cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5441/001/1.d73t7vt8/1
title: Western Gull-billed Tern Migration (2012-2019)

description: Goodenough KS, Patton RT. 2019. Satellite telemetry reveals strong fidelity to migration routes and wintering grounds for the gull-billed tern (Gelochelidon nilotica). Waterbirds. 42(4):400-410. doi:10.1675/063.042.0405
description: The western gull-billed tern (Gelochelidon nilotica) breeds in only 16 locations in southern California, USA and the Pacific coast and Gulf of California in Mexico. Relatively little information is available on migration and wintering locations for the population. This is the first project to use satellite telemetry to document Gull-billed Tern migration routes, important stop-over locations, and non-breeding areas for the northwestern-most breeding population that nests in San Diego, California. A total of eleven deployments occurred over a period of four breeding seasons. Of the 11 deployments, five terns provided information on complete migration cycles consisting of both a fall and a successive spring migration. Four terns provided information on two fall and one spring migration, and one tern provided information on three fall and three spring migrations. Migration routes in the fall and spring are similar, with individuals crossing inland over the Peninsular Mountain Range of Baja California to stop over in the Rio Colorado Delta of Mexico, before beginning southward travel along the continental Mexico coastline and reversing the route for spring migration. The wintering distribution of individuals from the San Diego breeding colony appears to be small, consisting of a 250-km span of coastal wetlands ranging from Bahía Tóbari, southern Sonora south to Santa María-La Reforma, northern Sinaloa, Mexico. Long term monitoring of individual movements suggests strong fidelity to both breeding and wintering grounds, with individuals returning to San Diego each season to breed and then returning to previously used winter locations.
DOI: 10.5441/001/1.d73t7vt8/2
title: Western Gull-billed Tern Migration (2012-2019)-reference-data

description: Goodenough KS, Patton RT. 2019. Satellite telemetry reveals strong fidelity to migration routes and wintering grounds for the gull-billed tern (Gelochelidon nilotica). Waterbirds. 42(4):400-410. doi:10.1675/063.042.0405
description: The western gull-billed tern (Gelochelidon nilotica) breeds in only 16 locations in southern California, USA and the Pacific coast and Gulf of California in Mexico. Relatively little information is available on migration and wintering locations for the population. This is the first project to use satellite telemetry to document Gull-billed Tern migration routes, important stop-over locations, and non-breeding areas for the northwestern-most breeding population that nests in San Diego, California. A total of eleven deployments occurred over a period of four breeding seasons. Of the 11 deployments, five terns provided information on complete migration cycles consisting of both a fall and a successive spring migration. Four terns provided information on two fall and one spring migration, and one tern provided information on three fall and three spring migrations. Migration routes in the fall and spring are similar, with individuals crossing inland over the Peninsular Mountain Range of Baja California to stop over in the Rio Colorado Delta of Mexico, before beginning southward travel along the continental Mexico coastline and reversing the route for spring migration. The wintering distribution of individuals from the San Diego breeding colony appears to be small, consisting of a 250-km span of coastal wetlands ranging from Bahía Tóbari, southern Sonora south to Santa María-La Reforma, northern Sinaloa, Mexico. Long term monitoring of individual movements suggests strong fidelity to both breeding and wintering grounds, with individuals returning to San Diego each season to breed and then returning to previously used winter locations.
DOI: 10.7479/g6vk-dr56
title: Insekten in 3D - Euglossa azureoviri

description: Die Insekten in 3D – wie hier die blauschillernde Orchideenbiene Euglossa azureoviri - werden aus rund 25.000 Aufnahmen zusammengefügt. Aus annähernd 400 Perspektiven werden Bilder mit einem 12-Megapixel-Sensor aufgenommen.
DOI: 10.6084/m9.figshare.13655975.v5
title: Characteristics of volunteers

description: Description of the volunteers including age, sex, height and others anthropometric data.<br><strong>CC BY-NC-SA licence<br></strong>
DOI: 10.5281/zenodo.4591436
title: rawdata to Evaluation of denoising strategies for task-based functional connectivity: Equalizing residual motion artifacts between rest and cognitively demanding tasks

description: Framesise Displacement raw plot (in mm)
DOI: 10.5281/zenodo.4591435
title: rawdata to Evaluation of denoising strategies for task-based functional connectivity: Equalizing residual motion artifacts between rest and cognitively demanding tasks

description: Framesise Displacement raw plot (in mm)
DOI: 10.5441/001/1.d73t7vt8
title: Data from: Satellite telemetry reveals strong fidelity to migration routes and wintering grounds for the gull-billed tern (Gelochelidon nilotica)

