Find research datasets worth reusing

Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h).

Text-fig. 24. Scanning electron microscope (SEM) images of "Stamen with zona-aperturate pollen"; Catefica locality, Portugal. a) Dorsal view of elongated anther showing the broad connective and very narrow pollen sacs; b) Lateral view of elongated anther showing the broad dorsal and ventral surfaces of the connectives and very narrow pollen sacs; c) Apex of elongated anther showing dorsal and ventral surfaces and very narrow pollen sacs; d) Lateral view of narrow pollen sac showing in situ pollen; e) Detail of pollen grain showing the solid band of exine above the aperture (asterisk); f) Detail of pollen grain showing the solid band of exine above the aperture (asterisk); g) Detail of tectum showing heterobrochate reticulum with lumina of two different sizes supported by long columellae (arrows); h) Detail of pollen grain showing the aperture extending over the ends of the grain (asterisks); i) Detail of tectum showing heterobrochate reticulum with lumina of two different sizes supported by long columellae (arrows). Specimen, Catefica 49-S171527 (a–i). Scale bars = 600 Μm (a, b), 100 Μm (c), 20 Μm (d), 6 Μm (e, f, h), 3 Μm (g), 1.5 Μm (i). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 24. Scanning electron microscope (SEM) images of "Stamen with zona-aperturate pollen"; Catefica locality, Portugal. a) Dorsal view of elongated anther showing the broad connective and very narrow pollen sacs; b) Lateral view of elongated anther showing the broad dorsal and ventral surfaces of the connectives and very narrow pollen sacs; c) Apex of elongated anther showing dorsal and ventral surfaces and very narrow pollen sacs; d) Lateral view of narrow pollen sac showing in situ pollen; e) Detail of pollen grain showing the solid band of exine above the aperture (asterisk); f) Detail of pollen grain showing the solid band of exine above the aperture (asterisk); g) Detail of tectum showing heterobrochate reticulum with lumina of two different sizes supported by long columellae (arrows); h) Detail of pollen grain showing the aperture extending over the ends of the grain (asterisks); i) Detail of tectum showing heterobrochate reticulum with lumina of two different sizes supported by long columellae (arrows). Specimen, Catefica 49-S171527 (a–i). Scale bars = 600 Μm (a, b), 100 Μm (c), 20 Μm (d), 6 Μm (e, f, h), 3 Μm (g), 1.5 Μm (i).

Text-fig. 29. Scanning electron microscope (SEM) images of stamens and pollen grains of cf. Endressistemon sp. 1 (a, b), cf. Endressistemon sp. 2 (c, d) and cf. Endressistemon sp. 3 (e–g); Catefica locality, Portugal. a) Two adhering stamens, each with a long, pointed extension of the connective; b) Monocolpate, reticulate pollen in situ in stamen from stamen pair in (a); c) Fragment of stamen with prominent apical extension of the connective; d) Reticulate, apparently monocolpate, pollen in situ in stamen fragment in (c); e) Stamen with basifixed anther, perhaps sessile, and with prominent, wing-like apical extensions of the connective; note the dehisced thecae with the anther wall curved back; f, g) Monocolpate, reticulate pollen in situ in stamen in (e). Specimens, Catefica 49-S107780 (a, b), Catefica 49-S107784 (c, d), Catefica 49-S107781 (e–g). Scale bars = 600 Μm (a, c, e), 6 Μm (b, d, f, g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 29. Scanning electron microscope (SEM) images of stamens and pollen grains of cf. Endressistemon sp. 1 (a, b), cf. Endressistemon sp. 2 (c, d) and cf. Endressistemon sp. 3 (e–g); Catefica locality, Portugal. a) Two adhering stamens, each with a long, pointed extension of the connective; b) Monocolpate, reticulate pollen in situ in stamen from stamen pair in (a); c) Fragment of stamen with prominent apical extension of the connective; d) Reticulate, apparently monocolpate, pollen in situ in stamen fragment in (c); e) Stamen with basifixed anther, perhaps sessile, and with prominent, wing-like apical extensions of the connective; note the dehisced thecae with the anther wall curved back; f, g) Monocolpate, reticulate pollen in situ in stamen in (e). Specimens, Catefica 49-S107780 (a, b), Catefica 49-S107784 (c, d), Catefica 49-S107781 (e–g). Scale bars = 600 Μm (a, c, e), 6 Μm (b, d, f, g).

