Proprietary Restrictions Research Articles

Survival Analysis Without Sharing of Individual Patient Data by Using a Gaussian Copula.

Cox regression and Kaplan-Meier estimations are often needed in clinical research and this requires access to individual patient data (IPD). However, IPD cannot always be shared because of privacy or proprietary restrictions, which complicates the making of such estimations. We propose a method that generates pseudodata replacing the IPD by only sharing non-disclosive aggregates such as IPD marginal moments and a correlation matrix. Such aggregates are collected by a central computer and input as parameters to a Gaussian copula (GC) that generates the pseudodata. Survival inferences are computed on the pseudodata as if it were the IPD. Using practical examples we demonstrate the utility of the method, via the amount of IPD inferential content recoverable by the GC. We compare GC to a summary-based meta-analysis and an IPD bootstrap distributed across several centers. Other pseudodata approaches are also considered. In the empirical results, GC approximates the utility of the IPD bootstrap although it might yield more conservative inferences and it might have limitations in subgroup analyses. Overall, GC avoids many legal problems related to IPD privacy or property while enabling approximation of common IPD survival analyses otherwise difficult to conduct. Sharing more IPD aggregates than is currently practiced could facilitate "second purpose"-research and relax concerns regarding IPD access.

Climate data from the Rocky Mountain Biological Laboratory (1975-2022).

The Rocky Mountain Biological Laboratory (RMBL) (Colorado, USA) is the site for many research projects spanning decades, taxa, and research fields from ecology to evolutionary biology to hydrology and beyond. Climate is a focus of much of this work and provides important context for the rest. There are five major sources of data on climate in the RMBL vicinity, each with unique variables, formats, and temporal coverage. These data sources include 1) RMBL resident billy barr, 2) the National Oceanic and Atmospheric Administration (NOAA), 3) the United States Geological Survey (USGS), 4) the United States Department of Agriculture (USDA), and 5) Oregon State University's PRISM Climate Group. Both the NOAA and the USGS have automated meteorological stations in Crested Butte, CO, approximately 10 km from the RMBL while the USDA has an automated meteorological station on Snodgrass Mountain, approximately 2.5 km from the RMBL. Each of these data sets has unique spatial and temporal coverage and formats. Despite the wealth of work on climate-related questions using data from the RMBL, previous researchers have each had to access and format their own climate records, make decisions about how to handle missing data, and recreate data summaries. Here we provide a single curated climate data set of daily observations covering the years 1975 to 2022 that blends information from all five sources and includes annotated scripts documenting decisions for handling data. This synthesized climate data will facilitate future research, reduce duplication of effort, and increase our ability to compare results across studies. The data set includes information on precipitation (water and snow), snowmelt date, temperature, wind speed, soil moisture and temperature, and stream flows, all of which are publicly available from a combination of sources. In addition to the formatted raw data, we provide several new variables that are commonly used in ecological analyses, including growing degree days, growing season length, a cold severity index, hard frost days, an index of El Niño-Southern Oscillation, and aridity (standardized precipitation evapotranspiration index). These new variables are calculated from the daily weather records. As appropriate, data are also presented as minima, maxima, means, residuals, and cumulative measures, for a variety of time scales including days, months, seasons, and years. The Rocky Mountain Biological Laboratory is a global research hub. Scientists on-site at the RMBL come from many countries and produce about 50 peer-reviewed publications each year, researchers from around the world also routinely make use of data from the RMBL for synthetic work, and educators around the United States use data from RMBL for teaching modules. This curated and combined data set will be of use to a wide audience. Along with the synthesized combined data set we include the raw data and the R code for cleaning the raw data and creating the monthly and yearly data sets, which facilitate adding additional years or data using the same standardized protocols. No copyright or proprietary restrictions are associated with the use of this data set; please cite this data paper when the data are used in publications or scientific events.

Nutrient and stoichiometric time series measurements of decomposing coarse detritus in freshwaters.

