Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

GTDB-Tk Phylogenetic Information for 102 MAGs from Columbia River hyporheic sediments

These are the phylogenetic analyses output for the GTDB-Tk that was run on the 102 MAGs from the Columbia River Hyporheic Zone. They form part of supplementary material from publication titled "Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments".

opencc-zeroNov 2022View details →

Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities. 2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability. 3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km2 sampling sites across a P. montanus hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies. 4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.

opencc-by-3.0-atApr 2022View details →

Planar Graph Classifier - Class Information

CSV files associating image files from the Planar Graph Classifier - Generated Graph Images (<a href="https://doi.org/10.5281/zenodo.6510092">10.5281/zenodo.6510092</a>) with planarity information. Class 0: graph drawn with networkx spring layout Class 1: graph drawn with networkx planar layout

opencc-by-4.0Jan 2022View details →

Compound Information in the EBI Metabolights Repository

Compound files from all studies in the EBI Metabolights database were stacked together. It has ~50K unique chemical names.

Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle"

Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle". The PDF file entitled "Supplementary material" contains the uncropped original western blots and autoradiographs published in the article. The PDF files entitled "Extended Data Fig.2,6,7,9,10 all panels" and "Figure 1,4 all panels" contain the original full-size confocal immunofluorescence images from which specific ROIs are published in the article. The Excel files "Source Data Principal Figures" and "Source Data Extended Figures" contain all the original datasets used for calculation and graphical representation of data published in the article.

openother-openMay 2022View details →

Physical Informed Deep Learning Reconstructs Missing Climate Information in the Antarctic

Here is the code and data corresponding to the Physical Informed Deep Learning Reconstructs Missing Climate Information in the Antarctic article. Reanalysis data In the reanalysis data folder, skin temperature data and wind speed data are in two different folders. The reanalysis data is the monthly average of the ERA-Interim from European Centre for Medium-Range Weather Forecasts (ECMWF) for 40 years from 1979 to 2018, with 1.5° latitude × 1.5° longitude resolution. The first 30 years are used as training data, and the next 10 years are used as test data. And the variables such as skin temperature (K, Kelvins) and surface wind speed (m/s, meter per second) are selected for experiments in Antarctic region (longitude (0°-360°), latitude (60°S-90°S)).  Station data The station data folder contains real observations from 180 weather stations in the Antarctic region. These include variables such as temperature, wind speed, and wind direction. PI-RFR The PI-RFR folder contains the code for this method, including training, testing, mask generation and network structure. Requirements: - Python >= 3.6 - PyTorch >= 1.6 - Numpy == 1.20.3 - NetCDF4 == 1.5.7 - h5py == 3.3.0 Train & Test To training or testing, use <pre><code class="language-python">python run.py python run.py --test</code></pre>

Project files provided as supporting information to the manuscript "Information-theoretical measures identify accurate low-resolution representations of protein configurational space"

The dataset contains the following compressed folder: -Notebooks.zip: This folder contains:   -python_script:         -RESREL.py: script performing the clusterization and computing the relevance resolution curves         -random_curves.py: script generating the random value and computing the corresponding RES-REV curves_s         -Cluster_distance_matrix.py: script returning the distance among clusters for a given partition.   -python_notebook:         -Exploratory_analysis.ipynb:  Analysis performed on the 12-protein_dataset         -DMAPS_ANTI.ipynb: Diffusion Map for the Antibody         -DMAPS_COV_1ake.ipynb: Diffusion Map + Inter-Intra state decomposition of covariance for 1ake Packages required for the usage of these python scripts/notebooks:   -numpy   -pandas   -matplotlib   -seaborn   -multiprocessing   -scipy   ======== RAW DATA ======== The raw data produced and employed in this study are available on a Google Drive folder at the following address: https://drive.google.com/drive/folders/1PasAUCgpR5-gdzUVEdyusgZIayQN0Le9 In this folder, together with the compressed Notebooks.zip folder, one can fin the compressed folder Data.zip, within which the following data are present: -12-protein_dataset:     -md.mdp: the .mdp file used in the MD simulations     -PROTEIN_PDB_CODE:         -Hk_{sel}.npy & Hs_{sel}.npy: the Rel & Res curves, sel=[all, CA, CB]         -RMSD_{sel}.npy: the RMSD matrix, sel=[all, CA, CB]         -npt.gro:protein+water+ions structure @TEO the equilibration (NVT+NPT)         -MSR_df.csv: a dataset containing the following columns                   'area' : area behind the Relevance-Resolution curve;                   'selection': the atomic selection (['all', 'CA', 'CB']) used to compute the RMSD matrix used for the clusterization (and consequently the Relevance-Resolution curves)                   'method': the linkage measure used in the clustering procedure, an integer in [0,6];                   'method_name': the linkage measure used in the clustering procedure, a string in ['average','ward','complete','single','centroid','median','weighted'];                   'rmsd_mean': the mean value of the rmsd vector along the trajectory computed wrt the first frame;                   'rmsd_var': the variance of the rmsd vector along the trajectory computed wrt the first frame;                   'rgy_mean': the mean value of the radius of gyration  along the trajectory;                   'rgy_var': the variance of the radius of gyration  along the trajectory;                   'rmsf_mean': the mean value of the rmsf;                   'rmsf_var': the variance of the rmsf;                   'RMSD_M_mean': the mean value of the RMSD matrix.                   'RMSD_M_var': the variance of the RMSD matrix.   -Random:     -curves.npy= 100K Relevance-Resolution Random curves for M=40001     -curves_s.npy= 100K Relevance-Resolution Random curves for M=15000   -validation_dataset:     -antibody:         -Hk_CB.npy & Hs_CB.npy: the Rel & Res curves         -RMSD_CB.npy: the RMSD matrix         -DIFF_{M}.npy: the eigenvalue/vector of the 10-D diffusion space         -Label_{method}.npy: the label vector for n_clusters     -1ake:         -Hk_{sel}.npy & Hs_{sel}.npy: the Rel & Res curves         -RMSD_{sel}.npy: the RMSD matrix         -DIFF_{M}.npy: the eigenvalue/vector of the 10-D diffusion space         -Label_{method}.npy: the label vector for n_clusters         -intra_{m}.npy: the intra-cluster covariance matrix         -inter_cov_{m}.npy: the inter-cluster correlation matrix   NOTE ===== The matrices of the cluster distances for adenylate kinase and antibody have been computed through the script Cluster_distance_matrix.py. These matrices have not been included in the dataset because of their large size; the raw data are however available upon request.

