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Fig. 28. Selected preserved specimens. A in Dead man's fingers point to new taxa: two new genera of New Zealand soft corals (Anthozoa, Octocorallia) and a revision of Alcyonium aurantiacum Quoy & Gaimard, 1833
Fig. 28. Selected preserved specimens. A. Ushanaia ferruginea gen. et sp. nov. B. U. fervens gen. et sp. nov. C. U. solida gen. et sp. nov. Note that most specimen lots include additional fragments that are not depicted. * = holotype.
The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia
<p>Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Both effects are likely to depend on prior selection on phenotypic and transcriptional plasticity in response to hypoxia, and may therefore show signs of local adaptation. Here we report the lifespan effects of chronic, mild, intermittent hypoxia (CMIH) and short-term survival in acute severe hypoxia (ASH) in four clones of <em>Daphnia magna</em> originating from either permanent or intermittent habitats, the latter regularly drying up with frequent hypoxic conditions. We show that CMIH extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to ASH. Exposure to CMIH did not protect against ASH; to the contrary, <em>Daphnia</em> from the CMIH treatment had lower ASH tolerance than normoxic controls. Few transcripts changed their abundance in response to the CMIH treatment in any of the clones. After 12 hours of ASH treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in mitochondrial and respiratory metabolism, oxygen transport, and, unexpectedly, gluconeogenesis showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to ASH than those from permanent habitats, there were no significant hypoxia-by-habitat of origin or CMIH-by-ASH interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.</p>
DeepSelectNet: Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing
<p>Curated dataset for the manuscript named "DeepSelectNet: Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing".</p> <p>Five publicly available datasets sequenced on ONT MinION/GridION were used for the experiments (see below for original sources). These datasets contained raw signal data in single-FAST5 format (one file per each read), which were converted to BLOW5 format using slow5tools to enable convenient and efficient file manipulation. Then, 40,000 reads containing at least 4500 signal samples were extracted from each dataset. From each dataset, 20,000 reads are for training (<species>/train-<species>.blow5) and the rest for testing (<species>/test-<species>.blow5). Basecalled reads for the dataset used for testing are also available (test-<species>.fastq). Guppy version 6.1.3 under dna_r9.4.1_450bps_hac mode was used. The reference genomes are also given (<species>/<species>-ref.fasta)</p> <p>Original datasets are from the following sources:<br> SARS-CoV-2: https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17<br> Zymo Metagenome: https://github.com/LomanLab/mockcommunity<br> Chlamydomonas: https://sra-download.ncbi.nlm.nih.gov/traces/era20/ERZ/003237/ERR3237140/Chlamydomonas_0.tar.gz<br> Saccharomyces cerevisiae: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA510813</p>
DataPad selection exports for Breathe Easy vignette
<p>These text files should be used for a manual run of our software, Breathe Easy. These text files are all manual selections added to the Datapad in LabChart for each of the files in the example dataset. If you are attempting to run a practice manual run of Breathe Easy, then these text files are required.</p>
A guiding diagram for the selection of a CiTO citation function for a given in-text citation
<p>A decision model for the selection of a Citation Typing Ontology (CiTO, <a href="http://purl.org/spar/cito">http://purl.org/spar/cito</a>) citation function to use for the annotation of the citation intent of an examined in-text citation based on its context. The first large row of the diagram contains three macro-categories: (1) “Reviewing …”, (2) “Affecting …”, and (3) “Referring …”. Each macro-category has at least two subcategories, and each subcategory refers to a set of citation functions. The first row defines the suitable citation functions for it with the help of a guiding sentence to be completed according to the chosen sub-category and citation function. </p> <p>To annotate the in-text citation intent using the guiding scheme (see Figure), we use a priority ranked strategy that works as follows: </p> <ol> <li>we match each in-text citation against at least one of the three macro-categories, i.e. “Reviewing ...”, “Affecting ...” and “Referring ...” (first row in Figure);</li> <li>for each macro-category we have selected in (1), we choose one or more citation functions from those provided by CiTO;</li> <li>in case we select only one citation function, then we annotate the in-text citation intent with such a value; otherwise</li> <li>we calculate the priority of each citation function we have selected by summing its value in parenthesis (from 0.1 to 0.6) with the corresponding value in the y-axis (from 10 to 50) and in the x-axis (from 1 to 8) shown in Figure. The smaller the sum, the more priority the citation function has. For instance, the priority of the citation function “confirms” is 11.2 that is higher than the one of the citation function “describes”, which is 43.2. Finally, we select the citation function that has higher priority and annotate the in-text citation function with it.</li> </ol>
