nada Kojovic ◽  
Martina Franchini ◽  
...  
Keyword(s):  
Large Scale ◽  
Developmental Stages ◽  
Temporal Dynamics ◽  
Brain Networks ◽  
Autism Spectrum ◽  
Brain Network ◽  
Clustering Methods ◽  
Early Developmental Stages ◽  
Spatio Temporal ◽  
Early Developmental

AbstractAutism spectrum disorders (ASD) are associated with disruption of large-scale brain network. Recently, we found that directed functional connectivity alterations of social brain networks are a core component of atypical brain development at early developmental stages in ASD. Here, we investigated the spatio-temporal dynamics of whole-brain neuronal networks at a subsecond scale in 113 toddlers and preschoolers (66 with ASD) using an EEG microstate approach. We first determined the predominant microstates using established clustering methods. We identified five predominant microstate (labeled as microstate classes A–E) with significant differences in the temporal dynamics of microstate class B between the groups in terms of increased appearance and prolonged duration. Using Markov chains, we found differences in the dynamic syntax between several maps in toddlers and preschoolers with ASD compared to their TD peers. Finally, exploratory analysis of brain–behavioral relationships within the ASD group suggested that the temporal dynamics of some maps were related to conditions comorbid to ASD during early developmental stages.

scholarly journals Spatio-Temporal Dynamics of Feed Grain Demand of Dairy Cows in China

2020 ◽  
Vol 12 (2) ◽  
pp. 663 ◽  
Author(s):  
Chao Yang Dong ◽  
Bei Bei Ma ◽  
Chun Xia LU
Keyword(s):  
Dairy Cows ◽  
Dairy Cow ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Hot Spot ◽  
Market Environment ◽  
Relative Level ◽  
Resource Endowment ◽  
Spatio Temporal ◽  
Feeding Technology

As the income of urban and rural residents has increased in recent decades in China, dairy products have become an important part of the Chinese diet. Therefore, keeping up with the growing demand for feed grain for dairy cows is a critical issue of feed grain security. Utilizing traditional statistical and spatial statistical methods, this study analyzes the spatio-temporal dynamics of dairy cow feed grain (DCFG) demand on the provincial, regional, and national levels across China from 1990 to 2016. Additionally, this paper explores the impacts of various factors on the spatio-temporal dynamics of DCFG demand using the Geo-Detector method. The results demonstrate that: (1) the temporal dynamics of DCFG demand can be divided into three stages of slow growth, rapid growth, and high-level stability, and the relative level of DCFG demand in the whole animal husbandry tends to decline; (2) at the regional and national levels, the spatial concentration of high DCFG demand has intensified; in particular, North China was the region where the largest demand for DCFG was localized and was increasing at the highest rate; (3) based on the hot spot analysis of provincial DCFG demand, the high and low demand provinces of DCFG have sharp characteristic contrast from north to south China; (4) the spatio-temporal dynamics of DCFG demand in China were essentially co-affected by the four groups of factors (e.g., resource endowment, feeding scale, feeding technology, and market environment), of which resource endowment and feeding scale were the dominant factors. Therefore, in the future, dairy cow feeding in China should promote grain-saving feeding technology, improve the utilization of forage, expand large-scale feeding, and create a good market environment to ensure the reasonable development and sustainability of DCFG demand.

scholarly journals Spatio-temporal information in an artificial olfactory mucosa

2008 ◽  
Vol 464 (2092) ◽  
pp. 1057-1077 ◽  
Author(s):  
Manuel A Sánchez-Montañés ◽  
Julian W Gardner ◽  
Timothy C Pearce
Keyword(s):  
Analytical Model ◽  
Temporal Dynamics ◽  
Stationary Phases ◽  
Formal Analysis ◽  
Discrimination Performance ◽  
Olfactory Mucosa ◽  
Temporal Information ◽  
Information Measure ◽  
Space And Time ◽  
Spatio Temporal

Deploying chemosensor arrays in close proximity to stationary phases imposes stimulus-dependent spatio-temporal dynamics on their response and leads to improvements in complex odour discrimination. These spatio-temporal dynamics need to be taken into account explicitly when considering the detection performance of this new odour sensing technology, termed an artificial olfactory mucosa. For this purpose, we develop here a new measure of spatio-temporal information that combined with an analytical model of the artificial mucosa, chemosensor and noise dynamics completely characterizes the discrimination capability of the system. This spatio-temporal information measure allows us to quantify the contribution of both space and time to discrimination performance and may be used as part of optimization studies or calculated directly from an artificial mucosa output. Our formal analysis shows that exploiting both space and time in the mucosa response always outperforms the use of space alone and is further demonstrated by comparing the spatial versus spatio-temporal information content of mucosa experimental data. Together, the combination of the spatio-temporal information measure and the analytical model can be applied to extract the general principles of the artificial mucosa design as well as to optimize the physical and operating parameters that determine discrimination performance.

scholarly journals Large-scale spiking circuit simulation of spatio-temporal dynamics in superior colliculus