opencc-zeroMay 2022View details →

Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys

Ecologists often study biodiversity by evaluating species occupancy and the relationship between occupancy and other covariates. Occupancy models are now widely used to account for false absences in field surveys and to reduce bias in estimates of covariate relationships. Existing occupancy models take as inputs binary detection/non-detection observations of species at each visit to each site. However, autonomous sensing devices and machine learning models are increasingly used to survey biodiversity, generating a new type of observation record (i.e., continuous-score data) that reflects the model's confidence a species is present in each autonomously sensed file, instead of binary detection/non-detection data. These data are not directly compatible with traditional binary occupancy modeling methods. Here, we develop a new occupancy model that models continuous scores on a visit level as a Gaussian mixture, combining a distribution of scores for files that do contain the species of interest and a distribution of scores for files that do not. The model takes as input continuous scores for each autonomously sensed and classified file, along with an optional small number of binary, manually verified detection and non-detection annotations. We present a simulation study that shows that over a range of empirically realistic parameters, our model outperforms traditional occupancy models that are based on binary annotation alone. We also apply this new model to an empirical case study using data generated from five machine learning classifiers applied to autonomous acoustic recordings gathered in the eastern United States. Because our occupancy model generalizes allowable input data beyond binary observations, it is particularly well-suited to the increasing volume of machine learning classified data in ecology and conservation.

Understanding Cultural Information Flow: A Qualitative study of a small social group

This study uses qualitative data to explore closely adoption and onward transmission. Interview data were collected in relation to housework regarding the perceived behaviour of participants’ parents, of themselves, and of their (grand)children (N=14). Observational data was also collected from the members of one of the families for triangulation purposes. Following the six-phase process of thematic analysis, we extracted three main themes: individual learning, horizontal transmission, and vertical transmission. While only few instances were categorised as ‘individual learning’, the instances of horizontal and vertical transmission were numerous, and included the transmission of dichotomous traits. Thus, we explored why some cultural variants outcompete others and how certain learning and teaching mechanisms lead to increased stability and longevity. Vertical congruence was observed during the transmission of a dichotomous cultural trait: transmitters who acquired two variants of the same trait (one horizontally and one vertically) chose to vertically transmit onward to learners – i.e., their (grand)children – the variant which they had previously acquired vertically (i.e., from their own parents or grandparents), even if they exhibited both variants themselves. Horizontal congruence was observed even in sibling-to-sibling transmission, as the transmitter (older sibling) transmitted onward to the learner (younger sibling) the cultural variants which he/she had previously acquired from a peer (even if these were in competition with vertically acquired alternatives). Finally, we discuss the effects of the mother/wife-transmitter, who can weaken the effects of the vertical-congruence effect in the case of her spouse and enhance them in the case of their children.

