Find research datasets worth reusing

Dataset for paper submission: "Revisiting the Long-Run Relationship Between Inward/Outward FDI and Income Inequality: New Evidence from the OECD"

The relatively small panel cointegration literature on the dynamics between FDI and income inequality predominantly finds that FDI will reduce income inequality in the long-run in developed countries. However, we point out an important technical oversight in the literature. Not accounting for cross-section dependence in panel data methodologies may yield unreliable results. Expanding on the work of @herzer/nunnenkamp:13, who pioneered the use of panel cointegration in the European context, we obtain different results when we account for cross-section dependence and employ economic procedures robust to it. Using a panel containing 16 OECD countries (1979-2017), 2 income inequality measures, and 4 FDI measures, we begin by showing strong evidence for the existence of cross-section dependence. Then, using second-generation econometric procedures, we do not find any evidence for a cointegrating relationship between inward FDI and income inequality. We do find evidence that outward FDI is cointegrated with income inequality; however, contrary to the main results of the literature, we find that it widens the income gap in the long-run. Additionally, our results support the view that fiscal policy is an important tool to reduce income inequality.

opencc-zeroAug 2022View details →

Drivers of within- and among-individual variation in risk-taking behaviour during reproduction in a long-lived bird

Plastic and selective mechanisms govern parental investment adjustments to predation threat. We investigated the relative importance of plasticity and selection in risk-taking propensity of incubating female common eiders Somateria mollissima facing unprecedented predation in SW Finland, Baltic Sea. Using a 12-year individual-based dataset, we examined within- and among-individual variation in flight initiation distance (FID), in relation to predation risk, nest detectability, individual traits and reproductive investment (NFID = 1009; Nindividual = 559). We expected females nesting in riskier environments (higher predation risk, lower nest concealment) to mitigate environmentally-imposed risk by exhibiting longer FIDs, and females investing more in current reproduction (older, in better condition or laying large clutches) to display shorter FIDs. The target of predation - adult or offspring - affected the mechanisms adapting risk-taking propensity; females plastically increased their FID under higher adult predation risk, while risk-avoiding breeders were predominant on islands with higher nest predation risk. Risk-taking females selected thicker nest cover, consistent with personality-matching habitat choice. Females plastically attenuated their antipredator response (shorter FIDs) with advancing age, and females in better body condition were more risk-taking, a result explained by selection processes. Future research should consider predator type when investigating the fitness consequences of risk-taking strategies.

opennotspecifiedSep 2022View details →

FIGURE. Petalidium parvifolium, flower and leaf morphology. A. Branchlet showing leaves that are not succulent; blade ± flat and margins without long, robust, multi-cellular trichomes and isolated, robust, stalked glandular trichomes. B. Flower in front view. C. Flower in lateral view. Scale bar = 5 mm. Photographs by W. Swanepoel. in Petalidium mannheimerae (Acanthaceae), a new species from Namibia and South Africa, with notes on the taxonomic identity of P. parvifolium

FIGURE. Petalidium parvifolium, flower and leaf morphology. A. Branchlet showing leaves that are not succulent; blade ± flat and margins without long, robust, multi-cellular trichomes and isolated, robust, stalked glandular trichomes. B. Flower in front view. C. Flower in lateral view. Scale bar = 5 mm. Photographs by W. Swanepoel.

Replication Package for Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects"

This replication package can be used for replicating results in the paper. It contains 1) a dataset of 290,255 repositories; and 2) Python scripts for training and interpreting models.  We recommend manually setup the required environment in a commodity Linux machine with at least 1 CPU Core, 8GB Memory and 100GB empty storage space. We conduct development and execute all our experiments on a Ubuntu 20.04 server with two Intel Xeon Gold CPUs, 320GB memory, and 36TB RAID 5 Storage. We use GHTorrent to restore historical states of 290,255 repositories with more than 57 commits, 4 PRs, 1 issue, 1 fork and 2 stars. The raw data of repositories are stored in `Replication Package/data/prodata.pkl`, and the contribution of features resulting from LIME model is stored in `Replication Package/data/limeres_m2_k1.pkl`. We sort items by the order in `Replication Package/data/randind.npy`, which can be used to reproduce the same results as in the paper.  `Replication Package/data/X_test_m2_k1.pkl` and `Replication Package/data/y_test_m2_k1.pkl` store the test dataset for the LIME model. You can run `Replication Package/fitdata.py` to get the results in Table III and IV, run `Replication Package/draw_compare_variable.py` to get Figure 2 and run `Replication Package/allvari_statistics.py` to get Table II. In `Replication Package/Variable_comparison_with_different_parameter.pdf`, we show the LIME results under different parameters. In `Replication Package/sample_pros.csv`, we also provide the list of randomly selected repositories in Section III.B.

