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opencc-zeroDec 2021View details →

Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations. Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters. Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations. Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation. Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.

Non-embeddability of standard contexts of lattices of integer partitions

We consider lattices of integer partitions ordered by dominance, and their standard contexts as studied in formal concept analysis. The present dataset provides evidence that the standard context of the partition lattice for \(n = 9\) cannot be embedded into the one for \(n = 10\). Further context and a detailed description of the files in the dataset can be obtained from the file context_embeddings.pdf (the code source for this file is given in context_embeddings.tex).

Symmetric embeddings between standard contexts of lattices of integer partitions

We consider lattices of integer partitions ordered by dominance, and their standard contexts as studied in formal concept analysis. The present dataset contains all 29 symmetric context embeddings of the standard context of the lattice of partitions of the integer 8 into the standard context of the lattice of 10. Further information and a detailed description of the files in the dataset can be obtained from the file context_embeddings.pdf (the code source for this file is given in context_embeddings.tex).

opencc-by-4.0Feb 2022View details →

Dataset created in the context of the project "Stable methodologies to evaluate and measure quality, interoperability, blockchain and reuse of open data in the agricultural field"

The project "Stable methodologies to evaluate and measure quality, interoperability, blockchain and reuse of open data in the agricultural field", whose website is https://datause.es/, is a project funded by the Ministry of Science and Innovation - State Research Agency, with reference PID2019-105708RB-C22. Within the framework of the project, a bibliographic search is carried out in all thematic categories of the Web of Science (WoS) related to agriculture and related areas. The search equation included the following categories: WC = (FOOD SCIENCE TECHNOLOGY OR PLANT SCIENCES OR FORESTRY OR AGRICULTURAL ENGINEERING OR AGRONOMY OR HORTICULTURE OR AGRICULTURE DAIRY ANIMAL SCIENCE OR AGRICULTURE MULTIDISCIPLINARY OR AGRICULTURAL ECONOMICS POLICY)  This data set shows the distribution of journals and the quartile they occupy in each of the thematic categories in 2019, with the aim of serving researchers in this area and for future data mining.

opencc-by-4.0Apr 2021View details →

Supplementary data to The vegetation of Chile and the EcoVeg approach in the context of the International Vegetation Classification project

The rar file contains a map of Macrogroups of Chile in ESRI shapefile format. Macrogroups are hierarchically included in the categories of division and formation of IVC classification. These categories can also be displayed using the table associated with the shapefile. Likewise, Chilean zonal vegetation units of Luebert & Pliscoff (2017) are included, so the crosswalk for generating the map of Macrogroups based on the Chilean zonal vegetation units is fully documented.

opencc-by-4.0Feb 2022View details →

State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data

These files can be categorized into three groups: (1) raw datasets obtained from public databases (i.e., GBIF, BOLD, and GenBank), (2) manually edited files needed for parsing and analysis, and (3) supplementary files for spatial analysis. All are used in the examination of gaps and biases present in Philippine biodiversity data, which can direct research on the taxa and spatial regions that need more sampling.

opencc-by-4.0Oct 2020View details →

Tara Pacific samples provenance and environmental context - version 2

This publication includes the provenance metadata and environmental context of all samples generated by the Tara Pacific Expedition. The metadata fields and parameters are detailed in the readme files. Provenance is given in a single UTF-8 encoded tab-separated-values file. Environmental context is provided in eleven UTF-8 encoded tab-separated-values files, all with the same structure, but each providing a different statistic:  <ul> <li>"n" = number of values</li> <li>"mean" = mean value</li> <li>"stdev" = standard deviation</li> <li>"P05" = 5 percentile, i.e. minimum (Q0)</li> <li>"P25" = 25 percentile, i.e. first quartile (Q1)</li> <li>"P50" = 50 percentile, i.e. median (Q2)</li> <li>"P75" = 75 percentile, i.e. third quartile (Q3)</li> <li>"P95" = 95 percentile, i.e. maximum (Q4)</li> <li>"dt" = lag in time, i.e. difference between the collection date/time of the sample and that of the environmental context provided</li> <li>"dxy" = lag in horizontal space, i.e. distance between the collection location of the sample and that of the environmental context provided</li> <li>"dz" = lag in vertical space, i.e. difference between the collection depth/altitude of the sample and that of the environmental context provided</li> </ul> Missing value terms are: <ul> <li>"nav" = not-available, i.e. the expected information is not given because it has not been collected or generated</li> <li>"npr" = not-provided, i.e. the expected information has been collected or generated but it is not given, i.e. a value may be available in a later version or may be obtained by contacting the data providers</li> <li>"nac" = confidential, i.e. the expected information has been collected or generated but is not available openly because of privacy concerns</li> <li>"nap" = not-applicable, i.e. no information is expected for this combination of parameter, environment and/or method, e.g. depth below seabed cannot be informed for a sample collected in the water or the atmosphere</li> </ul>

