scholarly journals bmotif: a package for motif analyses of bipartite networks

2018 ◽  
Author(s):  
Benno I. Simmons ◽  
Michelle J. M. Sweering ◽  
Maybritt Schillinger ◽  
Lynn V. Dicks ◽  
William J. Sutherland ◽  
...  
Keyword(s):  
Scale Structure ◽  
Individual Species ◽  
Mathematical Framework ◽  
List Type ◽  
Bipartite Networks ◽  
Diverse Range ◽  
Wide Range ◽  
Macro Scale ◽  
Plant Pollinator ◽  
Meso Scale

AbstractBipartite networks are widely-used to represent a diverse range of species interactions, such as pollination, herbivory, parasitism and seed dispersal. The structure of these networks is usually characterised by calculating one or more metrics that capture different aspects of network architecture. While these metrics capture useful properties of networks, they only consider structure at the scale of the whole network (the macro-scale) or individual species (the micro-scale). ‘Meso-scale’ structure between these scales is usually ignored, despite representing ecologically-important interactions. Network motifs are a framework for capturing this meso-scale structure and are gaining in popularity. However, there is no software available in R, the most popular programming language among ecologists, for conducting motif analyses in bipartite networks. Similarly, no mathematical formalisation of bipartite motifs has been developed.Here we introduce bmotif: a package for counting motifs, and species positions within motifs, in bipartite networks. Our code is primarily an R package, but we also provide MATLAB and Python code of the core functionality. The software is based on a mathematical framework where, for the first time, we derive formal expressions for motif frequencies and the frequencies with which species occur in different positions within motifs. This framework means that analyses with bmotif are fast, making motif methods compatible with the permutational approaches often used in network studies, such as null model analyses.We describe the package and demonstrate how it can be used to conduct ecological analyses, using two examples of plant-pollinator networks. We first use motifs to examine the assembly and disassembly of an Arctic plant-pollinator community, and then use them to compare the roles of native and introduced plant species in an unrestored site in Mauritius.bmotif will enable motif analyses of a wide range of bipartite ecological networks, allowing future research to characterise these complex networks without discarding important meso-scale structural detail.

Effects of Meso-Scale Structure and Interactions on Macro-Scale Mechanical Properties in Polymeric Materials

2004 ◽  
Vol 261-263 ◽  
pp. 747-752
Author(s):  
Akira Shinozaki ◽  
Masaki Omiya ◽  
Hisahiro Inoue ◽  
Kikuo Kishimoto
Keyword(s):  
Mechanical Properties ◽  
Network Models ◽  
Fem Analysis ◽  
Polymeric Materials ◽  
Scale Structure ◽  
Polymer Chains ◽  
Scale Interactions ◽  
Macro Scale ◽  
The Relationship ◽  
Meso Scale

The mechanical properties of polymers are strongly influenced by meso-scale structure such as entanglement, orientation, folded chain, etc. However, the relationship between the meso-scale structure and macro-scale mechanical properties of polymers has not been clarified. In this paper, network models of polymer chains are introduced to simulate the meso-scale interactions. From the FEM analysis of this model, the effects of interactions on macro-scale mechanical properties are investigated.

scholarly journals Broad-scale Applications of the Raspberry Pi: A Review and Guide for Biologists

2021 ◽  
Author(s):  
Jolle Wolter Jolles
Keyword(s):  
Scientific Community ◽  
Large Scale ◽  
Low Cost ◽  
Ease Of Use ◽  
Plant Phenotyping ◽  
Raspberry Pi ◽  
Ecosystem Monitoring ◽  
Diverse Range ◽  
Wide Range ◽  
Macro Scale

The field of biology has seen tremendous technological progress in recent years, fuelled by the exponential growth in processing power and high-level computing, and the rise of global information sharing. Low-cost single-board computers are predicted to be one of the key technological advancements to further revolutionise this field. So far, an overview of current uptake of these devices and a general guide to help researchers integrate them in their work has been missing. In this paper I focus on the most widely used single board computer, the Raspberry Pi. Reviewing its broad applications and uses across the biological domain shows that since its release in 2012 the Raspberry Pi has been increasingly taken up by biologists, both in the lab, the field, and in the classroom, and across a wide range of disciplines. A hugely diverse range of applications already exist that range from simple solutions to dedicated custom-build devices, including nest-box monitoring, wildlife camera trapping, high-throughput behavioural recordings, large-scale plant phenotyping, underwater video surveillance, closed-loop operant learning experiments, and autonomous ecosystem monitoring. Despite the breadth of its implementations, the depth of uptake of the Raspberry Pi by the scientific community is still limited. The broad capabilities of the Raspberry Pi, combined with its low cost, ease of use, and large user community make it a great research tool for almost any project. To help accelerate the uptake of Raspberry Pi’s by the scientific community, I provide detailed guidelines, recommendations, and considerations, and 30+ step-by-step guides on a dedicated accompanying website (raspberrypi-guide.github.io). I hope with this paper to generate more awareness about the Raspberry Pi and thereby fuel the democratisation of science and ultimately help advance our understanding of biology, from the micro- to the macro-scale.

