Find research datasets worth reusing

FIGURE 8 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 8 | Proportion of abstracts dealing with each Chondrichthyan order (number in parenthesis) on the Chondrichthyan Tree of Life cladogram (www.sharksrays.org, Naylor, 2022).

FIGURE 7 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 7 | Percentage, per event, of first authors' home institution regarding each of the five Brazilian regions: green, Northern (N); brown, Northeastern (NE); red, Midwestern (M); orange, Southeastern (SE); blue, Southern (S). EBI, Encontro Brasileiro de Ictiologia; SBEEL, Encontro da Sociedade Brasileira para o Estudo de Elasmobrânquios; ISPCNF, International Symposium on Phylogeny and Classification of Neotropical Fishes.

FIGURE 4 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 4 | Women as last authors in each event throughout the years. Blue circle = EBI (Encontro Brasileiro de Ictiologia), red square = SBEEL (Encontro da Sociedade Brasileira para o Estudo de Elasmobrânquios), yellow triangle = ISPCNF (International Symposium on Phylogeny and Classification of Neotropical Fishes). Continuous lines represent the data every two years.

FIGURE 1 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 1 | Research area per event over the years. EBI, Encontro Brasileiro de Ictiologia; SBEEL, Encontro da Sociedade Brasileira para o Estudo de Elasmobrânquios. ECO: Ecology, EVO: Evolution; PHY: Physiology, Others: Other research areas.

FIGURE 3 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 3 | At least one woman vs. no woman in authorship per event throughout the years. Blue circle = EBI (Encontro Brasileiro de Ictiologia), red square = SBEEL (Encontro da Sociedade Brasileira para o Estudo de Elasmobrânquios), yellow triangle = ISPCNF (International Symposium on Phylogeny and Classification of Neotropical Fishes); green cross, no woman. Continuous lines represent the data every two years.

FIGURE 2 in Three decades of Chondrichthyan research in Brazil assessed from conferences' abstracts: patterns, gaps, and expectations

FIGURE 2 | Proportion of abstracts with Chondrichthyan Systematics within Evolution (EVO) per event throughout the years. Blue circle = EBI (Encontro Brasileiro de Ictiologia), red square = SBEEL (Encontro da Sociedade Brasileira para o Estudo de Elasmobrânquios), yellow triangle = ISPCNF (International Symposium on Phylogeny and Classification of Neotropical Fishes). Continuous lines represent the data every two years.

opencc-by-4.0May 2019View details →

DATA FOR STUDY OF PRIVACY ATTITUDE OF USERS OF SOCIAL NETWORKING SITES AND THEIR EXPECTATIONS FROM LAW IN INDIA

<p>In the present study, on Indian population a disproportionate, stratified, purposive, convenience mixed sampling technique has been adopted in order to ensure proper representation of all the stakeholders concerned with regard to the issue of data privacy in India among the population of the study. The stratified sampling technique is popularly used for a large size population and where it is desirable to purposively have an adequate representation of the all the sub-groups. It is estimated that there are about 0.2 million Law Enforcement Officers (Directors General of Police to Assistant Sub- Inspector), 2.2 million Legal Professionals, including 21,586 Judges, 1.5 million Academicians, about 5000 Information Assurance and Privacy Experts, and 450 million Internet Users in India, out of which 196 million use SNSs. It may be clarified here that all these stakeholders are not only the users of social networking sites but also Indian citizens who are stakeholders in enactment and implementation of the privacy law as and when it is enacted.</p> <p>Based on the size of the total population, a statistically adequate sample size of 385, having a 95 per cent Confidence Level, 5 per cent Margin of Error (Confidence Interval), 0.5 Standard Deviation, a 1.96 Z-score was calculated.</p> <p> </p> <p> </p> <p> </p>

opencc-zeroDec 2021View details →

Data for: Resetting our expectations for parasites and their effects on species interactions: A meta-analysis

