Find research datasets worth reusing

Dataset for: Long-term soil warming decreases microbial phosphorus utilization by increasing abiotic phosphorus sorption and losses

Phosphorus (P) is an essential and often limiting element that could play a crucial role in terrestrial ecosystem responses to climate warming. However, it has yet remained unclear how different P cycling processes are affected by warming. Here we investigated the response of soil P pools and P cycling processes in a mountain forest after 14 years of soil warming (+4°C). Long-term warming decreased soil total P pools, likely due to higher outputs of P from soils by increasing net plant P uptake and downward transportation of colloidal and particulate P. Warming increased the sorption strength to more recalcitrant soil P fractions (absorbed to iron oxyhydroxides and clays), thereby further reducing bioavailable P in soil solution. As a response, soil microbes enhanced the production of acid phosphatase, though this was not sufficient to avoid decreases of soil bioavailable P and microbial biomass P (and biotic phosphate immobilization). This study therefore highlights how long-term soil warming triggers changes in biotic and abiotic soil P pools and processes, which can potentially aggravate the P constraints of the trees and soil microbes and thereby negatively affect the C sequestration potential of these forests.

Data from: Contrasting long-term trends in juvenile abundance of a widespread cold-water salmonid along a latitudinal gradient: Effects of climate, stream size and migration strategy

A changing climate reshapes the range distribution of many organisms, and species with relatively low thermal optima, like many salmonids, are increasingly expected to face local population extinctions at lower latitudes. Understanding where and how fast these changes are happening is of pivotal importance for successful mitigation and conservation efforts. We used an extensive electrofishing database to explore temporal trends of brown trout juveniles (Salmo trutta L.) in 218 locations from 174 Swedish streams, over the last 30 years (1991–2020). We hypothesized that 1) declines in abundance have occurred predominately in the warmer, southern regions, while increases have occurred in the colder, northern regions, 2) larger stream sizes may partly offset negative effects of climate, and 3) migrating and resident populations are affected differently by a warming climate. We found that abundance of brown trout juveniles generally declined in warmer regions, especially in smaller streams (≤ 6 m wide), while the abundance increased in colder regions. In larger streams, negative effects of higher temperatures were seemingly buffered, as we found lower rates of decline or even positive trends. The rate of change (i.e. the slopes of the trends in abundance) was more pronounced towards the climate extremes and was on average zero in regions with a normal annual air temperature (average temperature over 30-year period) around 5–6 ºC. Warmer climate had stronger effects on migrating compared to resident populations, suggesting that climate-induced loss of stream connectivity could be an additional factor that hinders recruitment in anadromous populations in a changing climate. Considering predictions of increasing temperatures and frequency of summer droughts, management of cold-water salmonid populations should focus on conserving and restoring riparian vegetation, wetlands, climate and thermal refugia, and habitat integrity overall. Such measures may, however, not suffice for small streams at lower latitudes, unless hydrological connectivity is maintained.

opencc-by-4.0Dec 2022View details →

Long-distance dispersal drives the genetic variation and historical demography of Quercus magnoliifolia and Quercus resinosa (Fagaceae) in the Mexican highlands

Genotypes of chloroplast microsatellites used in Albarrán-Lara et al. Data comprises six loci from 61 localities sampling in Mexico

Data from: Long-term trends in grassland bird relative abundance on focal grassland landscapes in Missouri

