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Data and original code for: Explaining the diversity of optical effects in Christmas beetles: climate, history, and mechanisms
<p><span>Beetles exhibit an extraordinary diversity of brilliant and colourful appearances. The mechanisms producing these optical effects have received some attention, but we know little about the ecological variables driving their evolution. Here we investigated environmental correlates of reflectivity and circular polarization produced by a combination of pigments and structures in optically diverse Christmas beetles (Scarabaeidae: Rutelinae). We quantified the optical properties of 261 specimens representing 46 species using spectrophotometry and calibrated photographs. Then, we examined associations between these properties and environmental variables such as temperature, humidity, and vegetation cover, controlling for body size and phylogenetic relatedness. Our results showed that larger beetles have higher reflectivity and occur in drier environments. Unexpectedly, near-infrared (NIR) reflectivity was not correlated with ecological variables. We observed no universal ecogeographical pattern for polarization but identified trade-offs with other optical properties: beetles without polarization-associated nanostructures had higher NIR reflectivity. Visible reflectivity seems less affected by nanostructures and is instead negatively correlated with the accumulation of pigments such as melanin. Our study highlights the value of a macroecological approach for testing alternative hypotheses to explain the diversity of optical effects in beetles and to understand the link between structure and function.</span></p>
The effects of PaPE-1 on amyloid beta-induced neurotoxicity
<p>Data related to the article Posttreatment with PaPE-1 Protects from Aβ-Induced Neurodegeneration Through Inhibiting the Expression of Alzheimer's Disease-Related Genes and Apoptosis Process That Involves Enhanced DNA Methylation of Specific Genes. These are biochemical, molecular and microscopic data. We aimed to verify the neuroprotective capacity of PaPE-1 against amyloid beta (Aβ)-induced toxicity. Fig 1 – the presence of amyloid beta in cellular cultures; Fig 2 – the effects of apoptosis inhibitors on amyloid beta-induced caspase-3 activity; Fig 3 – the effects of amyloid beta and PaPE-1 on caspase -3, -8, and -9 activities; Fig 4 – effects of amyloid beta and PaPE-1 on Calcein AM and Hoechst 33342 staining; Fig 5 – effects of amyloid beta and PaPE-1 on expression of apoptosis related factors; Fig 6 – effects of amyloid beta and PaPE-1 on methylation of specific genes; Fig 7 – effects of amyloid beta and PaPE-1 on the degree of neurodegeneration; Fig 8 - effects of amyloid beta and PaPE-1 on the membrane stain; Fig 9 - effects of amyloid beta and PaPE-1 on the expression of Alzheimer’s disease-related genes.</p>
Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."
<div> <p>All data and R code for</p> <p><strong>Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to <em>Daphnia</em> - a meta-analysis. <em>Microplastics and Nanoplastics</em>. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>)</strong></p> <p><em>Abstract</em></p> <p>Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus <em>Daphnia</em>. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in <em>Daphnia</em> spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.</p> </div>
Supplementary Data of the project "Cross Cultural Tears - A Systematic Investigation of the Interpersonal Effects of Emotional Crying Across Different Cultural Backgrounds"
<p>Supplementary Data related to the publication: </p> <div> <p>Zickfeld, J. et al. (2021). Tears evoke the intention to offer social support: A systematic investigation of the interpersonal effects of emotional crying across 41 countries. Journal of Experimental Social Psychology, 95, 104137. <a href="https://doi.org/10.1016/j.jesp.2021.104137" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.jesp.2021.104137 </a></p> </div>
Figure 2 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 2. Logarithmic in base 10 values of oxidative biomolecules level for each period collected (n = 6). Wilcox Test: P = 0.31. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Figure 1 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 1. (a) Osmotic fragility in percentage by saline concentration from both periods studied (GLM: F = 2.56, P = 0.03). No statistical differences were observed between individualized pairs of saline concentrations; (b) Overall osmotic fragility difference between periods considering only periods effect (GLM: F = 9.72, P = 0.01) (n = 6). Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Figure 3. Limnocoris submontandoni testis with clomazone 162 in Ecotoxicological effects of commercial herbicides on the reproductive system of aquatic arthropod Limnocoris submontandoni (Hemiptera: Naucoridae)
Figure 3. Limnocoris submontandoni testis with clomazone 162 mg / L, (A) Apparent enlargement of the testicular interstice and degeneration of some spermatoids (SPTI), with normal concentrations of spermatozoa (SPTZ) in the outer regions, (B) spermatocytes (SPTO) with normal appearance and sperm (SPTZ) with slight alteration of spermatids (SPTI), C) profusion of sperm (SPTZ) with a high degree of compaction, indicating high rates of spermatogenesis and integrity of tubular cells (arrowhead). Dye: Toluidine Blue.