Machine Learning Enabled Multi-Radio Access Technology Selection in 5G Networks
<p>In this paper, we present a machine learning algorithm for effective RAT selection in 5G networks by considering the geo-location (latitude and longitude) of the user as well as the received signal strength intensity (RSSI) from the base station as basic parameters, real live data from a 5G network base-station were collated, divided into training and testing data-sets, the training data-sets (input) were used to train models of supervised machine learning classification algorithm: Decision Tree (DT), Extra Tree (XTREE), Random Forest (RF), Gradient Boosting (GB), and eXtreme Gradient Boosting (XGBoost); these trained models are further tested with input test data-sets to predict/select the appropriate RAT (4G/5G) as labelled output. Evaluation of results showed a measure of accuracy of our chosen model of RAT selection; (XGBoost) at optimal level 93.86\%, which was further cross validated at 92.9\% when compared with other algorithms for its effectiveness on future data and mitigation ability on over-fitting and under-fitting issues, hence recommended for planning and optimization purposes in similar urban/dense-urban environment to assist in maintaining the rapidly increasing demand of network connections and devices.</p>
Multilevel selection on social network traits differs between sexes in experimental populations of forked fungus beetles
<p>Both individual and group behavior can influence individual fitness, but multilevel selection is rarely quantified on social behaviors. Social networks provide a unique opportunity to study multilevel selection on social behaviors, as they describe complex social traits and patterns of interaction at both the individual and group levels. In this study, we used contextual analysis to measure the consequences of both individual network position and group network structure on individual fitness in experimental populations of forked fungus beetles (<em>Bolitotherus</em> <em>cornutus</em>) with two different resource distributions. We found that males with high individual connectivity (strength) and centrality (betweenness) had higher mating success. However, group network structure did not influence their mating success. Conversely, we found that individual network position had no effect on female reproductive success but that females in populations with many social interactions experienced lower reproductive success. The strength of individual-level selection in males and group-level selection in females intensified when resources were clumped together, showing that habitat structure influences multilevel selection. Individual and emergent group social behavior both influence variation in components of individual fitness but impact male mating success and female reproductive success differently, setting up intersexual conflicts over patterns of social interactions at multiple levels. </p>
Supplementary Simulation Data for "Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation"
<p>Additional simulation data for "Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation", which has been submitted as a preprint to ChemRxiv.</p>
Text-fig. 6. Stratigraphic and phylogenetic placement inferred for fossil Fraxinus fruits. Only Fraxinus fossil fruits identified on the section level are included. The black color represents selected fossil fruits from published literature (excluding some Eocene North American occurrences not assigned to section), the red color represents the fossil fruits from the Lühe flora, Yunnan, Southwest China. The phylogenetic relationships are based on Hinsinger et al. (2013). in Fraxinus L. (Oleaceae) Fruits From The Early Oligocene Of Southwest China And Their Biogeographic Implications
Text-fig. 6. Stratigraphic and phylogenetic placement inferred for fossil Fraxinus fruits. Only Fraxinus fossil fruits identified on the section level are included. The black color represents selected fossil fruits from published literature (excluding some Eocene North American occurrences not assigned to section), the red color represents the fossil fruits from the Lühe flora, Yunnan, Southwest China. The phylogenetic relationships are based on Hinsinger et al. (2013).
Text-fig. 1. Bivariate diagram of length and width of the upper dentition of selected European small and middle size Amphicyoninae compared with the Tuchořice specimens. a: P4; b: M1; c: M2; d: m1; e: m2. Data from Schlosser (1899, 1904), Thenius (1949), Dehm (1950), Heizmann (1973), Ginsburg (1977, 1989), Peigné (2012). Dotted line – ranges of maximum and minimum values from the average of teeth of Cynelos lemanensis from Ulm (Peigné and Heizmann 2003). Abbreviations: L – length; W – width. in The Amphicyoninae (Amphicyonidae, Carnivora, Mammalia) Of The Early Miocene From Tuchořice, The Czech Republic
Text-fig. 1. Bivariate diagram of length and width of the upper dentition of selected European small and middle size Amphicyoninae compared with the Tuchořice specimens. a: P4; b: M1; c: M2; d: m1; e: m2. Data from Schlosser (1899, 1904), Thenius (1949), Dehm (1950), Heizmann (1973), Ginsburg (1977, 1989), Peigné (2012). Dotted line – ranges of maximum and minimum values from the average of teeth of Cynelos lemanensis from Ulm (Peigné and Heizmann 2003). Abbreviations: L – length; W – width.
