Find research datasets worth reusing

opencc-zeroJul 2021View details →

Natural history specimens collected and/or identified and deposited.

Natural history specimen data collected and/or identified by Richard Pyle, <a href="https://orcid.org/0000-0003-0768-1286">https://orcid.org/0000-0003-0768-1286</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.

opencc-by-4.0Jun 2021View details →

Panel: "Broken for All:: The case for persistent identifiers for digital cultural heritage resources AND Developer Track Session 2

This video contains two sessions from Open Repositories 2021: Panel: "Broken for All": the case for persistent identifiers for digital cultural heritage resources Turner, Adrian (1); Holmes-Wong, Deborah (2); Rafique, Zahid (2); Kunze, John (1); Lohnash, Megan (3); McKinley, Matthew (4), Lund, Allison (5) 1: California Digital Library; 2: University of Southern California Libraries; 3: California Revealed; 4: Omeka; 5: Metropolitan New York Library Council  Cultural heritage institutions within the United States have made significant investments in building unique digital collections, broadly disseminating them on the web and through networks such as the Digital Public Library of America (DPLA). The items within these collections are referenced and cited in a range of sources -- from Wikipedia and scholarly articles, to archival finding aids and classroom lesson plans. However, the application of persistent identifier schemes (e.g. DOI, ARK) for unique digital resources is relatively uncommon within the gallery, library, archive, and museum communities. Relatedly, many repositories and digital asset management systems (DAMS) widely used in these communities simply do not support persistent identifier schemes "out of the box." Hence, the URLs for the items are extremely fragile. If the collections are migrated to a different repository, the URLs can easily break -- impacting downstream networks, confounding researchers, and compounding the problem of link rot. This panel will discuss the critical role of persistent identifiers in digital collections management and dissemination and some of the challenges in applying them. It will feature case studies demonstrating how commonly-available licensed and open-source repositories can be adapted to support them. Developer Track Session 2: Constructing a Repository Test Strategy Built on Docker Containers Brady, Terrence W California Digital Library, United States of America The Merritt Digital Preservation system comprises a dozen microservices and supporting services. Our team found that it was not cost effective to maintain and patch a fleet of servers to support a development environment. Our solution was to replace our development server environment with a stack of dockerized services. Once the stack was containerized, we discovered that we were able to create 3 variants of our development stack with different persistence strategies for database content and cloud storage. With these variants, the team has been able to support a variety of testing scenarios. Deploying a Serverless Application as a Docker Image Brady, Terrence W California Digital Library, United States of America A serverless application consists of a defined runtime (such as Ruby 2.7 or Python 3) and a package of code. This presentation will illustrate 3 types of code packages of different complexity and will describe the challenges of bundling more complicated dependencies such as binary files. In December 2020, the AWS Lambda serverless architecture began to support Docker images as a deployment package. This packaging approach makes it possible to run tests against a code package before it is deployed. This presentation will demonstrate the test and deployment process for a serverless application within the Merritt digital preservation system. Other repository teams hosting their applications on AWS may discover some useful patterns for testing and deploying serverless code to AWS Lambda. Live Demo: Create a Developer Workspace Challenge Pottinger, Hardy Joseph California Digital Library, University of California, Office of the President, United States of America Creating a developer workspace, a place in which you can write and test your code, can seem a daunting task. Sure, someone might have done it before, and they might even share their notes with you, but following those notes and arriving in the same place is like following a treasure map and expecting to get rich. There’s a better way, and I’m willing to prove it. This demo aims to show the process one goes through to craft a development environment with pretty much any tool, but will use Lando to conserve time. Lando is a way to bootstrap a useable development environment. It's built on Docker, and is like Docker-Compose, but much more transparent. It handles the boring details and helps you actually start developing with code in your favorite IDE, and all the services you need in Docker. It's all about making the life of a developer easier. It won't give you an application container you can deploy, but you will develop a deeper understanding of how all the pieces fit together, and you'll have a tool which can deploy those pieces to dev/stage/prod if you wish. The audience will participate in this demo. Building Scalable Serverless Digital Repositories using Amplify Open-source Framework Chen, Yinlin; Jiang, Tingting; Hunter, Lee Virginia Tech, United States of America We develop digital repositories to disseminate different types of digital content and to promote the principles of open access. Our goal is not to provide access to information to just one individual institution or group but to anyone and everyone. With that ambitious goal in mind, how do we enable our digital repositories to have the high availability and flexible scaling capabilities necessary to face unforeseen demand? How do we utilize only the resources we need without the waste of overprovisioning resources? These are some of the most challenging issues that we face. To achieve our goals, we moved from the traditional monolithic, server-based approach to serverless cloud infrastructure. By leveraging the services that AWS provides we have been able to boost the performance of our repositories 10x compared to that of our previous implementation that was hosted in-house. Our repositories now automatically scale up and down to meet any kind of traffic demands, without our intervention. In this talk, we will demonstrate our scalable serverless digital repositories and show the opportunities to explore and reflect on the ways that repositories enable openness for all.

opencc-by-4.0Aug 2021View details →

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

Data deposition of the article 'Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence'

opencc-zeroAug 2021View details →

Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans

The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using C. elegans germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.