North American grassland birds have widely declined over the past 50 years, largely due to anthropogenic-driven loss of native prairie habitat. In response to these declines, many conservation programs have been implemented to help secure wildlife habitat on private and public lands. The Grasslands Coalition is one such initiative established to advance the conservation of grassland birds in Missouri. The Missouri Department of Conservation conducted annual point count surveys for comparison of grassland bird relative abundance between focal grassland areas and nearby paired (i.e., containing no targeted management) sites. We analyzed 17 years of point count data with a generalized linear mixed model in a Bayesian framework to estimate relative abundance and trends across focal or paired sites for nine bird species of management interest that rely on grasslands: barn swallow (Hirundo rustica), brown-headed cowbird (Molothrus ater), dickcissel (Spiza americana), eastern meadowlark (Sturnella magna), grasshopper sparrow (Ammodramus savannarum), Henslow's sparrow (A. henslowii), horned lark (Eremophila alpestris), northern bobwhite (Colinus virginianus), and red-winged blackbird (Agelaius phoeniceus). Relative abundance of all species except eastern meadowlarks declined regionally. Relative abundance of barn swallows, brown-headed cowbirds, dickcissels, eastern meadowlarks, Henslow's sparrows, and northern bobwhites was higher in focal than paired sites, though relative abundance trends were only improved in focal vs. paired areas for dickcissels and Henslow's sparrows. Relative abundance increased with increasing grassland cover at the local (250-m radius) scale for all species except horned larks and red-winged blackbirds and at the landscape (2,500-m radius) scale for all species except dickcissels, eastern meadowlarks, and northern bobwhites. Our results suggest focal areas contained greater relative abundances of several grassland species of concern, likely due to increased availability of grassland habitat at local and landscape scales. Further efforts to decrease landscape-scale fragmentation and improve habitat quality may be needed to achieve conservation goals.

Data from: Long-term forecast of thermal mortality with climate warming in riverine amphipods

Dataset and code to reproduce the figures in the associated publication

Multiplexed long-read plasmid validation and analysis using OnRamp

Plasmid read data and references from "Multiplexed long-read plasmid validation and analysis using OnRamp " Experiments: <ol> <li>AAZ605 - 7 plasmids</li> <li>AFQ178 - 9 plasmids</li> <li>ACK577 - 30 plasmids</li> <li>AEZ576 - 15 plasmids</li> <li>plasmids_ref_7.fasta</li> <li>plasmids_ref_9.fasta</li> <li>plasmids_ref_15.fasta</li> <li>plasmids_ref_30.fasta</li> </ol>

opencc-by-4.0Feb 2021View details →

Training, Validation and Test Sets for paper 'A Little Data goes a Long Way: Automating Seismic Phase Arrival Picking at Nabro Volcano with Transfer Learning'

Training, Validation and Test Data for model presented in paper 'A Little Data Goes A Long Way: Automating Seismic Phase Arrival Picking at Nabro Volcano with Transfer Learning', submitted to Journal of Geophysical Research: Solid Earth. Files: - train_events_2498.h5 = training set of seismic waveforms (events with P-/S-wave labelled arrivals only, i.e., no noise waveforms) - train_events_2498.pkl = event training set metadata (UTC P-/S-wave phase arrival times) - train_noise_2498.h5 = training set of seismic waveforms (noise sections only, i.e., no event waveforms) - train_noise_2498.pkl = noise training set metadata (UTC time for training noise waveforms) - val_events.h5 = validation set of seismic waveforms (events with P-/S-wave labelled arrivals only, i.e., no noise waveforms) - val_events.pkl = event validation set metadata (UTC P-/S-wave phase arrival times) - val_noise.h5 = validation set of seismic waveforms (noise sections only, i.e., no event waveforms) - val_noise.pkl = noise validation set metadata (UTC time for validation noise waveforms) - test.h5 = test set of seismic waveforms (events and noise) - test_events.pkl = event test set metadata (UTC P-/S-wave phase arrival times for test event waveforms) - test_noise.pkl = noise test set metadata (UTC time for test noise waveforms) - nabro_2011-247.mseed = 24 hours seismic data from Nabro Urgency Array (2011-09-04), saved in mseed format (e.g., can be read with obspy) - nabro_2011-269.mseed = 24 hours seismic data from Nabro Urgency Array (2011-09-26), saved in mseed format (e.g., can be read with obspy)   Further details and code for reading and using these files can be found at the GitHub repo for this paper: <a href="https://github.com/sachalapins/U-GPD">https://github.com/sachalapins/U-GPD</a>

opencc-by-4.0Feb 2022View details →

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Imaging data related to the "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures" manuscript