Replication Package for Paper "How Early Participation Determines Long-Term Sustained Activity in GitHub Projects"

opennotspecifiedSep 2022View details →

FIGURE. Disc cypselae and pappus in Callilepis taxa. A. Scanning electron micrograph of the laterally compressed disc cypsela of C. laureola var. laureola with one long and one short awn (Bester 13813, PRE). B. Digital image of the inner ray floret of C. leptophylla with laterally compressed ovary, one long awn and one short awn (Van Vuuren 1307, PRE). C. and D. Scanning electron micrographs of the disc cypselae of C. lancifolia: C, with one pappus awn and scales and D, no pappus awns, only scales (Koekemoer 5555, PRE). in A taxonomic revision of the genus Callilepis (Asteraceae) in South Africa

FIGURE. Disc cypselae and pappus in Callilepis taxa. A. Scanning electron micrograph of the laterally compressed disc cypsela of C. laureola var. laureola with one long and one short awn (Bester 13813, PRE). B. Digital image of the inner ray floret of C. leptophylla with laterally compressed ovary, one long awn and one short awn (Van Vuuren 1307, PRE). C. and D. Scanning electron micrographs of the disc cypselae of C. lancifolia: C, with one pappus awn and scales and D, no pappus awns, only scales (Koekemoer 5555, PRE).

Experimental data for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels

Experimental data set for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels. Provides all raw data needed to reproduce experimental graphs presented within the paper.

opennotspecifiedSep 2022View details →

Figure 25. Atypical maxilla 1, long palp with 3–4 in Morphological comparison and description of five new species of Hyalella (Crustacea: Amphipoda) from Veracruz and Mexico City

Figure 25. Atypical maxilla 1, long palp with 3–4 distal setae, and up to five distal setae on inner plate: Hyalella sp., male 6.8 mm, Lake Catemaco, Veracruz. Scale bar: 100 µm.

opencc-zeroSep 2022View details →

Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long-term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two lab and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2-, 3-, 4- and 5-strains for hundreds of generations and asked which fitness related phenotypes – maximum growth rate or relative competitive fitness – would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long-term co-existence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multi-genotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long-term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.

opencc-zeroDec 2021View details →

Long-term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

The coastal wetland is easily invaded by alien species due to its location in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to community restoration and species diversity protection. To reveal the long-term S. alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariquete, ruderal and unvegetated site) and soil depths (0–5 cm and 5–10 cm) in the Chongming island coastal salt marsh wetland. The results showed that the soil seed bank richness and species density under different vegetation types were higher than aboveground vegetation, and those of 0–5 cm seed banks were higher than 5–10 cm, except for the unvegetated site. The species richness and the S. alterniflora seed proportion in the seed banks under the S. alterniflora communities (S.AS) were lower and larger, respectively, than other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0–5 cm and 5–10 cm depths were interpreted 3.03% and 2.25% by aboveground communities, while 4.92% and 5.55% were interpreted by soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks' richness at the 0–5 cm depth and 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks' species density at the 0–5 cm depth and 5–10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0–5 cm seed banks' richness and species density, while its height and biomass only affected the 5–10 cm seed banks' species density. The microbial biomass of the 0–10 cm soil depth indirectly affected the richness and species density of the 0-5 cm seed bank, and only affected the richness of the 5–10 cm seed bank. Soil physical and chemical properties only indirectly affected the 0–5 cm seed banks' species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China and guidance for the protection and restoration of the native plant communities.

opencc-by-4.0Oct 2022View details →

Simulated Long-Film image dataset

This dataset contains simulated 10,368 Long-Film images and vertebrae centroid labels from projection of public CT images. The CT images are from SpineWeb [1] and The Cancer Imaging Archive [2]. Details of usage and generation process can be found in [3]. [1]    B. Glocker, J. Feulner, A. Criminisi, D.R. Haynor, E. Konukoglu, Automatic localization and identification of vertebrae in arbitrary field-of-view CT scans., Med. Image Comput. Comput. Assist. Interv. 15 (2012) 590–8. https://doi.org/10.1007/978-3-642-33454-2_73. [2]    K. Clark, B. Vendt, K. Smith, J. Freymann, J. Kirby, P. Koppel, S. Moore, S. Phillips, D. Maffitt, M. Pringle, L. Tarbox, F. Prior, The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository., J. Digit. Imaging. 26 (2013) 1045–57. https://doi.org/10.1007/s10278-013-9622-7. [3]    Huang Y, Jones CK, Zhang X, Johnston A, Waktola S, Aygun N, Witham TF, Bydon A, Theodore N, Helm PA, Siewerdsen JH, Uneri A. "Multi-perspective region-based CNNs for vertebrae labeling in intraoperative long-length images." Computer Methods and Programs in Biomedicine, 2022 (under review)

opencc-by-nc-4.0Sep 2021View details →

Figure 1 in Breeding biology of Long-tailed Cinclodes Cinclodes pabsti Sick, 1969 (Passeriformes: Furnariidae)

Figure 1. Location of the study area in the region of Campos de Cima da Serra, southern Brazil.