Decomposition of coarse detritus (e.g., dead organic matter larger than ~1 mm such as leaf litter or animal carcasses) in freshwater ecosystems is well described in terms of mass loss, particularly as rates that compress mass loss into one number (e.g., a first-order decay coefficient, or breakdown rate, 'k'); less described are temporal changes in elemental composition of these materials during decomposition, with important implications for elemental cycling from microbes to ecosystems. This stands in contrast to work in the terrestrial realm, where a focus on detrital elemental cycling has provided a sharper mechanistic understanding of decomposition, especially with specific processes such as immobilization and mineralization. Notably, freshwater ecologists often measure carbon (C), nitrogen (N), and phosphorus (P), and their stoichiometric ratios in decomposing coarse materials, including carcasses, wood, leaf litter, and more, but these measurements remain piecemeal. These detrital nutrients are measurements of the entire detrital-microbial complex and are integrative of numerous processes, especially nutrient immobilization and mineralization, and associated microbial growth and death. Thus, data relevant to an elemental, mechanistically-focused decomposition ecology are available in freshwaters, but have not been fully applied to that purpose. We synthesized published detrital nutrient and stoichiometry measurements at a global scale, yielding 4038 observations comprising 810 decomposition time series (i.e., measurements within a defined cohort of decomposing material through time) to build a basis for understanding the temporality of elemental content in freshwater detritus. Specifically, the dataset focuses on temporally and ontogenetically (mass loss)-explicit measurements of N, P, and stoichiometry (C:N, C:P, N:P). We also collected ancillary data, including detrital characteristics (e.g., species, lignin content), water physiochemistry, geographic location, incubation system type, and methodological variables (e.g., bag mesh size). These measurements are important to unlocking mechanistic insights into detrital ontogeny (the temporal trajectory of decomposing materials) that can provide a deeper understanding of heterotroph driven C and nutrient cycling in freshwaters. Moreover, these data can help bridge aquatic and terrestrial decomposition ecology, across plant or animal origin. By focusing on temporal trajectories of elements, this dataset facilitates cross-ecosystem comparison of fundamental decomposition controls on elemental fluxes and provides a strong starting point (e.g., via modeling efforts) for comparing processes such as immobilization and mineralization that are understudied in freshwaters. Time series from decomposing leaf litter, particularly in streams, are common in the dataset, but we also synthesized ontogenies of animal-based detritus, which tend to decompose rapidly compared to plant-based detritus which contains high concentrations of structural compounds such as lignin and cellulose. Although animal-based data were rare, comprising only three time series, their inclusion in this dataset underscores opportunities to develop an understanding of decomposition that encompasses all detrital types, from carrion to leaf litter. There are no copyright or proprietary restrictions on the dataset; please cite this data paper when reusing these materials.

MSR57 Survival Analysis without Sharing of Individual Person Data: An Antidote to “Data Available upon Request”?

Cox regression and Kaplan-Meier estimates are often needed in post-approval clinical research which requires access to individual person data (IPD). Think about a long-term treatment-effect review or a comparative effectiveness oncology study involving the IPD owned by a competitor. Here, IPD cannot always be shared due to privacy or proprietary restrictions, which complicates the making of such estimates. I propose a method that generates pseudodata replacing the IPD by only using non-disclosive IPD aggregates which are shared with a central computer and are input parameters to a Gaussian copula (GC) generating the pseudodata, allowing analysts to access completely anonymised versions of possibly multiple datasets on which to run analyses.

Comparing outcomes with the cloud-based and portable versions of an open-source hearing aid

The open-source speech processing platform (OSP) is an open-source hearing aid (HA), developed to overcome proprietary restrictions of commercial HAs and pave the way for innovative HA technology through rigorous and reproducible research. This study evaluates portable and cloud-based platforms of the OSP that will enable a wide range of lab and field applications. The two platforms share common software applications for HA signal processing and objective outcome assessments (HO2). The cloud-based platform is hosted on a web server whereas the portable platform is accessed on a browser via a WiFi-enabled portable communication device. Listeners with mild to moderately severe hearing loss or normal hearing completed a word identification task (Modified Rhyme Test) in a 6-alternate forced choice paradigm using the HO2 app. Words were mixed with different levels of speech-shaped noise; presented via calibrated headphones or behind-the-ear receivers-in-the-canal for cloud-based and portable platforms, respectively. Signals were processed with individualized gain and compression ratios based on a clinically validated prescriptive formula. Results-to-date from four listeners show comparable range of word identification scores between platforms. The full dataset will also compare phoneme-level scores and response time measures generated from the HO2 app. Clinical research applications will be discussed. [Work supported by NIH-R44DC020406.]

Integrated evidence-based extent of occurrence for North American bison (Bison bison) since 1500CE and before.