Text-fig. 9. Scanning electron microscope (SEM) images of stamens and pollen of Proencistemon portugallicus gen. et sp. nov. (a–g) and Proencistemon sp. (h–j); Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing almost sessile anthers; note short bracts at the base of the stamen whorl (arrow) and apparent paired arrangement of the stamens; b) Fragment of stamen whorl showing almost sessile anthers and apparent paired arrangement of the stamens; c) Pollen in situ from stamen whorl in (b) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d–g) Distal views of pollen in situ from pollen clump showing poorly defined trichotomocolpate aperture, semitectate-reticulate tectum (d–f), and fractured pollen wall with long, scattered columellae supporting narrow muri (g); h) Fragment of staminate inflorescence with narrow, almost sessile, stamens; i, j) Pollen from fragment of staminate inflorescence in (h) showing poorly defined trichotomocolpate aperture (i), semitectate-reticulate tectum (i, j) and long, scattered columellae supporting narrow muri (j). Specimens, Catefica 49-S266015 (a), Catefica 342-S122086 (b, c), Catefica 50-S170394 (d–g), Catefica 49-S107783 (h–j). Scale bars = 600 Μm (a, b, h), 6 Μm (c–f, i), 1.5 Μm (g, j). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 9. Scanning electron microscope (SEM) images of stamens and pollen of Proencistemon portugallicus gen. et sp. nov. (a–g) and Proencistemon sp. (h–j); Catefica locality, Portugal. a) Fragment of stamen whorl from staminate inflorescence showing almost sessile anthers; note short bracts at the base of the stamen whorl (arrow) and apparent paired arrangement of the stamens; b) Fragment of stamen whorl showing almost sessile anthers and apparent paired arrangement of the stamens; c) Pollen in situ from stamen whorl in (b) showing poorly defined trichotomocolpate aperture and semitectate-reticulate tectum; d–g) Distal views of pollen in situ from pollen clump showing poorly defined trichotomocolpate aperture, semitectate-reticulate tectum (d–f), and fractured pollen wall with long, scattered columellae supporting narrow muri (g); h) Fragment of staminate inflorescence with narrow, almost sessile, stamens; i, j) Pollen from fragment of staminate inflorescence in (h) showing poorly defined trichotomocolpate aperture (i), semitectate-reticulate tectum (i, j) and long, scattered columellae supporting narrow muri (j). Specimens, Catefica 49-S266015 (a), Catefica 342-S122086 (b, c), Catefica 50-S170394 (d–g), Catefica 49-S107783 (h–j). Scale bars = 600 Μm (a, b, h), 6 Μm (c–f, i), 1.5 Μm (g, j).

opencc-by-4.0Jan 2023View details →

Baseline assemblies for "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads" protocol

ntLink is a flexible de novo genome scaffolding toolkit which can be run in various modes depending on the desired user output, with multiple new functionalities recently introduced. Here, we provide the baseline assembly datasets used in the ntLink protocol paper "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads". The provided assemblies are ABySS (short-read) and Flye (long-read) assemblies of Caenorhabditis elegans genome sequencing data. The ABySS (v2.1.4) assembly utilized paired-end short reads (accession DRR008444), and was run with the following parameters: k=64 l=40 s=1000 q=15 B=10G j=8 kc=3 H=4 S=1000-10000 N=9.The C. elegans Flye (v2.5) assembly was run using Oxford Nanopore long reads (accession SRR10028109) and the following parameters: --nano-raw SRR10028109.fastq -g100m -t48.

