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Confirmation, consequences and causes of extensive polyphyly in the oak gall wasp genus Dryocosmus (Hymenoptera: Cynipidae: Cynipini)
No full textOak gall wasps are a species-rich group in which most genera induce galls on a single Fagaceae lineage (either a section within Quercus or a single non-oak genus). Preliminary data for the few exceptions (most notably Andricus, Callirhytis, Dryocosmus and Neuroterus) suggest that high apparent host plant diversity is an artefact of polyphyly resulting from inadequate morphological definition of genera. Here we demonstrate this issue in Dryocosmus, which (as currently defined) galls eight Fagaceae lineages, by reconstructing relationships among 35 species in the genus and 27 other Cynipini genera worldwide. Data for 1,871 base pairs of DNA sequence from one mitochondrial gene (cytochrome b) and three nuclear genes (28S D2, opsin, wingless) confirm that Dryocosmus comprises a polyphyletic assemblage of more host-specific lineages. Our analyses also strongly reject monophyly of Callirhytis. We survey the taxonomic issues underlying these problems in Dryocosmus and begin the taxonomic revision of this and closely related genera by (i) transferring D. asymmetricus to Neuroterus asymmetricus (Kinsey), comb. nov., (ii) transferring C. congregata to Melikaiella congregata (Ashmead), comb. nov., and C. clavula to Andricus clavula (Osten Sacken), comb. rev., (iii) reinstating Dryocosmus kunugiphagus Ide & Abe comb. rev., (iv) describing a new genus, Chrysolepisphex Stone, Nicholls, Melika & Tang, gen. nov. for Dryocosmus that gall chinquapins (Chrysolepis sp.), and (v) matching sexual and asexual generations of D. quercusnotha (Osten Sacken) and D. quercuspalustris (Osten Sacken). Our results provide a backbone for revision of Dryocosmus and highlight the need for Cynipini-wide revision of polyphyletic genera
Characterising vertical plug flow pneumatic conveying using CFD-DEM
No full textOpenFOAM and Aspherix simulation data for the paper, "Characterising vertical plug flow pneumatic conveying using CFD-DEM". It contains the full simulation data of the "base case", which corresponds to Section 4.1 of the paper. Also, the input files of the base cases of the parametric study sections, Sections 4.2 and 4.3 are also provided. The simulation was run using "CFDEMcoupling-Nonspherical-6.1.0" and "Aspherix-6.1.0". Aspherix is a proprietary software from DCS Computing and well recognised within the Discrete Element Method (DEM) research community.
In this simulation, plug flow pneumatic conveying is simulated in a vertical and circular pipe using velocity inlet and pressure outlet (P=0). The flow solver is "cfdemSolverPiso" provided within CFDEMCoupling, and its modified version for nonspherical particles, which is again included within the above-mentioned package, provided by DCS Computing GmbH.
### Contents
OpenFOAM and Aspherix simulation data are included in folders "CFD" and "DEM", respectively.
* CFD data is in the type of OpenFOAM format, which is well-known in the community. Its visualisation can be done on Paraview using the "controlDict.foam" file in CFD/system subfolder.
* DEM/post subfolder includes the simulation data output in vtk format. Further postprocessing can also be done by converting these vtk files to desired format.
* DEM/result.txt includes "(simulation time) (total number of particles) (total mass) (total translational specific energy) (total rotational specific energy)" in each row
Generation Scotland Mass Spectrometry Protein GWAS Summary Statistics
No full textThis dataset corresponds to the study "Genome-wide analysis of 439 mass spectrometry-based proteomic profiles in a population of 15,035 Scottish individuals". The files included are the summary statistics from genome-wide association studies (GWAS) of 439 mass spectrometry measured proteins in Generation Scotland. The GWAS was run using the fastGWA command in GCTA. Age, sex and 20PCs were included as covariates and a genetic relationship matrix (GRM) was used to account for family structure
Temporal changes to intestinal microbiome induced by stroke
No full textThese data contain 16s rRNS sequencing data from faecal material taken from naive animals and animals recovered 5 days, 2 weeks and 3 months after sham or stroke surgery. There are two independent experiments included with the acronyms SCM and RSM.
