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25 results for “integration and modularity”
Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia
<p><span><span><span><span><span><span><span><span><span><span><span>Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via the stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channeling morphological evolution along lines of least resistance—a process that may be particularly important in the accumulation of disparity among organisms with accretionary growth, as in many invertebrate systems. We use a time-calibrated phylogenetic hypothesis and high-density, 3D semilandmarking to analyze the relationship between modularity, integration, and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of body features that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve evolutionary-development and biomechanics. While the venerid body is tightly integrated in absolute terms, increasing modularity strength among subclades and ecologies appears to correlate with increasing disparity, indicating that shifts towards more mosaic evolution beget higher morphologic variance in this speciose family.</span></span></span></span></span></span></span></span></span></span></span></p>
MIntO: a Modular and Scalable Pipeline for Microbiome Metagenomic and Metatranscriptomic Meta-omics Data Integration
<p>To illustrate the use of MIntO, a set of 91 human fecal metagenomes from the Inflammatory Bowel Disease Multi’omics Database was selected (IBDMDB). We selected six participants diagnosed as non-IBD (P6018 (nIBD1), M2072 (nIBD2)); Crohn’s disease (H4006 (CD1) and H4020 (CD2)); and ulcerative colitis (H4019 (UC1) and H4035 (UC2)) that were followed for one year each. </p> <p>Here, we present the results from the <em>genome-based assembly-dependent</em> mode, where we used 91 metagenomic high-quality reads<strong> </strong>to recover 163 high-quality MAGs, which constituted a set of non-redundant genomes.</p>
Integrated modular Avionics - IMA by GMV
<p>This is an Cleansky2 Ubbick (Utility Building Blocks for Cockpit) project dissemination Action, done in 23th July 2018, presented in the Farnborough International Air Show 2018, ShowCentre, ETPS Road Farnborough, Hampshire,UK. Author José Neves(jose.neves@gmv.com). Title: "Integrated modular Avionics - IMA by GMV". This video features the GMV IMA products like SIMA, Arinc 664 Emulator, A664 Configurator and an overview of the development of XKY, a novel DO-178C DAL-A, safety critical, real time, partitioned operating system, developed under UBBICK project.</p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
tttrlib: modular software for integrating fluorescence spectroscopy and imaging
<p>This repository contains scripts and datasets associated with the manuscript "tttrlib: modular software for integrating fluorescence spectroscopy and imaging". The software is designed to facilitate the analysis of fluorescence spectroscopy and imaging data to enable integration with molecular modeling.</p> <p>The provided scripts encompass various functionalities, including:</p> <ul> <li>Single-molecule FRET (smFRET) analysis for studying conformational dynamics, particularly focusing on human guanylate binding protein 1 (hGBP1).</li> <li>Comprehensive image spectroscopy workflows applicable to murine guanylate binding protein 2 (mGBP2), featuring intensity and time-resolved analyses.</li> <li>Tools for burst variance analysis (BVA), multiparameter fluorescence detection, and correlative analysis of fluorescence lifetime and intensity.</li> </ul> <p>Datasets for both hGBP1 and mGBP2 are included to exemplify the software's capabilities in real-world applications.</p>
Simultaneous integration and modularity underlie the exceptional body shape diversification of characiform fishes
<p class="MsoNormal">Evolutionary biology has long striven to understand why some lineages diversify exceptionally while others do not. Most studies have focused on how extrinsic factors can promote differences in diversification dynamics, but a clade's intrinsic modularity and integration can also catalyze or restrict its evolution. Here, we integrate geometric morphometrics, phylogenetic comparative methods and visualizations of covariance to infer the presence of distinct modules in the body plan of Characiformes, an ecomorphologically diverse fish radiation. Strong covariances reveal a cranial module, and more subtle patterns support a statistically significant subdivision of the postcranium into anterior (precaudal) and posterior (caudal) modules. We uncover substantial covariation among cranial and postcranial landmarks, indicating body-wide evolutionary integration as lineages transition between compressiform and fusiform body shapes. A novel method of matrix subdivision reveals that within- and among-module covariation contributes substantially to the overall eigenstructure of characiform morphospace, and that both phenomena led to biologically important divergence among characiform lineages. Functional integration between the cranium and post-cranial skeleton appears to have allowed lineages to optimize the aspect ratio of their bodies for locomotion, while the capacity for independent change in the head, body and tail likely eased adaptation to diverse dietary and hydrological regimes. These results reinforce a growing consensus that modularity and integration synergize to promote diversification. </p>