Following the near extinction of bison (Bison bison) from its historic range across North America in the late 19th century, novel bison conservation efforts in the early 20th century catalyzed a popular widespread conservation movement to protect and restore bison among other species and places. Since Allen's initial delineation (1876) of the historic distribution of North American bison, subsequent attempts have been hampered by knowledge gaps about bison distribution and abundance prior to and following colonial arrival and settlement. For the first time, we applied a multidisciplinary approach to assemble a comprehensive, integrated geographic database and meta-analysis of bison occurrence over the last 200,000years, with particular emphasis on the 450years before present. We combined paleontology, archaeology, and historical ecology data for our database, which totaled 6438 observations. We derived the observations from existing online databases, published literature, and first-hand exploration journal entries. To illustrate the conservative maximum historical extent of occurrence of bison, we created a concave hull using observations occurring over the last 450years (n=3379 observations), which is the broadly accepted historical benchmark at 1500CE covering 59% of the North American continent. Although this distribution represents a historic extent of occurrence-merely delineating the maximum margins of the near-continental distribution-it does not replace a density-based approach reconstructing potential historical range distributions, which identifies core and marginal ranges. However, we envision the observations contained in this database will contribute to further research in the increasingly evidence-based disciplines of bison ecology, evolution, rewilding, management, and conservation. There are no copyright or proprietary restrictions on these data, and this data paper should be cited when the data are reused.

Utkin et al.'s dataset on specific leaf area.

Specific leaf area (SLA; one-sided leaf area per unit of dry mass) is a key trait indicating plant growth strategy and its responses to changing environments. Despite its high relevance for ecological research and recent efforts to mobilize the trait data, information on SLA in many plant lineages and biogeographic regions is still underrepresented. To assist in closing this gap, we translated and digitized a large dataset on SLA titled the Surface areas of forest plants by Anatoly I. Utikin, Lyudmila S. Ermolova, and Irina A. Utkina, published in Russian in 2008 (Nakua, Moscow, Russia) and previously not accessible to the great majority of people in the international research community. The book contains a compendium of SLA values collected by A. Utkin and his colleagues published between 1918 and 2006 containing research on ~1100 gymnosperm species from 562 genera and 139 families. Additionally, Utkin et al. provided useful information on the SLA ranges and SLA responses to changing illumination for several species. Also, the dataset contains ~200 references to research on SLA conducted between 1918 and 2006. The dataset is ready to use in various trait analyses. There are no copyright or proprietary restrictions for research or teaching purposes. The authors would appreciate notification when and how the data are used.

VTMaxHerp: A data set of voluntary thermal maximum temperatures of amphibians and reptiles from two Brazilian hotspots.

Amphibians and reptiles are ectothermic animals and therefore depend on environmental temperatures to maintain their physiological functions. Despite being poorly documented, data on thermal behavioral thresholds to avoid overheating in their habitats are essential to improve the understanding of their thermal ecology and physiology. Here we provide a data set of 312 individual voluntary thermal maximum (VTMax ) values, the maximum temperature tolerated by individuals before actively moving to a colder place, for 53 species of amphibians and reptiles of the Atlantic Forest and Cerrado savannas of southeastern South America. Voluntary thermal maximum values were recorded as the body temperature at which the individuals exited a heating box experimental setup. This data set comprises 25 species of 15 genera and eight families of amphibians and 28 species of 24 genera and 12 families of reptiles. Of the total number of individual records, 67.9% derived from the Cerrado and 32.0% derived from the Atlantic Forest ecoregions. Overall, lizards had higher VTMax than amphibians and snakes, and individuals in the Atlantic Forest had overall higher VTMax values than the ones in Cerrado. This data set is the first to compile VTMax values for South American herpetofauna, along with detailed experimental information such as heating rates and time to reach VTMax . This data set provides a baseline for understanding thermal tolerances and requirements of Neotropical ectothermic vertebrate species, which might be useful for future research on the impact of climate change and to test novel ecological hypotheses. There are no copyright or proprietary restrictions except that this data paper should be cited when data are used for publications. In addition, the authors would appreciated being informed of research projects or teaching purposes when these data are used.

Documenting pollinators, floral hosts, and plant-pollinator interactions in U.S. Pacific Northwest agroecosystems.