description: Goodenough KS, Patton RT. 2019. Satellite telemetry reveals strong fidelity to migration routes and wintering grounds for the gull-billed tern (Gelochelidon nilotica). Waterbirds. 42(4):400-410. doi:10.1675/063.042.0405
description: The western gull-billed tern (Gelochelidon nilotica) breeds in only 16 locations in southern California, USA and the Pacific coast and Gulf of California in Mexico. Relatively little information is available on migration and wintering locations for the population. This is the first project to use satellite telemetry to document Gull-billed Tern migration routes, important stop-over locations, and non-breeding areas for the northwestern-most breeding population that nests in San Diego, California. A total of eleven deployments occurred over a period of four breeding seasons. Of the 11 deployments, five terns provided information on complete migration cycles consisting of both a fall and a successive spring migration. Four terns provided information on two fall and one spring migration, and one tern provided information on three fall and three spring migrations. Migration routes in the fall and spring are similar, with individuals crossing inland over the Peninsular Mountain Range of Baja California to stop over in the Rio Colorado Delta of Mexico, before beginning southward travel along the continental Mexico coastline and reversing the route for spring migration. The wintering distribution of individuals from the San Diego breeding colony appears to be small, consisting of a 250-km span of coastal wetlands ranging from Bahía Tóbari, southern Sonora south to Santa María-La Reforma, northern Sinaloa, Mexico. Long term monitoring of individual movements suggests strong fidelity to both breeding and wintering grounds, with individuals returning to San Diego each season to breed and then returning to previously used winter locations.
DOI: 10.5281/zenodo.4515768
title: VolPy: automated and scalable analysis pipelines for voltage imaging datasets

description: Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (&gt;800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets.VolPy features motion correction, memory mapping, automated segmentation,denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation,we introduce a corpus of 24 manually annotated datasets from different preparations,brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy’s performance in spike extraction and scalability are state-of-the-art. File names contain 'L1'(mouse cortex) or 'TEG'(zebrafish tegmental area) are from the following paper: Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, et al. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.Science. 2019;365(6454):699–704. doi:10.1126/science.aav6416. File names contain 'HPC'(mouse hippocampus) are from the following paper: Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, et al. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics.Nature. 2019;569(7756):413.
description: Andrea Giovannucci is supported by the Arnold and Mabel Beckman Foundation and the Kavli Foundation. Kaspar Podgorski is supported by the Howard Hughes Medical Institute.
description: {"references": ["Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, et al. Brightand photostable chemigenetic indicators for extended in vivo voltage imaging.Science. 2019;365(6454):699\u2013704. doi:10.1126/science.aav6416.", "Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, et al. Voltage imaging andoptogenetics reveal behaviour-dependent changes in hippocampal dynamics.Nature. 2019;569(7756):413."]}
DOI: 10.5281/zenodo.4515767
title: VolPy: automated and scalable analysis pipelines for voltage imaging datasets

description: Voltage imaging enables monitoring neural activity at sub-millisecond and sub-cellular scale, unlocking the study of subthreshold activity, synchrony, and network dynamics with unprecedented spatio-temporal resolution. However, high data rates (&gt;800MB/s) and low signal-to-noise ratios create bottlenecks for analyzing such datasets. Here we present VolPy, an automated and scalable pipeline to pre-process voltage imaging datasets.VolPy features motion correction, memory mapping, automated segmentation,denoising and spike extraction, all built on a highly parallelizable, modular, and extensible framework optimized for memory and speed. To aid automated segmentation,we introduce a corpus of 24 manually annotated datasets from different preparations,brain areas and voltage indicators. We benchmark VolPy against ground truth segmentation, simulations and electrophysiology recordings, and we compare its performance with existing algorithms in detecting spikes. Our results indicate that VolPy’s performance in spike extraction and scalability are state-of-the-art. File names contain 'L1'(mouse cortex) or 'TEG'(zebrafish tegmental area) are from the following paper: Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, et al. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.Science. 2019;365(6454):699–704. doi:10.1126/science.aav6416. File names contain 'HPC'(mouse hippocampus) are from the following paper: Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, et al. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics.Nature. 2019;569(7756):413.
description: Andrea Giovannucci is supported by the Arnold and Mabel Beckman Foundation and the Kavli Foundation. Kaspar Podgorski is supported by the Howard Hughes Medical Institute.
description: {"references": ["Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, et al. Brightand photostable chemigenetic indicators for extended in vivo voltage imaging.Science. 2019;365(6454):699\u2013704. doi:10.1126/science.aav6416.", "Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, et al. Voltage imaging andoptogenetics reveal behaviour-dependent changes in hippocampal dynamics.Nature. 2019;569(7756):413."]}
DOI: 10.25345/c5fz3b
title: MassIVE MSV000087017 - Fish species identification in mixed samples using DNA sequencing and a proteomics-based approaches
title: With globally rising demands for food and increasing pressure on over-exploited food chains, feed and food adulteration has become an emerging problem, threatening both food security and food safety. In this context, development of sensitive molecular tools for food and feed authentication are key; on the one hand to ensure correct labelling of products to remedy safety concerns, on the other hand to tackle fraud such as the replacement of expensive food fish species with cheaper ones or with species that are endangered or unfit for human consumption. DNA metabarcoding approaches for distinguishing fish species in pure samples already are available; however, detection and quantification of fish species in highly processed and mixed products is still a challenge. In the present study, we use high throughput DNA sequencing and shot-gun proteomics to detect and differentiate seven fish species (Melanogrammus aeglefinus, Oreochromis niloticu, Gadus morhua, Salmo salar, Esox Lucius, Pangasianodon hypophthalmus, Xiphophorus maculatus), and to quantify the content of a mixture of three fish species. The results demonstrate that shotgun DNA sequencing in combination with mapping against masked reference genomes can be a useful tool for the identification of fish species and the relative amounts of each species in a mixed sample. Shotgun proteomics based on direct spectral comparison of tandem mass spectra allowed for the construction of phylogenetic trees which separated the seven fish samples accurately without using any genetic information. Spectral libraries built with tandem mass spectra allowed for the detection of species and estimation of quantities in mixed fish samples.
DOI: 10.6084/m9.figshare.3397603.v11
title: Custom toolbars and mini applications with Action Bar