Data from: Social disappointment and partner presence affect long-tailed macaque refusal behaviour in an "inequity aversion" experiment

Protest in response to unequal reward distribution is thought to have played a central role in the evolution of human cooperation. Some animals refuse food and become demotivated when rewarded more poorly than a conspecific, and this has been taken as evidence that non-human animals, like humans, protest in the face of inequity. An alternative explanation - social disappointment – shifts the cause of this discontent away from the unequal reward, to the human experimenter who could – but elects not to – treat the subject well. This study investigates whether social disappointment could explain frustration behaviour in long-tailed macaques, Macaca fascicularis. We tested 12 monkeys in a novel `inequity aversion' paradigm. Subjects had to pull a lever and were rewarded with low-value food; in half of the trials, a partner worked alongside the subjects receiving high-value food. Rewards were distributed either by a human or a machine. In line with the social disappointment hypothesis, monkeys rewarded by the human refused food more often than monkeys rewarded by the machine. Our study extends previous findings in chimpanzees and suggests that social disappointment plus social facilitation or food competition effects drive food refusal patterns.

Data set for the article "One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities"

The following are data and code used for statistical analysis and figure plotting in the manuscript Gorka et al. (2023) "One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities", Geoderma, <a href="https://doi.org/10.1016/j.geoderma.2023.116399">https://doi.org/10.1016/j.geoderma.2023.116399</a> It contains the following files: <ol> <li>Microbial PLFA and NLFA analysis files (contained in Fatty_acid_analysis.zip) <ul> <li>PLFA and NLFA abundance data, in nmol C g-1 dw (in fatty_acid_data.csv)</li> <li>Taxonomic specificities of fatty acids, needed for R-script to run (in phylum.csv)</li> <li>An R Script reproducing the statistical analysis, figure plotting and output for tables, as used in the manuscript (Fatty_acid_analysis.R)</li> </ul> </li> <li>Soil C and N stoichiometry analysis files (contained in TOC_TN_analysis.zip) <ul> <li>Dissolved organic C (DOC), total dissolved N (TN), and C and N in microbial biomass (Cmic, Nmic) abundance data, in mg g-1 dw (in toc_tn_data.csv)</li> <li>An R Script reproducing the statistical analysis, figure plotting and output for tables, as used in the manuscript (TOC_TN_analysis.R)</li> </ul> </li> </ol>

Long term photo - identification of european seabass

Identification of individuals of european seabass. Long term identification, two data collection of 32 seabass. Original and processed data. Data were collected in HCMR, Greece.The long-term scenario - for proving the stability of the visible features on the fish body for the identification of the fish during the long-term cultivation period. We used 32 fish individuals of seabass during 3 months experiment. Data were collected two times during this time. 32 fish were tagged for long-term identification. Trovan, 2 x 11.5 mm, ISO 11784/85 FDX-B PIT stages were used for tagging.

Datset related to article: "ACTB gene mutation in combined Dystonia-Deafness syndrome with parkinsonism: Expanding the phenotype and highlighting the long-term GPi DBS outcome"

Sanger sequences (.abi files) validating variants found with whole exome sequencing

Dataset for "A Double Dissociation between Savings and Long-Term Memory in Motor Learning"