opencc-by-4.0Oct 2022View details →

Methods for structural variant detection with long-read sequencing data

SV calls from different long-read based SV callers on sequencing data. SV results evaluated in Methods for structural variant detection with long-read sequencing data. NA24385_Pacbio_HiFi -> HiFi_L1 in paper NA24385_Pacbio_MtSinai -> CLR_L1 in paper NA24385_Pacbio_CLR_SRX7668835 -> CLR_L2 in paper NA24385_Pacbio_CLR_SRX6719924 -> CLR_L3 in paper NA24385_ONT_Promethion -> Nano_L1 in paper

opencc-zeroOct 2022View details →

Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main ABO allele groups: ABO*A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire ABO gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per ABO group were re-sequenced using Illumina and PacBio technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered four genetic variants putatively specific for ABO*A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

opencc-zeroOct 2022View details →

Data for: Estimating density dependence, environmental variance and long-term selection on a stage-structured life history

We model growth of a density-dependent stage-structured population undergoing small or moderate fluctuations around a deterministically stable equilibrium in a stochastic environment, assuming that a weighted sum of stage abundances, N, exerts density dependence on the stage-specific vital rates of survival and reproduction. We approximate the dynamics of N as a onedimensional stochastic process with three key parameters: the density-independent growth rate and the net density dependence and environmental variance in the life history. Comparisons of populations and species with different life histories are facilitated using the key parameters, which we show how to estimate from long-term demographic data on fluctuations in the vital rates. We also show that life history evolution is a stochastic maximization of a simple function of the key parameters. Elements in the long-term selection gradient acting on the life history can be expressed as sensitivities of this function with respect to density-independent, density-dependent, and stochastic components of the vital rates. Using years of demographic data on a great tit population, we estimate the key demographic parameters, which accurately predict the observed mean, coefficient of variation, and fluctuation rate of N, and also evaluate the long-term selection gradient on the population.

opennotspecifiedOct 2022View details →

FIGURE 2 in New genus and subgenus of South American long-horned bees (Apidae, Eucerini)

FIGURE 2. Savannychapis interrupta (Urban 1989): Female (Paratypus) in a) lateral and b) frontal views; specimen from Bahia, Brazil. Male in d) dorsal and e) frontal views; specimen from Mato Grosso, Brazil. g) detail of the three-segmented maxillary palpi, and h) sterna of male, to highlight the structure of S6 with two apicolateral carinae, not converging near the midline, and with basolateral depressions. Both specimens were studied by Dr. Danuncia Urban (DZUP) and used to confirm the identity of the vouchers included in the phylogenetic study subsidizing the proposal of the new genus. Scale bars = 2 mm.

opennotspecifiedOct 2022View details →

FIGURE 1 in New genus and subgenus of South American long-horned bees (Apidae, Eucerini)

FIGURE 1. Gaesischia (Gaesischioides) hyptidis (Ducke 1910): Female in a) lateral and b) frontal views. Male in c) lateral view, d) frontal view, e) sixtieth sterna (S6), and f) labrum. Specimens from Ceará, Brazil, studied by Danuncia Urban (DZUP) and used as references to confirm the identity of the vouchers used in the phylogenetic study subsidizing the proposal of this new taxon. Scale bars = 2 mm.

opencc-by-4.0Jul 2022View details →

How long is the last mile? Evaluating successful malaria elimination trajectories [Dataset]

Annual malaria case series were sought for 56 successful elimination programmes through an extensive non-systematic review of published and unpublished documents, including searches of PubMed (https://pubmed.ncbi.nlm.nih.gov/), Google Scholar (scholar.google.com), Google Books (books.google.com), WHO’s Institutional Repository for Information Sharing (https://apps.who.int/iris), online surveillance databases, and the authors’ existing collection of malaria-related books and reports. Several of these elimination programmes were implemented in regions that today have disputed jurisdictional claims or countries that no longer exist; their inclusion is to understand the impact of the historical programmes implemented there and no statement on their current geopolitical context is intended. When annual case totals were classified by origin, the number of locally acquired (i.e., autochthonous) cases was recorded separately from the number of imported cases. If not classified (as is typical until case incidence falls to very low levels), all reported cases were assumed to be locally acquired. Where locally acquired cases were further subclassified, indigenous and cryptic cases were tallied together, while introduced or induced cases were not included in case totals since such cases may arise sporadically in response to importation and are not considered to jeopardize elimination.  The first year in which zero indigenous or locally acquired cases were recorded was taken as the termination point of the case series, regardless of whether sporadic or resurgent local transmission occurred subsequently. While this definition of elimination is looser than that required for certification by WHO (i.e., three years with no indigenous transmission), it permits us to examine a wider range of elimination experiences, including some where success was not maintained. Secondary re-elimination efforts (where a year with zero local cases was achieved, malaria subsequently resurged, and then elimination was again achieved), as in the case of Mauritius or the former republics of the USSR, were not included.  Sources for the malaria case data are enumerated in the accompanying Word document. For questions or clarifications, please contact Justin Cohen at jcohen@clintonhealthaccess.org.

opencc-byFeb 2022View details →

Lowpoly Long Sword

Based in british sword from c. XIth century, probably saxon. Source: Objaverse 1.0 / Sketchfab