Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

Open Science as a nest that welcomes, as caring; and with openness to the world

New infographic proposal on Open Science after those of the umbrella and the mushroom; care and welcome are added

opencc-by-4.0Sep 2022View details →

Data from: Accounting for predator species identity reveals variable relationships between nest predation rate and habitat in a temperate forest songbird

Abstract Nest predation is the primary cause of nest failure in most ground-nesting bird species. Investigations of relationships between nest predation rate and habitat usually pool different predator species. However, such relationships likely depend on the specific predator involved, partly because habitat requirements vary among predator species. Pooling may therefore impair our ability to identify conservation-relevant relationships between nest predation rate and habitat. We investigated predator-specific nest predation rates in the forest-dependent, ground-nesting wood warbler Phylloscopus sibilatrix in relation to forest area and forest edge complexity at two spatial scales, and to the composition of the adjacent habitat matrix. We used camera traps at 559 nests to identify nest predators in five study regions across Europe. When analysing predation data pooled across predator species, nest predation rate was positively related to forest area at the local scale (1,000 m around nest), and higher where proportion of grassland in the adjacent habitat matrix was high but arable land low. Analyses by each predator species revealed variable relationships between nest predation rates and habitat. At the local scale, nest predation by most predators was higher where forest area was large. At the landscape scale (10,000 m around nest), nest predation by buzzards Buteo buteo was high where forest area was small. Predation by pine martens Martes martes was high where edge complexity at the landscape scale was high. Predation by badgers Meles meles was high where the matrix had much grassland but little arable land. Our results suggest that relationships between nest predation rates and habitat can depend on the predator species involved and may differ from analyses disregarding predator identity. Predator-specific nest predation rates, and their relationships to habitat at different spatial scales, should be considered when assessing the impact of habitat change on avian nesting success.

opencc-by-4.0May 2024View details →

Genotypes for Neurospora nested association mapping population

Genotype file that contains genotypes all the Neurospora association mapping population developed in Kronholm lab. See https://github.com/ikron/Neurospora_NAM_population The file is a tab-delimited text file in hapmap format and contains first contains the columns: rs    alleles    chrom    pos    strand    assembly    center    protLSID    assayLSID    panel    GCcode    and then the subsequent columns are strains identifiers. The column 'rs' is the name of the SNP, column 'alleles' shows which two alternative bases occur, the column 'chrom' is the chromosome, column 'pos' is the coordinate, columns 'strand', 'center', 'protLSID', 'assayLSID', 'panel' and 'GCcode' contain all missing data. They are included for hapmap format compatibility. The column 'assembly' indicates the version of the Neurospora crassa reference genome that the coordinates are based on. And in this case it is NC12 for all SNPs. Missing data is indicated by 'N'

opencc-by-4.0Sep 2024View details →

Data and Code for "Extracting reproductive parameters from GPS tracking data for a nesting raptor in Europe"

Understanding population dynamics requires estimation of demographic parameters. We build on existing approaches to develop a new tool that uses GPS tracking data to estimate breeding propensity and breeding success, and show that this tool yielded accurate predictions for two red kite populations in Central Europe. The tool is available as an R package at <a href="https://github.com/Vogelwarte/NestTool">https://github.com/Vogelwarte/NestTool</a> and will facilitate the estimation of demographic parameters from tracking data to inform population assessments. The files in this repository contain the data and analytical code to replicate the results of the publication in the Journal of Avian Biology (DOI: 10.1111/jav.03246). The version contained in this repository does not include updates and improvements that occurred after the 29 August 2024.

opencc-by-4.0Aug 2021View details →

Dataset for statistical analysis of the habituation between the nest builder Cornitermes cumulans termites and their inquiline Curvitermes cf. odontognathus

Here we present the dataset  used for statistical analysis of the work aiming to known if habituation could attenuate host-inquiline lethal interactions, which could favor cohabitation in termites. For that, we tested the effect of the prior heterospecific exposure time on the behaviour and survival of termite hosts and inquilines during an encounter. We used as a biological model the nest builder termites Cornitermes cumulans and their inquiline Curvitermes cf. odontognathus. We used prior heterospecific exposure times of 0, 60, 120, and 180 min where inquilines and builders were kept apart in a Petri-dish but sharing the headspace.

