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Chemical Engineering Science Apr 2021Motivated by analogies between the spread of infections and of chemical processes, we develop a model that accounts for infection and transport where infected...
Motivated by analogies between the spread of infections and of chemical processes, we develop a model that accounts for infection and transport where infected populations correspond to chemical species. Areal densities emerge as the key variables, thus capturing the effect of spatial density. We derive expressions for the kinetics of the infection rates, and for the important parameter , that include areal density and its spatial distribution. We present results for a batch reactor, the chemical process equivalent of the SIR model, where we examine how the dependence of on process extent, the initial density of infected individuals, and fluctuations in population densities effect the progression of the disease. We then consider spatially distributed systems. Diffusion generates traveling waves that propagate at a constant speed, proportional to the square root of the diffusivity and . Preliminary analysis shows a similar behavior for the effect of stochastic advection.
PubMed: 33518773
DOI: 10.1016/j.ces.2020.116347 -
Scientific Reports Nov 2022A semi-analytic admixed model formalism to study the stability effects of the inner crust regions against the local collective perturbations in non-rotating neutron...
A semi-analytic admixed model formalism to study the stability effects of the inner crust regions against the local collective perturbations in non-rotating neutron stars is proposed. It consists of the viscoelastic heavy neutron-rich nuclei, superfluid neutrons, and degenerate quantum electrons. A normal spherical mode analysis yields a generalized linear dispersion relation multiparametrically mimicking the inner crust features of neutron stars. A hybrid gravito-nucleo-acoustic (GNA) instability mode is found to be excited. It is demonstrated that the electron density and the inner crust curvature act as its accelerating and antidispersive agents. In contrast, the heavy neutron-rich nucleus and neutron densities act as decelerating factors. The heavy nucleus density, electron density, and geometric curvature act as its destabilizers. It is only the neutron density that acts as the GNA stabilizing agent. The heavy neutron-rich nucleus and neutron densities are found to act as dispersive broadening factors to it. The high-[Formula: see text] regions are the more unstable spectral windows indicating that the GNA mode plays a dominant role in the inner crust zone towards the local stability. Its fair reliability is indicated in light of the recent astronomic observed scenarios. It could be useful to explore acoustic mode signatures in non-rotating neutron stars and similar other compact astroobjects.
PubMed: 36411287
DOI: 10.1038/s41598-022-23854-x -
Information and Inference : a Journal... Jun 2022Estimation of density functions supported on general domains arises when the data are naturally restricted to a proper subset of the real space. This problem is...
Estimation of density functions supported on general domains arises when the data are naturally restricted to a proper subset of the real space. This problem is complicated by typically intractable normalizing constants. Score matching provides a powerful tool for estimating densities with such intractable normalizing constants but as originally proposed is limited to densities on [Formula: see text] and [Formula: see text]. In this paper, we offer a natural generalization of score matching that accommodates densities supported on a very general class of domains. We apply the framework to truncated graphical and pairwise interaction models and provide theoretical guarantees for the resulting estimators. We also generalize a recently proposed method from bounded to unbounded domains and empirically demonstrate the advantages of our method.
PubMed: 35721800
DOI: 10.1093/imaiai/iaaa041 -
Quantitative Imaging in Medicine and... Feb 2022Sjögren syndrome (SjS) is a systemic disease affecting exocrine, including ocular lacrimal, glands. It is uncertain whether ocular microvascular alterations are...
BACKGROUND
Sjögren syndrome (SjS) is a systemic disease affecting exocrine, including ocular lacrimal, glands. It is uncertain whether ocular microvascular alterations are associated with this disease. In this study, we evaluated retinal and conjunctival microvascular changes in SjS patients using optical coherence tomography angiography (OCTA).
METHODS
Twelve SjS patients (24 eyes) and 12 normal controls (24 eyes) were recruited to this study. Three-dimensional conjunctival and retinal OCTA images of each eye were captured and microvascular density was calculated. Each image was analyzed by retinal area based on the early treatment of diabetic retinopathy study method (R, S, L, and I) hemisphere segmentation method (SR, SL, IL, and IR); and central wheel division method (C1-C6). Correlation analyses were used to look for associations between retinal and conjunctival microvascular densities.
RESULTS
Superficial and deep retinal layer microvascular density was decreased in SjS patients compared with normal controls (P<0.05). This significant difference was found in both superficial and deep layers in S, L, SL, IL and C1-C3 regions, and additionally in the I and SR regions in the superficial layer. Conversely, in the conjunctiva microvascular density was higher in SjS patients than in controls. In SjS patients, a significant negative correlation was found between conjunctival and both superficial (r=-0.641; P=0.025) and deep (r=-0.958; P<0.0001) microvascular densities.
