Find research datasets worth reusing

opencc-by-4.0Apr 2023View details →

Set of Data from "Selective targeting of striatal parvalbumin-expressing interneurons for transgene delivery" https://doi.org/10.1016/j.jneumeth.2021.109105

PVCre (+/+) mice were injected in the right striatum with AAV2/1-hsyn-FLEX-eGFP AAV2/9-CBA-FLEX-eGFP  or AAV2/9-hsyn-FLEX-eGFP vectors. Two weeks after, cells were manually counted by a blind observer on 2D maximal intensity projections of confocal images transformed into the tiff format using the Multi-point tool in ImageJ. The GraphPad .pzfx files show the quantitative anaylsis of the proportion of GFP+ cells which were PV+ (specificty) , the proportion of PV+ cells which were GFP+ (efficiency), the proportion of PV+ cells in the injected striatum relative to to the injected striatum of PVCre (+/+) mice (absence of vector toxicity) and the proportion of PV+ cells in the striatum  of PVCre (+/+) mice versus wt mice.

opencc-by-4.0Jul 2022View details →

Dataset for "Single-Step Selective Oxidation of Methane by Iron-Oxo Species in the Metal-Organic Framework MFU-4l"

Dataset belonging to publication "Single-Step Selective Oxidation of Methane by Iron-Oxo Species in the Metal-Organic Framework MFU-4l"

Code, scripts and data for: Seasonality and competition select for variable germination behavior in perennials

The occurrence of within-population variation in germination behavior and associated traits such as seed size has long fascinated evolutionary ecologists. In annuals, unpredictable environments are known to select for bet-hedging strategies causing variation in dormancy duration and germination strategies. Variation in germination timing and associated traits is also commonly observed in perennials and often tracks gradients of environmental predictability. Although bet-hedging is thought to occur less frequently in long-lived organisms, these observations suggest a role of bet-hedging strategies in perennials occupying unpredictable environments. We use complementary analytical and evolutionary simulation models of within-individual variation in germination behavior in seasonal environments to show how bet-hedging interacts with fluctuating selection, life-history traits, and competitive asymmetries among germination strategies. We reveal substantial scope for bet-hedging to produce variation in germination behavior in long-lived plants, when "false starts" to the growing season results in either competitive advantages or increased mortality risk for alternative germination strategies. Additionally, we find that lowering adult survival may, in contrast to classic bet-hedging theory, result in less spreading of germination by decreasing density-dependent competition. These models extend insights from bet-hedging theory to perennials and explore how competitive communities may be affected by ongoing changes in climate and seasonality patterns.

Data for: Using radio frequency identification (RFID) technology to characterize nest site selection in wild Japanese tits (Parus minor)

Selecting a suitable nest site is critical to the survival and reproduction of birds. Prospecting allows individuals to gather information on the local quality of potential future breeding sites, which may help them make the best nest site selection decision. However, few studies have focused on the direct links between the prospecting activity of breeders and subsequent nest site selection. In this study, we investigated the prospecting pattern of Japanese tits (Parus minor) during the pre-breeding period of the first breeding attempt and whether nest site characteristics influence their nest box visiting behaviour and occupied nest site. We used radio frequency identification (RFID) to track the movements of Japanese tits visiting nest boxes and compared nest site characteristics between visited and unvisited (control) nest boxes, as well as between visited and occupied nest boxes. We found that Japanese tits started visiting nest boxes approximately 20 days before breeding, visited an average of 6 nest boxes and eventually chose the most visited nest box for breeding activities. Japanese tits were more likely to visit nest boxes that had less canopy cover and lower shrub density but a greater total number of surrounding trees and ultimately chose breeding nest boxes with a smaller entrance inclination, in nesting trees with a larger diameter at breast height (DBH) which were surrounded by trees with a larger DBH. Our results suggest that Japanese tits visit several potential breeding sites before choosing breeding nest boxes and that nest site characteristics can influence their prospecting activity and nest site selection.

opencc-by-4.0May 2023View details →

Data for: Selective elimination of enterovirus genotypes by activated sludge and chlorination

