Find research datasets worth reusing

opencc-zeroFeb 2021View details →

Data from: Holocene lake phosphorus species and primary producers reflect catchment processes in a small, temperate lake

This palaeo data set consists of a Holocene record from a small, temperate lake (Lake Fuglsø, Denmark). It comprises radiocarbon (14C)-dating, pollen, X-ray fluorescence scanning, carbon and nitrogen (contents and stable isotopes), phosphorus (P) pools (from sequential P extraction and 31P nuclear magnetic resonance spectroscopy), pigment, diatom, and plant macrofossil data. Our multi-proxy palaeolimnological study aimed to investigate how natural processes and anthropogenic land-use changes have affected sedimentary P forms and primary producers. We found three periods of human impact: (1) low disturbance from domestic grazing during the Early/Mid Neolithic (~3600 – ~2600 BC), (2) higher disturbance because of animal husbandry and some grain cultivation during the Late Bronze and Pre-Roman Iron Age (~800 BC – AD ~100) and (3) strong disturbance caused by domestic grazing, intensified crop cultivation and, in particular, by retting of fibre plants during the Middle Ages and Renaissance (AD ~1000 – ~1700). Cultural eutrophication during the latter phase caused unprecedented changes in the lake, including altered species composition, high production and strongly accelerated sediment accumulation rates. Generally, catchment deforestation was related to elevated proportions of metal (iron, aluminium, calcium)-bound P forms in the sediment, while high tree cover correlated with elevated proportions of P forms associated with organic material ("organic" P, humic-bound P, refractory organic P) and loosely bound P. During phases with forest in the catchment, silicon (Si) inputs to the lake were insufficient and diatom frustules were mostly absent in the sediments. In contrast, diatoms thrived in the lake when the landscape was open and erosional Si influx was high. This study is the first to show long-term (~eight millennia) and recurring Si limitation of diatoms, a finding that may explain the absence of diatoms in sediment records of other sites too. In summary, human land-use with preceding deforestation accelerated the transport of nutrients and elements from the terrestrial to the aquatic environment, leading to substantial and irreversible changes in Lake Fuglsø. Our study is a good example of the tight links between catchment processes and lake status, indicating that catchment dynamics should be considered in lake restoration projects, particularly for lowland lakes with high catchment:lake area ratios.

opencc-zeroMay 2020View details →

Data from: Disentangling the steps of the infection process responsible for juvenile disease susceptibility

1. Juveniles of diverse host taxa, including vertebrates, invertebrates and plants, are more susceptible to parasitic infections than adults, a phenomenon still poorly understood. 2. To shed light on the mechanisms underlying this host age effect, we investigated its expression during different steps of the infection process of a bacterial parasite of the planktonic crustacean Daphnia. To do so, we infected juvenile and adult Daphnia magna with the bacterium Pasteuria ramosa and monitored parasite development in experiments specific to different steps of the infection process. 3. We did not find an effect of host age on parasite attachment, but found a strong increase in the penetration time of the parasite into hosts with increasing age. Host age at exposure also affected within-host parasite development, which was delayed in old adult D. magna in comparison to young adults and juveniles. Furthermore, parasite clearance was observed only in old adults, suggesting that old hosts have a better immune response than young adults and juveniles. 4. Our results reveal a step-specific effect of host age on disease progression, giving support for different hypotheses explaining high juvenile disease susceptibility. While these mechanisms are likely to work independently from each other, earlier steps of the infection process influence later steps, and thus may respond more readily to selection than later steps. 5. Our results also highlight that clearance can occur both during early parasite establishment and surprisingly at progressed infection phases, an undocumented phenomenon in invertebrates, where late infections are often considered chronic, lasting until host death.

opencc-zeroDec 2015View details →

Data from: Fission–fusion processes weaken dominance networks of female Asian elephants in a productive habitat