CONCLUSIONS
The changed microvascular densities measured in deep and superficial retinal layers and in the conjunctiva demonstrate that OCTA is a promising method in differentiating the eyes from those with SjS.
PubMed: 35111627
DOI: 10.21037/qims-21-234 -
International Journal of Ophthalmology 2021To investigate the retinal vascular network alterations in eyes of patients with pterygium.
AIM
To investigate the retinal vascular network alterations in eyes of patients with pterygium.
METHODS
Totally 18 left eyes from 18 female pterygium patients and 18 left eyes from 18 female healthy control subjects were enrolled. Optical coherence tomography angiography (OCTA) images were generated of the superficial retinal layer and deeper retinal layer of the macular retina for each eye. The microvascular (MIR) and macrovascular (MAR) densities were calculated and MIR, MAR, and total microvascular (TMI) density was compared in the healthy control and pterygium groups.
RESULTS
In pterygium group, in the superficial retinal layer, the vascular density in superficial MIR, superior right (SR), inferior right (IR), right (R), superficial central annuli (SC)1, SC2, and SC3 decreased significantly in the macular area (<0.05). Furthermore, the vascular density in all those decreased regions except R, was significantly and negatively correlated with the disease course (=-0.6038 to -0.7762, =0.0008), and the area size of pterygium (=-0.6043 to -0.9508, <0.05). For the deeper retinal layer, the density of deep total microvessel (DTMI), deeper MIR, SR, IR, R, DC2, and DC3 decreased significantly in macular area of pterygium patients (<0.05). Furthermore, the vascular density in all those decreased regions was significantly and negatively correlated with the disease course (=-0.6901 to -0.7795, =0.0015), and the area size of pterygium (=-0.6043 to -0.9563, <0.05). No statistically significant differences and correlation was found in other region density (|r|<0.47, >0.05).
CONCLUSION
OCTA findings suggest that pterygium patients present with decreased retinal MIR density, and the major vascular alterations occurr mainly on the bitamporal side. The vascular density of the superficial SC1, SC2, SC3 adjacent to the foveal and deep layer of DC2, DC2 regions, significantly decreased.
PubMed: 34926200
DOI: 10.18240/ijo.2021.12.08 -
The Journal of Physical Chemistry. A Nov 2023While CCSD(T) is often considered the "gold standard" of computational chemistry, the scaling of its computational cost as N limits its applicability for large and...
While CCSD(T) is often considered the "gold standard" of computational chemistry, the scaling of its computational cost as N limits its applicability for large and complex molecular systems. In this work, we apply the density-based many-body expansion [ 2020, 120, e26228] in combination with CCSD(T). The accuracy of this approach is assessed for neutral, protonated, and deprotonated water hexamers, as well as (HO) and (HO) clusters. For the neutral water clusters, we find that already with a density-based two-body expansion, we are able to approximate the supermolecular CCSD(T) energies within chemical accuracy (4 kJ/mol). This surpasses the accuracy that is achieved with a conventional, energy-based three-body expansion. We show that this accuracy can be maintained even when approximating the electron densities using Hartree-Fock instead of using coupled-cluster densities. The density-based many-body expansion thus offers a simple, resource-efficient, and highly parallelizable approach that makes CCSD(T)-quality calculations feasible where they would otherwise be prohibitively expensive.
PubMed: 37871170
DOI: 10.1021/acs.jpca.3c04591 -
Oxford Open Neuroscience 2022To faithfully transmit and decode signals released from presynaptic termini, postsynaptic compartments of neuronal synapses deploy hundreds of various proteins. In... (Review)
Review
To faithfully transmit and decode signals released from presynaptic termini, postsynaptic compartments of neuronal synapses deploy hundreds of various proteins. In addition to distinct sets of proteins, excitatory and inhibitory postsynaptic apparatuses display very different organization features and regulatory properties. Decades of extensive studies have generated a wealth of knowledge on the molecular composition, assembly architecture and activity-dependent regulatory mechanisms of excitatory postsynaptic compartments. In comparison, our understanding of the inhibitory postsynaptic apparatus trails behind. Recent studies have demonstrated that phase separation is a new paradigm underlying the formation and plasticity of both excitatory and inhibitory postsynaptic molecular assemblies. In this review, we discuss molecular composition, organizational and regulatory features of inhibitory postsynaptic densities through the lens of the phase separation concept and in comparison with the excitatory postsynaptic densities.
PubMed: 38596704
DOI: 10.1093/oons/kvac003 -
Ecology May 2022Plants are often exposed to multiple herbivores and densities of these attackers (or corresponding damage intensities) often fluctuate greatly in the field....