Raw data underlying the journal article "Selective elimination of enterovirus genotypes by activated sludge and chlorination" by Larivé et al., Environmental Science: Water Research and Technology, 2023 (doi: 10.1039/d3ew00050h) One CSV file for each of Figures 2-6 of the main manuscript $ One CSV file for each of Figures S5, S6 and S7 of the Supplementary information. The data for Figures S2, S3 and S4 are summarized in a single CSV file.

opencc-by-4.0Apr 2023View details →

Deterministic evolution and stringent selection during pre-neoplasia

The earliest events during human tumor initiation, while poorly characterized, may hold clues to malignancy detection and prevention. Here we model occult pre-neoplasia by bi-allelically inactivating TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over two years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single cell sequencing of TP53 deficient gastric organoids similarly indicates progression towards malignant transcriptional programs. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programs repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference, and a striking degree of phenotypic convergence in pre-malignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and reveal evolutionary constraints and barriers to malignant transformation with implications for earlier detection and interception of aggressive, genome instable tumors.

opencc-zeroDec 2022View details →

Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

Background During domestication and subsequent improvement, plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. Results Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes, we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. Conclusions Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.

Data from: Vascularization underlies differences in sexually selected skin coloration in a wild primate

Male reproductive competition can select for condition-dependent, conspicuous traits that signal some aspect of fighting ability and facilitate assessment of potential rivals. However, the underlying mechanisms that link the signal to a male's current condition are difficult to investigate in wild populations. In this study, we used digital photographs and chest skin samples to investigate mechanisms of a visual signal used in male competition in a wild primate, the red chest patch in geladas (Theropithecus gelada) in the Simien Mountains National Park, Ethiopia. We analyzed photographs collected during natural and anesthetized conditions to understand variability in male and female chest redness, and we used chest skin biopsies to explore sex differences in gene expression. Male and female geladas showed similar average redness, but males exhibited a wider within-individual range in redness under natural conditions. These sex differences were reflected at the molecular level, with 10.5% of genes exhibiting significant sex differences in expression. Subadult males exhibited intermediate expression patterns between adult males and females, pointing to mechanisms underlying the development of the red chest patch. We found that genes more highly expressed in males were associated with blood vessel development and maintenance but not with androgen or estrogen activity. Together, our results suggest male gelada redness variability is driven by increased blood vessel branching in the chest skin, providing a potential link between male chest redness and current condition as increased blood circulation to exposed skin could lead to heat loss in the cold, high-altitude environment of geladas.

opencc-by-4.0May 2023View details →

Spatio-temporal Dynamics of Coworking Spaces Development: The Case of Selected Central European Capitals

The dataset provides geolocation coordinates and years of activity of coworking spaces in the selected Central European capitals - Bratislava, Budapest, Prague, and Warsaw.

Evolution of reproductive isolation in a long-term evolution experiment with Drosophila melanogaster: 30 years of divergent life history selection

We ask if three decades and over 1,500 generations of divergent life history selection on age at reproduction has resulted in the evolution of reproductive isolation (RI) between laboratory populations of Drosophila melanogaster. We tested for premating, postmating-prezygotic and postzygotic reproductive isolation between 3 replicate population pairs. Large evolved differences in body size between selection treatments suggested the potential for prezygotic barriers driven by sexual selection or physical incompatibilities between the sexes. Although a simple prediction would be preference for larger size, creating directional isolation, our results from individual mate choice trials indicate that populations from both selection treatments show a marked bias towards homotypic mate choice; indicative of prezygotic RI driven by sexual selection or sexual conflict. Hybridization between the focal populations resulted in the production of viable adult flies with intermediate size and developmental traits. We observed a suggestive but statistically non-significant trend of fitness decline in the F2 generation of hybrids, but no significant evidence suggesting the evolution of postmating-prezygotic or postzygotic RI. Our findings are in accord with extant literature that posits that premating RI evolves before postmating forms of RI.

opencc-by-4.0Sep 2022View details →

Figure 1 in The Chironomus species studied by Letha Karunakaran in Singapore, with a review of the status of selected South-East Asian Chironomus

Figure 1. Male hypopygium of Chironomus flaviplumus-Type B. Note that the anal point is not black and not sharply turned-down, and that the SVo is beaked and not gently curved.

opencc-by-4.0Jun 2023View details →

COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences

This upload contains pipeline configuration files, output data, scripts and data identifiers (GISAID EPI_ISL_ID) required to reproduce the results of the article entitled "COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences".