opencc-by-4.0Dec 2022View details →

Data from: Nest orientation and proximity to snow patches are important for nest site selection of a cavity breeder at high elevation

Abstract Reproductive timing and location are central to breeding success across taxa. Many species have evolved specific strategies to cope with environmental variability including shifts in timing of reproduction tracking resource availability or selecting favourable nest location. In mountain ecosystems, complex topography and pronounced seasonality result in particularly high spatiotemporal variability of environmental conditions, and the risk of climate-induced resource mismatches is particularly acute given that temperature is increasing more rapidly than in the lowlands. We investigated how a high-elevation passerine, the white-winged snowfinch Montifringilla nivalis, selects its nest site in relation to nest cavity characteristics, habitat composition and snow condition. We used a combination of field habitat mapping and satellite remote sensing to compare occupied nest sites with randomly selected pseudo-absence sites. In the first half of the breeding season, snowfinches preferred nest cavities oriented towards the morning sun while they used cavities proportional to their availability later on. This preference might relate to the nest microclimate offering eco-physiological advantages, namely thermoregulatory benefits for incubating adult and nestlings under the harsh conditions typically encountered in the alpine environment. Nest sites were consistently located in areas with greater-than-average snow cover at hatching date, likely mirroring the foraging preferences for tipulid larvae developing in meltwater along snowfields. Due to the particularly rapid climate shifts typical of mountain ecosystems, spatiotemporal mismatches between foraging grounds and nest sites are expected in the future, which may negatively influence demographic trajectories of the species concerned. The installation of well-designed nest boxes in optimal habitat configurations could to some extent help mitigate this risk.

opencc-by-4.0Dec 2022View details →

Cryptosporidium GP60 Nested-PCR

Video tutorial for Cryptosporidium spp. identification by nested-PCR on GP60 locus. Vision of <a href="https://zenodo.org/api/files/a60e7020-7da2-4f8c-856f-da3b5d0981b7/Cryptosporidium%20Nested-PCR%2018S%20rDNA_V2.mp4?versionId=4ac18f93-0faf-4b97-95f4-0df3b06739d7">Cryptosporidium Nested-PCR 18S rDNA_V2.mp4</a> is convenient for applying this tutorial.

opencc-by-4.0Feb 2023View details →

Nest survival data of Anthus hellmayri

File 1: a_hellmayri_survival.csv Nest survival data of Anthus hellmayri collected during 2017-2018, 2018-2019, and 2019-2020 breeding seasons in Punta Indio, Buenos Aires, Argentina. Used to estimate daily nest survival rates and include covariates in the models. File 2: Readme_a_hellmayri_survival.docx File conainting information about the columns and data File 3: script_ah.R Example code to be used in R software. This code leads to the main result of the paper.

