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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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Katile A, Sagara I, Cissoko M, Bationo CS, Dolo M, Thera I, Traore S, Kone M, Dembele P, Bocoum D, Sidibe I, Simaga I, Sissoko MS, Landier J, Gaudart J. Spatio-Temporal Variability of Malaria Incidence in the Health District of Kati, Mali, 2015-2019. Int J Environ Res Public Health 2022; 19:14361. [PMID: 36361240 PMCID: PMC9656757 DOI: 10.3390/ijerph192114361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Despite the implementation of control strategies at the national scale, the malaria burden remains high in Mali, with more than 2.8 million cases reported in 2019. In this context, a new approach is needed, which accounts for the spatio-temporal variability of malaria transmission at the local scale. This study aimed to describe the spatio-temporal variability of malaria incidence and the associated meteorological and environmental factors in the health district of Kati, Mali. METHODS Daily malaria cases were collected from the consultation records of the 35 health areas of Kati's health district, for the period 2015-2019. Data on rainfall, relative humidity, temperature, wind speed, the normalized difference vegetation index, air pressure, and land use-land cover were extracted from open-access remote sensing sources, while data on the Niger River's height and flow were obtained from the National Department of Hydraulics. To reduce the dimension and account for collinearity, strongly correlated meteorological and environmental variables were combined into synthetic indicators (SI), using a principal component analysis. A generalized additive model was built to determine the lag and the relationship between the main SIs and malaria incidence. The transmission periods were determined using a change-point analysis. High-risk clusters (hotspots) were detected using the SatScan method and were ranked according to risk level, using a classification and regression tree analysis. RESULTS The peak of the malaria incidence generally occurred in October. Peak incidence decreased from 60 cases per 1000 person-weeks in 2015, to 27 cases per 1000 person-weeks in 2019. The relationship between the first SI (river flow and height, relative humidity, and rainfall) and malaria incidence was positive and almost linear. A non-linear relationship was found between the second SI (air pressure and temperature) and malaria incidence. Two transmission periods were determined per year: a low transmission period from January to July-corresponding to a persisting transmission during the dry season-and a high transmission period from July to December. The spatial distribution of malaria hotspots varied according to the transmission period. DISCUSSION Our study confirmed the important variability of malaria incidence and found malaria transmission to be associated with several meteorological and environmental factors in the Kati district. The persistence of malaria during the dry season and the spatio-temporal variability of malaria hotspots reinforce the need for innovative and targeted strategies.
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Affiliation(s)
- Abdoulaye Katile
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Issaka Sagara
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Mady Cissoko
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Cedric Stephane Bationo
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
| | - Mathias Dolo
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Ismaila Thera
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Siriman Traore
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Mamady Kone
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Pascal Dembele
- Programme National de Lutte Contre le Paludisme, Bamako BP 233, Mali
| | - Djoouro Bocoum
- Direction Nationale de L’Hydraulique, Bamako BP 66, Mali
| | | | - Ismael Simaga
- Centre de Santé de Référence du District Sanitaire de Kati, Région de Koulikoro, Kati BP 594, Mali
| | - Mahamadou Soumana Sissoko
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
| | - Jordi Landier
- INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
| | - Jean Gaudart
- Malaria Research and Training Center (MRTC), FMOS-FAPH, Mali-NIAID-ICER, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 423, Mali
- APHM, INSERM, IRD, SESSTIM, ISSPAM, UMR1252, Hop Timone, BioSTIC, Biostatistic & ICT, Faculty of Medicine, Aix Marseille University, 13005 Marseille, France
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Saha P, Mukhopadhyay S. Unravelled multilevel transformation networks for predicting sparsely observed spatio-temporal dynamics. Philos Trans A Math Phys Eng Sci 2022; 380:20210198. [PMID: 35719071 DOI: 10.1098/rsta.2021.0198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/10/2022] [Indexed: 06/15/2023]
Abstract
In this paper, we address the problem of predicting complex, nonlinear spatio-temporal dynamics when available data are recorded at irregularly spaced sparse spatial locations. Most of the existing deep learning models for modelling spatio-temporal dynamics are either designed for data in a regular grid or struggle to uncover the spatial relations from sparse and irregularly spaced data sites. We propose a deep learning model that learns to predict unknown spatio-temporal dynamics using data from sparsely-distributed data sites. We base our approach on the radial basis function (RBF) collocation method which is often used for meshfree solution of partial differential equations. The RBF framework allows us to unravel the observed spatio-temporal function and learn the spatial interactions among data sites on the RBF-space. The learned spatial features are then used to compose multilevel transformations of the raw observations and predict its evolution in future time steps. We demonstrate the advantage of our approach using both synthetic and real-world climate data. This article is part of the theme issue 'Data-driven prediction in dynamical systems'.
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Affiliation(s)
- Priyabrata Saha
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Saibal Mukhopadhyay
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Vohryzek J, Cabral J, Vuust P, Deco G, Kringelbach ML. Understanding brain states across spacetime informed by whole-brain modelling. Philos Trans A Math Phys Eng Sci 2022; 380:20210247. [PMID: 35599554 PMCID: PMC9125224 DOI: 10.1098/rsta.2021.0247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/23/2021] [Indexed: 05/26/2023]
Abstract
In order to survive in a complex environment, the human brain relies on the ability to flexibly adapt ongoing behaviour according to intrinsic and extrinsic signals. This capability has been linked to specific whole-brain activity patterns whose relative stability (order) allows for consistent functioning, supported by sufficient intrinsic instability needed for optimal adaptability. The emergent, spontaneous balance between order and disorder in brain activity over spacetime underpins distinct brain states. For example, depression is characterized by excessively rigid, highly ordered states, while psychedelics can bring about more disordered, sometimes overly flexible states. Recent developments in systems, computational and theoretical neuroscience have started to make inroads into the characterization of such complex dynamics over space and time. Here, we review recent insights drawn from neuroimaging and whole-brain modelling motivating using mechanistic principles from dynamical system theory to study and characterize brain states. We show how different healthy and altered brain states are associated to characteristic spacetime dynamics which in turn may offer insights that in time can inspire new treatments for rebalancing brain states in disease. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Jakub Vohryzek
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, UK
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Psychiatry, University of Oxford, Oxford, UK
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Spain
| | - Joana Cabral
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, UK
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Peter Vuust
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Gustavo Deco
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Spain
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Morten L. Kringelbach
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, Oxford, UK
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Psychiatry, University of Oxford, Oxford, UK
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Bartha FA, Juhász N, Marzban S, Han R, Röst G. In Silico Evaluation of Paxlovid's Pharmacometrics for SARS-CoV-2: A Multiscale Approach. Viruses 2022; 14:1103. [PMID: 35632843 PMCID: PMC9146265 DOI: 10.3390/v14051103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Paxlovid is a promising, orally bioavailable novel drug for SARS-CoV-2 with excellent safety profiles. Our main goal here is to explore the pharmacometric features of this new antiviral. To provide a detailed assessment of Paxlovid, we propose a hybrid multiscale mathematical approach. We demonstrate that the results of the present in silico evaluation match the clinical expectations remarkably well: on the one hand, our computations successfully replicate the outcome of an actual in vitro experiment; on the other hand, we verify both the sufficiency and the necessity of Paxlovid's two main components (nirmatrelvir and ritonavir) for a simplified in vivo case. Moreover, in the simulated context of our computational framework, we visualize the importance of early interventions and identify the time window where a unit-length delay causes the highest level of tissue damage. Finally, the results' sensitivity to the diffusion coefficient of the virus is explored in detail.
