Congestion-gradient driven transport on complex networks

We present a study of transport on complex networks with routing based on local information. Particles hop from one node of the network to another according to a set of routing rules with different degrees of congestion awareness, ranging from random diffusion to rigid congestion-gradient driven flow. Each node can be either source or destination for particles and all nodes have the same routing capacity, which are features of ad-hoc wireless networks. It is shown that the transport capacity increases when a small amount of congestion awareness is present in the routing rules, and that it then decreases as the routing rules become too rigid when the flow becomes strictly congestion-gradient driven. Therefore, an optimum value of the congestion awareness exists in the routing rules. It is also shown that, in the limit of a large number of nodes, networks using routing based on local information jam at any nonzero load. Finally, we study the correlation between congestion at node level and a betweenness centrality measure.Comment: 11 pages, 8 figure

High contrast ultrasonic imaging of resin-rich regions in graphite/epoxy composites using entropy

This study compares different approaches for imaging a near-surface resin-rich defect in a thin graphite/epoxy plate using backscattered ultrasound. The specimen was created by cutting a circular hole in the second ply; this region filled with excess resin from the graphite/epoxy sheets during the curing process. Backscat-tered waveforms were acquired using a 4 in. focal length, 5MHz center frequency broadband transducer, scanned on a 100 × 100 grid of points that were 0.03 × 0.03 in. apart. The specimen was scanned with the defect side closest to the transducer. Consequently, the reflection from the resin-rich region cannot be gated from the large front-wall echo. At each point in the grid 256 waveforms were averaged together and subsequently used to produce peak-to-peak, Signal Energy (sum of squared digitized waveform values), as well as entropy images of two different types (a Renyi entropy, and a joint entropy). As the figure shows, all of the entropy images exhibit better border delineation and defect contrast than the either the peak-to-peak or Signal Energy. The best results are obtained using the joint entropy of the backscattered waveforms with a reference function. Two different references are examined. The first is a reflection of the insonifying pulse from a stainless steel reflector. The second is an approximate optimum obtained from an iterative parametric search. The joint entropy images produced using this reference exhibit three times the contrast obtained in previous studies

Entropy vs. Energy Waveform Processing: A Comparison Based on the Heat Equation

Virtually all modern imaging devices collect electromagnetic or acoustic waves and use the energy carried by these waves to determine pixel values to create what is basically an “energy” picture. However, waves also carry “information,” as quantified by some form of entropy, and this may also be used to produce an “information” image. Numerous published studies have demonstrated the advantages of entropy, or “information imaging”, over conventional methods. The most sensitive information measure appears to be the joint entropy of the collected wave and a reference signal. The sensitivity of repeated experimental observations of a slowly-changing quantity may be defined as the mean variation (i.e., observed change) divided by mean variance (i.e., noise). Wiener integration permits computation of the required mean values and variances as solutions to the heat equation, permitting estimation of their relative magnitudes. There always exists a reference, such that joint entropy has larger variation and smaller variance than the corresponding quantities for signal energy, matching observations of several studies. Moreover, a general prescription for finding an “optimal” reference for the joint entropy emerges, which also has been validated in several studies

Dominance of photo over chromatic acclimation strategies by habitat-forming mesophotic red algae

Funding was provided by a Leverhulme Trust Research Project grant no. (RPG-2018-113) to H.L.B., G.A.T. and I.D.W.S., an Engineering and Physical Sciences Research Council grant (EP/L017008/1) to G.A.T. and I.D.W.S., and a São Paulo Research Foundation (FAPESP) individual grant (#2016/14017-0) to G.H.P.-F.Red coralline algae are the deepest living macroalgae, capable of creating spatially complex reefs from the intertidal to 100+ m depth with global ecological and biogeochemical significance. How these algae maintain photosynthetic function under increasingly limiting light intensity and spectral availability is key to explaining their large depth distribution. Here, we investigated the photo- and chromatic acclimation and morphological change of free-living red coralline algae towards mesophotic depths in the Fernando do Noronha archipelago, Brazil. From 13 to 86 m depth, thalli tended to become smaller and less complex. We observed a dominance of the photo-acclimatory response, characterized by an increase in photosynthetic efficiency and a decrease in maximum electron transport rate. Chromatic acclimation was generally stable across the euphotic-mesophotic transition with no clear depth trend. Taxonomic comparisons suggest these photosynthetic strategies are conserved to at least the Order level. Light saturation necessitated the use of photoprotection to 65 m depth, while optimal light levels were met at 86 m. Changes to the light environment (e.g. reduced water clarity) due to human activities therefore places these mesophotic algae at risk of light limitation, necessitating the importance of maintaining good water quality for the conservation and protection of mesophotic habitats.Publisher PDFPeer reviewe