Data, scripts and supplementary information for analysis of the functioning of a three-species microcosm under cadmium pressure

Data files of different experiments conducted with a three-species microcosm + Rscript for infering paremeters from a mechanistic EDO based model describing the functioning of the microcosm and the effect of cadmium + JAGS script of the model + supplementary information

opencc-zeroDec 2021View details →

Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on non-invasive samples, making it challenging to generate large amounts of high-quality genetic data for many elusive and at-risk species. We developed and optimized a Genotyping-in-Thousands by sequencing (GT-seq) panel using non-invasive samples to inform the management of invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high-quality tissue and non-invasive fecal and hair samples to simultaneously distinguish individuals, identify sex and reconstruct kinship among deer sampled across the archipelago, then provided a proof-of-concept application using field-collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high-quality tissue samples genotyped using restriction-site associated DNA sequencing (92.4%), while genotyping discordance between paired high-quality tissue and non-invasive samples was low (0.50%). The panel will be used to inform future invasive species operations (culls or eradications) in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT-seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where non-invasive genetic sampling is employed.

opencc-zeroJun 2022View details →

Zehneria neorensis: Additional phylogenies and sequence information

Basic data and supplement for Ranjan et al. 2022, Biogeography of Zehneria (Cucurbitaceae) and a New Species from India, Systematic Botany. Zehneria is one of the most diverse genera in Cucurbitaceae with 75 accepted species mainly in Southeast Asia and tropical Africa. We describe Zehneria neorensis, a new species from Neora Valley in the mountains of West Bengal, India, which has 7–10 cm long twisted fruiting pedicels, the longest pedicels reported in the genus so far. Based on morphological data, we also suggest the transfer of Melothria morobensis to the genus Zehneria. With a molecular phylogenetic and global biogeographic analysis based on 3856 nucleotides of plastid and nuclear ribosomal DNA, we demonstrate that the genus Zehneria most likely originated on the African continent 24 (30-19) million years ago and spread from there at least five times to Madagascar and three times to Asia. Zehneria neorensis represents an independent colonization event from Africa to India about 11 (15–7) million years ago. Three lineages reached New Guinea/Australia and finally moved into Polynesia. We infer a rate of at least 20 long-distance dispersal (LDD) events per 10 million years in the genus. This high LDD frequency is most likely a result of the small berry fruits and small flattened seeds of Zehneria, which seem perfectly adapted to long-distance bird dispersal. Field observations are needed to investigate a potential effect of the newly discovered extended and coiling pedicels in Zehneria neorensis on seed dispersal efficiency. The new species adds to a growing list of rather old Cucurbitaceae lineages in the Himalayan foothills, supporting the hypothesis of long climatic stability in the region.

Multishell Diffusion MR Tractography Yields Morphological and Microstructural Information of the Anterior Optic Pathway: A Proof-of-Concept Study in Patients with Leber's Hereditary Optic Neuropathy. RAW DATA

Raw data used to prepare Figures and Tables in article "Multishell Diffusion MR Tractography Yields Morphological and Microstructural Information of the Anterior Optic Pathway: A Proof-of-Concept Study in Patients with Leber’s Hereditary Optic Neuropathy", accepted for publication at International Journal of Environmental Research and Public Health, 27 May 2022.