Long-term daily hydrometeorological drought indices, soil moisture, and evapotranspiration for ICOS ecosystem sites

Standardized drought indices to support research at ICOS ecosystem sites. Dataset to Nature Scientific Data submission. "The dataset comprises four files for each of the 101 sites: "[site_name]_input" contains the observational data extracted from E-OBS, PET estimates as well as the simulated soil water storage and actual evapotranspiration from mHM; and threemore files for each of the standardized drought indices ("SSMI_[site_name]", "SPI_[site_name]", "SPEI_[site_name]"). Details on the variables, their units and their origin are given in Tab. 1. For the SPI and SPEI, the file of each site contains the estimates for various aggregation times, ranging from 5 to 730 days in steps of 5 days from 5 to 365 and steps of 10 days from 370 to 730. Each data file has a daily temporal resolution and covers the time span from 1950 to 2021."

opencc-by-4.0Jan 2023View details →

Dataset for: 'Patterns in the Plankton – Spatial distribution and long-term variability of copepods on the Agulhas Bank'

This dataset contains environmental data (in situ temperature and chlorophyll a) and integrated biomass (mg C m-2) data for a number of copepod taxa, as well as total copepod biomass and abundance, on the Agulhas Bank, South Africa, as predicted by a Generalized Additive Model (GAM), during late austral spring (October-December) from 1988 to 2011. Mean environmental and copepod biomass parameters for each area and year are also provided. Relevant information on sampling and statistical analysis of spatial distributions has been extracted from the paper. Please see paper for full details and figures, including supplementary data; <a href="https://doi.org/10.1016/j.dsr2.2023.105265">https://doi.org/10.1016/j.dsr2.2023.105265</a>. Please see the Word document Huggett_et_al_2023_README.docx for a list of the data files and descriptions of the contents.

opencc-by-4.0Jan 2023View details →

Monthly nitrogen point-source loading dataset for the Long Island Sound Watershed

The attached dataset and code accompanies a Data in Brief article, "Monthly nitrogen point-source loading dataset for the Long Island Sound Watershed." Abstract: Quantifying point source nitrogen loads to the Long Island Sound watershed is important because they contribute to the annual occurrence of hypoxia in Long Island Sound. However, the data are not easily accessible and are not available at a central location, making it difficult to characterize the magnitude of loading, seasonal patterns and long-term trends. For the period between April 1989 and September 2021, we gathered all available monthly nitrogen data for wastewater treatment plants within the Long Island Sound watershed from the U.S. Environmental Protection Agency Integrated Compliance Information System-National Pollutant Discharge Elimination System (ICIS-NPDES) and Permit Compliance System, and Connecticut Department of Energy and Environmental Protection databases. Data were checked for quality assurance and unreasonable outliers were imputed with means of other observations within the same year and season. Estimates were also imputed for missing observations. We publish both raw data with missing observations and a curated dataset with imputed estimates for missing observations. Monthly point source nitrogen load data can be used for water quality modeling and to infer, by subtraction, the relative contribution of nonpoint sources to gauged watershed loads. Additionally, the scripts used to reformat data from the ICIS could be repurposed to collect similar data in other regions.

openother-openFeb 2023View details →

Data and code from: Three decades of wildlife-vehicle collisions in a protected area: main roads and long-distance commuting trips to migratory prey increase spotted hyena roadkills in the Serengeti

This is the first release. Potential updates will be available on GitHub: <a href="https://github.com/MarwanNaciri/Three_decades_of_spotted_hyena_roadkill_in_a_protected_area">https://github.com/MarwanNaciri/Three_decades_of_spotted_hyena_roadkill_in_a_protected_area</a>

opencc-zeroFeb 2023View details →

Data for: Coordination of care is facilitated by delayed feeding and collective arrivals in the long-tailed tit

When multiple carers invest in a shared brood, there is likely to be conflict among individuals over how much each carer invests. This conflict results in suboptimal investment to the detriment of all carers. It has been proposed that conditional cooperation, i.e. 'turn-taking' or 'alternation', may resolve this conflict by preventing exploitation. This contentious idea has received some empirical support, but distinguishing active alternation from that expected via passive processes has proved challenging. The aim of this study was to use detailed observations of provisioning to examine whether carers at biparental (parents only) and cooperative (parents and helpers) nests of the long-tailed tit Aegithalos caudatus behave in a context-dependent manner that enhances the level of alternation. First, we show that carers who had been the last to feed waited near the nest (loitering) for longer before feeding when they next arrived at the nest and allowed others to feed first, thus facilitating alternation. Secondly, we found that the arrival of carers near the nest and their subsequent feeds were tightly synchronised, with overlapping loitering periods, allowing them to monitor the effort of other carers. Finally, we show that measures of coordination were influenced by carers arriving in a status-dependent order, with breeding females consistently arriving first and helpers last. Together, these results show how patterns of alternation and synchrony arise in long-tailed tits and reveal the behavioural mechanisms underpinning coordination of care.