Figure 1 in Ecotoxicological effects of commercial herbicides on the reproductive system of aquatic arthropod Limnocoris submontandoni (Hemiptera: Naucoridae)
Figure 1. Photomicrographs of the control group of Limnocoris submontandoni, (A) helical distribution of the seminiferous tubule with germ cells, spermatogonia (SPGO), spermatocytes (SPTO), spermatids (SPTI), sperms (SPTZ), (B) spermatocytes (SPTO) and spermatids (SPTI) in different degrees of maturation, (C) spermatocytes (SPTO) with slightly colored areas (*) displaced to one of the cell poles, spermatids (SPTI) with different degrees of maturation, acrosome vesicle (arrows), elongation of slightly colored structures (**), elongated cells forming the tubular wall (arrowhead), core (n), (D) Spermatids (SPTI) in different degrees of maturation, spermatozoa (SPTZ) forming compact bundles and very elongated nucleus, nucleus (n) and acrosome vesicles (arrows) of some spermatoids and (E) Compact sperm bundles (SPTZ), sperm nuclei (n), tubular wall cells (arrowhead) and tracheole (tr). Dye: Toluidine Blue.
Figure 3 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 3. Logarithmic in base 10 values of (a) Enzymatic activity level of glutathione peroxidase – GPx and (b) activity of glutathione reductase - GR of red blood cells in hibernation and active periods (n = 6). T-test, P = 0.68 and P = 0.10, respectively. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Fig. 1 in Flower thrips (Thysanoptera: Thripidae and Phlaeothripidae) species complex on Florida blackberries and the effect of blackberry cultivar
Fig. 1. Numbers of flower thrips sampled from 6 blackberry cultivars. a) Mean total numbers of thrips larvae and adults per flower. b) Mean numbers of thrips adults and c) mean numbers of thrips larvae per flower on each sampling date. Error bars represent SE. Treatments with the same letter are not significantly different at P <0.05. Significant differences for the last 3 sampling weeks in (c) are described in the text.
FedscGen: privacy-aware federated batch effect correction of single-cell RNA sequencing data -- Preprocessed datasets
<div> <div> <div> <div> <p>This dataset accompanies the publication "FedscGen: Privacy-Aware Federated Batch Effect Correction of Single-Cell RNA Sequencing Data" and includes eight single-cell RNA sequencing (scRNA-seq) datasets used to benchmark the FedscGen and scGen methods. The datasets are provided in <code>.h5ad</code> format and include comprehensive metadata necessary for replication and further analysis.</p> <h3>Datasets</h3> <p>We analyze various datasets to compare FedscGen against scGen (centralized) in terms of batch correction. For simplicity, we refer to the dataset by abbreviations:</p> <ol> <li> <p><strong>Cell Line (CL)</strong>:</p> <ul> <li>Derived from the 293t_jurkat experiment with three batches: Zheng et al., 2017.</li> </ul> </li> <li> <p><strong>Human Dendritic Cells (HDC)</strong>:</p> <ul> <li>scRNA-seq data of human dendritic cells across two batches: Villani et al., 2017.</li> </ul> </li> <li> <p><strong>Human Pancreas (HP)</strong>:</p> <ul> <li>Consolidated data from five sources with 14,767 cells each: Baron et al., 2016; Muraro et al., 2016; Segerstolpe et al., 2016; Wang et al., 2016; Xin et al., 2016.</li> </ul> </li> <li> <p><strong>Mouse Brain (MB)</strong>:</p> <ul> <li>Merged datasets with 691,600 and 141,606 cells: Saunders et al., 2018; Rosenberg et al., 2018.</li> </ul> </li> <li> <p><strong>Mouse Cell Atlas (MCA)</strong>:</p> <ul> <li>Data focusing on 11 cell types from various organs: Han et al., 2018; The Tabula Muris Consortium, 2018.</li> </ul> </li> <li> <p><strong>Mouse Hematopoietic Stem and Progenitor Cells (MHSPC)</strong>:</p> <ul> <li>Data from SMART-seq2 and MARS-seq protocols: Nestorowa et al., 2016; Paul et al., 2015.</li> </ul> </li> <li> <p><strong>Mouse Retina (MR)</strong>:</p> <ul> <li>Data from two unassociated laboratories with 26,830 and 44,808 cells: Macosko et al., 2015; Shekhar et al., 2016.</li> </ul> </li> <li> <p><strong>PBMC (human Peripheral Blood Mononuclear Cell)</strong>:</p> <ul> <li>scRNA-seq data with two batches: Zheng et al., 2017.</li> </ul> </li> </ol> <p><strong>Usage Notes</strong>: Each dataset is provided in <code>.h5ad</code> format, compatible with common single-cell analysis tools such as Scanpy. Detailed metadata is included within each file.</p> <p><strong>Keywords</strong>: Single-cell RNA sequencing, scRNA-seq, Batch effect correction, Privacy-aware, Federated learning, scGen, FedscGen, Clinical multi-center studies, Genomics, Bioinformatics</p> <p><strong>Contact</strong>: For questions or further information, please contact Mohammad Bakhtiari at <a href="mailto:mohammad.bakhtiari@uni-hamburg.de.">mohammad.bakhtiari@uni-hamburg.de.</a></p> <p><strong>License</strong>: Creative Commons Attribution 4.0 International (CC BY 4.0)</p> </div> </div> </div> </div> <div> <div> <div> </div> </div> </div>
Data from Investigating the effects of diurnal and nocturnal pollinators on male and female reproductive success and on floral trait selection in Silene dioica