Plants are often exposed to multiple herbivores and densities of these attackers (or corresponding damage intensities) often fluctuate greatly in the field. Plant-mediated interactions vary among herbivore species and with changing feeding intensity, but little is known about how herbivore identity and density interact to determine plant responses and herbivore fitness. Here, we investigated this question using Triadica sebifera (tallow) and two common and abundant specialist insect herbivores, Bikasha collaris (flea beetle) and Heterapoderopsis bicallosicollis (weevil). By manipulating densities of leaf-feeding adults of these two herbivore species, we tested how variations in the intensity of leaf damage caused by flea beetle or weevil adults affected the performance of root-feeding flea beetle larvae and evaluated the potential of induced tallow root traits to predict flea beetle larval performance. We found that weevil adults consistently decreased the survival of flea beetle larvae with increasing leaf damage intensities. In contrast, conspecific flea beetle adults increased their larval survival at low damage then decreased larval survival at high damage, resulting in a unimodal pattern. Chemical analyses showed that increasing leaf damage from weevil adults linearly decreased root carbohydrates and increased root tannin, whereas flea beetle adults had opposite effects as weevil adults at low damage and similar effects as them at high damage. Furthermore, across all feeding treatments, flea beetle larval survival correlated positively with concentrations of carbohydrates and negatively with concentration of tannin, suggesting that root primary and secondary metabolism might underlie the observed effects on flea beetle larvae. Our study demonstrates that herbivore identity and density interact to determine systemic plant responses and plant-mediated effects on herbivores. In particular, effects are species-specific at low densities, but converge at high densities. These findings emphasize the importance of considering herbivore identity and density simultaneously when investigating factors driving plant-mediated interactions between herbivores, which advances our understanding of the structure and composition of herbivore communities and terrestrial food webs.
Topics: Animals; Carbohydrates; Coleoptera; Herbivory; Plant Roots; Plants; Tannins; Weevils
PubMed: 35072958
DOI: 10.1002/ecy.3647 -
Ecology and Evolution Oct 2023The western honey bee, , lives worldwide in approximately 102 million managed hives but also wild throughout much of its native and introduced range. Despite the... (Review)
Review
The western honey bee, , lives worldwide in approximately 102 million managed hives but also wild throughout much of its native and introduced range. Despite the global importance of as a crop pollinator, wild colonies have received comparatively little attention in the scientific literature and basic information regarding their density and abundance is scattered. Here, we review 40 studies that have quantified wild colony density directly ( = 33) or indirectly using genetic markers ( = 7) and analyse data from 41 locations worldwide to identify factors that influence wild colony density. We also compare the density of wild and managed colonies at a regional scale using data on managed colonies from the Food and Agriculture Organization (FAO). Wild colony densities varied from 0.1 to 24.2/km and were significantly lower in Europe (average of 0.26/km) than in Northern America (1.4/km), Oceania (4.4/km), Latin America (6.7/km) and Africa (6.8/km). Regional differences were not significant after controlling for both temperature and survey area, suggesting that cooler climates and larger survey areas may be responsible for the low densities reported in Europe. Managed colony densities were 2.2/km in Asia, 1.2/km in Europe, 0.2/km, in Northern America, 0.2/km in Oceania, 0.5/km in Latin America and 1/km in Africa. Wild colony densities exceeded those of managed colonies in all regions except Europe and Asia. Overall, there were estimated to be between two and three times as many wild colonies as managed worldwide. More wild colony surveys, particularly in Asia and South America, are needed to assess the relative density of wild and managed colonies at smaller spatial scales.
PubMed: 37841222
DOI: 10.1002/ece3.10609 -
Proceedings of the National Academy of... Oct 2021Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional...
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of animal cells appears tuned close to a two-dimensional liquid-liquid critical point. In some examples, cytoplasmic proteins aggregate at plasma membrane domains, forming structures such as the postsynaptic density and diverse signaling clusters. Here we examine the physics of these surface densities, employing minimal simulations of polymers prone to phase separation coupled to an Ising membrane surface in conjunction with a complementary Landau theory. We argue that these surface densities are a phase reminiscent of prewetting, in which a molecularly thin three-dimensional liquid forms on a usually solid surface. However, in surface densities the solid surface is replaced by a membrane with an independent propensity to phase separate. We show that proximity to criticality in the membrane dramatically increases the parameter regime in which a prewetting-like transition occurs, leading to a broad region where coexisting surface phases can form even when a bulk phase is unstable. Our simulations naturally exhibit three-surface phase coexistence even though both the membrane and the polymer bulk only display two-phase coexistence on their own. We argue that the physics of these surface densities may be shared with diverse functional structures seen in eukaryotic cells.
Topics: Animals; Cell Membrane; Cytoplasm; Polymers; Post-Synaptic Density; Proteins; Thermodynamics
PubMed: 34599097
DOI: 10.1073/pnas.2103401118