opencc-zeroFeb 2023View details →

Data for: Large-scale long-term passive-acoustic monitoring reveals spatiotemporal activity patterns of boreal bats

The distribution ranges and spatio-temporal patterns in the occurrence and activity of boreal bats are yet largely unknown due to their cryptic lifestyle and lack of suitable and efficient study methods. We approached the issue by establishing a permanent passive-acoustic sampling setup spanning the area of Finland to gain an understanding on how latitude affects bat species composition and activity patterns in northern Europe. The recorded bat calls were semi-automatically identified for three target taxa; Myotis spp., Eptesicus nilssonii or Pipistrellus nathusii and the seasonal activity patterns were modeled for each taxa across the seven sampling years (2015–2021). We found an increase in activity since 2015 for E. nilssonii and Myotis spp. For E. nilssonii and Myotis spp. we found significant latitude -dependent seasonal activity patterns, where seasonal variation in patterns appeared stronger in the north. Over the years, activity of P. nathusii increased during activity peak in June and late season but decreased in mid season. We found the passive-acoustic monitoring network to be an effective and cost-efficient method for gathering bat activity data to analyze spatio-temporal patterns. Long-term data on the composition and dynamics of bat communities facilitates better estimates of abundances and population trend directions for conservation purposes and predicting the effects of climate change.

opencc-by-4.0Feb 2023View details →

Data for "A snapshot of the long term evolution of a distributed tectonic plate boundary" submitted to Science Advances

This compressed folder contains data presented in Figures of the following paper: "A snapshot of the long term evolution of a distributed tectonic plate boundary" by M. Dalaison, R. Jolivet, L. Le Pourhiet; submitted to Science Advances in February 2023 Please open the README.txt file for details about the folder's content

opencc-zeroFeb 2023View details →

Long-term coastal macrobenthic Community Trajectory Analysis reveals habitat-dependent stability patterns

Long-term monitoring programs are fundamental to detecting changes in ecosystem health and understanding ecological processes. In the current context of increasing anthropogenic threats on marine ecosystems, understanding the dynamics and response of communities becomes essential. We used data collected over 14 years in the REBENT benthic coastal invertebrates monitoring program, at a regional scale in the North-East Atlantic, covering a total of 26 sites and 979 taxa. Four distinct habitats were studied: two biogenic habitats associated with foundation species in the intertidal and subtidal zones and two bare sedimentary habitats in the same respective tidal zones. We used Community Trajectory Analysis, a statistical approach that allows for quantitative measures and comparisons of temporal trajectories of ecosystems. We compared observed community trajectories to trajectories simulated under a non-directional null model in order to better understand the dynamics of the communities, their potential drivers, and the role of the studied habitats in these dynamics. Despite strong differences in the community compositions between sites and habitats, the communities followed non-directional dynamics during the 14 years monitored, which suggested stability at the regional scale. However, the shape, size, and direction of the trajectories of benthic communities were more similar within than among habitats, also suggesting the influence of the nature of the habitat on community dynamics. Results showed a higher variability in community composition in the first years of the monitoring in the intertidal bare habitat and confirmed the role of biogenic habitats in maintaining temporal stability. They also highlighted the need to apprehend the role of transient and rare species and the scale of observation in temporal beta diversity analyses. Finally, our study confirmed the usefulness of Community Trajectory Analysis to link observed trajectory patterns to fundamental ecological processes.

opencc-by-4.0Feb 2023View details →

Chateau Champs - very long focal length dataset for Structure from Motion algorithms

This dataset contains a photogrammetric acquisition (99 images) of a sculpture head located in Château de Champs-sur-Marne, France. The images were taken with the full-frame Canon EOS 5D Mark II and a focal length of 1000mm.

opencc-by-4.0Feb 2023View details →

Earthquake catalogs for: A specific earthquake processing workflow for studying long-lived explosive volcanic eruptions with application to the 2008 Okmok eruption