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Affiliation(s)
- Ferenc A. Bartha
- Bolyai Institute, University of Szeged, H-6720 Szeged, Hungary; (S.M.); (G.R.)
| | - Nóra Juhász
- Bolyai Institute, University of Szeged, H-6720 Szeged, Hungary; (S.M.); (G.R.)
| | - Sadegh Marzban
- Bolyai Institute, University of Szeged, H-6720 Szeged, Hungary; (S.M.); (G.R.)
| | - Renji Han
- School of Sciences, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Gergely Röst
- Bolyai Institute, University of Szeged, H-6720 Szeged, Hungary; (S.M.); (G.R.)
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Shimadzu S, Furuya T, Ozawa Y, Fukuda H, Kondo Y. Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope. Quant Plant Biol 2022; 3:e15. [PMID: 37077981 PMCID: PMC10095866 DOI: 10.1017/qpb.2022.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 05/03/2023]
Abstract
Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence reporters causes autofluorescence and photobleaching. Unlike fluorescence reporters, luminescence proteins do not require excitation light, and therefore offer an alternative reporter for long-term and quantitative spatio-temporal analysis. We established an imaging system for luciferase, which enabled monitoring cell fate marker dynamics during vascular development in a vascular cell induction system called VISUAL. Single cells expressing the cambium marker, proAtHB8:ELUC, had sharp luminescence peaks at different time points. Furthermore, dual-color luminescence imaging revealed spatio-temporal relationships between cells that differentiated into xylem or phloem, and cells that transitioned from procambium to cambium. This imaging system enables not only the detection of temporal gene expression, but also facilitates monitoring of spatio-temporal dynamics of cell identity transitions at the single cell level.
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Affiliation(s)
- Shunji Shimadzu
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Science, Kobe University, Kobe, Japan
| | - Tomoyuki Furuya
- Graduate School of Science, Kobe University, Kobe, Japan
- College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yasuko Ozawa
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroo Fukuda
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto University of Advanced Science, Kameoka, Japan
| | - Yuki Kondo
- Graduate School of Science, Kobe University, Kobe, Japan
- Author for correspondence: Y. Kondo, E-mail:
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Marzban S, Han R, Juhász N, Röst G. A hybrid PDE-ABM model for viral dynamics with application to SARS-CoV-2 and influenza. R Soc Open Sci 2021; 8:210787. [PMID: 34737874 PMCID: PMC8564626 DOI: 10.1098/rsos.210787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/11/2021] [Indexed: 05/08/2023]
Abstract
We propose a hybrid partial differential equation-agent-based (PDE-ABM) model to describe the spatio-temporal viral dynamics in a cell population. The virus concentration is considered as a continuous variable and virus movement is modelled by diffusion, while changes in the states of cells (i.e. healthy, infected, dead) are represented by a stochastic ABM. The two subsystems are intertwined: the probability of an agent getting infected in the ABM depends on the local viral concentration, and the source term of viral production in the PDE is determined by the cells that are infected. We develop a computational tool that allows us to study the hybrid system and the generated spatial patterns in detail. We systematically compare the outputs with a classical ODE system of viral dynamics, and find that the ODE model is a good approximation only if the diffusion coefficient is large. We demonstrate that the model is able to predict SARS-CoV-2 infection dynamics, and replicate the output of in vitro experiments. Applying the model to influenza as well, we can gain insight into why the outcomes of these two infections are different.
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Affiliation(s)
- Sadegh Marzban
- Bolyai Institute, University of Szeged, Szeged 6720, Hungary
| | - Renji Han
- Bolyai Institute, University of Szeged, Szeged 6720, Hungary
| | - Nóra Juhász
- Bolyai Institute, University of Szeged, Szeged 6720, Hungary
| | - Gergely Röst
- Bolyai Institute, University of Szeged, Szeged 6720, Hungary
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Cecilia H, Arnoux S, Picault S, Dicko A, Seck MT, Sall B, Bassène M, Vreysen M, Pagabeleguem S, Bancé A, Bouyer J, Ezanno P. Dispersal in heterogeneous environments drives population dynamics and control of tsetse flies. Proc Biol Sci 2021; 288:20202810. [PMID: 33529565 PMCID: PMC7893214 DOI: 10.1098/rspb.2020.2810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Spatio-temporally heterogeneous environments may lead to unexpected population dynamics. Knowledge is needed on local properties favouring population resilience at large scale. For pathogen vectors, such as tsetse flies transmitting human and animal African trypanosomosis, this is crucial to target management strategies. We developed a mechanistic spatio-temporal model of the age-structured population dynamics of tsetse flies, parametrized with field and laboratory data. It accounts for density- and temperature-dependence. The studied environment is heterogeneous, fragmented and dispersal is suitability-driven. We confirmed that temperature and adult mortality have a strong impact on tsetse populations. When homogeneously increasing adult mortality, control was less effective and induced faster population recovery in the coldest and temperature-stable locations, creating refuges. To optimally select locations to control, we assessed the potential impact of treating them and their contribution to the whole population. This heterogeneous control induced a similar population decrease, with more dispersed individuals. Control efficacy was no longer related to temperature. Dispersal was responsible for refuges at the interface between controlled and uncontrolled zones, where resurgence after control was very high. The early identification of refuges, which could jeopardize control efforts, is crucial. We recommend baseline data collection to characterize the ecosystem before implementing any measures.