scholarly journals Standard Astronomical Sources for the Space Telescope

1985 ◽  
Vol 111 ◽  
pp. 357-360
Author(s):  
Ralph C. Bohlin
Keyword(s):  
List Type ◽  
Scientific Instruments ◽  
Diverse Range ◽  
Space Telescope ◽  
Wide Range ◽  
Flat Field ◽  
Imaging Polarimetry ◽  
Working Groups ◽  
Measurement Capabilities

The Space Telescope (ST) will require many types of standard sources for a diverse range of calibrations to be performed after launch. The scientific instruments are sensitive to a wide range of wavelengths from 1050 to 11,000Å and encompass a broad range of measurement capabilities including astrometry, photometry, imaging, polarimetry, and spectroscopy. To verify proper operations of each instrument and to provide quantitative calibrations, a diverse range of standard sources and fields are required. In order to select targets that satisfy the requirements of the Instrument Definition Teams and the long term responsibilities of the Science Institute, six groups containing a total of 25 astronomers are defining the calibration targets to be observed after launch. The six categories of ST standard sources are: 1)Ultraviolet Spectrophotometric2)Ground Based Spectrophotometric and Photometric3)Wavelength4)Astrometric5)Polarimetric6)Spatially Flat FieldThe data in these categories will be collected from the literature or through new observing programs as appropriate. These six reports of the working groups outline the calibrations and proposed targets for all of the scientific instruments on ST. The collected data on each set of standard sources should be published in the refereed literature.

scholarly journals SARS-CoV-2 acquisition and immune pathogenesis among school-aged learners in four diverse schools

2021 ◽  
Author(s):  
Dan M. Cooper ◽  
Michael Z. Zulu ◽  
Allen Jankeel ◽  
Izabela Coimbra Ibraim ◽  
Jessica Ardo ◽  
...  
Keyword(s):  
Immune Responses ◽  
Low Income ◽  
Neutralizing Antibodies ◽  
Mitigation Strategies ◽  
Student Diversity ◽  
List Type ◽  
Diverse Range ◽  
Humoral And Cellular Immunity ◽  
Wide Range ◽  
Diverse Schools

Abstract Background Understanding SARS-CoV-2 infection in children is necessary to reopen schools safely. Methods We measured SARS-CoV-2 infection in 320 learners [10.5 ± 2.1 (sd); 7–17 y.o.] at four diverse schools with either remote or on-site learning. Schools A and B served low-income Hispanic learners; school C served many special-needs learners, and all provided predominantly remote instruction. School D served middle- and upper-income learners, with predominantly on-site instruction. Testing occurred in the fall (2020), and 6–8 weeks later during the fall-winter surge (notable for a tenfold increase in COVID-19 cases). Immune responses and mitigation fidelity were also measured. Results We found SARS-CoV-2 infections in 17 learners only during the surge. School A (97% remote learners) had the highest infection (10/70, 14.3%, p < 0.01) and IgG positivity rates (13/66, 19.7%). School D (93% on-site learners) had the lowest infection and IgG positivity rates (1/63, 1.6%). Mitigation compliance [physical distancing (mean 87.4%) and face-covering (91.3%)] was remarkably high at all schools. Documented SARS-CoV-2-infected learners had neutralizing antibodies (94.7%), robust IFN-γ + T cell responses, and reduced monocytes. Conclusions Schools can implement successful mitigation strategies across a wide range of student diversity. Despite asymptomatic to mild SARS-CoV-2 infection, children generate robust humoral and cellular immune responses. Impact Successful COVID-19 mitigation was implemented across a diverse range of schools. School-associated SARS-CoV-2 infections reflect regional rates rather than remote or on-site learning. Seropositive school-aged children with asymptomatic to mild SARS-CoV-2 infections generate robust humoral and cellular immunity.

scholarly journals Uncovering indirect interactions in bipartite ecological networks

