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Eco-evolutionary consequences of living with close relatives: Resistance to herbivores and climatic stress increases with investment into mycorrhiza in adult oaks
<p><span>1. Mycorrhizas are known to increase plant resistance to herbivores and climatic stress. However, it is unknown if particularly hostile environments select for increased investment of plants into mycorrhiza. </span></p> <p><span>2. We studied hostile biotic environments: phylogenetically proximate neighbourhoods known to increase herbivory and pedoclimatic stress. In a common garden, we studied the resistances, tri-trophic interactions and microclimate of 28-years-old oaks (Quercus petraea), descending from provenances of contrasting phylogenetic neighbourhoods.</span></p> <p><span> 3. We found that oaks descending from phylogenetically proximate neighbourhoods had increased ectomycorrhizal enzymatic activities without affecting mycorrhization rate of root tips. We also found that increased ectomycorrhizal enzymatic activity decreased damages by one group of specialist herbivores (leaf-miners), without affecting another (galls) or generalists (ectophages). Consistently, descendants from phylogenetically proximate neighbourhoods showed decreased damage by leaf miners. We finally found that oaks descending from phylogenetically proximate neighbourhoods were most capable of maintaining leaf chlorophyll under heat-induced drought, reflecting their increased ectomycorrhizal enzymatic activities. </span></p> <p><span>4. Synthesis. Overall, oaks living with closely related neighbours can rapidly evolve increased investment into ectomycorrhizas and thereby resistances to herbivores and climatic stress, ultimately facilitating coexistence among closely related neighbours. </span><span>While phylogenetically diverse forests remain essential for maintaining biodiversity, the selection regimes in less diverse forests can be used as a source of native genotypes resistant to future climate change, rather than using exotic populations and species as a source pool.</span></p>
Transhumeral Loading During Advanced Upper Extremity Activities of Daily Living
<p>Percutaneous osseointegrated (OI) implants for direct skeletal attachment of upper extremity prosthetics represent an alternative to traditional socket suspension that may yield improved patient function and satisfaction. This is especially true in high-level, transhumeral amputees where prosthetic fitting is challenging and abandonment rates remain high. However, maintaining mechanical integrity of the bone-implant interface is crucial for safe clinical introduction of this technology. The collection of population data on the transhumeral loading environment will aid in the design of compliance and overload protection devices that mitigate the risk of periprosthetic fracture. We collected marker-based upper extremity kinematic data from non-amputee volunteers during advanced activities of daily living (AADLs) that applied dynamic loading to the humerus. These kinematic data are available for download and will aid in the development of overload protection devices and appropriate post-operative rehabilitation protocols that balance return to an active lifestyle with patient safety.</p>
Living in mixed-sex groups limits sexual selection in coloration and pelage appendages in bovids
<p>Among mammals, bovids provide some of the most striking examples of sexual dimorphism in colouration and pelage appendages, such as beards and manes. This dimorphism is usually assumed to have evolved through sexual selection on males in the context of intra- or intersexual communication. However, the sexes look similar in several bovid species thought to be characterized by large opportunities for sexual selection, hinting at fitness costs of dimorphic traits due to other selection pressures. This study applies the comparative method with phylogenetic control to identify the factors promoting and constraining the evolution of dimorphism in colouration and pelage appendages across bovids. We found that trait dimorphism correlated positively with large breeding group size, an indicator of the intensity of sexual selection, and negatively with male territoriality, which is also likely to affect the operation of sexual selection. The relative rarity of colour and pelage dimorphism in species with territorial mating systems may be explained by weaker sexual selection due to difficulty in monopolizing females and/or sexual selection targeting other traits, such as territorial quality as an extended phenotype. We also found that colour and pelage dimorphism were reduced in species spending more time in mixed-sex groups outside the breeding season, possibly due to increased predation costs from non-uniformity This suggests that benefits from integration into mixed-sex groups select against the extravagant male morphologies otherwise promoted by sexual selection.</p>
Preliminary results: Predicted cooling effect, lives saved and associated economic value from public green spaces in Paris
<p><span>This dataset represents preliminary results predicting the cooling effect from public green spaces in Paris for the 10th, 22nd and 24th July 2019, the lives saved and associated economic valuation.</span></p> <p>The data format is a shapefile with coordinate reference system RGF93 v1 / Lambert-93 (EPSG:2154).</p> <p>Please see the README file for description of the variable names. </p> <p>Full results will be shared in due course, alongside all code and a detailed description of the method. If you would like to know more about the method or would like to be informed when the full results and method are published, please contact Jo Garrett at j.k.garrett@Exeter.ac.uk</p>