<p>Despite the ubiquitous nature of parasitism, how parasitism alters the outcome of host species interactions such as competition, mutualism, and predation remain unknown. Using a phylogenetically informed meta-analysis of 154 studies, we examined how the mean and variance in the outcomes of species interactions differed between parasitized and non-parasitized hosts. Overall, parasitism did not significantly affect the mean or variance of host species interaction outcomes, nor did the shared evolutionary histories of hosts and parasites have an effect. Instead, there was considerable variation in outcomes, ranging from strongly detrimental to strongly beneficial for infected hosts. Trophically-transmitted parasites increased the negative effects of predation, parasites increased and decreased the negative effects of interspecific competition for parasitized and non-parasitized heterospecifics, respectively, and parasites had particularly strong negative effects on host species interactions in freshwater and marine habitats, yet were beneficial in terrestrial environments. Our results illuminate the diverse ways in which parasites modify critical linkages in ecological networks, implying that whether the cumulative effects of parasitism are considered detrimental depends not only on the interactions between hosts and their parasites, but also on the many other interactions that hosts experience.</p>

opencc-zeroNov 2022View details →

Expectation-Maximization enables phylogenetic dating under a Categorical Rate Model

<div> <div> <div> <p>Dating phylogenetic trees to obtain branch lengths in the unit of time is essential for many downstream applications but has remained challenging. Dating requires inferring mutation rates that can change across the tree. While we can assume to have information about a small subset of nodes from the fossil record or sampling times (for fast-evolving organisms), inferring the ages of the other nodes essentially requires extrapolation and interpolation. Assuming a clock model that defines a distribution over rates, we can formulate dating as a constrained maximum likelihood (ML) estimation problem. While ML dating methods exist, their accuracy degrades in the face of model misspecification where the assumed parametric statistical clock model vastly differs from the true distribution. Notably, existing methods tend to assume rigid, often unimodal rate distributions. A second challenge is that the likelihood function involves an integral over the continuous domain of the rates and often leads to difficult non-convex optimization problems. To tackle these two challenges, we propose a new method called Molecular Dating using Categorical-models (MD-Cat). MD-Cat uses a categorical model of rates inspired by non-parametric statistics and can approximate a large family of models by discretizing the rate distribution into k categories. Under this model, we can use the Expectation-Maximization (EM) algorithm to co-estimate rate categories and branch lengths in the time unit. Our model has fewer assumptions about the true clock model than parametric models such as Gamma or LogNormal distribution. Our results on two simulated and real datasets of Angiosperms and HIV and a wide selection of rate distributions show that MD-Cat is often more accurate than the alternatives, especially on datasets with nonmodal or multimodal clock models.</p> </div> </div> </div>

opencc-by-4.0Apr 2023View details →

SPEAC Webinar: Use of background rates for observed / expected analysis

<p>The SPEAC team organized a webinar on April 24th, 2023, focused on the use of background rates for observed/expected analysis. The webinar featured three presentations, followed by a Q&A session. More details:</p> <ul> <li>Background rates of AESI for COVID-19, how have they been used? by Miriam Sturkenboom (SPEAC) - [00:00 - 10: 58]</li> <li>FDA COVID-19 vaccine safety surveillance: Use of background rates and observed/expected analyses by Brendan Day (US FDA-CBER) - [10:58 - 23:58]</li> <li>COVID-19 vaccines: Observed-to-expected analyses by Maria Gordillo Maranon and Catherine Cohet (EMA) -  [23:58 - 23:58]</li> <li>Q&A - [39:57 - 58:59]</li> </ul> <p>The recording can be accessed below. </p>

opencc-by-4.0Feb 2023View details →

Farmers' expectations and acceptance of new technologies involved in circular agriculture at the farm level