opencc-by-4.0Apr 2023View details →

A Dataset of French Trade Directories from the 19th Century for Nested NER task

This dataset is composed of pages and entries extracted from French directories published between 1798 and 1861. The purpose of this dataset is to evaluate the performance of Nested Named Entity Recognition approaches on 19th century French documents, regarding both clean and noisy texts (due to the OCR engine). Source dataset This dataset has been built from this source dataset : <pre><code class="language-markdown">N. Abadie, S. Baciocchi, E. Carlinet, J. Chazalon, P. Cristofoli, B. Duménieu and J. Perret, A Dataset of French Trade Directories from the 19th Century (FTD), version 1.0.0, May 2022, online at https://doi.org/10.5281/zenodo.6394464.</code></pre> Our experiments // Paper Details about our experiments on nested NER approaches are given in our paper (<a href="https://hal.science/hal-03994759v2">the pre-print version is available here</a>). <pre><code class="language-markdown">Tual, S., Abadie, N., Chazalon, J., Duménieu, B., & Carlinet, E. (2023). A Benchmark of Nested NER Approaches in Historical Structured Documents. Proceedings of the 17th International Conference on Document Analysis and Recognition, San José, California, USA. 2023. Springer. https://hal.science/hal-03994759v2</code></pre> Our code is available on <a href="https://github.com/soduco/paper-nestedner-icdar23-code">Git-Hub</a>. Dataset overview The following list describes the keys of the .JSON file which contain the complete materials of our experiments. - id : Entry unique ID in a given page - box : Bounding box of the entry in the scanned directory page - book : Source directory of the entry (*see more information bellow*) - page : Page ID in a given directory - valid_box : Is the bbox of the entry valid ? (*all bbox are valid here*) - text_ocr_ref` : OCR extracted and manually corrected text of the entry - nested_ner_xml_ref :  text_ocr_ref with nested ner entities - text_ocr_pero : OCR extracted text of the entry with PERO-OCR engine (best engine according to Abadie et al. experiment) - has_valid_ner_xml_pero : Is entities mapping between nested-ner entities annotated by hand on the ref text and pero ocr text correct ? (in our experiments, we only use entries with True value) - nested_ner_xml_pero : Annotated noisy entries produced with PERO OCR - text_ocr_tess : OCR extracted text of the entry with Tesseract engine (*not used in our expriments*) - nested_ner_xml_tess : Is entities mapping between nested-ner entities annotated by hand on the ref text and tesseract text correct? (not used in our experiments) - has_valid_ner_xml_tess : Annotated noisy entries produced with Tesseract. (not used in our experiments) Nested entities are annotated using XML tags. Our hierachy of entities is a *Part Of* a two-levels hierarchy. It means that bottom entities are contained in a top level entity.   Source documents // Copyright and licence This section has been copied from the <a href="https://zenodo.org/record/6394464">original dataset description</a>. The images were extracted from the original source https://gallica.bnf.fr, owned by the *Bibliothèque nationale de France* (French national library). Original contents from the Bibliothèque nationale de France can be reused non-commercially, provided the mention "Source gallica.bnf.fr / Bibliothèque nationale de France" is kept.   => Researchers do not have to pay any fee for reusing the original contents in research publications or academic works. Original copyright mentions extracted from <a href="https://gallica.bnf.fr/edit/und/conditions-dutilisation-des-contenus-de-gallica">https://gallica.bnf.fr/edit/und/conditions-dutilisation-des-contenus-de-gallica</a> on March 29, 2022. The original contents were significantly transformed before being included in this dataset. All derived content is licensed under the permissive *Creative Commons Attribution 4.0 International* license. Links to original contents are given in the window bellow :

opencc-by-4.0Jul 2023View details →

Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) I: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for H2O

We present all of the data across our SNR and abundance study for the molecule H2O for an exoEarth twin. The wavelength range is from 0.515-1 micron, with 25 evenly spaced 20% bandpasses in this range. The SNR ranges from 3-16, and the abundance values range from log10(VMR)  = -3.5 to -1.5 in steps of 0.5 and 0.25 (all presented in VMR in the associated table). We present the lower and upper wavelength per bandpass, the input H2O value (abundance case), the retrieved H2O value (presented as the log10(VMR)), the lower and upper limits of the 68% credible region (presented as the log10(VMR)), and the log-Bayes factor for H2O. For more information about how these were calculated, please see Bayesian Analysis for Remote Biosignature Identification on exoEarths (BARBIE) I: Using Grid-Based Nested Sampling in Coronagraphy Observation Simulations for H2O, accepted and currently available on arXiv.  To open this csv as a Pandas dataframe, use the following command: your_dataframe_name = pd.read_csv(f'zenodo_table.csv', dtype={'Input H2O': str})

openCC (other)Nov 2024View details →

American Goshawk habitat data from nest stands and random points within the Minidoka Ranger District, Sawtooth National Forest, USA