Wildlife following people: A multidisciplinary assessment of the ancient colonization of the Mediterranean Basin by a long-lived raptor
<p>Here, we used a multidisciplinary approach to a) reconstruct the process of colonization of the Mediterranean Basin by a long-lived bird of prey, the Bonelli's eagle (<em>Aquila fasciata</em>), and b) test the hypothesis that this colonization was unintentionally favored by anatomically modern humans through a release of competition by dominant species, primarily golden eagles (<em>A. chrysaetos</em>). For this, we used distribution, genetics, fossils, and ecological data. Data archived in Dryad includes all genetic information (<strong>Genetic_data.xlsx</strong>) and a portion of the ecological data (<strong>Ecological_data-provinces.xlsx</strong>, <strong>Ecological_data-nuclei.xlsx</strong>, <strong>Ecological_data-GLMs.xlsx</strong>, <strong>Ecological_data-reciprocal_occupation.xlsx</strong>), while the remaining data can be accessed from a) tables included in the manuscript and b) the original sources.</p>
Towards intelligent living facades: On electrical activity of ordinary moss \emph{Brachythecium rutabulum}
<p>Electrical recordings of of ordinary moss \emph{Brachythecium rutabulum}. Data for the paper Towards intelligent living facades: On electrical activity of ordinary moss \emph{Brachythecium rutabulum}</p>
Live video/audio recording of Hamas rocket attack and rushing for bomb shelter at Weizmann Institute campus, Rehovot, Israel
<p>In the early morning of October 7, 2024, terrorists launched an attack with rockets and death squads on Israel. For several days, an enormous number of rockets was launched by Hamas terrorists in the Gaza strip on Israel.</p> <p>This is a real live video recording of escaping from an apartment in Rehovot, Israel, to the nearby Luftschutzbunker (Shelter).</p> <div> <div>This was one of the massive (Qassam) rocket attacks by Hamas terrorists launched from Gaza strip towards north of Israel, here at Rehovot near Weizmann Institute of Science. The rockets were intercepted by the iron dome system. Several families with children were already inside the Shelter.</div> </div> <div>The scene was recorded in the evening of 7th October 2023. Several attacks happened before that first day of the 2023 Israel-Hamas war. The earliest was 06:30 am in the morning on the Shabat.</div> <div>The rocket attacks stopped at night after the Israeli Air Force had begun raids on the Gaza strip.</div>
Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats.
<p>This data set includes the R scripts (combined into one R markdown document) and input files needed to create the main text figures and major analyses for the paper "Grieneisen L, Hays A, Cook E, Blekhman R, and Tecot S. 2024. Temporal patterns of gut microbiota in lemurs (<em>Eulemur rubriventer</em>) living in intact and disturbed habitats. American Journal of Primatology." </p>
Data for: Reliable biogeography requires fossils: Insights from a new species-level phylogeny of extinct and living carnivores
<p>A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geologic events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.</p>
Figure 2 in Monitoring the feeding and parental care behavior of a pair of free-living owls (Tyto furcata) in the nest during the reproductive period in Rio de Janeiro, Brazil
Figure 2. The first egg of the couple of Tyto furcata. Campos dos Goytacazes, RJ.
Demo Live Cell Imaging Dataset for PetaKit5D
<p>Demo dataset for PetaKit5D (<a href="https://github.com/abcucberkeley/LLSM5DTools">https://github.com/abcucberkeley/PetaKit5D</a>). </p> <p>The dataset is for the large field of view live cell imaging of LLC-PK1 cells of nuclei and endoplasmic reticulum (ER). It contains two time points with two channels. Each time point and channel contains 4 volumetric tiles. Some demos in PetaKit5D use this dataset to demonstrate the usage.</p> <p>Please cite our paper (<a href="https://doi.org/10.1101/2023.12.31.573734">https://doi.org/10.1101/2023.12.31.573734</a>) if you use this dataset in your research:</p> <p><code>Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua L. Lillvis, Alexander Kuhn, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N. Killilea, Eric Betzig, Srigokul Upadhyayula. Image processing tools for petabyte-scale light sheet microscopy data. bioRxiv 2023.12.31.573734; doi: <a href="https://doi.org/10.1101/2023.12.31.573734">https://doi.org/10.1101/2023.12.31.573734</a></code></p>
Data from: Extreme mitochondrial reduction in a novel group of free-living metamonads
<p>Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway through lateral gene transfer. One of the isolates, <em>Skoliomonas litria</em>, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.</p>
Sample data for "Live Cell Fluorescence Microscopy – An End-to-End Workflow for High-Throughput Image and Data Analysis"