2018 ◽  
Author(s):  
Benno I. Simmons ◽  
Alyssa R. Cirtwill ◽  
Nick J. Baker ◽  
Lynn V. Dicks ◽  
Daniel B. Stouffer ◽  
...  
Keyword(s):  
Ecological Networks ◽  
Indirect Interactions ◽  
Ecological Communities ◽  
Bipartite Networks ◽  
New Paradigm ◽  
Diverse Range ◽  
Constituent Species ◽  
Quantitative Analyses ◽  
Plant Pollinator ◽  
New Framework

AbstractIndirect interactions play an essential role in governing population, community and coevolutionary dynamics across a diverse range of ecological communities. Such communities are widely represented as bipartite networks: graphs depicting interactions between two groups of species, such as plants and pollinators or hosts and parasites. For over thirty years, studies have used indices, such as connectance and species degree, to characterise the structure of these networks and the roles of their constituent species. However, compressing a complex network into a single metric necessarily discards large amounts of information about indirect interactions. Given the large literature demonstrating the importance and ubiquity of indirect effects, many studies of network structure are likely missing a substantial piece of the ecological puzzle. Here we use the emerging concept of bipartite motifs to outline a new framework for bipartite networks that incorporates indirect interactions. While this framework is a significant departure from the current way of thinking about networks, we show that this shift is supported by quantitative analyses of simulated and empirical data. We use simulations to show how consideration of indirect interactions can highlight ecologically important differences missed by the current index paradigm. We extend this finding to empirical plant-pollinator communities, showing how two bee species, with similar direct interactions, differ in how specialised their competitors are. These examples underscore the need for a new paradigm for bipartite ecological networks: one incorporating indirect interactions.

Multi-Scale Investigation on Residual Strength of Jacket Platform With Fatigue Crack Damage

2015 ◽  
Author(s):  
Ren Hua Wang ◽  
Xiang Zou ◽  
Pei Lin Dou ◽  
Yuan Yuan Fang ◽  
Guang-en Luo
Keyword(s):  
Fatigue Crack ◽  
Residual Strength ◽  
Scale Structure ◽  
Scale Model ◽  
Wave Load ◽  
Jacket Platform ◽  
Multi Scale ◽  
Extreme Load ◽  
Macro Scale ◽  
Meso Scale

Fatigue crack damage caused by the wave load brings the structure of jacket platform in service potential failure risk when subjected to the extreme load. However, there is lack of efficient method to evaluate the influence of crack damage on the structural performance because of the huge scale difference between the meso-scale damage and the macro-scale structure. Based on the multi-scale finite element method (FEM), to improve the efficiency of structural analysis, the damaged region of the structure is modeled with fine FE mesh (shell element) to describe the fatigue crack, and the undamaged area is modeled with coarse FE mesh (beam element). Furthermore, the applicability and superiority of this multi-scale model was validated through comparing the results obtained from the beam, multi-scale and shell models. The influence of the time-varying crack damage on the residual strength of jacket platform is then revealed based on the multi-scale FE model. The results show that the proposed multi-scale method can accurately describe fatigue crack damage in the macro-scale structure, and be applied to investigate the influence of meso-scale structural damage under the extreme load condition.

scholarly journals Dynamic visualisation of million-tip trees: the OneZoom project

2020 ◽  
Author(s):  
Yan Wong ◽  
James Rosindell
Keyword(s):  
Science Communication ◽  
Tree Of Life ◽  
Individual Species ◽  
List Type ◽  
Data Synthesis ◽  
Wide Range ◽  
Complete Tree ◽  
Client Side ◽  
Guided Tours

AbstractThe complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on a relatively old mobile device.The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in and supporting multiple applications including exhibition kiosks and digital art.After eight years of work, our tree of life explorer is now broadly complete, it has attracted over 1.3 million users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.

scholarly journals Extinction models of robustness for weighted ecological networks

2017 ◽  
Author(s):  
Miranda S. Bane ◽  
Michael J. O. Pocock ◽  
Richard James
Keyword(s):  
Network Structure ◽  
Structural Heterogeneity ◽  
Ecological Networks ◽  
List Type ◽  
Bipartite Networks ◽  
Opposing Effects ◽  
The Impact ◽  
Plant Pollinator ◽  
Binary Networks ◽  
New Framework