<table> <tbody> <tr> <td>Dataset description </td> <td>Data correspond to 149 farmers from four EU countries (Spain, Italy, Croatia, and the Czech Republic). This database contains information about farmer characteristics, farm structural characteristics, and farm management, and also contains preferences and attitudinal constructs (such as agribusiness objectives, and environmental attitudes and opinions) and variables related to questions about the potential adoption of the proposed innovations</td> </tr> <tr> <td>Collection</td> <td> Data was collected online from March to August 2021, using a survey instrument, administered to farmers face to face.</td> </tr> <tr> <td>Utility</td> <td>The data provides insight into farmer acceptance of five different circular agricultural innovations designed to reduce nutrient loss at the farm level and focused on improving environmental sustainability.</td> </tr> </tbody> </table> <p> </p> <p> </p>

opencc-zeroJul 2023View details →

Male sexual signaling and expected effects of hatchery-induced sperm competition vary with water depth at which whitefish are caught

<div> <div> <div> <div> <p>Salmonids like whitefish (<em>Coregonus</em> spp.) are often propagated in supportive breeding. Spawners are caught from their spawning locations, their gametes mixed, and the resulting offspring reared in a protected environment before being released into the wild. This procedure can affect sexual selection, for example, by enhancing the importance of sperm competition or by reducing the relevance of sexual signals. While it is often unclear how sperm competitiveness is affected by a male's overall genetic quality, there is accumulating evidence that sexual signals reveal good genes and that mate choice based on such signals can increase offspring viability (Auld et al. 2019). Therefore, supportive breeding may affect the genetic variance and the mean genetic quality of next generations. We sampled whitefish from various locations along a depth gradient to test how male characteristics that are likely to affect sexual selection under natural conditions correlate with characteristics that affect hatchery-induced sperm competition. Whitefish are external fertilizers, and multi-male spawning and hence sperm competition is common under natural conditions. Mate choice is not sufficiently understood but could be based on breeding tubercles. These are small conical structures that grow on scales before the breeding sea- son and fall off shortly afterwards. The size of breeding tubercles varies much among males and has repeatedly been found to correlate positively with offspring viability (Wedekind et al. 2001; Keka ̈la ̈inen et al. 2010). Male dominance is typically depend- ent on body size (Auld et al. 2019) and could also be relevant in whitefish. Body size itself can reflect individual inbreeding coefficients (Su et al. 1996) and be an indicator of heritable genetic quality in small or structured populations (Neff and Pitcher 2008). In another fish with a somewhat comparable mating system, the size of breeding tubercles and male size was not correlated but could both be used to predict male reproductive success under close to natural conditions (Jacob et al. 2009). We study whitefish from Lake Hallwil (Switzerland). This lake has suffered so much from anthropogenic eutrophication that it is being artificially aerated since 1985. Three hatcheries around the lake are likely to have played a key role in maintaining the whitefish population, as concluded also from a recent mark–recapture experiment (Vonlanthen 2015). However, eutrophication combined with possible hybridization in hatcheries can have led to a speciation reversal (Vonlanthen et al. 2012) and may thereby have destroyed any genetic structure linked to water depth. Hatchery protocols now focus on maintaining over-all genetic variance by pooling milt of many males before adding the mix to eggs of multiple females. Milt volume varies among sires, for example, because males often lose milt when being pulled up from deep locations (Figure 1), an effect that likely depends on how much the swim bladder is inflated by the change in pressure. This variance in milt volume is likely to affect the genetic variance that, in combination with the average genetic quality, may then affect the long-term survival of a population. The extent to which hatchery protocols affect genetic quality can be estimated by the correlations between male quality indicators and traits that affect hatchery-induced sperm competition, that is, sperm number, velocity, and longevity (summarized here as "milt potency," see also Supplementary Material). Many breeding protocols are likely to promote genetic quality if male attractiveness or dominance are positively correlated to milt potency. If there are no such correlations or negative ones because of life-history trade-offs, hatchery-induced sperm competition is likely to reduce the average genetic quality in future generations. We sampled fish from various depths and determined their age, size, breeding ornamentation, and milt potency (see methods in the Supplementary Material) to test whether and how different male characteristics affect reproductive success in supportive breeding in a heavily managed population.</p> </div> </div> </div> </div>