Ecosystem engineer morphological traits and taxon identity shape biodiversity across the euphotic-mesophotic transition

Funding was provided by a Leverhulme Trust Research Project grant (no. RPG-2018-113) to H.L.B., G.A.T. and I.D.W.S., an Engineering and Physical Sciences Research Council grant (no. EP/L017008/1) to G.A.T. and I.D.W.S., and a São Paulo Research Foundation (FAPESP) individual grant (no. 2016/14017-0) to G.H.P.F.The euphotic-mesophotic transition is characterized by dramatic changes in environmental conditions, which can significantly alter the functioning of ecosystem engineers and the structure of their associated communities. However, the drivers of biodiversity change across the euphotic-mesophotic transition remain unclear. Here, we investigated the mechanisms affecting the biodiversity-supporting potential of free-living red coralline algae-globally important habitat creators-towards mesophotic depths. Across a 73 m depth gradient, we observed a general decline in macrofaunal biodiversity (fauna abundance, taxon richness and alpha diversity), but an increase in beta-diversity (i.e. variation between assemblages) at the deepest site (86 m depth, where light levels were less than 1% surface irradiance). We identified a gradient in abundance decline rather than distinct ecological shifts, driven by a complex interaction between declining light availability, declining size of the coralline algal host individuals and a changing host taxonomy. However, despite abundance declines, high between-assemblage variability at deeper depths allowed biodiversity-supporting potential to be maintained, highlighting their importance as coastal refugia.PostprintPeer reviewe

Severe childhood malaria syndromes defined by plasma proteome profiles

BACKGROUND Cerebral malaria (CM) and severe malarial anemia (SMA) are the most serious life-threatening clinical syndromes of Plasmodium falciparum infection in childhood. Therefore it is important to understand the pathology underlying the development of CM and SMA, as opposed to uncomplicated malaria (UM). Different host responses to infection are likely to be reflected in plasma proteome-patterns that associate with clinical status and therefore provide indicators of the pathogenesis of these syndromes. METHODS AND FINDINGS Plasma and comprehensive clinical data for discovery and validation cohorts were obtained as part of a prospective case-control study of severe childhood malaria at the main tertiary hospital of the city of Ibadan, an urban and densely populated holoendemic malaria area in Nigeria. A total of 946 children participated in this study. Plasma was subjected to high-throughput proteomic profiling. Statistical pattern-recognition methods were used to find proteome-patterns that defined disease groups. Plasma proteome-patterns accurately distinguished children with CM and with SMA from those with UM, and from healthy or severely ill malaria-negative children. CONCLUSIONS We report that an accurate definition of the major childhood malaria syndromes can be achieved using plasma proteome-patterns. Our proteomic data can be exploited to understand the pathogenesis of the different childhood severe malaria syndromes

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.

Microglia, the resident immune cells of the brain, rapidly change states in response to their environment, but we lack molecular and functional signatures of different microglial populations. Here, we analyzed the RNA expression patterns of more than 76,000 individual microglia in mice during development, in old age, and after brain injury. Our analysis uncovered at least nine transcriptionally distinct microglial states, which expressed unique sets of genes and were localized in the brain using specific markers. The greatest microglial heterogeneity was found at young ages; however, several states-including chemokine-enriched inflammatory microglia-persisted throughout the lifespan or increased in the aged brain. Multiple reactive microglial subtypes were also found following demyelinating injury in mice, at least one of which was also found in human multiple sclerosis lesions. These distinct microglia signatures can be used to better understand microglia function and to identify and manipulate specific subpopulations in health and disease

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software