<p><strong>data_all_OdEx.csv</strong>: all data about phenotypes or reproductive success at the individual scale</p> <ul> <li>ID : ID name</li> <li>nGrSemis_min : seed number needed to be sowned to get enough seedlings</li> <li>nGrGerm : seed number effectively sowned</li> <li>nGrGerm_OK : number of germinated seed</li> <li>TauxGerm : germination rate</li> <li>nFruits_MAX : maximal number of fruit that the plant could have produced</li> <li>nFruits_OK : effective number of fruits that the plant had produced</li> <li>nFruits_OK_avecPred : effective number of fruits that the plant had produced ignoring predation</li> <li>nFruits_pred : number of predated fruits</li> <li>mean_nbSeeds : mean number of seeds per fruit</li> <li>sd_nbSeeds : sd number of seeds per fruit</li> <li>mean_nbOv : mean ovule non fertilize per fruit</li> <li>sd_nbOv : sd ovule non fertilize per fruit</li> <li>mean_nbOvTOT : mean ovule number per flower</li> <li>sd_nbOvTOT : sd ovule number per flower</li> <li>prodTOT : total number of seed produced including germination rate</li> <li>FS : Fruit-set</li> <li>SS : Seed-set</li> <li>prodTOTsg : total number of seed produced without germination rate</li> <li>nbFlo_run0 : flower number at the beginning of the experiment</li> <li>nbFlo_run1 : flower number at the first measurement</li> <li>mean_nbFlo : mean flower number</li> <li>MeanFec : mean seed sired per males according to MEMM model</li> <li>MeanDelta : mean delta pollen dispersion according to MEMM model</li> <li>MeanMRS : mean male reproductive success (including female RS) according to MEMM model</li> <li>MedFec : same as above with the median</li> <li>MedDelta : same as above with the median</li> <li>MedMRS : same as above with the median</li> <li>VarFec : same as above with the variance</li> <li>VarDelta : same as above with the variance</li> <li>VarMRS : same as above with the variance</li> <li>ciFec : Same as above with confidence interval</li> <li>ciDelta : Same as above with confidence interval</li> <li>ciMRS : Same as above with confidence interval</li> <li>MS_Res : mating success</li> <li>mean_lFl : mean corolla width</li> <li>mean_hFl : mean calyx height</li> <li>QttTOT : pollen number per flower</li> <li>pop : which originate population</li> <li>cohort : which cohort</li> </ul> <p><strong>data_seeds_OdEx.csv</strong> : all data about seed number of weight as well as unfertilized ovule at the fruit scale for female RS</p> <ul> <li>ID : ID name</li> <li>noFruit : ID fruit</li> <li>poids : seed weight</li> <li>nbSeeds : number of seeds</li> <li>nbOv : number of unfertilized ovule</li> <li>moySeeds : mean seed size</li> <li>varSeeds : variance in seed size</li> </ul> <p><strong>data_poll_OdEx.csv</strong> : all data about pollinator observation session</p> <ul> <li>ID : ID name</li> <li>session : observation session number</li> <li>nbVis : number of independent insect attracted</li> <li>nbVisTot : number of total visit</li> <li>binVis : individual visited or not</li> </ul>
Dataset for "Self-heating effects and switching dynamics in graphene multiterminal Josephson junctions"
<p>Dataset containing raw measurement data and simulation results for the manuscript "Self-heating effects and switching dynamics in graphene multiterminal Josephson junctions".</p>
Negative parental and offspring environmental effects of macroalgae on coral recruitment are linked with alterations in the coral larval microbiome
<p>The persistence of reef-building corals is threatened by macroalgal competitors leading to a major demographic bottleneck in coral recruitment. Whether parental effects exist under coral-algal competition and whether they influence offspring performance via microbiome alterations represent major gaps in our understanding of the mechanisms by which macroalgae may hinder coral recovery. We investigated the diversity, variability and composition of the microbiome of adults and larvae of the coral <em>Pocillopora acuta</em> and surrounding benthic substrate on algal-removed and algal-dominated bommies. We then assessed the relative influence of parental and offspring environmental effects on coral recruitment processes by reciprocally exposing coral larvae from two parental origins (algal-removed and algal-dominated bommies) to algal-removed and algal-dominated environmental conditions. Dense macroalgal assemblages impacted the microbiome composition of coral larvae. Larvae produced by parents from algal-dominated bommies were depleted in putative beneficial bacteria and enriched in opportunistic taxa. These larvae had a significantly lower survival compared to larvae from algal-removed bommies regardless of environmental conditions. In contrast, algal-induced parental and offspring environmental effects interacted to reduce the survival of coral recruits. Together our results demonstrate negative algal-induced parental and offspring environmental effects on coral recruitment that could be mediated by alterations in the offspring microbiome.</p>
Train and Evaluation Code, Road Classification Models and Test set of the paper "Insights into the Effects of Image Overlap and Image Size on Semantic Segmentation Models Trained for Road Surface Area Extraction from Aerial Orthophotography"