Abstract
Stroke survivors experience a plethora of complications during recovery, including gastrointestinal symptoms. Intestinal dysfunction is reported to occur rapidly following stroke in both humans and animal models and alterations such as reduced barrier integrity, lymphocyte loss, and an altered microbiota have been suggested to contribute to poor neurological outcomes. Despite the persistence of gastrointestinal symptoms in many stroke survivors, how the intestinal environment changes over the course of stroke recovery remains poorly understood. Here, we use an experimental model of ischemic stroke to profile the gastrointestinal tract over a three month period of recovery.We have shown that experimental stroke leads to structural alterations to the colon, impaired transit times and an altered bacterial community composition. No impairments to barrier function were detected at any time point and transit times recover within 2 weeks post stroke. In contrast, structural and bacterial community alterations remain up to 3 months post stroke and are accompanied by abnormalities that develop only during chronic recovery, such as altered antibody coating of bacteria. These results suggest that the gastrointestinal system is dynamically altered over the course of experimental stroke recovery and that certain defects persist chronically after stroke.Data are Fastq files of samples taken from individual animals in the experiment. File name contains experiment acronym, time point and treatment. Positive and negative control Fastq files are also include
Supplemental data for Comparative rhizotaxy of fossil and living isoetalean rhizomorphs reveals development through rootlet intercalation within a triangular lattice
No full textSupplemental data: Background and Aims: The Isoetales are a clade of lycopsids that evolved colossal arborescent forms during their Palaeozoic prime but today are represented solely by the small herbaceous monogeneric Isoetes. Despite the differences in scale of taxa in the clade the rooting system of all members consists of two-parts, a rhizomorph from which rootlets develop in a regular pattern termed rhizotaxy. Rhizomorphs are highly diverse in different members leading to different terminology being used to describe rhizotaxy in different lineages. Here we set out to investigate how conserved rhizotaxy was between taxa and to provide a standard geometric definition, and developmental interpretation of rhizotaxy applicable to all members. Methods: We developed a pipeline to quantitatively describe rhizotaxy. This pipeline allowed rootlet arrangement to be captured in 3D, before being visualsed on a 2D lattice where Deluany Triangulation could be applied. This method offers a standard method to investigate rhizotaxy across disparate rhizomorphs. Next, to investigate the evolution and development of rhizotaxy we applied our pipeline to a 3D model we generated of the rooting system of the extinct Carboniferous lycopsids Oxroadia. Finally, we made direct observations of rootlet development in Isoetes using time course imaging. Key Results: We demonstrate that rhizotaxy can be described as an equallateral triangular lattice for all members of the Isoetales including Oxroadia. By combining evidence from direct observation of rootlet development in Isoetes with inferences of rootlet development and the early stages of sporophyte ontogeny of Oxroadia we conclude that the conserved rhizotaxy developed by the process of rootlet intercalation. Conclusions: We provide a single geometric definition, and predicted developmental mechanism for rhizotaxy that applies to all Isoetales. Our findings call into question the literal interpretation that the rhizomorph is a modified shoot
Modelling of what-where-when episodic-like memories in rats
No full textEpisodic memories contain information about the nature of an event, the place where it happened and the time when it occurred. In animals, the term “episodic-like memory” is preferred to refer to mnemonic instances containing these three features, commonly referred to as “what-where-when”. Models to study episodic-like memory have been proposed in corvidae and rodents, although their use in the neuroscience research has been limited due to certain limitations and potential ambiguities. While the neurological correlates of “what-where-when” have been identified in neuronal types such as place and time cells, it is unclear how they contribute to form a unitary representation, or how this information can be accessed during memory recall, either holistically or differentially. Here, we outline two new behavioural paradigms based on the everyday memory task that we have developed to model what and when components as well as ‘where’ information. In experiment 1 (E1), we demonstrate that rats are able to learn two distinct food positions on a daily basis and retrieve them independently. In E2, we establish that rats can learn that two flavours are replenished at different times after an initial sampling, thus use the temporal component to guide their decision making. These two tasks can therefore provide the basis to study how the item, location and time information of a memory are stored and accessed by the brain. This should be observable in single-unit recording or calcium-imaging studies.