Dominance hierarchies are expected to form in response to socioecological pressures and competitive regimes. We assess dominance relationships among free-ranging female Asian elephants (Elephas maximus) and compare them with those of African savannah elephants (Loxodonta africana), which are known to exhibit age-based dominance hierarchies. Both species are generalist herbivores, however, the Asian population occupies a more productive and climatically stable environment relative to that of the African savannah population. We expected this would lower competition relative to the African taxon, relaxing the need for hierarchy. We tested whether 1) observed dominance interactions among individuals were transitive, 2) outcomes were structured either by age or by social unit according to 4 independent ranking methods, and 3) hierarchy steepness among classes was significant using David's score. Elephas maximus displayed less than a third the number of dominance interactions as observed in L. africana, with statistically insignificant transitivity among individuals. There was weak but significant order as well as steepness among age-classes but no clear order among social units. Loxodonta africana showed significant transitivity among individuals, with significant order and steepness among age-classes and social units. Elephas maximus had a greater proportion of age-reversed dominance outcomes than L. africana. When dominance hierarchies are weak and nonlinear, signals of dominance may have other functions, such as maintaining social exclusivity. We propose that resource dynamics reinforce differences via influence on fission–fusion processes, which we term "ecological release." We discuss implications of these findings for conservation and management when animals are spatially constrained.

opencc-zeroDec 2017View details →

Data from: Pattern and process in hominin brain size evolution are scale-dependent

A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates, and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to have been generated primarily by processes operating within hypothesized lineages – 64% or 88% depending on whether one uses a more or less speciose taxonomy, respectively. These processes were supplemented by the appearance in the fossil record of larger-brained Homo species and the subsequent disappearance of smaller-brained Australopithecus and Paranthropus taxa. When the estimated rate of within-lineage ECV increase is compared to an exponential model that operationalizes generation-scale evolutionary processes, it suggests that the observed data were the result of episodes of directional selection interspersed with periods of stasis and/or drift; all of this occurs on too fine a time scale to be resolved by the current human fossil record, thus producing apparent gradual trends within lineages. Our findings provide a quantitative basis for developing and testing scale-explicit hypotheses about the factors that led brain size to increase during hominin evolution.

opencc-zeroApr 2020View details →

Data from: The relevance of gene flow with wild relatives in understanding the domestication process

The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the domestication process depends on having an adequate representation of wild relatives. Cultivated maize (Zea mays spp. mays) is one of the most important crops in the world, with a long and a relatively well documented history of domestication. The current consensus points towards a single domestication event from teosinte Zea mays spp. parviglumis from the Balsas Basin in Southwest central Mexico. However, the underlying diversity of teosintes from lowlands Z. mays spp. parviglumis and highlands Zea mays spp. mexicana) was not taken into account in early studies. We used 32,739 SNPs obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members of Zea. We then inferred levels of gene flow among teosinte populations and maize, the degree of population structure of Zea mays subspecies, and potential domestication location of maize. We confirmed a strong geographic structure within Z. mays spp. parviglumis and documented multiple gene flow events with other members of the genus, including an event between Z. mays spp. mexicana and maize. Our results suggest that the likely ancestor of maize may have been domesticated not in the Balsas Basin as previously thought, but in Jalisco or in the Pacific coast, and that different populations of the teosinte subspecies have contributed to modern maize's gene pool. Our results points towards a long period of domestication marked by gene flow with wild relatives, making domestication a long and ongoing process.