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low: in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low:
Pest defenses under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations
<p>Whilst droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e., height growth, drought avoidance based on water-use efficiency inferred from δ<sup>13</sup>C, and pest resistance based on defense traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ<sup>13</sup>C and increased the evolutionary potential of height growth and δ<sup>13</sup>C across populations. We found, however, no pronounced gradient in defenses and their evolutionary potential along populations or test sites. Response to selection was weak in defenses across test sites, but high for height growth, particularly at warm test sites. Response to selection of δ<sup>13</sup>C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with limited evolutionary influence from pest (biotic) pressures.</p>
Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster: scripts and files
<p>Pipeline and analysis scripts as well as final data files</p>
StorAge Selection theory: a visual introduction
<p>This short video provides an introduction to the theory of StorAge Selection, or SAS. SAS is used to simulate material transport through complex systems, like rain water through a watershed and into a stream.</p> <p>The animations in this video were produced using mesas.py: https://github.com/charman2/mesas/</p>
The Missing Link Between Black Holes in High-Mass X-ray Binaries and Gravitational-Wave Sources: Observational Selection Effects
<p>Data tables containing the calculated binary parameters used to acquire all results in <a href="https://arxiv.org/abs/2210.01825v1">arXiv:2210.01825v1</a>. The file "xrb_params_illustris_z0.05_sample.csv" contains data for the z<0.05 sampled population and the file xrb_params_illustris_z20_sample.csv contains data for the z<20 sampled population.</p>
Data used in the paper: Historical and current environmental selection on functional traits of trees in the Atlantic Forest biodiversity hotspot
<p>This repository contains phylogenetic and functional trait data, raster files, and tables with sampling information and references used in the article "Historical and current environmental selection on functional traits of trees in the Atlantic Forest biodiversity hotspot" by Silva, J.L.A., Souza, A., and Vitória, A.P. Journal of Vegetation Science, <a href="https://doi.org/10.1111/jvs.13049">https://doi.org/10.1111/jvs.13049</a> .</p> <p>Description of files:</p> <p>(1) "Species-level_Trait_Data_Silva_et_al._2021.csv": This file contains species-specific mean trait values and the plant growth form of the 2,122 studied species, whenever available. Trait values were compiled from public sources such as original papers, master and doctoral dissertations, and global trait databases.</p> <p>(2) "Phylogenetic_Tree_Silva_et_al._2021.txt": This file contains the phylogenetic tree of the 2,122 studied species.</p> <p>(3) "CWM_Trait_Maps.zip": This file contains seven rasters of spatially contiguous surfaces produced by Ordinary Kriging Interpolation using Community-Weighted Means (CWM) of each functional trait.</p> <p>(4) "References-abundance-data.csv": This file contains sampling details and the references used to compile species abundance data for each studied site.</p> <p>(5) "References-trait-data.csv": This file contains sampling details and the references used to compile functional trait data.</p> <p> </p>
Multiwavelength classification of X-ray selected galaxy cluster candidates using convolutional neural networks
<p>Classification dataset used in Kosiba et al. 2020 (10.1093/mnras/staa1723) consisting of candidate clusters in the XCLASS survey</p> <p>Training and testing images and corresponding labels low-z (clusters, 0<z<0.3), hi-z (clusters, z>0.3), nearby galaxy, point source (point, double source, star/AGN), and other (artefact, edge)</p>
Reproductive compensation and selection among viable embryos drive the evolution of polyembryony
<p>Simple polyembryony -- where one gametophyte produces multiple embryos with different sires but the same maternal haplotype -- is common among vascular plants. We develop an infinite-site, forward population genetics model showing that together polyembryony's two benefits -- "reproductive compensation" achieved by providing a backup for inviable embryos, and the opportunity to favor the fitter of surviving embryos, can favor its evolution. Our model tests how these factors can favor the evolution of polyembryony, and how these underlying benefits of polyembryony shape the genetic load under a range of biological parameters. While these two benefits are difficult to disentangle in nature, we construct variant models of polyembryony that either only include or only exclude the opportunity for reproductive compensation. We find that reproductive compensation strongly favors the evolution of polyembryony, and that polyembryony is favored much more weekly in its absence, suggesting that the benefit of a backup embryo is a major force favoring polyembryony. Remarkably we find nearly identical results in cases in which mutations impact either embryo or post-embryonic fitness (no pleiotropy), and in cases in which mutations have identical fitness effects embryo or post-embryonic fitness (extreme pleiotropy). Finally, we find that the consequences of polyembryony depends on its function – polyembryony results in a decrease in mean embryonic fitness when acting as a mechanism of embryo compensation, and ultimately increases mean embryonic fitness when we exclude this potential benefit.</p>
CONSOLE_WP2_Task2.2_Data collection, selection and diagnosis of reasons for successes and failures of initiatives in Europe_second level diagnosis_2022.10.25
<p>This dataset contains data on the second level analysis of existing and highly potential contract solutions throughout Europe within the EU-H2020 project CONSOLE (CONtract Solutions for Effective and lasting delivery of agri-environmental-climate public goods by EU agriculture and forestry).</p> <p>The dataset is organized in one document (.rtf). The document represents the list of the 26 in-depth case studies, including data on case study ID, AECPGs addressed, performance description and evaluation. The dataset is related to the Deliverable 2.3.</p>
CONSOLE_WP2_Task2.2_Data collection, selection and diagnosis of reasons for successes and failures of initiatives in Europe_first level diagnosis_2022.10.25
<p>This dataset contains data on the first level analysis of existing and highly potential contract solutions throughout Europe within the EU-H2020 project CONSOLE (CONtract Solutions for Effective and lasting delivery of agri-environmental-climate public goods by EU agriculture and forestry).</p> <p>The dataset is organized in one document (.rtf) with two main chapters. The first part contains the information gained for the first level diagnosis based on Task 2.2 and Deliverable 2.1 and the second half of the document contains updated information on the case studies connected to Deliverable 2.6.The analyses performed with this dataset can be found in Deliverable 2.4.</p> <p>The first chapter represents the list on the 60 first level case studies and the second chapter contains the 61 updated case studies, including data on case study ID, NUTS location, short description, AECPGs addressed, main contractual features, a simplified SWOT.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.