Nest-switch and nest site selection pattern in the double-brooded Japanese tits (Parus minor)

Most studies on nest site selection in multiple-brooded birds indicate that breeders tend to reuse the original nest site for subsequent breeding attempts within the same season. However, there are also some instances that many breeders may choose to move and build a new nest. The factors of habitat affecting nest switching of multiple-brooded avian species are poorly investigated. In this study, we investigated whether facultatively double-brooded Japanese tits (Parus minor) adapt their nest site characteristics in response to changes in environmental conditions during the second breeding attempt. Our results showed that second breeding nest boxes of Japanese tits had lower shrub height and fewer total number of tree species, but taller nest box height and higher shrub density compared to the control nest boxes. Compared with first-breeding nest boxes, second-breeding nest boxes used by Japanese tits had lower shrub height and higher shrub density. Our results suggested that Japanese tits selected nest sites for second breeding based on nest site characteristics, which may be related to food availability or predator avoidance.

Reduced strength and increased variability of extinction selectivity during mass extinctions

Two of the traits most often observed to correlate with extinction risk in marine animals are geographic range and body size. However, the relative effects of these two traits on extinction risk has not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographic range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographic range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographic range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographic range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.

Supplementary tables for: Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel's lambda model

Phylogenetic generalized least squares (PGLS) regression is widely used to detect evolutionary correlations. In contrast to the equal treatment of analyzed traits in conventional correlation methods such as Pearson and Spearman's rank tests, we must designate one trait as the independent variable and the other as the dependent variable. However, in our PGLS regression analyses (using Pagel's λ model) of both empirical and simulated datasets, switching independent and dependent variables yielded many conflicting results. A serious problem with PGLS regression that has not been noticed before is that selecting an inappropriate trait as the dependent variable will often result in an error. To assess correlations in simulated data, we established a gold standard by analyzing changes in traits along phylogenetic branches. Next, we tested seven potential criteria for dependent variable selection: log-likelihood, Akaike information criterion, R2, p-value, Pagel's λ, Blomberg et al.'s K, and the estimated λ in <a name="_Hlk136010442"></a>Pagel's λ model. We determined that the last three criteria performed equally well in selecting the dependent variable and were superior to the other four. For practicality, we suggest using the trait with a higher λ or K value as the dependent variable in future PGLS regressions. In analyzing the evolutionary relationship between two traits, we should designate the trait with a stronger phylogenetic signal as the dependent variable even if it could logically assume the cause in the relationship.

Elevational differences in migration phenology of Lazuli Buntings do not support selection-based hypotheses for protandry

Documenting and understanding sex-specific variation in migratory phenology is important for predicting avian population dynamics. In spring, males often arrive on the breeding grounds before females (protandry), though whether these patterns result from fitness benefits versus sex-specific constraints on arrival timing remains poorly understood. Sex-specific variation in the timing of fall migration is less well-documented than in spring, in part because documenting fall departures is often limited by cryptic behaviors, lower vocalization rates, and shifting territory boundaries during this time of year. We used two years of high-resolution encounter data from radio-frequency identification (RFID)-equipped bird feeders to monitor the daily presence of male and female Lazuli Buntings (Passerina amoena) throughout the breeding season at a high and a low elevation site in Cache County, Utah, USA. These encounter data were used to estimate daily arrival and departure probabilities and to investigate possible differences in migration timing in relation to sex and elevation. At low elevation, male arrival (n=15) preceded female arrival (n=16) by approximately one week, consistent with previous research that has documented protandry in other migratory songbirds. At high elevation, however, no significant differences were found between male (n=19) and female arrival (n=6). In fall, we found little difference in departure dates between elevation or sex, or between years. Our observations are most consistent with constraint-based hypotheses explaining protandry, possibly relating to sex-specific constraints operating during the non-breeding period. We additionally emphasize the need for quantifying uncertainty in phenological estimates and importance of addressing potential differences across demographic groups.