AbstractAnalysis of ecological networks is a valuable approach to understanding the vulnerability of systems to environmental change. The tolerance of ecological networks to co-extinctions, resulting from sequences of primary extinctions, is a widely-used tool for modelling network ‘robustness’. Previously, these ‘extinction models’ have been developed for and applied mostly to binary networks and recently used to predict cascades of co-extinctions in plant-pollinator networks. There is a need for robustness models that can make the most of the weighted data available and most importantly there is a need to understand how the structure of a network affects its robustness.Here, we developed a framework of extinction models for bipartite ecological networks (specifically plant-pollinator networks). In previous models co-extinctions occurred when nodes lost all their links, but by relaxing this rule (according to a set threshold) our models can be applied to binary and weighted networks, and can permit structurally correlated extinctions, i.e. the potential for avalanches of extinctions. We tested how the average and the range of robustness values is impacted by network structure and the impact of structurally-correlated extinctions sampling non-uniformly from the distribution of random extinction sequences.We found that the way that structurally-correlated extinctions are modelled impacts the results; our two ecologically-plausible models produce opposing effects which shows the importance of understanding the model. We found that when applying the models to networks with weighted interactions, the effects are amplified and the variation in robustness increases. Variation in robustness is a key feature of these extinction models and is driven by the structural heterogeneity (i.e. the skewness of the degree distribution) of nodes (specifically, plant nodes) in the network.Our new framework of models enables us to calculate robustness with weighted, as well as binary, bipartite networks, and to make direct comparisons between models and between networks. This allows us to differentiate effects of the model and of the data (network structure) which is vital for those making ecological inferences from robustness models. The models can be applied to mutualistic and antagonistic networks, and can be extended to food webs.

Comparison of Deterministic and Linear Cosine Spatial Filtering of Transmission Electron Micrographs

1972 ◽  
Vol 30 ◽  
pp. 596-597
Author(s):  
David A. Ansley
Keyword(s):  
Spherical Aberration ◽  
Focal Length ◽  
Chromatic Aberration ◽  
Spatial Filter ◽  
Operating Conditions ◽  
Objective Lens ◽  
List Type ◽  
Spatial Filters ◽  
Transmission Electron ◽  
Wide Range

The coherence of the electron flux of a transmission electron microscope (TEM) limits the direct application of deconvolution techniques which have been used successfully on unmanned spacecraft programs. The theory assumes noncoherent illumination. Deconvolution of a TEM micrograph will, therefore, in general produce spurious detail rather than improved resolution.A primary goal of our research is to study the performance of several types of linear spatial filters as a function of specimen contrast, phase, and coherence. We have, therefore, developed a one-dimensional analysis and plotting program to simulate a wide 'range of operating conditions of the TEM, including adjustment of the:(1) Specimen amplitude, phase, and separation(2) Illumination wavelength, half-angle, and tilt(3) Objective lens focal length and aperture width(4) Spherical aberration, defocus, and chromatic aberration focus shift(5) Detector gamma, additive, and multiplicative noise constants(6) Type of spatial filter: linear cosine, linear sine, or deterministic

Triply-periodic nanostructures in surfactant, block copolymer, and biomembrane systems, and simulation of TEMs

1993 ◽  
Vol 51 ◽  
pp. 884-885
Author(s):  
David M. Anderson ◽  
Tomas Landh
Keyword(s):  
Liquid Crystalline ◽  
Diblock Copolymers ◽  
Cubic Phase ◽  
List Type ◽  
Interpenetrating Networks ◽  
Triply Periodic ◽  
Wide Range ◽  
Bicontinuous Cubic ◽  
Phase Liquid ◽  
Dividing Surface

First discovered in surfactant-water liquid crystalline systems, so-called ‘bicontinuous cubic phases’ have the property that hydropnilic and lipophilic microdomains form interpenetrating networks conforming to cubic lattices on the scale of nanometers. Later these same structures were found in star diblock copolymers, where the simultaneous continuity of elastomeric and glassy domains gives rise to unique physical properties. Today it is well-established that the symmetry and topology of such a morphology are accurately described by one of several triply-periodic minimal surfaces, and that the interface between hydrophilic and hydrophobic, or immiscible polymer, domains is described by a triply-periodic surface of constant, nonzero mean curvature. One example of such a dividing surface is shown in figure 5.The study of these structures has become of increasing importance in the past five years for two reasons:1)Bicontinuous cubic phase liquid crystals are now being polymerized to create microporous materials with monodispersed pores and readily functionalizable porewalls; figure 3 shows a TEM from a polymerized surfactant / methylmethacrylate / water cubic phase; and2)Compelling evidence has been found that these same morphologies describe biomembrane systems in a wide range of cells.

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