opencc-zeroMar 2020View details →

Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree

Motivation: Sap flow sensors are crucial instruments to understand whole-tree water use. The lack of direct calibration of the available methods on large trees and the application of several data-processing procedures may jeopardize our understanding of water uptake dynamics by increasing the uncertainties around sensor-based estimates. We directly compared the heat ratio method (HRM) sap flow measurements to water uptake measured gravimetrically using the cut-tree method on a large mature aspen tree to quantify those uncertainties for ten consecutive days. Dataset: In this dataset, we provide sap flux density (ten-minutes intervals; g.cm-2.hr-1; corrected for wounding and sapwood thermal diffusivity) obtained from four HRM sap flow sensors installed at 2.5 m high on the focus tree (20 m tall, 60 years old trembling aspen in the boreal mixedwood region of Alberta) between July 18th and August 22nd 2017. We present the code and data (weather data from neighboring weather station) used to calculate whole-tree sap flux (L.hr-1) from each of the individual sensors using different methods of radial integration of sap flux density across the sapwood area estimated via different calculations, as well as different zero-flow corrections used. The cut-tree procedure was applied to the focus tree, and gravimetric measurements of water uptake (ten-minutes intervals) were made using a recording scale. We directly compared the different estimates of hourly, daily and cumulative sap flows obtained with gravimetric measurement of water uptake. We present the code providing the statistical analysis and results reported in the associated publication (Merlin, M., Solarik, K.A., Landhäusser, S.M. Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree. 2020. Agricultural and Forest Meteorology, http://dx.doi.org/10.1016/j.agrformet.2020.107926)

opencc-zeroDec 2017View details →

Data from: How sea-level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes

Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea-level change interacted with variable near-shore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the Last Glacial Maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38 °N) to Reforma, Sinaloa, Mexico (~25 °N). We assessed range-wide genetic structure and diversity of three co-distributed tidal estuarine fishes (California Killifish, Shadow Goby, Longjaw Mudsucker) along ~4,600 km using mitochondrial control region and cytB sequence, and 16–20 microsatellite loci from a total of 524 individuals. Results show that glacial-associated sea-level change limited estuarine habitat to few, widely separated refugia at glacial lowstand, and present-day genetic clades were sourced from specific refugia. Habitat increased during postglacial sea-level rise and refugial populations admixed in newly formed habitats. Continental shelves with active tectonics and/or low sediment supply were steep and hosted fewer, smaller refugia with more genetically differentiated populations than on broader shelves. Approximate Bayesian computation favored the refuge-recolonization scenarios from habitat models over isolation by distance and seaway alternatives, indicating isolation at lowstand is a major diversification mechanism among estuarine (and perhaps other) coastal species. Because sea-level change is a global phenomenon, we suggest this top-down physical control of extirpation-isolation-recolonization may be an important driver of genetic diversification in coastal taxa inhabiting other topographically complex coasts globally during the Mid- to Late Pleistocene and deeper timescales.

opencc-zeroDec 2017View details →

Data from: Response to persistent er stress in plants: a multiphasic process that transitions cells from prosurvival activities to cell death

The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of ZmIRE1 for promiscuous ribonuclease activity that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of alternative RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amidst a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.

opencc-zeroDec 2013View details →

Data from: Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5′-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.

openbsd-3-clauseNov 2015View details →

Learning stochastic process-based models of dynamical systems from knowledge and data - Libraries, incomplete models and data

The archive contains all libraries of domain knowledge, the incomplete models and the data used in the experiments described in the manuscript titled "Learning stochastic process-based models of dynamical systems from knowledge and data" pubilshed in BMC Systems Biology

SARWIND LG-Mod (v4.01) output data with reference to the Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind)

A zipped folder containing SARWIND LG-Mod (v4.01) output data obtained by processing the Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind). Pre-processed data derived from the Sentinel-1 SAR image have been obtained by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components have been provided by the Numerical Weather Model (NWM) SKYRON. These Earth Observation (EO) data have been used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016) for the sea surface wind field retrieval. The available Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, has been acquired on the 7th Dec 2014, 05:51:54.