Data for "A Double Dissociation between Savings and Long-Term Memory in Motor Learning" For analysis code and any updates, please visit  https://github.com/AlkisMH/Savings_vs_Long_Term_Memory For any questions, please contact Alkis Hadjiosif (alkis [at] seas [dot] harvard [dot] edu; ahadjiosif [at] gmail [dot] com) These .mat files contain data collected for Experiments 1-4 and S1, used to reproduce Figures 1-6 and S1 in the paper. Data for each experiment are in the form of a Matlab structure, with each field consisting of a [Num_trials x Num_participants] matrix. The fields are: TN: Trial Number VF: Whether visual feedback was given during the trial (1: online visual feedback; 2: no visual feedback) Rotation: The visuomotor rotation imposed on each trial (in degrees). CCW is positive, CW is negative. Wait: Whether, right before the trial, a wait time was imposed (1) or not (0). Trials immediately following breaks are indicated by (2). Instruction: Whether an instruction was given for the trial (1) or not (0). Only present in Experiment 3. Note that Experiment 3 includes: -> Two specific instruction trials during learning and and two during relearning, before and after the 1-minute wait ("Move your hand to the center of the target","Move your hand to the far end of the target") -> Six random instruction trials before initial learning and six before relearning ("Move your hand to the left/right/near/far end of the target"), to familiarize participants with the instruction process ITI: Time (in seconds) since the last trial (regardless of direction). theta_target: Target direction (in degrees) relative to the 12 o'clock position. Only included for Experiment 4: target is always at 12 o'clock for Experiments 1-3. theta: = reaching direction relative to theta_target, measured 150ms into the movement. Note that this is flipped based on the rotation sign so that adaptation towards the imposed visuomotor rotation is always positive. theta_end: = reaching direction relative to theta_target, measured at the end of movement. Only included for Experiment 4: it is to be used for the no visual feedback blocks in Experiment 4. Note for Experiment 4: the last two blocks (last 114 trials) were done on day 2.

Supporting data for "Long distance multiplexed quantum teleportation from a telecom photon to a solid-state qubit"

This repository contains the data supporting the article "Long distance multiplexed quantum teleportation from a telecom photon to a solid-state qubit" by Dario Lago-Rivera, Jelena V. Rakonjac, Samuele Grandi and H. de Riedmatten. The individual .zip files contain the raw detection files for the main results of the article, i.e. the short distance teleportation, the teleportation results as a function of the repetition rate of the experiment and the teleportation experiment across 1 km of optical fibre.

MinION plasmid deep long read sequencing for sequence verification

We sequenced four plasmid constructs, each with a whole MinION flowcell, for use in developing and testing a sequence verification procedure. The resulting pipeline can sequence verify plasmid constructs, generating a consensus sequence with associated confidence of each base, adhering to strict acceptance criteria . The data contained herein are a subset of the complete data; 30 fast5 files for each plasmid, to be used as example data.   datHL_001519: BCRxV.TF.1 datHL_001521: BCRxV.VSVG.1 datHL_001617: BCRxV.GagPolRev.1 datHL_001620: BCRxV.VSVG.1_mutant

opencc-zeroDec 2022View details →

Trinity College Botanic Garden long-term monitoring program

Botanic gardens hold large, documented, and accessible collections of living plants. These represent unique subsets of taxa from different biogeographical regions growing under common environmental conditions, connecting people to global plant research and conservation efforts while offering a place beneficial for human health and wellbeing. Despite Botanic Gardens being an ideal setting for climate change research, their potential for comparative, long-term studies and outreach in the field is still underutilised. As part of its ten-year strategy, Trinity College Botanic Garden (TCBG) aims to tap this potential and establish a programme for long-term (>30 years) monitoring of key physiological performances in its living woody plant collection. The programme will also assess particulate pollution (PM10 and PM2.5) interception by the same trees, pairing climate change and urban green research. Importantly, the project will include the design of a transferable protocol, produce vouchered herbarium specimens as a future historical archive and as a pedagogical tool, and support the garden outreach strategy, so as to nurture its link with both Trinity College Dublin and local communities, ensuring the garden's legacy into the future.