ROS 2 Bags acquired from AgRob Modular-e during the IV SCORPION Integration (Aymavilles, Italy)
<p>ROS 2 Bags acquired with the AgRob Modular-e robot during the IV SCORPION Integration in Cave des Onze Communes vineyard (Aymavilles, Italy), between 13 and 15 June 2023.<br><br>Main topics available include:<br>- Robot odometry (/odom) [nav_msgs/msg/Odometry]<br>- Redshift UM7 IMU data (/eut_sensors/imu/data) [sensor_msgs/msg/Imu]<br>- RS-LIDAR 3D scans (/rslidar_points) [sensor_msgs/msg/PointCloud2]<br>- Livox MID-70 scans in proprietary format (/livox/lidar) [livox_ros_driver/msg/CustomMsg]<br>- U-Blox ZED-F9P base receiver GNSS coordinates (/base/fix) [sensor_msgs/msg/NavSatFix]<br>- U-Blox ZED-F9P heading data from base-rover moving baseline setup (/rover/navheading) [sensor_msgs/msg/Imu]<br><br>Datasets description:<br><br>2023-06-13T161127Z - Robot navigating across two crop rows, closing a loop, with RS-LIDAR, Livox MID-70 and IMU data available.<br>2023-06-13T170852Z - Same as previous, but with GNSS data from SCORPION receiver (no data from U-Blox)<br>2023-06-13T175518Z - Robot navigating across three crop rows, forming an 8. No IMU or odometry data available.<br>2023-06-14T174658Z - Robot navigating along five crop rows with Livox data, base+rover GNSS, IMU and wheel odometry.<br>2023-06-15T110725Z - Robot navigating along four crop rows (forming loops), with RS-LIDAR data, base+rover GNSS, IMU and wheel odometry. Dataset interrupted in the middle of last row when returning to base.<br>2023-06-15T110725Z - Robot navigating along three crop rows (forming an 8), with RS-LIDAR data, base+rover GNSS, IMU and wheel odometry.<br><br>The measured transformations (estimated) between robot and sensor frames are found below (format: [x y z yaw pitch roll]). Please note these are not recorded with the datasets and must be included as static transforms using the tf2_ros package.</p><p>"base_footprint" to "imu_link": ["-0.05", "0", "0.759", "0", "0", "0"]<br>"imu_link" to "rslidar": ["0", "0", "-0.05464", "3.14159", "0", "0"]<br>"imu_link" to "livox_frame": ["0.0698", "0", "-0.14464", "0", "0", "0"]<br>"imu_link" to "gps_base": ["-0.025", "0", "0.27396", "3.14159", "0.0", "0"]<br>"gps_base" to "gps_rover": ["0.7", "0", "0", "0", "0", "0"]</p>
Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia
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Simultaneous integration and modularity underlie the exceptional body shape diversification of characiform fishes
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Data from: Ontogenetic changes in the phenotypic integration and modularity of leaf functional traits
1.Changes in resource availability, functional demands, hormonal regulation and developmental constraints can promote differences in the expression of leaf traits during plant development and foster changes in the targets of natural selection. As a consequence, the pattern and magnitude of covariation among traits, and therefore their phenotypic integration and modularity are equally expected to change throughout ontogeny. However, these changes have not been described yet. 2.We measured leaf economic, defensive and morphological traits in plants of Turnera velutina and estimated the magnitude and pattern of foliar integration and modularity for juvenile and reproductive individuals. In addition, we assessed the relationship between plant biomass and foliar integration within and among ontogenetic stages. 3.Both the pattern and magnitude of foliar integration changed across plant ontogeny. Foliar integration was lower in juvenile than in reproductive plants, and the pattern of phenotypic integration and modularity was different between ontogenetic stages: whereas leaves from juvenile plants showed two functional modules related to plant defence and leaf economy, traits from reproductive plants had greater interconnectivity and hence lower modularity. 4.The relationship between plant biomass and foliar integration was negative within each ontogenetic stage but positive between ontogenetic stages, suggesting that processes intrinsic to plant development influenced the magnitude of foliar integration to a greater extent than plant size. 5.Our findings indicate that plants can change the patterns of covariation among leaf traits during their development. Whereas a lower foliar integration in juvenile plants could allow for greater lability to explore a multi-trait phenotypic space, canalization of leaf attributes along ontogeny should promote greater phenotypic integration, constraining the number of multi-trait combinations that plants can express. Hence, we suggest that ontogenetic changes in foliar integration allow plants to deal with changing selective dynamics and physiological priorities along their development.