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Affiliation(s)
| | | | | | - Ahmadou Dicko
- Cirad, INRAE, ASTRE, University of Montpellier, Montpellier, France
| | - Momar Talla Seck
- Institut Sénégalais de Recherches Agricoles, Laboratoire National d'Elevage et de Recherches Vétérinaires, Dakar-Hann, Senegal
| | - Baba Sall
- Direction des Services vétérinaires, Ministère de l'Elevage et des Productions animales, Sphères ministérielles de Diamniadio, Bât. C, 3ème étage, Senegal
| | - Mireille Bassène
- Institut Sénégalais de Recherches Agricoles, Laboratoire National d'Elevage et de Recherches Vétérinaires, Dakar-Hann, Senegal
| | - Marc Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, 1400 Vienna, Austria
| | - Soumaïla Pagabeleguem
- Insectarium de Bobo-Dioulasso - Campagne d'Eradication des Tsé-tsé et Trypanosomoses (IBD-CETT), Bobo-Dioulasso 01, BP 1087, Burkina Faso.,Université de Dédougou (UDDG), BP 176, Burkina Faso
| | - Augustin Bancé
- Centre International de Recherche-Développement sur l'Elevage en Zone Subhumide (CIRDES), Bobo-Dioulasso 01 01 BP 454, Burkina Faso
| | - Jérémy Bouyer
- Cirad, INRAE, ASTRE, University of Montpellier, Montpellier, France.,Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, 1400 Vienna, Austria.,UMR 'Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides', Cirad, Montpellier, France
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Deepa Maheshvare M, Raha S, Pal D. A Graph-Based Framework for Multiscale Modeling of Physiological Transport. Front Netw Physiol 2021; 1:802881. [PMID: 36925576 PMCID: PMC10013063 DOI: 10.3389/fnetp.2021.802881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022]
Abstract
Trillions of chemical reactions occur in the human body every second, where the generated products are not only consumed locally but also transported to various locations in a systematic manner to sustain homeostasis. Current solutions to model these biological phenomena are restricted in computability and scalability due to the use of continuum approaches in which it is practically impossible to encapsulate the complexity of the physiological processes occurring at diverse scales. Here, we present a discrete modeling framework defined on an interacting graph that offers the flexibility to model multiscale systems by translating the physical space into a metamodel. We discretize the graph-based metamodel into functional units composed of well-mixed volumes with vascular and cellular subdomains; the operators defined over these volumes define the transport dynamics. We predict glucose drift governed by advective-dispersive transport in the vascular subdomains of an islet vasculature and cross-validate the flow and concentration fields with finite-element-based COMSOL simulations. Vascular and cellular subdomains are coupled to model the nutrient exchange occurring in response to the gradient arising out of reaction and perfusion dynamics. The application of our framework for modeling biologically relevant test systems shows how our approach can assimilate both multi-omics data from in vitro-in vivo studies and vascular topology from imaging studies for examining the structure-function relationship of complex vasculatures. The framework can advance simulation of whole-body networks at user-defined levels and is expected to find major use in personalized medicine and drug discovery.
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Affiliation(s)
- M Deepa Maheshvare
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Soumyendu Raha
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
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Tabasi M, Alesheikh AA. Spatiotemporal Variability of Zoonotic Cutaneous Leishmaniasis Based on Sociodemographic Heterogeneity. The Case of Northeastern Iran, 2011-2016. Jpn J Infect Dis 2020; 74:7-16. [PMID: 32611974 DOI: 10.7883/yoken.jjid.2020.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Zoonotic cutaneous leishmaniasis (ZCL) is one of the most prevalent zoonoses in Iran, especially in central and northeastern Iran. This research aimed to examine whether there were spatiotemporal clusters of ZCL cases, and if so, whether there were differences in clustering according to age, sex, area of residence, and occupation. Spatial analysis, including global and local spatial autocorrelations, inverse distance weighting, and space-time scan statistics, were used to determine potential clusters in the villages of Golestan from 2011-2016. Several spatially significant (p < 0.05) clusters were observed in the north and northeastern regions, and most persisted until the last year of the study period. Children (0-10 years) living in rural settings were more likely to have an infection than those living in other areas. Although the disease was centered in the northern regions, housekeepers, females, and patients aged 21-30 and 41-50 years were found to be the high-risk groups in the southern areas. The seasonal pattern indicated that the outbreak mainly began in late summer, peaked in October, and diminished in December. By exploring spatiotemporal variations of ZCL by sociodemographic information, this study was able to identify priority areas for decision-makers in healthcare and resource allocation.
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Affiliation(s)
- Mohammad Tabasi
- Department of Geospatial Information System, Faculty of Geodesy and Geomatics Engineering, K.N. Toosi University of Technology, Iran
| | - Ali Asghar Alesheikh
- Department of Geospatial Information System, Faculty of Geodesy and Geomatics Engineering, K.N. Toosi University of Technology, Iran
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11
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Mérillet L, Kopp D, Robert M, Mouchet M, Pavoine S. Environment outweighs the effects of fishing in regulating demersal community structure in an exploited marine ecosystem. Glob Chang Biol 2020; 26:2106-2119. [PMID: 31883434 DOI: 10.1111/gcb.14969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 05/08/2023]
Abstract
Global climate change has already caused bottom temperatures of coastal marine ecosystems to increase worldwide. These ecosystems face many pressures, of which fishing is one of the most important. While consequences of global warming on commercial species are studied extensively, the importance of the increase in bottom temperature and of variation in fishing effort is more rarely considered together in these exploited ecosystems. Using a 17 year time series from an international bottom trawl survey, we investigated covariations of an entire demersal ecosystem (101 taxa) with the environment in the Celtic Sea. Our results showed that over the past two decades, biotic communities in the Celtic Sea were likely controlled more by environmental variables than fisheries, probably due to its long history of exploitation. At the scale of the entire zone, relations between taxa and the environment remained stable over the years, but at a local scale, in the center of the Celtic Sea, dynamics were probably driven by interannual variation in temperature. Fishing was an important factor structuring species assemblages at the beginning of the time series (2000) but decreased in importance after 2009. This was most likely caused by a change in spatial distribution of fishing effort, following a change in targeted taxa from nephrops to deeper water anglerfish that did not covary with fishing effort. Increasing bottom temperatures could induce additional changes in the coming years, notably in the cold-water commercial species cod, hake, nephrops, and American plaice. We showed that analyzing covariation is an effective way to screen a large number of taxa and highlight those that may be most susceptible to future simultaneous increases in temperature and changes in exploitation pattern by fisheries. This information can be particularly relevant for ecosystem assessments.