The abundance and diversity of pollinator populations are in global decline. Managed pollinator species, like honey bees, and wild species are key ecosystem service providers in both natural and managed agroecosystems. However, relatively few studies have exhaustively characterized pollinator populations in diverse agroecosystems over multiple years, while also thoroughly documenting plant-pollinator interactions. Yet, such studies are needed to fulfill the national pollinator protection plans that have been released by the United States and other nations. Our research is among the first studies to respond to these directives by systematically documenting bee and plant biodiversity, bee-plant interactions, and bee-mediated pollen movement in farming systems of the Pacific Northwest, USA. Our data provides insight into the processes mediating pollinator and plant community assembly, persistence, and resilience across landscapes with variable crop and landscape diversity and agroecosystem management practices. These data will also contribute to the development of a United States pollinator database, supporting the United States' plan to promote pollinators. With few publicly available data sets that systematically take account of agroecosystem practices, plant populations, and pollinators, our research will provide future users the means to conduct synesthetic studies of pollinators and ecosystem function in a period of rapid and global pollinator declines. There are no copyright or proprietary restrictions for research or teaching purposes. Usage of the data set must be cited.

ATLANTIC POLLINATION: a data set of flowers and interaction with nectar-feeding vertebrates from the Atlantic Forest.

Flowering plant species and their nectar-feeding vertebrates exemplify some of the most remarkable biotic interactions in the Neotropics. In the Brazilian Atlantic Forest, several species of birds (especially hummingbirds), bats, and non-flying mammals, as well as one lizard feed on nectar, often act as pollinators and contribute to seed output of flowering plants. We present a dataset containing information on flowering plants visited by nectar-feeding vertebrates and sampled at 166 localities in the Brazilian Atlantic Forest. This dataset provides information on 1902 unique interactions among 515 species of flowering plants and 129 species of potential vertebrate pollinators and the patterns of species diversity across latitudes. All plant-vertebrate interactions compiled were recorded through direct observations of visits, and no inferences of pollinators based on floral syndromes were included. We also provide information on the most common plant traits used to understand the interactions between flowers and nectar-feeding vertebrates: plant growth form, corolla length, rate of nectar production per hour in bagged flowers, nectar concentration, flower color and shape, time of anthesis, presence or absence of perceptible fragrance by human, and flowering phenology as well as the plant's threat status by International Union for Conservation of Nature (IUCN) classification. For the vertebrates, status of threat by IUCN classification, body mass, bill or rostrum size are provided. Information on the frequency of visits and pollen deposition on the vertebrate's body is provided from the original source when available. The highest number of unique interactions is recorded for birds (1771) followed by bats (110). For plants, Bromeliaceae contains the highest number of unique interactions (606), followed by Fabaceae (242) and Gesneriaceae (104). It is evident that there was geographical bias of the studies throughout the southeast of the Brazilian Atlantic Forest and that most effort was directed to flower-hummingbird interactions. However, it reflects a worldwide tendency of more plants interacting with birds compared with other vertebrate species. The lack of similar protocols among studies to collect basic data limits the comparisons among areas and generalizations. Nevertheless, this dataset represents a notable effort to organize and highlight the importance of vertebrate pollinators in this hotspot of biodiversity on Earth and represents the data currently available. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or scientific events.

DAMA: the global Distribution of Alien Mammals database.

We developed the DAMA (Distribution of Alien Mammals) database, a comprehensive source reporting the global distribution of the 230 species of mammals that have established self-sustaining and free-ranging populations outside their native range due to direct or indirect human action. Every alien range is accompanied by information on its invasion stage, pathway, method of introduction, and date of introduction. We collected information from 827 different sources (scientific literature, books, risk assessments, reports, online biodiversity databases and websites), and used it to draw alien range maps for these species following the IUCN mapping framework. DAMA comprises 2,726 range polygons, covering 199 countries, 2,190 level 1 administrative areas, and 11 zoogeographic realms for the period 21500 BC-AD 2017. The most represented orders among introduced mammal species are Rodentia (n = 58, 25.22%), Cetartiodactyla (n = 49 species, 21.30%), Carnivora (n = 30 species, 13.04%), Diprotodontia (n = 28, 12.17%), and Primates (n = 26, 11.30%). Mammal species have been frequently introduced for hunting (n = 100), pet trade (n = 57), conservation (n = 51), and fauna improvement (n = 42). The majority of range polygons are placed on islands (n = 2,196, 80.56%), encompass populations that have moved beyond establishment and into the invasion stage (n = 1,655, 60.71%), and originated from 1500 AD to the present (n = 1,496, 54.88%). Despite inheriting literature biases towards more studied regions (e.g., developed countries), DAMA is the most up-to-date picture of alien mammal global distribution and can be used to investigate their invasion ecology across different biogeographical regions. There are no copyright or proprietary restrictions; IUCN range maps were modified into a derivative work according to the IUCN's terms of service.