opencc-by-4.0Mar 2022View details →

Analytical Center of University Cultural Productions in the Context of the Conflict (caPAZ)

This dataset comprises a collection of journalistic articles written by young university students in Colombia, which is a product of the project: Analytical Center of University Cultural Productions in the Context of the Conflict (caPAZ), funded by the Ministry of Science, Technology and Innovation (Minciencias) and the National Center for Historical Memory (CNM) of Colombia (under the code: 1349-872-76354, agreement 872 of 2020) This corpus includes news written by the 8 colleges media of the Colombian Network of College Journalism from 2001 to 2021. The dataset includes digital news, for a total of 2373 news items related to the armed conflict, the memory of the victims and the peace process in Colombia. These news items were collected through a web-scraping technique, using 3 lemmatized keywords (conflicto armado, memoria de las víctimas y proceso de paz), with the aim of identifying these regular expressions in the logical operators that run through the HTML structure of each Web page

opencc-by-4.0Mar 2022View details →

Planned behaviour in the COVID-19 context

This dataset contains information about the intentions of Spanish tourists to travel to destinations that have a low impact of COVID-19, their risk perceptions in times of uncertainty, and past behaviour.

Fig. 6 in Gis Modelling Of The Distribution Of Terrestrial Tortoise Species: Testudo Graeca And Testudo Hermanni (Testudines, Testudinidae) Of Eastern Europe In The Context Of Climate Change

Fig. 6. Result of the analysis of Binomial tests (CliMond 2090 (2081–2100)): A — T. graeca; B — T. hermanni.

Fig. 3 in Gis Modelling Of The Distribution Of Terrestrial Tortoise Species: Testudo Graeca And Testudo Hermanni (Testudines, Testudinidae) Of Eastern Europe In The Context Of Climate Change

Fig. 3. Niche clustering (Geographic space, CliMond 1975 (1970–2000)) from: A — T. graeca (1. T. g. ibera, 2. T. nikolskii, 3. T. g. anamurensis, 4. T. g. floweri, 5. T. g. antakyensis, 6. T. g. pallasi, 7. T. g. armenica, 8. T. g. perses, buxtoni, 9. T. g. terrestris); B — T. hermanni (1. T. h. hermanni, 2. T. h. hervegovinensis, 3. T. h. boettgeri), red circles showing the approximate ranges of subspecies according to "Turtles…, 2017" World" (2017).

Fig. 2 in Gis Modelling Of The Distribution Of Terrestrial Tortoise Species: Testudo Graeca And Testudo Hermanni (Testudines, Testudinidae) Of Eastern Europe In The Context Of Climate Change

Fig. 2. The "Ecological envelope" — relationship bio01 "Annual mean temperature", °C & bio12 "Annual precipitation", mm (DivaGis): A — T. graeca; B — T. hermanni.

Fig. 5 in Gis Modelling Of The Distribution Of Terrestrial Tortoise Species: Testudo Graeca And Testudo Hermanni (Testudines, Testudinidae) Of Eastern Europe In The Context Of Climate Change

Fig. 5. Potential (probabilistic) model of T. hermanni world expansion built in the Maxent program based on the CliMond: A — 1975 (1970–2000); B — 2090 (2081–2100)) climatic data and GBIF data (2021). Areas of the highest habitat suitability (> 0.3–0.5) are colored in red and areas of the lowest (<0.2) — in blue (SAGA GIS).