The dataset contains the data represented in the main and supplementary figures.Data structure is described in README.tx
Grass communities differ floristically under different dominant trees in savannas in Thailand and Cambodia
No full textAbstract
Aims: Southeast Asian savannas are some of the least studied ecosystems, with understanding of their function and resilience limited by a lack of understanding of grass species richness and composition. Since savannas are characterised by their grassy ground layer we conducted field surveys in Thailand and Cambodia to assess grass community composition under different dominant tree genera.
Methods: We conducted field surveys in four savanna ecosystems characterised by (i) Dipterocarpus, (ii) Pinus, (iii) Pterocarpus, and (iv) Shorea tree genera. In each we recorded grass species composition and richness. We assessed differences in composition using PERMANOVA, patterns of grass species discovery using species accumulation curves, and common species with relative frequency distributions.
Results: In total we recorded 160 unique grass species. These savannas support distinct grassy assemblages, with diverse patterns of species accumulation, richness and overlap. Common grasses were frequently shared between ecosystems. Grass assemblages were functionally similar, comprising mostly C4, perennial species. Across the ecosystems, grass communities were mostly composed of tribe Andropogoneae although we recorded common fire-adapted C3 grasses including Vietnamosasa ciliata (A.Camus) T.Q.Nguyen and Vietnamosasa pusilla (A.Chev. & A.Camus) T.Q.Nguyen.
Conclusion: The savanna ecosystems of Thailand and Cambodia are characterised by Dipterocarpus, Pinus, Pterocarpus and Shorea tree species, which support distinct grass assemblages. Diversity varies across savanna landscapes with the highest grass species diversity found in the Dipterocarpus and Shorea savannas. Increased sampling is necessary to fully characterise the grass flora of Southeast Asian savannas and their responses to environment.
The dataset comprises floristic surveys of the ground layer of savannas in Cambodia and Thailand
Data from: Malaria parasites adjust liver stage development to synchronise the blood stage of infections with host daily rhythms.
No full textSynchronised multiplication of Plasmodium parasites within red blood cells causes periodic malaria fevers. Aligning blood-stage development with the vertebrate host’s feeding-fasting rhythm facilitates within-host survival and between-host transmission. We use the rodent model Plasmodium chabaudi to test when, following development in the liver, the blood stage of infection begins. We find egress from the liver into the blood is aligned with the time of day of rhythmic host feeding, but only in wild type hosts, with egress occurring after a fixed period of pre-erythrocytic development in hosts without a functional canonical clock. However, perturbing the duration over which parasites enter the bloodstream does not affect their multiplication rate in the first few IDCs, suggesting any fitness benefits from times egress may occur later during the infection
Prevalence and characteristics of dental and periodontal disease in Western European hedgehogs (Erinaceus europaeus) admitted into an animal shelter in northwestern Germany
No full textThis data set was created during a study aiming to collect information on the prevalence and characteristics of dental and periodontal disease in Western European hedgehogs (Erinaceus europaeus) admitted into an animal shelter in northwestern Germany. Immediately upon arrival, information on hedgehog health and history was documented on an arrival protocol. Once the overall health status of the hedgehog allowed general anaesthesia, a full body examination, including a dental assessment, was conducted and documented on a veterinary examination protocol. Indices judging gingivitis, calculus, gingival recession, and tooth mobility were assessed and added up to an overall dental examination index representing the severity of the disease
Visual Data for Paper: "LAS-on-Edge: A Real-Time Laser Absorption Spectroscopic Water Vapor Sensor on Edge Computing Platforms"
No full textThese two videos shows the online monitored water vapor temperature and concentration as well as the water mist diffusion process and the flame variation, respectively