CASA: An Alternative Smartphone-Based ADAS

Advanced driving assistance system (ADAS) is an electronic system that helps the driver navigate roads safely. A typical ADAS, however, is suited to specific brands of vehicle and, due to proprietary restrictions, has non-extendable features. Project CASA is an alternative, low-cost generic ADAS. It is an app deployable on smartphone or tablet. The real-time data needed by the app to make sense of its environment are stored in the vehicle or on the cloud, and are accessible as web services. They are used to determine the current driving context, and, if needed, decide actions to prevent an accident or keep road navigation safe. Project CASA is an undertaking of a consortium of industrial and academic partners. A use case scenario is tested in the laboratory (virtual) and on the road (actual) to validate the appropriateness of CASA. It is a contribution to safe driving. CASA’s contribution also lies in its approach in the semantic modeling of the context of the environment, the vehicle and the driver, and on the modeling of rules for fusion of data and fission process yielding an action to be implemented. In addition, CASA proposes a secured means of transmitting data using light, via light fidelity (LiFi), itself an alternative means of wireless vehicle–smartphone communication.

Multi-tissue and multi-isotope (δ13 C, δ15 N, δ18 O and 87/86 Sr) data for early medieval human and animal palaeoecology.

Human isotopic ecology at its core aims to study humans as a part of their environments, as animals within an ecosystem. We are complex animals with complicated foodways and mobility patterns that are hard to address without large multifaceted data sets. As biomolecular data from archaeological remains proliferates scientists are now at the stage where we are able to collate large bodies of data and undertake complex meta-analyses and address the complexities of human ecology and past socioenvironmental dynamics. Here we present a data set of 862 entries of new primary isotopic data (37 faunal bone, 235 human enamel carbonate with a subset of 18 for 87/86 Sr, 347 human bone, 243 human bulk dentine) within a larger data set compiled from available legacy data. It contains a total of 8,910 isotopic entries from ancient humans and animals relating to diet and mobility from the late Roman period into the Middle Ages (c. 400-1200 AD). It includes carbon, nitrogen, oxygen, and strontium isotope ratios from human bone, human dentine, faunal bone, and human bioapatite from thousands of individuals, and hundreds of sites found across 26 modern countries in western Europe. Studies have previously focused on only one of these aspects, compiling data sets for one tissue, or common isotopic pairing, or focusing on a particular site or region at a smaller scale for multi-isotope multitissue studies. This is the largest and first multitissue, multi-isotope, multiproxy data set of its kind from premodern populations. In publishing this data set, we hope to inspire more synthetic and meta-analytical work on human isotopic ecology. Insights from these data should lead to greater understanding of diet, agriculture, climate change, human-animal interactions, mobility/migration, and much more in the past. It is hoped that these insights into past socioenvironmental dynamics will help inform current discourse on human-environmental interactions. There are no copyright or proprietary restrictions on the data; these data papers should be cited when these data are used in publications. Additionally, we would like to hear from other researchers who use these data sets in teaching or for their own research.

COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.

The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits, and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life habit, phenology, behavior, home range, and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.

Life-history traits, geographical range, and conservation aspects of reef fishes from the Atlantic and Eastern Pacific.

Reef fish represent one of the most diverse vertebrate groups on Earth, with over 7,000 species distributed around the globe. This richness is not evenly distributed geographically. The Atlantic (AT) and the Eastern Pacific (EP) encompass 30% of the global fish fauna. These areas have been considered the most isolated from the marine biodiversity hotspot in the Indo-Pacific due to distinct physical barriers, such as the Tethyan closure and the distance between the EP and the western Pacific. Despite their comparatively lower species richness, these realms host unique fish assemblages characterized by a remarkable proportion of regional endemics and species with large body size. Here, we present the largest database of life-history traits and biogeographical and conservation aspects presently available for the reef fish fauna of the AT and the EP realms. The database includes 21 traits distributed into behavioral (home range, diel activity, group size, level in the water column, three measures of preferred temperature), morphological (maximum body size, size class, body shape, aspect ratio, caudal fin, mouth position), and ecological (trophic level, diet, spawning strategy, depth of occurrence, two allometric constants, pelagic larval duration, and life span), as well as biogeographical (geographic range index, range extension, species distribution in 20 marine provinces, latitude north and south of occurrence, total number of provinces where species occur, occurrence in the AT and EP), and conservation aspects (IUCN status, vulnerability and global market price). We compiled these data through a careful review of 104 local checklists published between 1982 and 2020, online repositories, local reports, books, and monographs on specific families or genera. We limited our database to localities situated between latitudes 51°N and 45°S that including shallow and upper mesophotic biogenic and/or rocky reefs habitats. Our database covers 2,198 species belonging to 146 families and 655 reef fish genera distributed in two marine realms (1,458 in the AT, 829 in the EP, and 89 in both realms) and 20 marine provinces. This database of reef fish offers the opportunity to explore novel ecological and evolutionary questions at different scales and provides tools for species conservation based on these traits. There are no copyright or proprietary restrictions for research or teaching purposes.