description: The Action Bar ImageJ plugin facilitates creation of additional custom toolbars, using simple macro-like toolbar description file. Readers will learn how to setup a basic action bar, and how to use the latest features of this plugin. Button actions are basically macro programs, so action bars can interact with all standard ImageJ components. Primary use of these custom toolbars is to keep at hand often used commands, plugins and macros, but toolbars sets can be turned into mini applications with minimal effort. With these highly task-oriented applications, end users can focus on just using a simple system with absolutely no prior knowledge of ImageJ. This paper is aimed at ImageJ users with some previous experience with the macro language. First version was published in June 2006, and this is the support material for a workshop I first gave at the 2008 ImageJ conference in Luxembourg.
DOI: 10.17632/gf8ppgyssf.1
title: Data for: The Effect of Chinese Herb Solid Drink Versus Lactulose on Gut Microbiota in Rats with Slow Transit Constipation Induced by Compound Diphenoxylate

description: Data legends data weight: The body weight data of rats on Mondays, Wednesdays, Fridays and Sundays during the experiment were recorded. data food intake: The food intake data of rats on the 19th. day and the 36th. day. data intestin transit: The time from charcoal meal solution oral administered to the first dark fecal defecation of rats on the 19th. day and the 38th. day. data moisture content: The moisture content of feces. data MTL: The concentration of motilin in serum of rats. data VIP: The concentration of vasoactive intestinal peptide in serum of rats. data SP: The concentration of P substance in serum of rats. data gastrin: The concentration of gastrin in serum of rats. data Chao1, ACE, Shannon: The Chao1 index, ACE index, Shannon index from Assay of feces sample by 16S rDNA and sequencing of rats. data Firmicutes, Bacteroidetes, FB value: The abundance of Firmicutes, Bacteroidetes, and the ratio of the abundance of Firmicutes and the abundance of Bacteroidetes from Assay of feces sample by 16S rDNA and sequencing of rats. data Lactobacillus, Blautia, Ruminococcus, Ruminococcus, Roseburia, Dehalobacterium, Eubacterium, Akkermansia, Streptococcus, prevotella, paraprevotella: The abundance of Lactobacillus, Blautia, Ruminococcus, Ruminococcus, Roseburia, Dehalobacterium, Eubacterium, Akkermansia, Streptococcus, Prevotella, Paraprevotella from Assay of feces sample by 16S rDNA and sequencing of rats.
DOI: 10.6084/m9.figshare.14186558
title: Genome sequence

description: We performed a standard DNA extraction from a single, field-collected <i>Formica aquilonia</i> × <i>Formica polyctena</i> haploid male and assembled its genome using ~ 60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4,687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenoptera BUSCOs and was scaffolded using the pseudo-chromosomal assembly of a related species, <i>F. selysi</i> (28 scaffolds, N50 = 8.49 Mb).
DOI: 10.6084/m9.figshare.14186534
title: Protein sequences