<p>This repository contains:</p> <ul> <li> <p>Sample data for the "Live Cell Fluorescence Microscopy – From Sample Preparation to Numbers and Plots" methodology paper by Zahumensky & Malinsky. The paper describes the preparation of live yeast cell samples for microscopy, the subsequent semi-automatic analysis of the microscopy images using our custom-written Fiji macros, and automatic processing of the output (Results table) from the image analys using custom-written R scripts. The data provided here are real experimental data from two publications of our group: Zahumensky et al., 2022 and Vesela et al., 2023</p> </li> <li> <p>"Results tables" from the Fiji based analysis</p> </li> <li> <p>Outputs of the processing of these Results tables using our R scripts, in the form of summary tables, graphs, and statistical analyses</p> </li> </ul>
Intervention fidelity and factors affecting the process of a mobile phone text messaging intervention among adolescents living with HIV: A convergent mixed methods study in southern Ethiopia
<p><em>Objective:</em> To assess the intervention fidelity and explore contextual factors affecting the process of a mobile phone text messaging intervention in improving adherence to and retention in care among adolescents living with HIV, their families, and their healthcare providers in southern Ethiopia.</p> <p><em>Design:</em> A convergent mixed-methods design guided by the process evaluation theoretical framework and the RE-AIM framework was used alongside a randomised controlled trial to examine the fidelity and explore the experiences of participants in the intervention.</p> <p><em>Setting:</em> Six hospitals and five health centres providing HIV treatment and care to adolescents in five zones in southern Ethiopia. Participants: adolescents (aged 10–19), their families and their healthcare providers.</p> <p><em>Intervention:</em> Mobile phone text messages daily for 6 months or standard care (control). Results: 306 participants were enrolled in the process evaluation. Among the intervention participants (N =153), 171 (55.9%) of whom were men, most resided in an urban area 225 (73.5%), and participants had a mean age of 15 (2.62). The overall experiences of implementing the text messages reminder intervention were described as helpful in terms of treatment support for adherence but had room for improvement. During the study, 30,700 text messages were sent, and fidelity was high, with 99.4% successfully receiving text messages during the intervention. Barriers such as failed text messages delivery, limitations in phone ownership, and technical limitations affected fidelity. Technical challenges can hinder maintenance, but a belief in the future of digital communication permeates the experiences of the text messages reminders.</p> <p><em>Conclusions: </em>Overall fidelity was high, and participants' overall experiences of mobile phone text messages were expressed as helpful. Contextual factors, such as local telecommunications networks and local electric power, as well as technical and individual factors must be considered when planning future interventions.</p>
Fig. 3 in Skin Microbiome Of Free-Living European Pond Turtle (Emys Orbicularis (L.)) On The Northern Border Of Its Range In Silene Nature Park, Latvia
Fig. 3. Gram-positive (A) and Gram-negative bacteria (B) under the microscope. Magnification x1000.
Fig. 2 in Skin Microbiome Of Free-Living European Pond Turtle (Emys Orbicularis (L.)) On The Northern Border Of Its Range In Silene Nature Park, Latvia
Fig. 2. Sampled turtle with the biotope (Photo: M. Pupins).
Fig. 1 in Free-living freshwater nematodes in Vlasina Lake (Serbia, Pčina District, Surdulica Municipality)
Fig. 1. Vlasina Lake (Photo: Stefan Stoichev).
SN2N's 3D dataset of outer mitochondrial membrane network of live COS-7 cells labeled with Tom20-mCherry on SD-SIM sysytem.
Open the record for dataset details and reuse information.
Separable processes for live "in-person" and "zoom-like" faces
<p>Increased reliance on Zoom-like (webcam) platforms for interpersonal communications has raised the question of how this new virtual format compares to real face-to-face interactions. This question is also relevant to current models of face processing. Neural coding of simulated faces engages feature-selective processes in the ventral visual stream and two-person live face-to-face interactions engage additional face processes in the lateral and dorsal visual streams. However, it is not known if and/or how live in-person face processes differ from live virtual face processes because the faces and tasks are essentially the same. Current views of functional specificity predict no neural difference between the virtual and live conditions. Here we compare the same live faces viewed both over a video format and in person with measures of functional near-infrared spectroscopy (fNIRS), eye tracking, pupillometry, and electroencephalography (EEG). Neural activity was increased in dorsal regions for in-person face gaze and was increased in ventral regions for virtual face gaze. Longer dwell times on the face, increased arousal indexed by pupil diameter, increased neural oscillation power in the theta band, and increased cross-brain coherence were also observed for the in-person face condition. These findings highlight the fundamental importance of real faces and natural interactions for models of face processing.</p>
Figure 4 in Assessments of environmental variables affecting the spatiotemporal distribution and habitat preferences of living Ostracoda (Crustacea) species in the Enez Lagoon Complex (Enez-Evros Delta, Turkey)
Figure 4. Salinity tolerance diagram of Ostracoda determined in the Enez lagoons.
ScienceDex guides
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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.