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Affiliation(s)
- Laurène Mérillet
- UMR 7204 MNHN-UPMC-CNRS, Centre d'Ecologie et de Sciences de la COnservation, Paris, France
- Ifremer, Unité de Sciences et Technologies halieutiques, Laboratoire de Technologie et Biologie Halieutique, Lorient, France
| | - Dorothée Kopp
- Ifremer, Unité de Sciences et Technologies halieutiques, Laboratoire de Technologie et Biologie Halieutique, Lorient, France
| | - Marianne Robert
- Ifremer, Unité de Sciences et Technologies halieutiques, Laboratoire de Technologie et Biologie Halieutique, Lorient, France
| | - Maud Mouchet
- UMR 7204 MNHN-UPMC-CNRS, Centre d'Ecologie et de Sciences de la COnservation, Paris, France
| | - Sandrine Pavoine
- UMR 7204 MNHN-UPMC-CNRS, Centre d'Ecologie et de Sciences de la COnservation, Paris, France
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12
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Celotto M, De Luca C, Muratore P, Resta F, Allegra Mascaro AL, Pavone FS, De Bonis G, Paolucci PS. Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques. Methods Protoc 2020; 3:E14. [PMID: 32023996 PMCID: PMC7189682 DOI: 10.3390/mps3010014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
Slow waves (SWs) are spatio-temporal patterns of cortical activity that occur both during natural sleep and anesthesia and are preserved across species. Even though electrophysiological recordings have been largely used to characterize brain states, they are limited in the spatial resolution and cannot target specific neuronal population. Recently, large-scale optical imaging techniques coupled with functional indicators overcame these restrictions, and new pipelines of analysis and novel approaches of SWs modelling are needed to extract relevant features of the spatio-temporal dynamics of SWs from these highly spatially resolved data-sets. Here we combined wide-field fluorescence microscopy and a transgenic mouse model expressing a calcium indicator (GCaMP6f) in excitatory neurons to study SW propagation over the meso-scale under ketamine anesthesia. We developed a versatile analysis pipeline to identify and quantify the spatio-temporal propagation of the SWs. Moreover, we designed a computational simulator based on a simple theoretical model, which takes into account the statistics of neuronal activity, the response of fluorescence proteins and the slow waves dynamics. The simulator was capable of synthesizing artificial signals that could reliably reproduce several features of the SWs observed in vivo, thus enabling a calibration tool for the analysis pipeline. Comparison of experimental and simulated data shows the robustness of the analysis tools and its potential to uncover mechanistic insights of the Slow Wave Activity (SWA).
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Affiliation(s)
- Marco Celotto
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- IIT—Neural Computation Lab, CNCS@UniTn, 38068 Rovereto, Italy
| | - Chiara De Luca
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- INFN, 00185 Rome, Italy;
- PhD Program in Behavioural Neuroscience,“Sapienza” University of Rome, 00185 Rome, Italy
| | - Paolo Muratore
- Department of Physics, “Sapienza” University of Rome, 00185 Rome, Italy; (M.C.); (C.D.L.); (P.M.)
- PhD Program in Cognitive Neuroscience, SISSA, 34136 Trieste, Italy
| | - Francesco Resta
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
| | - Anna Letizia Allegra Mascaro
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
- Istituto di Neuroscienze, CNR, 56124 Pisa, Italy
| | - Francesco Saverio Pavone
- LENS, University of Florence, 50019 Florence, Italy; (F.R.); (A.L.A.M.); (F.S.P.)
- Department of Physics, University of Florence, 50019 Florence, Italy
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13
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Zwetsloot MJ, Goebel M, Paya A, Grams TEE, Bauerle TL. Specific spatio-temporal dynamics of absorptive fine roots in response to neighbor species identity in a mixed beech-spruce forest. Tree Physiol 2019; 39:1867-1879. [PMID: 31504991 DOI: 10.1093/treephys/tpz086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/07/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Absorptive fine roots are an important driver of soil biogeochemical cycles. Yet, the spatio-temporal dynamics of those roots in the presence of neighboring species remain poorly understood. The aim of this study was to analyze shifts in absorptive fine-root traits in monoculture or mixtures of Fagus sylvatica [L.] and Picea abies [L.] Karst. We hypothesized that root competition would be higher under single-species than mixed-species interactions, leading to changes in (i) root survivorship, diameter and respiration and (ii) spatio-temporal patterns of root growth and death. Using minirhizotron methods, we monitored the timing and location of absorptive fine-root growth and death at an experimental forest in southern Germany from 2011 to 2013. We also measured root respiration in the spring and fall seasons of 2012 and 2013. Our findings show that the absorptive fine roots of F. sylvatica had a 50% higher risk of root mortality and higher respiration rates in the single-species compared to mixed-species zones. These results support our hypothesis that root competition is less intense for F. sylvatica in mixture versus monoculture. We were unable to find confirmation for the same hypothesis for P. abies. To analyze spatio-temporal patterns of absorptive fine-root production and mortality, we used a mixed-effects model considering root depth (space) and seasons (time) simultaneously. This analysis showed that F. sylvatica shifts root production towards shallower soil layers in mixed-species stands, besides significant seasonal fluctuations in root production depths for both species. Ultimately, the impact of neighbor species identity on root traits observed in this study has important implications for where, when and how fast root-facilitated carbon cycling takes place in single-species versus mixed-species forests. In addition, our study highlights the need for inclusion of absorptive fine-root spatio-temporal dynamics when examining belowground plant interactions and biogeochemical cycles.
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Affiliation(s)
- Marie J Zwetsloot
- School of Integrative Plant Science, Cornell University, 236 Tower Road, Ithaca, NY 14853, USA
- Soil Biology Group, Wageningen University, Droevendaalsesteeg 3, 6708 PB Wageningen, the Netherlands
| | - Marc Goebel
- Department of Natural Resources, Cornell University, 111 Fernow Hall, Ithaca, NY 14853, USA
| | - Alex Paya
- School of Integrative Plant Science, Cornell University, 236 Tower Road, Ithaca, NY 14853, USA
| | - Thorsten E E Grams
- Ecophysiology of Plants, Technical University of Munich, Am Hochanger 13, 85354 Freising, Germany
| | - Taryn L Bauerle
- School of Integrative Plant Science, Cornell University, 236 Tower Road, Ithaca, NY 14853, USA
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14
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McLean M, Mouillot D, Lindegren M, Villéger S, Engelhard G, Murgier J, Auber A. Fish communities diverge in species but converge in traits over three decades of warming. Glob Chang Biol 2019; 25:3972-3984. [PMID: 31376310 DOI: 10.1111/gcb.14785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Describing the spatial and temporal dynamics of communities is essential for understanding the impacts of global environmental change on biodiversity and ecosystem functioning. Trait-based approaches can provide better insight than species-based (i.e. taxonomic) approaches into community assembly and ecosystem functioning, but comparing species and trait dynamics may reveal important patterns for understanding community responses to environmental change. Here, we used a 33-year database of fish monitoring to compare the spatio-temporal dynamics of taxonomic and trait structure in North Sea fish communities. We found that the majority of variation in both taxonomic and trait structure was explained by a pronounced spatial gradient, with distinct communities in the southern and northern North Sea related to depth, sea surface temperature, salinity and bed shear stress. Both taxonomic and trait structure changed significantly over time; however taxonomically, communities in the south and north diverged towards different species, becoming more dissimilar over time, yet they converged towards the same traits regardless of species differences. In particular, communities shifted towards smaller, faster growing species with higher thermal preferences and pelagic water column position. Although taxonomic structure changed over time, its spatial distribution remained relatively stable, whereas in trait structure, the southern zone of the North Sea shifted northward and expanded, leading to homogenization. Our findings suggest that global environmental change, notably climate warming, will lead to convergence towards traits more adapted for novel environments regardless of species composition.