description: We annotated the genome with the Braker2 pipeline (Brůna, Hoff, Lomsadze, Stanke, & Borodovsky, 2020; v2.1.5, Hoff, Lomsadze, Borodovsky, & Stanke, 2019). Both RNAseq- and protein-derived hints were used to train GeneMark-ETP, which predictions were in turn used to train Augustus and obtain the final gene set. All protein data available for Arthropoda were downloaded from OrthoDB (v10, Kriventseva et al. 2019, https://v100.orthodb.org/download/odb10_arthropoda_fasta.tar.gz, last accessed 22.07.2020) and aligned using ProtHint. This dataset contains 2.6 million sequences and encompasses 170 species, including 40 of the same order (Hymenoptera) and 17 of the same family (Formicidae). RNAseq data produced above was aligned against the hard-masked genome using STAR (v2.7.2, Dobin et al., 2013), and secondary alignments were removed with SAMtools (v1.10, Li et al., 2009). After the Braker2 run, protein sequences of all gene models not supported by at least one hint were blasted against the Uniprot database (UniProt Consortium, 2019) and all models without any hit on Aculeata (wasps, bees and ants) were discarded from the final gene set. Finally, functional annotation was carried with EnTAP (v0.10.3, Hart et al., 2020) using the EggNOG (Huerta-Cepas et al., 2016), Uniprot and RefSeq databases.
DOI: 10.6084/m9.figshare.14186522
title: Genome annotation

description: We annotated the genome with the Braker2 pipeline (Brůna, Hoff, Lomsadze, Stanke, & Borodovsky, 2020; v2.1.5, Hoff, Lomsadze, Borodovsky, & Stanke, 2019). Both RNAseq- and protein-derived hints were used to train GeneMark-ETP, which predictions were in turn used to train Augustus and obtain the final gene set. All protein data available for Arthropoda were downloaded from OrthoDB (v10, Kriventseva et al. 2019, https://v100.orthodb.org/download/odb10_arthropoda_fasta.tar.gz, last accessed 22.07.2020) and aligned using ProtHint. This dataset contains 2.6 million sequences and encompasses 170 species, including 40 of the same order (Hymenoptera) and 17 of the same family (Formicidae). RNAseq data produced above was aligned against the hard-masked genome using STAR (v2.7.2, Dobin et al., 2013), and secondary alignments were removed with SAMtools (v1.10, Li et al., 2009). After the Braker2 run, protein sequences of all gene models not supported by at least one hint were blasted against the Uniprot database (UniProt Consortium, 2019) and all models without any hit on Aculeata (wasps, bees and ants) were discarded from the final gene set.
DOI: 10.6084/m9.figshare.14171315
title: Harbour seal offshore foraging data

description: netcdf files containing pressure, accelerometer, magnetometer data sampled at 1 Hz, GPS and timing of prey capture attempts for harbour seals during offshore foraging trips in the Wadden Sea, Germany.
DOI: 10.25390/caryinstitute.11801052.v19
title: Cary Institute Environmental Monitoring Program Current Year Data 2021

description: The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, and water pollution and other streamwater chemistry. Our solar radiation monitoring includes diffuse and global photosynthetically active radiation (PAR), diffuse and global shortwave radiation, net radiation and UV. Long-term monitoring of solar radiation provides us with an understanding of atmospheric energy dynamics, which can affect natural and human systems. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:<br>Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2018 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org.<br>Those wishing to publish data from Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact data manager Vicky Kelly, kellyv@caryinstitute.org.<br>For complete data for previous years and for complete metadata, please see appropriate items for the Cary Institute Environmental Monitoring Program at https://caryinstitute.figshare.com/
DOI: 10.6084/m9.figshare.14186566.v1
title: Table S1. Gaussberg: volcanology and petrology

description: Published whole-rock analyses of lamproites from Gaussberg
DOI: 10.6084/m9.figshare.14186566
title: Table S1. Gaussberg: volcanology and petrology

description: Published whole-rock analyses of lamproites from Gaussberg
DOI: 10.17632/f9vm3c4d7v.1
title: Polytrauma: missed fractures hand/forearm

description: We wanted to assess how many fractures of hand and forearm, that were diagnosed 77 late (later than 24 h after admisison), were visible in the WBCT on retrospection. Additionally, the influence of the time of day of the WBCT and slice thickness on the occurrence of late diagnoses should be examined.
DOI: 10.17632/35bx8pw9bj.1
title: Comparing risk with VaR models in COVID-19 pandemic period

description: This dataset contains all variables used to estimate and backtest VaR models in TUNINDEX stock index.
DOI: 10.17632/k7fp4986pr.2
title: Supplementary data

description: The effect of relative humidity and formulation variables on chewable xylitol-sorbitol tablets