<p>This repository contains the Python scripts built for training and evaluation of the implementation, together with the test data and the resulting road segmentation models corresponding to the paper "Insights into the Effects of Image Overlap and Image Size on Semantic Segmentation Models Trained for Road Surface Area Extraction from Aerial Orthophotography". The scripts make use of the Tensorflow with Keras framework and their additional required dependencies.</p> <p>The training and validation set is based on the binary SROADEX dataset (<a href="../records/6482346">https://zenodo.org/records/6482346</a>) that was re-split into tiles that feature the image resolutions (256 x 256, 512 x 512, and 1024 x 1024 pixels) and image overlaps (0% and 12.5%) considered in this study. The data have been generated using scripts developed in Python using Open Source libraries (GDAL/OGR and MapScript) for rasterization of vector cartography that represents the axes of the different types of roads (urban, interurban and rural). This binary road data contains information from 16 full orthoimages (28.5 km * 18.5 km) with spatial resolution of 0.5 m/pixel from the insular and peninsular Spanish territory. Due to the size on disk of approximately 492 gigabytes, this training and validation data is only available upon request from the corresponding author. The test set has been generated from a novel area from Palencia (Spain) and features 18 million pixels labelled with the positive "Road" class. The test sets are provided in the repository for each resolution (with no overlap), so that additional DL models can be evaluated on the same data and compared with the results achieved in this study.</p> <p>The structure of the information shared in this repository is as follows:<br>The scripts have been grouped by tile resolution (256, 512 and 1024). First, the test set and the evaluation script can be found. For each tile resolution, there are two subfolders (corresponding to the "no overlap" and "12.5% overlap"). In each case, the Python scripts for training the models in the three repetitions are shared, and the trained models (H5 format) are shared in compressed form. Finally, for each resolution we also share the testing dataset which consists of two folders.</p> <p>The material is distributed under a CC-BY 4.0 license.</p>
Figure 7 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 7. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) weed germination/emergence, (B) seedling radicle/root length, (C) plant height, and (D) leaf area when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.
Figure 3 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 3. Overall water-stress effects on germination/emergence of grass and broadleaf weeds (top) and six weed families—Asteraceae, Fabaceae, Convolvulaceae, Amaranthaceae, Rubiaceae, and Poaceae (bottom). The vertical black dashed line represents zero effect. The black dots are overall mean effect sizes, and the black lines are 99% confidence intervals (CIs).The values in parentheses are the number of observations followed by the number of studies for each pair-wise comparison. The mean effect sizes were considered significantly different when their 99% CIs did not include zero.
Figure 4 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 4. The log response ratio for germination and seedling radicle length of broadleaf (green dots/line) and grass (red dots/line) weed species as a function of water-stress intensity. Water stress increased as solution osmotic potential (ψsolution) decreased and vice versa.The subgroups for germination are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −0.8, −0.8 to −1.0, −1.0 to −1.4, and <−1.4 MPa, while the subgroups for radicle length are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −1.0, and <−1.0 MPa. Only ψsolution-based studies were used in this analysis. For each subgroup, the solid dots and lines represent mean effect sizes and their corresponding 99% confidence intervals (CIs).The mean effect sizes were considered significantly different when their 99% CIs did not include zero. Similarly, the water-stress effects were significantly different for each subgroup and among weed types only when their 99% CIs did not overlap with one another. The fitted lines represent a four-parameter logistic regression model, and the coefficients of the models are presented in Table 2.
Figure 1 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 1. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses; Page and McKenzie 2021) flow diagram highlighting the selection procedure of 86 scientific published papers included in the meta-analysis.
Figure 8 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 8. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) branches/tillers per plant, (B) leaves per plant, (C) inflorescences per plant, (D) seeds per plant, (E) total biomass, (F) root biomass, (G) shoot biomass, and (H) root:shoot ratio, when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.
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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.