Soil dynamics in forest restoration: a data set for temperate and tropical regions.

Restoring forest ecosystems has become a global priority. Yet, soil dynamics are still poorly assessed among restoration studies and there is a lack of knowledge on how soil is affected by forest restoration process. Here, we compile information on soil dynamics in forest restoration based on soil physical, chemical, and biological attributes in temperate and tropical forest regions. It encompasses 50 scientific papers across 17 different countries and contains 1,469 points of quantitative information of soil attributes between reference (e.g., old-growth forest) and restored ecosystems (e.g., forests in their initial or secondary stage of succession) within the same study. To be selected, studies had to be conducted in forest ecosystems, to include multiple sampling sites (replicates) in both restored and reference ecosystems, and to encompass quantitative data of soil attributes for both reference and restored ecosystems. We recorded in each study the following information: (1) study year, (2) country, (3) forest region (tropical or temperate), (4) latitude, (5) longitude, (6) soil class, (7) past disturbance, (8) restoration strategy (active or passive), (9) restoration age, (10) soil attribute type (physical, chemical, or biological); (11) soil attribute, (12) soil attribute unit, (13) soil sampling (procedures), (14) date of sampling, (15) soil depth sampled, (16) soil analysis, (17) quantitative values of soil attributes for both restored and reference ecosystems, (18) type of variation (standard error of deviation) for both restored and reference ecosystems, and (19) quantitative values of the variation for both restored and reference ecosystems. These were the most common data available in the selected studies. This extensive database on the extent soil physical, chemical, and biological attributes differ between reference and restored ecosystems can fill part of the existing gap on both soil science and forest restoration in terms of (1) which are the critical soil attributes to be monitored during forest restoration? and (2) how do environmental factors affect soil attributes in forest restoration? The data will be made available to the scientific community for further analyses on both soil science and forest restoration. Soil information gaps during the forest restoration process and their general patterns can be addressed using this data set. There are no copyright or proprietary restrictions.

The body size and temperature dependence of organismal locomotion.

The speed and maneuverability of organisms are central to their fitness, determining the strength and outcome of many species interactions that drive population and community-level processes. While locomotion is influenced by many internal and external factors, body size and temperature are two key factors governing organismal locomotion. Biologists have been measuring locomotor performance, particularly maximum speed, for over a century. Studies have tended to focus on single species or groups of species that are either phylogenetically related, functionally similar, or use the same habitat. Few studies compare locomotor performance across a diverse range of taxa or locomotor modes, very few have incorporated locomotor traits other than maximum speed, and the data are not accessible in a single database with standardized units. Here, we present a data set we compiled from the literature that contains 2,951 measurements of locomotor performance for five traits (exploratory speed, maximum speed, maximum acceleration, minimum powered turn radius, and maximum angular speed) that are important in the daily lives of many organisms. This represents the most diverse and comprehensive database on animal locomotion yet published and includes 884 species spanning 23 orders of magnitude of body size. Together with body size (mass and length) and temperature (body and ambient), we also provide data on trophic group and habitat (aerial, terrestrial, aquatic). In publishing our data set, we hope to encourage others to contribute to a continued effort to build this locomotion database and to analyze these data for underlying patterns. Interspecific analyses can help elucidate how organismal locomotion varies with important morphological and physiological traits and environmental conditions, revealing generalities and deviations in organismal locomotion. Additionally, intraspecific analyses, which are possible for a number of species in our data set, can help corroborate these patterns and deviations and explore potential mechanisms that could underlie these patterns. Insights from these analyses should uncover drivers of locomotor performance and contribute to an understanding about how locomotion shapes ecological processes across scales. There are no copyright or proprietary restrictions, except this data paper should be cited when data are used for publication. In addition, we would appreciate hearing for which research projects or teaching exercises these data are used.