This data supported analysis of American Goshawk (Astur atricapillus) nest stand habitat and was collected within the Minidoka Ranger District of the Sawtooth National Forest in southern Idaho and northern Utah from 2017-2020. The central goal of this research was to develop management tools that demonstrate the utility of conducting analyses at multiple spatial scales as well as using both parametric and machine learning approaches. The stand-level dataset includes variables collected by hand in the field at nest stands and paired random forested sites 300 meters away. It also includes some terrain variables based on remote sensing data. Variables included in the stand-level data table include nest, distance to edge, distance to road, distance to water, division, dominant tree species, canopy closure, Stand Density Index (SDI), Trees per hectare, elevation, slope, Topographic Position Index (TPI), northness, eastness, Diameter at Breast Height (DBH), DBH variance, tree height, tree height variance, and crown depth. We recommend that the stand-level data be used to identify relevant variables and their thresholds for forest managers due to its high resolution. The forest-wide dataset includes only variables collected using various remote sensing datasets at nests and random forested points throghout the Minidoka Ranger District of the Sawtooth National Forest. Variables included in the forest-wide data table include nest, canopy closure, elevation, slope, TPI, northness, eastness, distance to road, distance to water, distance to edge, tree height, and crown depth. We recommend that the forest-wide data be used to identify areas of high suitability for goshawk occupancy across the study area along with sites that could become suitable habitat with management intervention. Latitude and longitude data, while used in our analyses, are excluded from the data tables to protect breeding goshawks from disturbance.

openCustomJan 2020View details →

Nest-mediated seed dispersal study from mixed habitats in North Georgia and Western North Carolina

Many plant seeds travel on the wind and through animal ingestion or adhesion; however, an overlooked dispersal mode may lurk within those dispersal modes. Viable seeds may remain attached or embedded within materials birds gather for nest building. Our objective was to determine if birds inadvertently transport seeds when they forage for plant materials to build, insulate, and line nests. We also hypothesized that nest-mediated dispersal might be particularly useful for plants that use mating systems with self-fertilized seeds embedded in their stems. We gathered bird nests in temperate forests and fields in eastern North America and germinated the plant material. We also employed experimental nest boxes and performed nest dissections to rule out airborne and fecal contamination. We found that birds collect plant stem material and mud for nest construction and inadvertently transport the seeds contained within. Experimental nest boxes indicated that bird nests were not passive recipients of seeds (e.g., carried on wind), but arrived in the materials used to construct nests. We germinated 144 plant species from the nests of 23 bird species. A large proportion of the nest germinants were graminoids containing self-fertilized seeds inside stemsâ€”suggesting that nest dispersal may be an adaptive benefit of closed mating systems. Avian nest building appears as a dispersal pathway for hundreds of plant species, including many non-native species, at distances of at least 100â€“200 m. We propose a new plant dispersal guild to describe this phenomenon, caliochory (calio = Greek for nest).

openCC0Jan 2025View details →

DPP01 Drought experiment nested within the phosphorus plots experiment at Konza Prairie

We explore how nutrient-altered tallgrass prairie responds to drought. Seven years of nutrient treatments (control, nitrogen (N), phosphorus (P), and N+P) resulted in significantly different plant communities. Within this experimental context we imposed a three-year drought followed by three years of recovery from drought. We hypothesized (1) the plant functional types would have different responses to drought; (2) the different community types would vary in their resistance to drought; and (3) the control and P treated plots, where N is limited, will have a greater increase in standing biomass production in the previously droughted plots compared to the non-droughted plots.

openCC (other)Mar 2025View details →

Boulder Chickadee Study nest temperature data, Boulder County, Colorado, 2024.

Incubation is a crucial part of the avian life cycle; eggs must be kept warm enough for embryos to develop. As egg temperatures drop rapidly when not being actively incubated, birds must balance the thermal requirements of their developing offspring with their own energy requirements when deciding to make a feeding trip. Incubation behavior can vary with ambient temperature, and across the breeding cycle. Here, we examine the incubation behavior of black-capped (Poecile atricapillus) and mountain (P. gambeli) chickadees where they live together in the Front Range of the Colorado Rocky Mountains. We deployed iButton temperature monitors in and around chickadee nests to record nest and ambient temperatures during the incubation period. For each deployment, we visually inspected temperature data to determine whether incubation was detected. For each deployment in which incubation was detected we quantified incubation behavior using the incR R package. Across the four nests for which incubation was detected, females (the incubating sex) spent about 85% of the day incubating, and left the nest about 32 times per day for an average of 6.7 minutes. On average, nest temperatures were maintained around 35˚C.