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Affiliation(s)
- Matthew McLean
- Unité Halieutique de Manche et mer du Nord, IFREMER, Boulogne-sur-Mer, France
- MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier Cedex, France
| | - David Mouillot
- MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier Cedex, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Martin Lindegren
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
| | - Sébastien Villéger
- MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier Cedex, France
| | - Georg Engelhard
- Centre for Environment, Fisheries & Aquaculture Science (Cefas), Lowestoft, UK
- Collaborative Centre for Sustainable Use of the Seas (CCSUS), University of East Anglia, Norwich, UK
| | - Juliette Murgier
- Unité Halieutique de Manche et mer du Nord, IFREMER, Boulogne-sur-Mer, France
| | - Arnaud Auber
- Unité Halieutique de Manche et mer du Nord, IFREMER, Boulogne-sur-Mer, France
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15
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Beltrame L, Dunne T, Vineer HR, Walker JG, Morgan ER, Vickerman P, McCann CM, Williams DJL, Wagener T. A mechanistic hydro-epidemiological model of liver fluke risk. J R Soc Interface 2019; 15:rsif.2018.0072. [PMID: 30158179 PMCID: PMC6127180 DOI: 10.1098/rsif.2018.0072] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/27/2018] [Indexed: 01/13/2023] Open
Abstract
The majority of existing models for predicting disease risk in response to climate change are empirical. These models exploit correlations between historical data, rather than explicitly describing relationships between cause and response variables. Therefore, they are unsuitable for capturing impacts beyond historically observed variability and have limited ability to guide interventions. In this study, we integrate environmental and epidemiological processes into a new mechanistic model, taking the widespread parasitic disease of fasciolosis as an example. The model simulates environmental suitability for disease transmission at a daily time step and 25 m resolution, explicitly linking the parasite life cycle to key weather–water–environment conditions. Using epidemiological data, we show that the model can reproduce observed infection levels in time and space for two case studies in the UK. To overcome data limitations, we propose a calibration approach combining Monte Carlo sampling and expert opinion, which allows constraint of the model in a process-based way, including a quantification of uncertainty. The simulated disease dynamics agree with information from the literature, and comparison with a widely used empirical risk index shows that the new model provides better insight into the time–space patterns of infection, which will be valuable for decision support.
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Affiliation(s)
| | - Toby Dunne
- Department of Civil Engineering, University of Bristol, Bristol, UK
| | - Hannah Rose Vineer
- School of Biological Sciences, University of Bristol, Bristol, UK.,Bristol Veterinary School, University of Bristol, Bristol, UK.,Cabot Institute, University of Bristol, Bristol, UK
| | - Josephine G Walker
- School of Biological Sciences, University of Bristol, Bristol, UK.,Cabot Institute, University of Bristol, Bristol, UK.,Bristol Medical School, University of Bristol, Bristol, UK
| | - Eric R Morgan
- Cabot Institute, University of Bristol, Bristol, UK.,School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | | | | | - Diana J L Williams
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Thorsten Wagener
- Department of Civil Engineering, University of Bristol, Bristol, UK.,Cabot Institute, University of Bristol, Bristol, UK
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16
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Pu L, Zhang S, Yang J, Chang L, Bai S. Spatio-Temporal Dynamics of Maize Potential Yield and Yield Gaps in Northeast China from 1990 to 2015. Int J Environ Res Public Health 2019; 16:E1211. [PMID: 30987325 DOI: 10.3390/ijerph16071211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Maize yield has undergone obvious spatial and temporal changes in recent decades in Northeast China. Understanding how maize potential yield has changed over the past few decades and how large the gaps between potential and actual maize yields are is essential for increasing maize yield to meet increased food demand in Northeast China. In this study, the spatial and temporal dynamics of maize potential yield in Northeast China from 1990 to 2015 were simulated using the Global Agro-ecological Zones (GAEZ) model at the pixel level firstly. Then, the yield gaps between actual and potential yields were analyzed at city scale. The results were the following. (1) The maize potential yield decreased by about 500 kg/ha and the potential production remained at around 260 million tonnes during 1990–2000. From 2000 to 2015, the maize potential yield and production increased by approximately 1000 kg/ha and 80 million tonnes, respectively. (2) The maize potential yield decreased in most regions of Northeast China in the first decade, such as the center area (CA), south area (SA), southwest area (SWA), and small regions in northeast area (NEA), due to lower temperature and insufficient rainfall. The maize potential yield increased elsewhere. (3) The maize potential yield increased by more than 1000 kg/ha in the center area (CA) in the latter 15 years, which may be because of the climate warming and sufficient precipitation. The maize potential yield decreased elsewhere and Harbin in the center area (CA). (4) In 40 cities of Northeast China, the rates of actual yield to potential yield in 17 cities were higher than 80%. The actual yields only attained 50–80% of the potential yields in 20 cities. The gaps between actual and potential yields in Hegang and Dandong were very large, which need to be shrunk urgently. The results highlight the importance of coping with climate change actively, arranging crop structure reasonably, improving farmland use efficiency and ensuring food security in Northeast China.
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17
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Chen HW, Xu J, Liu N, Hong JJ, Qi SY, Yuan H. Spatio-temporal dynamics of ecosystem service value of green land in Shenyang, Northeast China. Ying Yong Sheng Tai Xue Bao 2018; 29:3391-3397. [PMID: 30325165 DOI: 10.13287/j.1001-9332.201810.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Urban green land is an important component of urban natural ecosystems, with critical ecosystem service functions. Based on the land use data of Shenyang in 2005, 2010 and 2015, this study estimated ecosystem service value (ESV) according to "equivalent value per unit area of ecosystem services for various ecosystems in China" and then analyzed its spatio-temporal characteristics and change rate. The results showed that arable land area significantly reduced by 3.5% from 2005 to 2010 and 10.9% from 2010 to 2015, respectively. Wood land area increased slightly, and the area of meadow increased by 17.2%. The ESV of green land in Shenyang increased from 11.76×108 yuan in 2005 to 23.48×108 yuan in 2010, and then decreased to 11.29×108 yuan in 2015. The annual change of ESV showed significant difference among different districts, with the highest occurring in Yuhong, Shenbei and Heping districts. The coefficient of variation (CV) was 64.9%, 60.4% and 40.8%, respectively. The ESV of green land varied significantly among diffe-rent districts, with higher values occurring in Huanggu, Shenbei and Dongling districts. Soil conservation function had the highest ESV, accounting for 15% of the total ESV. The food production function had the lowest ESV. The changes of ESV in Shenyang might be attributed to the urban expansion, agricultural land conversion, and green space construction.