2014 ◽  
Vol 15 (S1) ◽  
Author(s):  
Richard E Veale ◽  
Tadashi Isa ◽  
Masatoshi Yoshida
Keyword(s):  
Superior Colliculus ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Circuit Simulation ◽  
Spatio Temporal

scholarly journals Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene

2016 ◽  
Vol 283 (1827) ◽  
pp. 20152152 ◽  
Author(s):  
Jennifer J. Crees ◽  
Chris Carbone ◽  
Robert S. Sommer ◽  
Norbert Benecke ◽  
Samuel T. Turvey
Keyword(s):  
Large Scale ◽  
Temporal Dynamics ◽  
Human Impacts ◽  
Biodiversity Loss ◽  
Mammal Species ◽  
The Holocene ◽  
Range Change ◽  
Spatio Temporal ◽  
Patterns And Processes ◽  
Species Specific

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18 700 mammalian zooarchaeological records for the last 11 700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of ‘static’ past baselines to inform current-day environmental management and restoration.

scholarly journals Spatio-temporal dynamics of dengue in Brazil: seasonal travelling waves and determinants of regional synchrony

2018 ◽  
Author(s):  
Mikhail Churakov ◽  
Christian J. Villabona-Arenas ◽  
Moritz U.G. Kraemer ◽  
Henrik Salje ◽  
Simon Cauchemez
Keyword(s):  
Large Scale ◽  
Temporal Dynamics ◽  
Mosquito Control ◽  
Human Mobility ◽  
Travelling Waves ◽  
Seasonal Pattern ◽  
Temporal Analysis ◽  
Vector Ecology ◽  
Spatio Temporal ◽  
Dengue Epidemics

AbstractDengue continues to be the most important vector-borne viral disease globally and in Brazil, where more than 1.4 million cases and over 500 deaths were reported in 2016. Mosquito control programmes and other interventions have not stopped the alarming trend of increasingly large epidemics in the past few years.Here, we analyzed monthly dengue cases reported in Brazil between 2001 and 2016 to better characterize the key drivers of dengue epidemics. Spatio-temporal analysis revealed recurring travelling waves of disease occurrence. Using wavelet methods, we characterised the average seasonal pattern of dengue in Brazil, which starts in the western states of Acre and Rondônia, then travels eastward to the coast before reaching the northeast of the country. Only two states in the north of Brazil (Roraima and Amapá) did not follow the countrywide pattern and had inconsistent timing of dengue epidemics throughout the study period.We also explored epidemic synchrony and timing of annual dengue cycles in Brazilian regions. Using gravity style models combined with climate factors, we showed that both human mobility and vector ecology contribute to spatial patterns of dengue occurrence.This study offers a characterization of the spatial dynamics of dengue in Brazil and its drivers, which could inform intervention strategies against dengue and other arboviruses.Author summaryIn this paper we studied the synchronization of dengue epidemics in Brazilian regions. We found that a typical dengue season in Brazil can be described as a wave travelling from the western part of the country towards the east, with the exception of the two most northern equatorial states that experienced inconsistent seasonality of dengue epidemics.We found that the spatial structure of dengue cases is driven by both climate and human mobility patterns. In particular, precipitation was the most important factor for the seasonality of dengue at finer spatial resolutions.Our findings increase our understanding of large scale dengue patterns and could be used to enhance national control programs against dengue and other arboviruses.

scholarly journals Video Question Answering via Hierarchical Spatio-Temporal Attention Networks

2017 ◽  
Author(s):  
Zhou Zhao ◽  
Qifan Yang ◽  
Deng Cai ◽  
Xiaofei He ◽  
Yueting Zhuang
Keyword(s):  
Visual Information ◽  
Large Scale ◽  
Question Answering ◽  
Temporal Dynamics ◽  
Temporal Attention ◽  
Attention Networks ◽  
Learning Framework ◽  
Spatio Temporal ◽  
The Given ◽  
Video Question Answering

Open-ended video question answering is a challenging problem in visual information retrieval, which automatically generates the natural language answer from the referenced video content according to the question. However, the existing visual question answering works only focus on the static image, which may be ineffectively applied to video question answering due to the temporal dynamics of video contents. In this paper, we consider the problem of open-ended video question answering from the viewpoint of spatio-temporal attentional encoder-decoder learning framework. We propose the hierarchical spatio-temporal attention network for learning the joint representation of the dynamic video contents according to the given question. We then develop the encoder-decoder learning method with reasoning recurrent neural networks for open-ended video question answering. We construct a large-scale video question answering dataset. The extensive experiments show the effectiveness of our method.

scholarly journals Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

2019 ◽  
Author(s):  
Sonja Blasche ◽  
Yongkyu Kim ◽  
Ruben Mars ◽  
Eleni Kafkia ◽  
Maria Maansson ◽  
...  
Keyword(s):  
Species Interactions ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Niche Partitioning ◽  
Metabolic Cooperation ◽  
Stable Coexistence ◽  
Milk Fermentation ◽  
Complex Microbial Community ◽  
Spatio Temporal ◽  
Natural Milk

SummaryMicrobial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.

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