ROS 2 Bag acquired from AgRob Modular-e during the V SCORPION Integration (Quinta do Seixo, Portugal)
<p>ROS 2 Bag acquired with the AgRob Modular-e robot during the V SCORPION Integration in Quinta do Seixo (Valença do Douro, Portugal), on October 26, 2023.<br><br>Dataset description:<br>rosbag2_2023_10_26-16_22_30 - Robot navigating across four crop rows in a steep slope vineyard, returning to the main road.<br><br>Main topics available include:<br>- Redshift UM7 IMU data (/eut_sensors/imu/data)<br>- RS-LIDAR 3D scans (/rslidar_points)<br>- U-Blox GNSS coordinates with RTK precision (/base/fix)<br>- U-Blox heading data from moving baseline setup (/rover/navheading)<br> </p>
Extension of Towards Large Scale Automated Algorithm Design by Integrating Modular Benchmarking Frameworks
<p>This provides the dataset and the corresponding parsing scripts that extend the "Towards Large Scale Automated Algorithm Design by Integrating Modular Benchmarking Frameworks" study.</p>
Data from: Effects of environmental disturbance on phenotypic variation: an integrated assessment of canalization, developmental stability, modularity and allometry in lizard head shape
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Data from: Ontogenetic changes in the phenotypic integration and modularity of leaf functional traits
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Data from: Functional integration for enrolment constrains evolutionary variation of phacopid trilobites despite developmental modularity
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Data from: Evolutionary covariation in geometric morphometric data: analyzing integration, modularity, and allometry in a phylogenetic context
Quantifying integration and modularity of evolutionary changes in morphometric traits is crucial for understanding how organismal shapes evolve. For this purpose, comparative studies are necessary, which need to take into account the phylogenetic structure of interspecific data. This study applies several of the standard tools of geometric morphometrics, which mostly have been used in intraspecific studies, in the new context of analyzing integration and modularity based on comparative data. Morphometric methods such as principal component analysis, multivariate regression, partial least squares and modularity tests can be applied to phylogenetically independent contrasts of shape data. We illustrate this approach in an analysis of cranial evolution in 160 species from all orders of birds. Mapping the shape information onto the phylogeny indicates that there is a significant phylogenetic signal in skull shape. Multivariate regression of independent contrasts of shape on independent contrasts of size reveals clear evolutionary allometry. Regardless of whether or not a correction for allometry is used, evolutionary integration between the face and braincase is strong, and tests reject the hypothesis that the face and braincase are separate evolutionary modules. These analyses can easily be applied to other taxa and can be combined with other morphometric tools to address a wide range of questions about evolutionary patterns and processes.
Data from: Integration and modularity of teleostean pectoral fin shape and its role in the diversification of acanthomorph fishes
Phenotypic integration and modularity describe the strength and pattern of interdependencies between traits. Integration and modularity have been proposed to influence the trajectory of evolution, either acting as constraints or facilitators. Here, we examine trends in the integration and modularity of pectoral fin morphology in teleost fishes using geometric morphometrics. We compare the fin shapes of the highly diverse radiation of acanthomorph fishes to lower teleosts. Integration and modularity are measured using two-block partial least squares analysis and the covariance ratio coefficient between the radial bones and lepidotrichia of the pectoral fins. We show that the fins of acanthomorph fishes are more tightly integrated but also more morphologically diverse and faster evolving compared to non-acanthomorph fishes. The main pattern of shape covariation in non-acanthomorphs is concordant with the main trajectory of evolution between non-acanthomorphs and acanthomorphs. Our findings support a facilitating role for integration during the acanthomorph diversification. Potential functional consequences and developmental mechanisms of fin integration are discussed.
Figure 1 from: Haston E, Cubey R, Pullan M, Atkins H, Harris D (2012) Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach. ZooKeys 209: 93-102. https://doi.org/10.3897/zookeys.209.3121
Figure 1 - Diagrammatic overview of the digitisation workflows at the Royal Botanic Garden Edinburgh (RBGE)
A loop-type modular soft robot with integrated locomotion and manipulation capability
<p>Modular Soft Robot.</p>
Data from: Integration and modularity of teleostean pectoral fin shape and its role in the diversification of acanthomorph fishes
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