Fig. 4 in Gis Modelling Of The Distribution Of Terrestrial Tortoise Species: Testudo Graeca And Testudo Hermanni (Testudines, Testudinidae) Of Eastern Europe In The Context Of Climate Change

Fig. 4. Potential (probabilistic) model of T. graeca expansion built in the Maxent program based on the CliMond: A — 1975 (1970–2000); B — 2090 (2081–2100)) climatic data and GBIF data (2021 a). Areas of the highest habitat suitability (> 0.3–0.5) are colored in red and areas of the lowest (<0.2) — in blue (SAGA GIS).

opencc-zeroApr 2022View details →

Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.

opencc-zeroApr 2022View details →

Context-dependence in the symbiosis between Dictyostelium discoideum and Paraburkholderia

Symbiotic interactions change with environmental context. Measuring these context-dependent effects in hosts and symbionts is critical to determining the nature of symbiotic interactions. We investigated context-dependence in the symbiosis between social amoeba hosts and their inedible Paraburkholderia bacterial symbionts, where the context is the abundance of host food bacteria. Paraburkholderia have been shown to harm hosts dispersed to food-rich environments, but aid hosts dispersed to food-poor environments by allowing hosts to carry food bacteria. Through measuring symbiont density and host spore production, we show that this food context matters in three other ways. First, it matters for symbionts, who suffer a greater cost from competition with food bacteria in the food-rich context. Second, it matters for host-symbiont conflict, changing how symbiont density negatively impacts host spore production. Third, data-based simulations show that symbiosis often provides a long-term fitness advantage for hosts after rounds of growth and dispersal in variable food-contexts, especially when conditions are harsh with little food. These results show how food context can have many consequences for the Dictyostelium-Paraburkholderia symbiosis and that both sides can frequently benefit.

opencc-by-4.0Jul 2021View details →

Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.

Uploaded under this Zenodo DOI is the following: 1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs). 2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files. 3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments.  4. Excel worksheets that contain the numerical source data for all qPCR bar plots.

opencc-zeroDec 2021View details →

Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus)

To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than non-hybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to non-hybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and non-hybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus non-repeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time while controls did not, though trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus non-hybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.

opencc-by-nc-4.0May 2022View details →

A TripAdvisor Dataset for Dyadic Context Analysis

There are many contexts where dyadic data are present. In social networks, users are linked to a variety of items, defining interactions. In the social platform of TripAdvisor, users are linked to restaurants by means of reviews posted by them. Using the information of these interactions, we can get valuable insights for forecasting, proposing tasks related to recommender systems, sentiment analysis, text-based personalisation or text summarisation, among others. Furthermore, in the context of TripAdvisor there is a scarcity of public datasets and lack of well-known benchmarks for model assessment. We present six new TripAdvisor datasets from the restaurants of six different cities: London, New York, New Delhi, Paris, Barcelona and Madrid. If you use this data, please cite the following paper under submission process (<a href="https://arxiv.org/abs/2205.01759">preprint - arXiv</a>) We exclusively collected the reviews written in English from the restaurants of each city. The tabular data is comprised of a set of six different CSV files, containing numerical, categorical and text features: <ul> <li>parse_count: numerical (integer), corresponding number of extracted review by the web scraper (auto-incremental)</li> <li>author_id: categorical (string), univocal, incremental and anonymous identifier of the user (UID_XXXXXXXXXX)</li> <li>restaurant_name: categorical (string), name of the restaurant matching the review</li> <li>rating_review: numerical (integer), review score in the range 1-5</li> <li>sample: categorical (string), indicating “positive” sample for scores 4-5 and “negative” for scores 1-3</li> <li>review_id: categorical (string), univocal and internal identifier of the review (review_XXXXXXXXX)</li> <li>title_review: text, review title</li> <li>review_preview: text, preview of the review, truncated in the website when the text is very long</li> <li>review_full: text, complete review</li> <li>date: timestamp, publication date of the review in the format (day, month, year)</li> <li>city: categorical (string), city of the restaurant which the review was written for</li> <li>url_restaurant: text, restaurant url</li> </ul>