opencc-by-4.0Mar 2022View details →

Non-informative dataset to be used with GA-VirReport workflow

Input dataset of plant chloroplast, mitochondria and rRNA

The Practical Value of Information Literacy in the Workplace

This video was produced for an information literacy course at the University of Ottawa's École School of Information Studies (ÉSIS). It is shared as an open education resource to be (re)used to teach viewers about the value of information literacy in the workplace. The video aims to briefly outline workplace literacy expectations for novice job seekers wanting to increase their employability. The video’s objective is to make (under)graduate students aware of the key information literacy skills that employers are looking for in new hires, and provide some suggested resources to improve or acquire these skills. The video is meant to be a starting point to build on students' awareness of information literacy skills and how these skills will be valuable in the workplace. This builds on the core concept of "Information Has Value" from the Association of College & Research Libraries' <a href="https://www.ala.org/acrl/sites/ala.org.acrl/files/content/issues/infolit/framework1.pdf">Framework for Information Literacy for Higher Education</a> (2015). Learning objectives include knowing why an employee needs information, where and how information can be found, and how information is used and presented in the workplace. The video was produced using Microsoft PowerPoint, Canva, Slidesgo and Screencast-o-matic. The following references were used to inform the video content:  Cheuk, B. (2008). Delivering business value through information literacy in the workplace. Libri, 58(3), 137–143. <a href="https://doi.org/10.1515/libr.2008.015">https://doi.org/10.1515/libr.2008.015</a>  Geisinger, K. F. (2016). 21st century skills: What are they and how do we assess them? Applied Measurement in Education, 29(4), 245–249.<a href="https://doi.org/10.1080/08957347.2016.1209207"> https://doi.org/10.1080/08957347.2016.1209207</a> Hamlett, A. (2021). Getting to work. Journal of Information Literacy, 15(2), 166–177.<a href="https://doi.org/10.11645/15.2.2857"> https://doi.org/10.11645/15.2.2857</a> Hart Research Associates. (2015). Falling short? College learning and career success. Selected findings from online surveys of employers and college students conducted on behalf of the Association of American Colleges & Universities. <a href="https://dgmg81phhvh63.cloudfront.net/content/user-photos/Research/PDFs/2015employerstudentsurvey.pdf">https://dgmg81phhvh63.cloudfront.net/content/user-photos/Research/PDFs/2015employerstudentsurvey.pdf</a> Head, A. J. (2012). Learning curve: How college graduates solve information problems once they join the workplace. SSRN Electronic Journal.<a href="https://doi.org/10.2139/ssrn.2165031"> https://doi.org/10.2139/ssrn.2165031</a> Head, A. J. (2016). Staying smart: How today’s graduates continue to learn once they complete college. SSRN Electronic Journal.<a href="https://doi.org/10.2139/ssrn.2712329"> https://doi.org/10.2139/ssrn.2712329</a> Head, A. J., Hoeck, M. V., Eschler, J., & Fullerton, S. (2013). What information competencies matter in today’s workplace? Library and Information Research, 37(114), 74–104.<a href="https://doi.org/10.29173/lirg557"> https://doi.org/10.29173/lirg557</a> Hoffman, N. (2016). Guttman Community College puts “work” at the center of learning: An approach to student economic mobility. Change, 48(4), 14–23.<a href="https://doi.org/10.1080/00091383.2016.1198167"> https://doi.org/10.1080/00091383.2016.1198167</a> Jewell, P., Reading, J., Clarke, M., & Kippist, L. (2020). Information skills for business acumen and employability: A competitive advantage for graduates in Western Sydney. Journal of Education for Business, 95(2), 88–105.<a href="https://doi.org/10.1080/08832323.2019.1610346"> https://doi.org/10.1080/08832323.2019.1610346</a> Rainie, L., & Anderson, J. (2017). The future of jobs and jobs training. Pew Research Center. <a href="https://www.proquest.com/docview/1904675911?parentSessionId=ZC%2F3xfG3CZGmYbJM0fE4NhuW5HQPbFkfieMUZFD57mU%3D&pq-origsite=primo&">https://www.proquest.com/docview/1904675911?parentSessionId=ZC%2F3xfG3CZGmYbJM0fE4NhuW5HQPbFkfieMUZFD57mU%3D&pq-origsite=primo&</a>

Searching for Information on Social Media - An OER on information literacy

This open educational resource video offers digital immigrants and strangers the skills to find authoritative information on social media. With a focus on the ACRL's information literacy framework threshold concepts of "Authority is contextual and constructed" and "Information has value". It is intended for use and re-use in information literacy educational contexts. We have included the video file, a transcript and the slides used to make the OER. This video was made with PowerPoint with final editing touches in DaVinci Resolve 16.

Student Creativity in Information Literacy Instruction - OER video for high school educators

This video was produced in an information literacy course at the School of Information Studies (ÉSIS) at the University of Ottawa, Canada, in Spring 2022. It is shared as an open educational resource (OER) using CC-BY license to be re(used) to teach viewers about creativity in the context of information literacy. This video is meant to help educators teach information literacy to their high school students using creativity. The learning objective includes understanding methods to incorporate creativity in the instruction of information literacy through the form of content creation. The main goal is to engage the viewers and incentivize the target audience to implement creativity in their educational methods related to information literacy. This video was created in screencast-o-matic and edited using the same program and Lightworks. The slides used are from a presentation template from SlidesCarnival and illustrations by Sergei Tikhonov. The references used to create this project are displayed at the end of the video.

Magnetic field line information from sunspot simulation in 10.5281/zenodo.6385593

This dataset contains magnetic field line information from the dataset corresponding to 10.5281/zenodo.6385593

opencc-zeroJun 2022View details →

Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information

The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace's Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and a burst of dispersal west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagos east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.

Supporting Information for "Wave heating during the helium flash and lithium-enhanced clump stars"

"data" contains the data used to generate the plots in this paper. "batches" contains a log of nearly every MESA run performed in this work (including ~all failed experiments). These are stored as Python3 Pickle files. Experiments were run using the RemoteExperiments software package (https://github.com/adamjermyn/remote_experiments). See the documentation there for further information on the data format for these files. "Stokes_Experiments" contains a git repository which includes both the final version of the code used in our canonical run as well as the full history of (nearly) all experiments we performed along the way. Each experiment is a commit (detached from any branch) with the commit message "patch". "Scripts" contains both the scripts we used to run these experiments and those we used to analyze them and make the plots in the paper. Further detail is given in the paper itself.