When the neighborhood matters: contextual selection on seedling traits in native and non-native California grasses

Plants interact extensively with their neighbors, but the evolutionary consequences of variation in neighbor identity are not well understood. Seedling traits are likely to experience selection that depends on the identity of neighbors because they influence competitive outcomes. To explore this, we evaluated selection on seed mass and emergence time in two California grasses, the native perennial Stipa pulchra and the non-native annual Bromus diandrus, in the field with six other native and non-native neighbor grasses in individual and mixed species treatments. We also quantified characteristics of each neighbor treatment to further investigate factors influencing their effects on fitness and phenotypic selection. Selection favored larger seeds in both focal species and this was largely independent of neighbor identity. Selection generally favored earlier emergence in both focal species, but neighbor identity influenced the strength and direction of selection on emergence time in S. pulchra but not B. diandrus. Greater light interception, higher soil moisture, and greater productivity of neighbors was associated with more intense selection for earlier emergence and larger seeds. Our findings suggest that changes in plant community composition can alter patterns of selection in seedling traits, and that these effects can be associated with measurable characteristics of the community.

opencc-by-nc-4.0Jun 2023View details →

Wikidata Thematic Subgraph Selection

Wikidata Thematic Subgraph Selection These datasets have been designed to train and evaluate algorithms to select thematic subgraphs of interest in a large knowledge graph from seed entities of interest. Specifically, we consider Wikidata. Given a set of seed QIDs of interest, a graph expansion is performed following P31, P279, and (-)P279 edges. Traversed classes that thematically deviates from seed QIDs of interest should be pruned. Datasets thus consist of classes reached from seed QIDs that are labeled as "to prune" or "to keep". Available datasets <table> <tbody><tr> <th>Dataset</th> <th># Seed QIDs</th> <th># Labeled decisions</th> <th># Prune decisions</th> <th>Min prune depth</th> <th>Max prune depth</th> <th># Keep decisions</th> <th>Min keep depth</th> <th>Max keep depth</th> <th># Reached nodes up</th> <th># Reached nodes down</th> </tr> </tbody><tbody> <tr> <td><a href="data/dataset1">dataset1</a></td> <td>455</td> <td>5233</td> <td>3464</td> <td>1</td> <td>4</td> <td>1769</td> <td>1</td> <td>4</td> <td>1507</td> <td>2593609</td> </tr> <tr> <td><a href="data/dataset2">dataset2</a></td> <td>105</td> <td>982</td> <td>388</td> <td>1</td> <td>2</td> <td>594</td> <td>1</td> <td>3</td> <td>1159</td> <td>1247385</td> </tr> </tbody> </table> Each dataset folder contains <ul> <li><code>datasetX.csv</code>: a CSV file containing one seed QID per line (not the complete URL, just the QID). This CSV file has no header.</li> <li><code>datasetX_labels.csv</code>: a CSV file containing one seed QID per line and its label (not the complete URL, just the QID)</li> <li><code>datasetX_gold_decisions.csv</code>: a CSV file with seed QIDs, reached QIDs, and the labeled decision (1: keep, 0: prune)</li> <li><code>datasetX_Y_folds.pkl</code>: folds to train and test models based on the labeled decisions</li> </ul> <code>dataset1-2</code> consists of using <code>dataset1</code> for training and <code>dataset2</code> for testing. License Datasets are available under the <a href="https://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC</a> license.

opencc-by-4.0Jun 2023View details →

An Adaptive Channel Selection Method for Assimilating the Hyperspectral Infrared Radiances

1. The channel sets selected by the ER-based selection method with different thresholds. 2. The analysis fields assimilated by the ER-based selection method and the adaptive method. 3. Note: The compressed file 'clearsky/allsky' contains four files with different thresholds of the ER-based selection method (ER0.8, ER0.85, ER0.9, ER0.95) and six files with different thresholds of the adaptive method (PaPb0.9, PaPb0.95, PaPb0.96, PaPb0.97, PaPb0.98, PaPb0.99), along with one file for all channels.