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Affiliation(s)
- Hong Wei Chen
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, Shenyang 110044, China
| | - Jing Xu
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
| | - Na Liu
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
| | - Jiao Jiao Hong
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
| | - Shu Yan Qi
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, Shenyang 110044, China
| | - Hao Yuan
- College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China
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18
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Kottaram A, Johnston L, Ganella E, Pantelis C, Kotagiri R, Zalesky A. Spatio-temporal dynamics of resting-state brain networks improve single-subject prediction of schizophrenia diagnosis. Hum Brain Mapp 2018; 39:3663-3681. [PMID: 29749660 PMCID: PMC6866493 DOI: 10.1002/hbm.24202] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 02/01/2023] Open
Abstract
Correlation in functional MRI activity between spatially separated brain regions can fluctuate dynamically when an individual is at rest. These dynamics are typically characterized temporally by measuring fluctuations in functional connectivity between brain regions that remain fixed in space over time. Here, dynamics in functional connectivity were characterized in both time and space. Temporal dynamics were mapped with sliding-window correlation, while spatial dynamics were characterized by enabling network regions to vary in size (shrink/grow) over time according to the functional connectivity profile of their constituent voxels. These temporal and spatial dynamics were evaluated as biomarkers to distinguish schizophrenia patients from controls, and compared to current biomarkers based on static measures of resting-state functional connectivity. Support vector machine classifiers were trained using: (a) static, (b) dynamic in time, (c) dynamic in space, and (d) dynamic in time and space characterizations of functional connectivity within canonical resting-state brain networks. Classifiers trained on functional connectivity dynamics mapped over both space and time predicted diagnostic status with accuracy exceeding 91%, whereas utilizing only spatial or temporal dynamics alone yielded lower classification accuracies. Static measures of functional connectivity yielded the lowest accuracy (79.5%). Compared to healthy comparison individuals, schizophrenia patients generally exhibited functional connectivity that was reduced in strength and more variable. Robustness was established with replication in an independent dataset. The utility of biomarkers based on temporal and spatial functional connectivity dynamics suggests that resting-state dynamics are not trivially attributable to sampling variability and head motion.
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Affiliation(s)
- Akhil Kottaram
- Department of Biomedical Engineering, The University of Melbourne, Victoria, 3010, Australia
| | - Leigh Johnston
- Department of Biomedical Engineering, The University of Melbourne, Victoria, 3010, Australia
- Department of Electrical and Electronic Engineering, The University of Melbourne, Victoria, 3010, Australia
- Florey Institute for Neurosciences and Mental health, Parkville, Victoria, 3052, Australia
| | - Eleni Ganella
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Victoria, 3010, Australia
- Cooperative Research Centre for Mental Health, Carlton, Victoria, 3053, Australia
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Victoria, 3010, Australia
- Department of Psychiatry, The University of Melbourne, Victoria, 3010, Australia
- Florey Institute for Neurosciences and Mental health, Parkville, Victoria, 3052, Australia
- North Western Mental Health, Melbourne Health, Parkville, Victoria, Australia
- Centre for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne, Victoria, 3053, Australia
- Cooperative Research Centre for Mental Health, Carlton, Victoria, 3053, Australia
| | - Ramamohanarao Kotagiri
- Department of Computing and Information Systems, The University of Melbourne, Victoria, 3010, Australia
| | - Andrew Zalesky
- Department of Biomedical Engineering, The University of Melbourne, Victoria, 3010, Australia
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Victoria, 3010, Australia
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Winkler DE, Butz RJ, Germino MJ, Reinhardt K, Kueppers LM. Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants. Front Plant Sci 2018; 9:1140. [PMID: 30108605 PMCID: PMC6079221 DOI: 10.3389/fpls.2018.01140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/13/2018] [Indexed: 05/30/2023]
Abstract
The spatial patterning of alpine plant communities is strongly influenced by the variation in physical factors such as temperature and moisture, which are strongly affected by snow depth and snowmelt patterns. Earlier snowmelt timing and greater soil-moisture limitations may favor wide-ranging species adapted to a broader set of ecohydrological conditions than alpine-restricted species. We asked how plant community composition, phenology, plant water relations, and photosynthetic gas exchange of alpine-restricted and wide-ranging species differ in their responses to a ca. 40-day snowmelt gradient in the Colorado Rocky Mountains (Lewisia pygmaea, Sibbaldia procumbens, and Hymenoxys grandiflora were alpine-restricted and Artemisia scopulorum, Carex rupestris, and Geum rossii were wide-ranging species). As hypothesized, species richness and foliar cover increased with earlier snowmelt, due to a greater abundance of wide-ranging species present in earlier melting plots. Flowering initiation occurred earlier with earlier snowmelt for 12 out of 19 species analyzed, while flowering duration was shortened with later snowmelt for six species (all but one were wide-ranging species). We observed >50% declines in net photosynthesis from July to September as soil moisture and plant water potentials declined. Early-season stomatal conductance was higher in wide-ranging species, indicating a more competitive strategy for water acquisition when soil moisture is high. Even so, there were no associated differences in photosynthesis or transpiration, suggesting no strong differences between these groups in physiology. Our findings reveal that plant species with different ranges (alpine-restricted vs. wide-ranging) could have differential phenological and physiological responses to snowmelt timing and associated soil moisture dry-down, and that alpine-restricted species' performance is more sensitive to snowmelt. As a result, alpine-restricted species may serve as better indicator species than their wide-ranging heterospecifics. Overall, alpine community composition and peak % cover are strongly structured by spatio-temporal patterns in snowmelt timing. Thus, near-term, community-wide changes (or variation) in phenology and physiology in response to shifts in snowmelt timing or rates of soil dry down are likely to be contingent on the legacy of past climate on community structure.