opencc-zeroMar 2023View details →

Long-term seed bank persistence in Arctomecon californica

Seed banks, the collection of viable seeds in the soil, are particularly important determinants of population survival in highly variable environments. Predictions of increased stochasticity in the amount and timing of precipitation in desert environments raise the question of how seed banks of desert species will respond to climate change, and ultimately, whether these species will persist. Here, we present data from our long-term studies of germination requirements and seed bank dynamics in a rare desert gypsophile perennial, Arctomecon californica (Las Vegas bearpoppy). Arctomecon californica is a relatively short-lived plant that recruits from seed in sequences of unusually favorable years. We used germination experiments, an in situ seed bank study, and a 15-year field seed retrieval study to examine factors affecting seed bank persistence. In the germination study, a majority of seeds remained dormant, despite a wide variety of treatments, suggesting that a large proportion of the seed dispersed each year has cue-nonresponsive dormancy. Our seed bank study showed that seed density varied widely between sites, among transects, and among samples within a transect. The patchiness of seeds in the soil highlights the importance of protecting large areas where A. californica populations are known to have existed in the past. The seed retrieval study provided strong evidence that this species has a long-lived seed bank in which only a small fraction of seeds (roughly 5%) become nondormant each year, allowing seed banks of this species to last up to 20 years without a seed production event. Whether this impressive life history strategy can maintain the species in the face of climate change depends on the future frequency of the well-timed precipitation that allows for establishment of new cohorts of adult plants.

opencc-zeroMar 2023View details →

Data from: Long-term capture data uncover shifts in the daily activity patterns of Amazonian birds

Although the duration of biological rhythms varies from milliseconds to decades, daily cycles are especially widespread for individual organisms. These circadian rhythms are synchronized by light-dark cycles, which govern predictable changes in other microclimate variables. Despite the fixed, regular nature of these abiotic cycles at low latitudes, little is known about how different animals structure activity along these gradients. We used 25 years of capture-recapture data and ~25,000 unique captures to characterize 'activity' (time of capture) for 65 species of Amazonian birds in the lowest forest stratum (0–2.5 m). To quantify vertical niche breadths, we also measured foraging heights for these same species in the field. Activity peaked within the first two hours after sunrise for most species (71%), while others peaked 1–3 hours later (29%). This difference was associated with an apparent preference for specific vertical strata, as terrestrial and near-ground birds peaked ~1 hour after sunrise, while birds from higher strata delayed their first bouts of activity in the lower understory (by an average of 40 to 100 minutes). Peak capture times also correlated with long-term abundance trends, as only species with the earliest capture times showed strong declines, suggesting that associations with mid- or late-morning microclimates may contribute to resiliency in birds typical of higher strata. Because arboreal species largely avoid the lower understory in the early morning, when terrestrial birds are active, we infer that they are poorly adapted to low-light environments. However, with their broad vertical niches and reliance on brighter microhabitats, we suggest that an arboreal lifestyle diminishes specialization and may increase the capacity to cope with a wider range of daily microclimate conditions. We predict that subtle, but important, shifts in daily activity patterns would materialize if other biodiversity-monitoring programs could analyze similar temporal datasets.

opencc-zeroMar 2023View details →

Short-term, but not long-term grooming reciprocity in a species with high fission-fusion dynamics

Reciprocity allows animals to balance the costs and benefits of cooperative interactions by switching roles over time. Reciprocity can be based on two different processes: partner control and partner choice. Although not mutually exclusive, the relative roles of the two processes remain debated. We investigated grooming reciprocity in wild Geoffroy's spider monkeys (Ateles geoffroyi), a species with low grooming rates and reduced opportunities for group members to interact due to a high degree of fission-fusion dynamics. We assessed separately the roles of partner control and partner choice in grooming exchanges and investigated the factors affecting reciprocity. We found short-term reciprocity based on partner-control with reciprocation occurring within 401 s after receiving grooming. In contrast, we did not find evidence for long-term reciprocity based on partner choice. Short-term reciprocity based on partner control was not affected by kinship, whereas reduced time spent together in the same subgroup increased the probability of short-term grooming reciprocation. Our results suggest the opportunity to interact is a potent modulator of reciprocity. In species characterized by a high degree of fission-fusion dynamics and low grooming rates, short-term reciprocation based on partner control can be favoured at the expense of partner choice.