Sentinel-1A (2014/12/07, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ additional SKYRON reference wind) for SARWIND LG-Mod (v4.01)

A zipped folder containing pre-processed data from a Sentinel-1 SAR image by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components provided by the Numerical Weather Model (NWM) SKYRON is also added in the folder. These Earth Observation (EO) data can be used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016), with the aim at retrieving the sea surface wind field by exploiting the single co-polarized Sentinel-1 image available. In particular, the latter is the Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, acquired on the 7th Dec 2014, 05:51:54

Sentinel-1A (2014/12/31, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ additional SKYRON reference wind) for SARWIND LG-Mod (v4.01)

SARWIND LG-Mod (v4.01) output data with reference to the Sentinel-1A (2014/12/31, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind)

A zipped folder containing SARWIND LG-Mod (v4.01) output data obtained by processing the Sentinel-1A (2014/12/31, Camargue), EW, GRD, MR, VV-polarized, descending orbit, SNAP pre-processed data (+ the additional SKYRON reference wind). Pre-processed data derived from the Sentinel-1 SAR image have been obtained by using the Sentinel Application Platform (SNAP), ver. 3.0.3, distributed by the European Space Agency (ESA). The reference wind components have been provided by the Numerical Weather Model (NWM) SKYRON. These Earth Observation (EO) data have been used as inputs to the SARWIND LGMod algorithm, ver. 4.01, developed by Rana Fabio Michele (2014-2016) for the sea surface wind field retrieval. The available Sentinel-1, Extra Wide Swath Mode, Ground Range, Multi-look, Detected, Medium Resolution, Vertical polarisation on transmit, Vertical polarisation on receive, Descending orbit, C-band SAR image, has been acquired on the 31st Dec 2014, 05:51:53.

opencc-by-4.0Feb 2017View details →

Data for Gaussian-Process-Based Emulators for Building Performance Simulation

The ZIP folder contains the MAT files you need to rerun the experiment described in Rastogi, Parag, Mohammad Emtiyaz Khan, and Marilyne Andersen. 2017. “Gaussian-Process-Based Emulators for Building Performance Simulation.” In Proceedings of BS 2017. San Francisco, CA, USA: IBPSA. ------------------------------------------------------------- The two m-scripts (MATLAB) help you to load the results reported in the paper. Make sure to CHECK the file paths inside the scripts, especially to the MAT files. Usually, the paths should be fine if you update the variable pathMATfolder inside the script RunThis.m . There are two types of MAT files inside the folder called "Data" : 1. Original data (building simulations) --> gpdata_BaseSimulation.mat 2. Errors and predictions - errs_BaseSimulation_N_M.mat and ystore_BaseSimulation_N_M.mat --> The first contains all the error quantities and the second the 'y' predictions. The number N represents the run number (subset of master training data set sampled for the given run). The number M can take only two values - 1 or 2. The models for heating load are represented by 1 and for cooling by 2. 3. Metadata - trainN* --> These files contain metadata for setting up the plots. See github repository https://github.com/paragrastogi/GPregressionInBS.git for more scripts. See www.paragrastogi.com or www.ibpsa.org for the conference paper.

opencc-by-4.0Feb 2017View details →

Underlying data for Slimani et al. Identification of dominant hydrogeochemical processes for groundwaters in the Algerian Sahara supported by inverse modeling of chemical and isotopic data

The data hereafter underlie the paper by Slimani et al. doi:10.5194/hess-20-1-2016, appeared to Hydrol. Earth Syst. Sci., 20, 1-23, 2016. 1. File Tableaux_data.xls This is an Excel sheet file. It contains: - raw analytical data, mostly in mg/L; - data converted in mmol/L; - data corrected from the defect of cations - anions balance; the correction is made proportionally. - the previous data completed with logarithms of activities, computed by Phreeqc, for calcium, sulfate, carbonate and water; those data are used to plot equilibrium diagrams for calcite and gypsum (figure 6); - for Phreatic aquifer only, saturation indexes for halite, anhydrite, calcite, dolomite and gypsum, along with distance from south to north, used in figure 7. 2. Directory Phreeqc_res Contains the input file with all samples from CI, CT and Phr in a single file, and the selected output file. All calculations were made with version phreeqc-3.1.2 and database sit.dat. 3. Directory Inverse models This directory contains inverse models for computing transformations: - from CI (average) to CT (average): - from CT (average) to Phr (pole I, average); - from pure water to Phr (pole II, sample P036); - for mixing Phr pole I and II, and try to explain a sample typical of medium mixing ratio, sample P068.