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Affiliation(s)
- Daniel E. Winkler
- School of Natural Sciences, University of California, Merced, Merced, CA, United States
- United States Geological Survey, Southwest Biological Science Center, Moab, UT, United States
| | - Ramona J. Butz
- Department of Forestry & Wildland Resources, Humboldt State University, Arcata, CA, United States
- Pacific Southwest Region, United States Department of Agriculture Forest Service, Eureka, CA, United States
| | - Matthew J. Germino
- United States Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, United States
| | - Keith Reinhardt
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
| | - Lara M. Kueppers
- Energy & Resource Group, University of California, Berkeley, Berkeley, CA, United States
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20
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Wedgwood KCA, Richardson SJ, Morgan NG, Tsaneva-Atanasova K. Spatiotemporal Dynamics of Insulitis in Human Type 1 Diabetes. Front Physiol 2016; 7:633. [PMID: 28082906 PMCID: PMC5186767 DOI: 10.3389/fphys.2016.00633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/05/2016] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes (T1D) is an auto-immune disease characterized by the selective destruction of the insulin secreting beta cells in the pancreas during an inflammatory phase known as insulitis. Patients with T1D are typically dependent on the administration of externally provided insulin in order to manage blood glucose levels. Whilst technological developments have significantly improved both the life expectancy and quality of life of these patients, an understanding of the mechanisms of the disease remains elusive. Animal models, such as the NOD mouse model, have been widely used to probe the process of insulitis, but there exist very few data from humans studied at disease onset. In this manuscript, we employ data from human pancreases collected close to the onset of T1D and propose a spatio-temporal computational model for the progression of insulitis in human T1D, with particular focus on the mechanisms underlying the development of insulitis in pancreatic islets. This framework allows us to investigate how the time-course of insulitis progression is affected by altering key parameters, such as the number of the CD20+ B cells present in the inflammatory infiltrate, which has recently been proposed to influence the aggressiveness of the disease. Through the analysis of repeated simulations of our stochastic model, which track the number of beta cells within an islet, we find that increased numbers of B cells in the peri-islet space lead to faster destruction of the beta cells. We also find that the balance between the degradation and repair of the basement membrane surrounding the islet is a critical component in governing the overall destruction rate of the beta cells and their remaining number. Our model provides a framework for continued and improved spatio-temporal modeling of human T1D.
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Affiliation(s)
- Kyle C. A. Wedgwood
- Centre for Biomedical Modelling and Analysis, University of ExeterExeter, UK
| | | | - Noel G. Morgan
- University of Exeter Medical School, University of ExeterExeter, UK
| | - Krasimira Tsaneva-Atanasova
- College for Engineering, Mathematics and Physical Sciences, University of ExeterExeter, UK
- Engineering and Physical Sciences Research Council Centre for Predictive Modelling in Healthcare, University of ExeterExeter, UK
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21
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Li S, Gilbert L, Harrison PA, Rounsevell MDA. Modelling the seasonality of Lyme disease risk and the potential impacts of a warming climate within the heterogeneous landscapes of Scotland. J R Soc Interface 2016; 13:rsif.2016.0140. [PMID: 27030039 DOI: 10.1098/rsif.2016.0140] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/04/2016] [Indexed: 12/22/2022] Open
Abstract
Lyme disease is the most prevalent vector-borne disease in the temperate Northern Hemisphere. The abundance of infected nymphal ticks is commonly used as a Lyme disease risk indicator. Temperature can influence the dynamics of disease by shaping the activity and development of ticks and, hence, altering the contact pattern and pathogen transmission between ticks and their host animals. A mechanistic, agent-based model was developed to study the temperature-driven seasonality of Ixodes ricinus ticks and transmission of Borrelia burgdorferi sensu lato across mainland Scotland. Based on 12-year averaged temperature surfaces, our model predicted that Lyme disease risk currently peaks in autumn, approximately six weeks after the temperature peak. The risk was predicted to decrease with increasing altitude. Increases in temperature were predicted to prolong the duration of the tick questing season and expand the risk area to higher altitudinal and latitudinal regions. These predicted impacts on tick population ecology may be expected to lead to greater tick-host contacts under climate warming and, hence, greater risks of pathogen transmission. The model is useful in improving understanding of the spatial determinants and system mechanisms of Lyme disease pathogen transmission and its sensitivity to temperature changes.
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Affiliation(s)
- Sen Li
- Environmental Change Institute, University of Oxford, South Parks Road, Oxford OX1 3QY, UK
| | - Lucy Gilbert
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Paula A Harrison
- Environmental Change Institute, University of Oxford, South Parks Road, Oxford OX1 3QY, UK Centre for Ecology and Hydrology, Library Avenue, Lancaster LA1 4AP, UK
| | - Mark D A Rounsevell
- School of GeoSciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
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22
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Viña A, McConnell WJ, Yang H, Xu Z, Liu J. Effects of conservation policy on China's forest recovery. Sci Adv 2016; 2:e1500965. [PMID: 27034980 PMCID: PMC4803489 DOI: 10.1126/sciadv.1500965] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/19/2016] [Indexed: 05/28/2023]
Abstract
Forest loss is one of the most pervasive land surface transformations on Earth, with drastic effects on global climate, ecosystems, and human well-being. As part of biodiversity conservation and climate change mitigation efforts, many countries, including China, have been implementing large-scale policies to conserve and restore forests. However, little is known about the effectiveness of these policies, and information on China's forest dynamics at the national level has mainly relied on official statistics. In response to international calls for improved reliability and transparency of information on biodiversity conservation and climate change mitigation efforts, it is crucial to independently verify government statistics. Furthermore, if forest recovery is verified, it is essential to assess the degree to which this recovery is attributable to policy, within the context of other relevant factors. We assess the dynamics of forest cover in China between 2000 and 2010 and evaluate the effectiveness of one of the largest forest conservation programs in the world-the Natural Forest Conservation Program (NFCP). Results indicate that forest cover has significantly increased in around 1.6% of China's territory and that the areas exhibiting forest gain experienced a combined increase in net primary productivity (ca. 0.9 Tg of carbon). Among the variables evaluated at county level, the NFCP exhibited a significantly positive relation with forest gain, whereas reduction in rural labor showed a negative relationship with both forest loss and gain. Findings such as these have global implications for forest conservation and climate change mitigation efforts.
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Affiliation(s)
- Andrés Viña
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - William J. McConnell
- Center for Global Change and Earth Observations, Michigan State University, East Lansing, MI 48823, USA
| | - Hongbo Yang
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - Zhenci Xu
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - Jianguo Liu
- Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
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Zaytsev AV, Segura-Peña D, Godzi M, Calderon A, Ballister ER, Stamatov R, Mayo AM, Peterson L, Black BE, Ataullakhanov FI, Lampson MA, Grishchuk EL. Bistability of a coupled Aurora B kinase-phosphatase system in cell division. eLife 2016; 5:e10644. [PMID: 26765564 PMCID: PMC4798973 DOI: 10.7554/elife.10644] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/13/2016] [Indexed: 01/08/2023] Open
Abstract
Aurora B kinase, a key regulator of cell division, localizes to specific cellular locations, but the regulatory mechanisms responsible for phosphorylation of substrates located remotely from kinase enrichment sites are unclear. Here, we provide evidence that this activity at a distance depends on both sites of high kinase concentration and the bistability of a coupled kinase-phosphatase system. We reconstitute this bistable behavior and hysteresis using purified components to reveal co-existence of distinct high and low Aurora B activity states, sustained by a two-component kinase autoactivation mechanism. Furthermore, we demonstrate these non-linear regimes in live cells using a FRET-based phosphorylation sensor, and provide a mechanistic theoretical model for spatial regulation of Aurora B phosphorylation. We propose that bistability of an Aurora B-phosphatase system underlies formation of spatial phosphorylation patterns, which are generated and spread from sites of kinase autoactivation, thereby regulating cell division.
