Emerging dynamics from high-resolution spatial numerical epidemics.
Ontology highlight
ABSTRACT:
SUBMITTER: Thomine O
PROVIDER: S-EPMC8568339 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify.
| S-EPMC3443149 | biostudies-literature
Project description:Self-organized lipid bilayers together with proteins are the essential building blocks of biological membranes. Membranes are associated with all living systems as they make up cell boundaries and provide basic barriers to cellular organelles. It is of interest to study the dynamics of individual molecules in cell membranes as the mechanism of how biological membranes function at the single molecule remains to be elucidated. In this letter we describe a study in which we incubate rat basophilic leukemia cells with a fluorescently labeled cell membrane component on a surface containing zero-mode waveguides (ZMWs). We used the ZMW to confine fluorescent excitation to an approximately 100-nm region of the membrane to monitor lipid diffusion along the cellular membrane. We showed that confinement with a ZMW largely reduced fluorescent contributions from the cytosolic pool that is present when using a more standard technique such as laser-induced confocal microscopy. We show that optical confinement with ZMWs is a facile way to probe dynamic processes on the membrane surface.
| S-EPMC1305672 | biostudies-literature
Project description:Mesoscale dynamics accounts for a significant part of the ocean kinetic energy and plays a crucial role in its mixing. The presented data were generated by numerical simulation and reveal mesoscale patterns of circulation of the upper 15-m layer of the Caspian Sea. The currents in 2003-2005 are reconstructed in an eddy-resolving ocean general circulation model SZ-COMPAS using a realistic forcing. The data arrays have a very high resolution: ∼2 km in space and 4 hours in time. This is sufficient to resolve most of mesoscale features of the sea dynamics as well as a wide range of their temporal spectrum, including inertial oscillations (with period ∼18 hours), synoptic and seasonal variability. The dataset includes: (1) raw model data on the velocity vector fields on three top-layer horizons (surface, 7 m, and 15 m) in 2003, (2) the same fields averaged over every month in 2003-2005, and (3) two video-files visualizing surface currents in 2003-2005 in which sea salinity is used to trace dynamical structures. The data can be used by marine researchers to explore the Caspian Sea dynamics and its impact on the sea biogeochemical condition.
| S-EPMC7153301 | biostudies-literature
Project description:Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.
| S-EPMC10624634 | biostudies-literature
Project description:BackgroundBacterial meningitis causes a high burden of disease in the African meningitis belt, with regular seasonal hyperendemicity and sporadic short, but intense, localized epidemics during the late dry season occurring at a small spatial scale [i.e., below the district level, in individual health centers (HCs)]. In addition, epidemic waves with larger geographic extent occur every 7-10 y. Although atmospheric dust load is thought to be an essential factor for hyperendemicity, its role for localized epidemics remains hypothetic.ObjectivesOur goal was to evaluate the association of localized meningitis epidemics in HC catchment areas with the dust load and the occurrence of cases in the same population early in the dry season.MethodsWe compiled weekly reported cases of suspected bacterial meningitis at the HC resolution for 14 districts of Burkina Faso for the period 2004-2014. Using logistic regression, we evaluated the association of epidemic HC-weeks with atmospheric dust [approximated by the aerosol optical thickness (AOT) satellite product] and with the observation of early meningitis cases during October-December.ResultsAlthough AOT was strongly associated with epidemic HC-weeks in crude analyses across all HC-weeks during the meningitis season [odds ratio (OR) [Formula: see text]; 95% CI: 4.90, 9.50], the association was no longer apparent when controlling for calendar week (OR [Formula: see text]; 95% CI: 0.60, 1.50). The number of early meningitis cases reported during October-December was associated with epidemic HC-weeks in the same HC catchment area during January-May of the following year (OR for each additional early case [Formula: see text]; 95% CI: 1.06, 1.21).ConclusionsSpatial variations of atmospheric dust load do not seem to be a factor in the occurrence of localized meningitis epidemics, and the factor triggering them remains to be identified. The pathophysiological mechanism linking early cases to localized epidemics is not understood, but their occurrence and number of early cases could be an indicator for epidemic risk. https://doi.org/10.1289/EHP2752.