opencc-zeroAug 2021View details →

Data from: Identifying extracellular vesicles from single cells

Extracellular vesicles (EVs) are constantly secreted from both eukaryotic and prokaryotic cells. EVs, including those referred to as exosomes, may have an impact on cell signaling and an incidence in diseased cells. In this manuscript, a platform to capture, quantify, and phenotypically classify the EVs secreted from single cells is introduced. Microfluidic chambers of about 300 pL are employed to trap and isolate individual cells. The EVs secreted within these chambers are then captured by surface-immobilized monoclonal antibodies (mAbs), irrespectively of their intracellular origin. Immunostaining against both plasma-membrane and cytosolic proteins was combined with highly sensitive, multi-color total internal reflection fluorescence microscopy (TIRFM) to characterize the immobilized vesicles. The data analysis of high-resolution images allowed the assignment of each detected EV to one of 15 unique populations, and demonstrated the presence of highly-heterogeneous phenotypes even at the single-cell level. The analysis also revealed that each mAb isolates phenotypically-different EVs, and more vesicles were effectively immobilized when CD63 was targeted instead of CD81. Finally, we demonstrate how an heterogeneous suppression in the secreted vesicles is obtained when the enzyme neutral sphingomyelinase is inhibited.

opencc-by-4.0Jan 2021View details →

Dataset for "A novel method to identify sub-seasonal clustering episodes of extreme precipitation events and their contributions to large accumulation periods"

Dataset for "A novel method to identify sub-seasonal clustering episodes of extreme precipitation events and their contributions to large accumulation periods". Added file "Obs_metrics_all.RData" containing p-value for significance test of the clustering metric S_cl. Accepted version (August 2021).

opencc-zeroAug 2021View details →

Identifying priority giant anteater (Myrmecophaga tridactyla) populations for conservation in São Paulo State, Brazil

Habitat loss is the main threat to biodiversity conservation worldwide. Some species may be particularly susceptible to the effects of fragmentation and the isolation of populations. The impacts of human activity on wild animal populations may be understood through relationships between individual genetic data and spatial landscape variables, particularly when considering local population dynamics influenced by fragmented habitats. Thus, the objective of this study was to analyze the population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla) using an individual sampling scheme (ISS) on a regional geographic scale. Data were collected from 41 specimens from twenty different locations in São Paulo State, Brazil, and six polymorphic microsatellite loci were genotyped. Our results indicate that barriers to gene flow exist and have segregated individuals of the farther away areas into two spatially structured clusters. The populations were also found to have high genetic diversity. The experimental sampling approach used herein enabled an analysis of the population dynamics of the giant anteater on a regional scale, as well as the identification of priority populations for genetic resource conservation for this species. The results reflect the need for adequate management plans. The efficacy of the sampling scheme may vary based on the study model used, but we argue that the use of an ISS combined with suitable molecular markers and statistical methods may serve as an important tool for initial analyses of threatened or vulnerable species, particularly in anthropized regions where species populations are small or hard to characterize.

Fig. 13 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 13. Distribution map of Ngirhaphium in Southeast Asia

Fig. 9 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 9. Distribution map of Ngirhaphium meieri, new species and Ngirhaphium thaicum, new species.

Fig. 7 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 7. Ngirhaphium meieri, new species, female habitus. Scale = 1 mm.

Fig. 6 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 6. Ngirhaphium meieri, new species, male habitus (photo: Abdulloh Samoh). Scale = 1 mm.

Fig. 3 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 3. Ngirhaphium thaicum, new species male habitus. Scale = 1 mm.

Fig. 4 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia

Fig. 4. Ngirhaphium thaicum, new species habitus female. Scale = 1 mm.

opencc-by-4.0Nov 2009View details →

Fig. 3 in The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar

Fig. 3. Photograph of living Miniopterus brachytragos captured near Ambanizana, Masoala Peninsula

opencc-by-4.0Sep 2021View details →

Dataset : Identifying locations susceptible to micro-anatomical reentry using a spatial network representation of atrial fibre maps

<ul> <li>The three files in the dataset are:</li> </ul> 1) Healthy Sheep Atria Fibre Orientation Dataset 300µm 2) Heart Failure Sheep Atria Fibre Orientation Dataset 300µm 3) Human Atria Fibre Orientation Dataset 330µm <ul> <li>Data is stored as numpy binary files. Given below is an example .py script to open the flat datasets:</li> </ul>     import numpy as np     data = np.load("Human_330um.npy") <ul> <li>Volume and fibre orientation dataset stored in flat format as given below:</li> </ul>     i, j, k, v1, v2, v3, ...  repeated for each voxel           where (i, j, k) are voxel coordinates and (v1, v2, v3) are vector components corresponding to fibre orientation within that voxel.

opencc-by-4.0Oct 2021View details →

Houska_et_al_Dataset_Identifying the drivers of discharge and instream nitrate concentrations using Random Forest

Dataset and Python code to perform a Random Forest regression analysis on mesured discharge and nitrate concentration data at sixteen points within the Sschwingbach Earth Observatory (SEO) located in Hüttenberg, Hesse, Germany.

opencc-zeroOct 2021View details →

Data from: Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed C. glaucofraenum to be three morphologically similar species (C. glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to C. dicrus, host gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly P. tortugensis. The pharodes–coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but P. tortugensis is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether P. tortugensis is truly a widespread generalist, or instead represents a group of more specialized cryptic species.

opencc-zeroOct 2021View details →

Natural history specimens collected and/or identified and deposited.

Natural history specimen data collected and/or identified by Tim Adriaens, <a href="https://orcid.org/0000-0001-7268-4200">https://orcid.org/0000-0001-7268-4200</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.

opencc-zeroJun 2023View details →

Natural history specimens collected and/or identified and deposited.

Natural history specimen data collected and/or identified by James Lendemer, <a href="https://orcid.org/0000-0003-1186-0711">https://orcid.org/0000-0003-1186-0711</a>. Claims or attributions were made on Bionomia, <a href="https://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.