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Affiliation(s)
- Anatoly V Zaytsev
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Dario Segura-Peña
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Maxim Godzi
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Abram Calderon
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Edward R Ballister
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Rumen Stamatov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Alyssa M Mayo
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Laura Peterson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Fazly I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Federal Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Department of Physics, Moscow State University, Moscow, Russia
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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Watts AG, Schlichting PE, Billerman SM, Jesmer BR, Micheletti S, Fortin MJ, Funk WC, Hapeman P, Muths E, Murphy MA. How spatio-temporal habitat connectivity affects amphibian genetic structure. Front Genet 2015; 6:275. [PMID: 26442094 PMCID: PMC4561841 DOI: 10.3389/fgene.2015.00275] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/14/2015] [Indexed: 11/13/2022] Open
Abstract
Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.
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Affiliation(s)
- Alexander G Watts
- Department of Ecology & Evolutionary Biology, University of Toronto Toronto, ON, Canada
| | - Peter E Schlichting
- Department of Natural Resources Management, Texas Tech University Lubbock, TX, USA
| | - Shawn M Billerman
- Department of Zoology and Physiology, University of Wyoming Laramie, WY, USA ; Program in Ecology, University of Wyoming Laramie, WY, USA
| | - Brett R Jesmer
- Department of Zoology and Physiology, University of Wyoming Laramie, WY, USA ; Program in Ecology, University of Wyoming Laramie, WY, USA
| | - Steven Micheletti
- School of Biological Sciences, Washington State University Pullman, WA, USA
| | - Marie-Josée Fortin
- Department of Ecology & Evolutionary Biology, University of Toronto Toronto, ON, Canada
| | - W Chris Funk
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University Fort Collins, CO, USA
| | - Paul Hapeman
- Department of Biology, Central Connecticut State University New Britain, CT, USA
| | - Erin Muths
- Fort Collins Science Center, U.S. Geological Survey Fort Collins, CO, USA
| | - Melanie A Murphy
- Program in Ecology, University of Wyoming Laramie, WY, USA ; Department of Ecosystem Science and Management, University of Wyoming Laramie, WY, USA
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25
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Sagl G, Blaschke T, Beinat E, Resch B. Ubiquitous geo-sensing for context-aware analysis: exploring relationships between environmental and human dynamics. Sensors (Basel) 2012; 12:9800-22. [PMID: 23012571 PMCID: PMC3444129 DOI: 10.3390/s120709800] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/12/2012] [Accepted: 07/17/2012] [Indexed: 11/16/2022]
Abstract
Ubiquitous geo-sensing enables context-aware analyses of physical and social phenomena, i.e., analyzing one phenomenon in the context of another. Although such context-aware analysis can potentially enable a more holistic understanding of spatio-temporal processes, it is rarely documented in the scientific literature yet. In this paper we analyzed the collective human behavior in the context of the weather. We therefore explored the complex relationships between these two spatio-temporal phenomena to provide novel insights into the dynamics of urban systems. Aggregated mobile phone data, which served as a proxy for collective human behavior, was linked with the weather data from climate stations in the case study area, the city of Udine, Northern Italy. To identify and characterize potential patterns within the weather-human relationships, we developed a hybrid approach which integrates several spatio-temporal statistical analysis methods. Thereby we show that explanatory factor analysis, when applied to a number of meteorological variables, can be used to differentiate between normal and adverse weather conditions. Further, we measured the strength of the relationship between the 'global' adverse weather conditions and the spatially explicit effective variations in user-generated mobile network traffic for three distinct periods using the Maximal Information Coefficient (MIC). The analyses result in three spatially referenced maps of MICs which reveal interesting insights into collective human dynamics in the context of weather, but also initiate several new scientific challenges.
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Affiliation(s)
- Günther Sagl
- Doctoral College Geographic Information Science, University of Salzburg, Schillerstrasse 30, 5020 Salzburg, Austria
| | - Thomas Blaschke
- Centre for Geoinformatics, University of Salzburg, Schillerstrasse 30, 5020 Salzburg, Austria; E-Mails: (T.B.); (E.B.)
| | - Euro Beinat
- Centre for Geoinformatics, University of Salzburg, Schillerstrasse 30, 5020 Salzburg, Austria; E-Mails: (T.B.); (E.B.)
| | - Bernd Resch
- Institute for Geoinformatics and Remote Sensing, University of Osnabrück, Barbarastrasse 22b, 49076 Osnabrück, Germany; E-Mail:
- SENSEable City Lab, Massachusetts Institute of Technology, 9-209, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Solinas S, Nieus T, D'Angelo E. A realistic large-scale model of the cerebellum granular layer predicts circuit spatio-temporal filtering properties. Front Cell Neurosci 2010; 4:12. [PMID: 20508743 PMCID: PMC2876868 DOI: 10.3389/fncel.2010.00012] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 03/18/2010] [Indexed: 11/21/2022] Open
Abstract
The way the cerebellar granular layer transforms incoming mossy fiber signals into new spike patterns to be related to Purkinje cells is not yet clear. Here, a realistic computational model of the granular layer was developed and used to address four main functional hypotheses: center-surround organization, time-windowing, high-pass filtering in responses to spike bursts and coherent oscillations in response to diffuse random activity. The model network was activated using patterns inspired by those recorded in vivo. Burst stimulation of a small mossy fiber bundle resulted in granule cell bursts delimited in time (time windowing) and space (center-surround) by network inhibition. This burst–burst transmission showed marked frequency-dependence configuring a high-pass filter with cut-off frequency around 100 Hz. The contrast between center and surround properties was regulated by the excitatory–inhibitory balance. The stronger excitation made the center more responsive to 10–50 Hz input frequencies and enhanced the granule cell output (with spikes occurring earlier and with higher frequency and number) compared to the surround. Finally, over a certain level of mossy fiber background activity, the circuit generated coherent oscillations in the theta-frequency band. All these processes were fine-tuned by NMDA and GABA-A receptor activation and neurotransmitter vesicle cycling in the cerebellar glomeruli. This model shows that available knowledge on cellular mechanisms is sufficient to unify the main functional hypotheses on the cerebellum granular layer and suggests that this network can behave as an adaptable spatio-temporal filter coordinated by theta-frequency oscillations.
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Affiliation(s)
- Sergio Solinas
- Department of Physiology, University of Pavia and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia Pavia, Italy
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