| S-EPMC6375477 | biostudies-literature
Project description:We present a new method of formation photoplethysmographic images with high spatial resolution from video recordings of a living body in the reflection geometry. The method (patent pending) is based on lock-in amplification of every pixel of the recorded video frames. A reference function required for synchronous detection of cardiovascular pulse waves is formed from the same frames. The method is featured by ability to visualize dynamic changes in cardiovascular pulse wave during the cardiac (or respiratory) cycle. We demonstrate that the system is capable to detect the minimal irritations of the body such as gentle scratching of the skin by own finger.
| S-EPMC3072138 | biostudies-other
Project description:The extensive collection of glossy (gl) and eceriferum (cer) mutants of maize and Arabidopsis have proven invaluable in dissecting the branched metabolic pathways that support cuticular lipid deposition. This bifurcated pathway integrates a fatty acid elongation-decarbonylative branch and a fatty acid elongation-reductive branch, which collectively has the capacity to generate hundreds of cuticular lipid metabolites. In this study, a combined transgenic and biochemical strategy was implemented to explore and compare the physiological function of three homologous genes, Gl2, Gl2-like, and CER2, in the context of this branched pathway. These biochemical characterizations integrated new extraction chromatographic procedures with high spatial resolution mass spectrometric imaging methods to profile the cuticular lipids on developing floral tissues transgenically expressing these transgenes in wild-type or cer2 mutant lines of Arabidopsis. Collectively, these datasets establish that both the maize Gl2 and Gl2-like genes are functional homologs of the Arabidopsis CER2 gene. In addition, the dynamic distribution of cuticular lipid deposition follows distinct floral organ localization patterns indicating that the fatty acid elongation-decarbonylative branch of the pathway is differentially localized from the fatty acid elongation-reductive branch of the pathway.
| S-EPMC8082717 | biostudies-literature
Project description:Novel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.
| S-EPMC6901486 | biostudies-literature
Project description:High-resolution and wide field-of-view (FOV) microscopic imaging plays a central role in diverse applications such as high-throughput screening and digital pathology. However, conventional microscopes face inherent trade-offs between the spatial resolution and FOV, which are fundamental limited by the space-bandwidth product (SBP) of the optical system. The resolution-FOV tradeoff can be effectively decoupled in Fourier ptychography microscopy (FPM), however, to date, the effective imaging NA achievable with a typical FPM system is still limited to the range of 0.4-0.7. Herein, we report, for the first time, a high-NA illumination based resolution-enhanced FPM (REFPM) platform, in which a LED-array-based digital oil-immersion condenser is used to create high-angle programmable plane-wave illuminations, endowing a 10×, 0.4 NA objective lens with final effective imaging performance of 1.6 NA. With REFPM, we present the highest-resolution results with a unprecedented half-pitch resolution of 154 nm at a wavelength of 435 nm across a wide FOV of 2.34 mm2, corresponding to an SBP of 98.5 megapixels (~50 times higher than that of the conventional incoherent microscope with the same resolution). Our work provides an important step of FPM towards high-resolution large-NA imaging applications, generating comparable resolution performance but significantly broadening the FOV of conventional oil-immersion microscopes.
| S-EPMC5430655 | biostudies-literature
Project description:Theory predicts that selection for pathogen virulence and horizontal transmission is highest at the onset of an epidemic but decreases thereafter, as the epidemic depletes the pool of susceptible hosts. We tested this prediction by tracking the competition between the latent bacteriophage ? and its virulent mutant ?cI857 throughout experimental epidemics taking place in continuous cultures of Escherichia coli. As expected, the virulent ?cI857 is strongly favored in the early stage of the epidemic, but loses competition with the latent virus as prevalence increases. We show that the observed transient selection for virulence and horizontal transmission can be fully explained within the framework of evolutionary epidemiology theory. This experimental validation of our predictions is a key step towards a predictive theory for the evolution of virulence in emerging infectious diseases.
| S-EPMC3597519 | biostudies-literature