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Data from: Linking pollen foraging of megachilid bees to their nest bacterial microbiota

Solitary bees build their nests by modifying the interior of natural cavities and they provision them with food by importing collected pollen. As a result, the microbiota of the solitary bee nests may be highly dependent on introduced materials. In order to investigate how the collected pollen is associated with the nest microbiota, we used metabarcoding of the ITS2 rDNA and the 16S rDNA to simultaneously characterize the pollen composition and the bacterial communities of 100 solitary bee nest chambers belonging to seven megachilid species. We found a weak correlation between bacterial and pollen alpha-diversity and significant associations between the composition of pollen and that of the nest microbiota, contributing to the understanding of the link between foraging and bacteria acquisition for solitary bees. Since solitary bees cannot establish bacterial transmission routes through eusociality, this link could be essential for obtaining bacterial symbionts for this group of valuable pollinators.

opencc-zeroAug 2020View details →

opencc-by-4.0Feb 2015View details →

Figure 1 in Observations on the nesting behaviour of the spider wasp Eragenia congrua (Hymenoptera: Pompilidae), with the first record of the host

Figure 1. (A) Jacaranda tree (Jacaranda copaia) with the nests of Eragenia congrua; (B) detail of the bark of Jacaranda tree with three closed old nests of E. congrua indicated by arrows. (C, D) Females of E. congrua on the bark of a Jacaranda tree.

opencc-by-4.0Feb 2015View details →

Figure 4 in Observations on the nesting behaviour of the spider wasp Eragenia congrua (Hymenoptera: Pompilidae), with the first record of the host

Figure 4. (A) Female of Eragenia congrua with bent gaster and curved wing tip; (B) mandible of a female of E. congrua; (C) terminal portion of metasoma of a female of E. congrua; (D) detail of the bristles in the terminal portion of metasoma of a female of E. congrua.

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Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data for 130 samples of Chiromantis rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change, and periods of isolation and secondary contact. Species distribution models were used to identify regions of climatic stability that could have served as forest refugia since the Last Interglacial. Results: Population structure within Chiromantis rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent-based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Main conclusions: Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo-Congolian forest. Population demographic inferences help connect patterns of genetic variation to diversification model predictions. The diversification history of Chiromantis rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation, and adaptive evolution along environmental gradients.

opencc-zeroAug 2020View details →

opencc-zeroJan 2016View details →

Daily Activity and Nest Occupation Patterns of Fox Squirrels (Sciurus niger) Throughout the Year

The daily distribution of activity has been studied in detail in ground squirrels in the field as well as in the laboratory, but studies of tree squirrels have been few and generally limited to the sampling of behavior of groups of animals. In this study, the authors investigated the general activity and nest occupation patterns of fox squirrels in a natural setting using temperature-sensitive data loggers that measure activity as changes in the microenvironment of the animal. Data were obtained from 25 distinct preparations, upon 13 unique squirrels, totaling 1385 recording days. Fox squirrels exhibited robust daily rhythmicity of locomotor activity, comparable to that of laboratory rats and gerbils. The animals were clearly diurnal, with a predominantly unimodal activity pattern, although individual squirrels occasionally exhibited bimodal patterns, particularly in the spring and summer. Even during the short days of winter (9 hours), the squirrels typically left the nest after dawn and returned before dusk, spending only about 7 hours out of the nest each day. Although the duration of the daily active phase did not change with the seasons, the squirrels exited the nest earlier in the day when the days became longer in the summer and exited the nest later in the day when the days became shorter in the winter, thus tracking dawn along the seasons. During the few hours each day spent outside the nest, fox squirrels seemed to spend most of the time sitting or lying. These findings suggest that fox squirrels may have adopted a slow life history strategy.