Repository for the seismic catalogs from Garza-Giron et al. (2023a,b). These include the catalog with absolute locations using NonLinLoc (Lomax et al., 2001; Lomax and Curtis, 2001), and the relocated catalogs using hypoDD (Waldhauser and Ellsworth, 2000) and GrowClust (Trugman and Shearer, 2017). The header of the CSV files is as follows: Date (year/month/day), Time (hr:min:sec:msec), Latitude (decimal degrees), Longitude (decimal degrees), Depth (km), Magnitude (Ml calculated for this study), Event_type (VT:vulcano-tectonic;LP:long-period), Number of stations where the event was detected, ID References: <div>Garza‐Giron, R., Brodsky, E. E., Spica, Z. J., Haney, M. M., & Webley, P. W. (2023a). A specific earthquake processing workflow for studying long‐lived, explosive volcanic eruptions with application to the 2008 Okmok Volcano, Alaska, eruption. Journal of Geophysical Research: Solid Earth, e2022JB025882.</div> <div> </div> <div> <div>Garza‐Girón, R., Brodsky, E. E., Spica, Z. J., Haney, M. M., & Webley, P. W. (2023b). Earthquakes record cycles of opening and closing in the enhanced seismic catalog of the 2008 Okmok Volcano, Alaska, eruption. Journal of Geophysical Research: Solid Earth, 128(7), e2023JB026893.</div> <div> </div> </div> Lomax A, Curtis A (2001) Fast, probabilistic earthquake location in 3-D models using oct-tree importance sampling. Geophys Res Abstracts, 3:955. Lomax, A., Zollo, A., Capuano, P., and Virieux, J. (2001). Precise, absolute earthquake location under Somma‐Vesuvius volcano using a new 3D velocity model.Geophysical Journal International,146, 313–331. Trugman, D. T., and Shearer, P. M. (2017). GrowClust: A hierarchical clustering algorithm for relative earthquake relocation, with application to the Spanish Springs and Sheldon, Nevada, earthquake sequences. Seismological Research Letters, 88(2A), 379-391. Waldhauser, F., and Ellsworth, W. L. (2000). A double-difference earthquake location algorithm: Method and application to the northern Hayward fault, California. Bulletin of the Seismological Society of America, 90(6), 1353-1368.

Long term mean Potential Evapotranspiration (PET) and Actual Evapotranspiration (EAT) estimates using World-Wide HYPE and different PET-formula

Data of the article "Which Potential Evapotranspiration Formula to Use in Hydrological Modelling World-wide? " (Pimentel et al. 2023, Water Resources Research, <a href="https://doi.org/10.1029/2022WR033447">https://doi.org/10.1029/2022WR033447</a>)

opencc-zeroMar 2023View details →

Compositionally constrained sites drive long branch attraction

Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce "compositional constraint analysis", a method to investigate the effect of site-specific amino acid diversity on phylogenetic inference, and show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signal under models ignoring across-site compositional heterogeneity and thus contribute to topological bias and long branch attraction artifacts. We demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-PMSF, a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals.

De novo assembly of a long-read Amblyomma americanum genome

Genome assemblies of Amblyomma americanum generated from PacBio HiFi sequencing of 50 individual female ticks. This repository contains the unphased diploid assembly generated by the Flye assembler (Arcadia_Amblyomma_americanum_asm001.fasta). In addition, there are two associated fasta files containing sequences generated by submitting the unphased diploid assembly to separation by the Purge_Dups pipeline (purged pseudo-haploid assembly and haplotig assembly). Flye assembler: https://github.com/fenderglass/Flye Purge_Dups pipeline: https://github.com/dfguan/purge_dups NCBI Bioproject: PRJNA932813

The cost of movement: assessing energy expenditure in a long-distant ectothermic migrant under climate change

Functions to simulate monarch migration under set weather conditions. Data for repsirometry measurements and weather stations are also included in ZIP folders. Functions include working example of movement based on literature values for thresholds. Functions can be modified for other species as needed. Weather station data were collected from NOAA LCD stations. Alternative data sources include Wunderground Personal Weather Station datasets. However, Wunderground requires an API to access their data unless you have a PWS in their system. Connecting a PWS to wunderground provides you an API key for accessing data.

Data accompanying the paper "The electron flow in marine sediments experiencing microbial long-distance electron transport"

Data accompanying the paper "The electron flow in marine sediments experiencing microbial long-distance electron transport"