opencc-by-4.0Mar 2017View details →

Pre-processed PubMed data for a study of coauthorship

This dataset was collected from the PubMed portal to MEDLINE and other repositories of biomedical research (https://www.ncbi.nlm.nih.gov/pubmed/). Analysis of the dataset led to the paper "Effects of research complexity and competition on the incidence and growth of coauthorship in biomedicine", published in PLOS One (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173444). The raw data were pre-processed using the script "clean.r" in the project directory on GitHub (https://github.com/corybrunson/coauthor) to obtain the file presented here. The dataset is formatted as a data table (https://cran.r-project.org/web/packages/data.table/index.html), a class of data frame in R, and saved as a .RData file, which can be loaded into an R session via `load("path/to/dataset/pmDat.RData")`. The fields are as follows: <ul> <li>`pmid` - the unique publication identifier (PMID) used by PubMed</li> <li>`jid` - the unique journal identifier used by PubMed</li> <li>`issn` - the (print) ISSN of the journal</li> <li>`ym` - the month and year of publication</li> <li>`nau` - the number of authors credited by the publication (up to any limits imposed by PubMed, and counting each author collective as a single author)</li> <li>`cau` - whether any corporate author was credited</li> <li>`rev` - whether the publication was tagged as a review</li> <li>`trial` - whether the publication was tagged as a clinical trial</li> <li>`npmt` - the number of MeSH terms assigned to the publication that were flagged as "major" topics</li> <li>`nmh` - the number of top-level MeSH headings assigned to the publication</li> <li>`supp` - whether the publication was tagged as having received financial support</li> <li>`ng` - the number of grants acknowledged by the publication</li> <li>`co` - the country in which the journal was published</li> </ul> Note that the field values for any publication can be validated by searching for the PMID in PubMed.

opencc-by-4.0May 2017View details →

Experimental data for the paper "Scalable Fine-Grained Proofs for Formula Processing"

We provide here the binary, options and experimental data for our CADE paper and the companion report. Setup The tarball containing the source code of veriT used in our experiments is available here. The command line parameters of veriT used in each of the configurations described in the paper are: <ul> <li>Basic: "--old-processing --disable-sym --disable-simp --disable-unit-simp --disable-unit-subst-simp --disable-ackermann --disable-bclause"</li> <li>Extended: "--old-processing --disable-sym --disable-unit-simp --disable-unit-subst-simp --disable-ackermann --disable-bclause"</li> <li>Complete: "--old-processing"</li> <li>with proofs: "--proof=/dev/null --proof-with-sharing"</li> <li>with new code: remove parameter "--old-processing"</li> </ul> The benchmarks are from the SMT-LIB categories QF_ALIA, QF_AUFLIA, QF_IDL, QF_LIA, QF_LRA, QF_RDL, QF_UF, QF_UFIDL, QF_UFLIA, QF_UFLRA, AUFLIA, AUFLIRA, UF, UFIDL, UFLIA, and UFLRA. Our experiments were conducted on servers equipped with two Intel Xeon E5-2630 v3 processors, with eight cores per processor, and 126 GB of memory. The time limit was set to 30 s.

opencc-by-4.0Jun 2024View details →

MAB-SWOT CPIES Level 2 Processed Data

<div> These are the hourly (P#.mat) and lowpass filtered (P#lp.mat) files from the current- and pressure- sensor equipped inverted echo sounders (CPIESs) deployed as part of the MAB-SWOT program.  Version 2 of this dataset (1) includes data from P3 and (2) uses corrected clock drifts to determine each instruments' time base.  A description of the processing and details about the experiment can be found at: Wang, Y. D., & Andres, M. (2025). SWOT Adopt a Crossover Field Campaign—Cape Hatteras (MAB-SWOT) Current and Pressure Sensor Equipped Inverted Echo Sounder (CPIES) Technical Report (Version 2). Zenodo. <a href="https://doi.org/10.5281/zenodo.12583849" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.16851887</a>     </div>