Nikolaeva et al.'s reference book on seed dormancy and germination.

Despite the recent advances in seed science research, information on seed dormancy and germination traits is still missing for many lineages of the seed plants. We translated and digitized a huge data set on seed dormancy and germination from the Reference Book On Dormant Seed Germination by M. Nikolaeva, M. Razumova, and V. Gladkova published in Russian in 1985 and previously not readily accessible to the great majority of people in the international scientific community interested in seeds. The data set contains information on the seed dormancy classification (sensu Nikolaeva et al., 1985; Baskin and Baskin, 2004), dormancy-breaking conditions/germination, and for some of the included species storage behaviour, of seeds of nearly 3000 gymnosperm and angiosperm species from 843 genera and 164 families occurring worldwide. Additionally, the data set contains about 550 references, many of them unknown to seed scientists, to seed ecology research conducted between 1926 and 1985. The data set should be of value to applied, basic, and theoretical plant biologists, ecologists, and evolutionary biologists interested in the various aspects of regeneration of plants from seeds. There are no copyright or proprietary restrictions for research or teaching purposes. The originator of the data would appreciate notification when and how the data are used. When used in published analyses, this paper should be referred to as the data source.

Trees of Amazonian Ecuador: a taxonomically verified species list with data on abundance and distribution.

We compiled a data set for all tree species collected to date in lowland Amazonian Ecuador in order to determine the number of tree species in the region. This data set has been extensively verified by taxonomists and is the most comprehensive attempt to evaluate the tree diversity in one of the richest species regions of the Amazon. We used four main sources of data: mounted specimens deposited in Ecuadorian herbaria only, specimen records of a large-scale 1-hectare-plot network (60 plots in total), data from the Missouri Botanical Garden Tropicos® database (MO), and literature sources. The list of 2,296 tree species names we provide in this data set is based on 47,486 herbarium records deposited in the following herbaria: Alfredo Paredes Herbarium (QAP), Catholic University Herbarium (QCA), Herbario Nacional del Ecuador (QCNE), Missouri Botanical Garden (MO), and records from an extensive sampling of 29,768 individuals with diameter at breast height (dbh) ≥10cm recorded in our plot network. We also provide data for the relative abundance of species, geographic coordinates of specimens deposited in major herbaria around the world, whether the species is native or endemic, current hypothesis of geographic distribution, representative collections, and IUCN threat category for every species recorded to date in Amazonian Ecuador. These data are described in Metadata S1 and can be used for macroecological, evolutionary, or taxonomic studies. There are no copyright restrictions; data are freely available for noncommercial scientific use (CC BY 3.0). Please see Metadata S1 (Class III, SectionB.1: Proprietary restrictions) for additional information on usage.

CauseSpec: a database of global terrestrial vertebrate cause-specific mortality.

As wildlife populations continue to decline worldwide, human-caused mortality of terrestrial vertebrates is of increasing importance. However, there is a limited understanding of how direct anthropogenic mortality compares in magnitude to natural mortality. Here, we present CauseSpec, a database of global terrestrial vertebrate cause-specific mortality. We compiled studies that used telemetry to monitor terrestrial vertebrates and determine cause of death. We distinguished between anthropogenic and natural mortality and also documented the specific mortality source where possible (e.g., harvest, vehicle collision, predation, and starvation). This database consists of 1,134 studies that collectively monitored the fates of 123,747 individual animals. From this, there are 43,998 deaths of known cause among 307 species. It is an updated version of the data set used in Hill etal. (2019) and will continue to be updated in the future. These data can be combined with data on species morphology and behavior to examine how species attributes influence susceptibility to various mortality sources. Our database also includes the geographic coordinates of the study site so that site attributes can be included in analyses. We also distinguish between adults and juveniles where possible, allowing for age-specific mortality analyses. Study start and end dates are available as well so that analyses of temporal changes in mortality are possible. Last, users can select all cause-specific mortality studies from a single species to perform a species-level analysis. The data set will allow users to circumvent a literature search, facilitating more rapid publication of large-scale vertebrate mortality studies and elucidating mortality patterns of terrestrial vertebrates around the world. There are no copyright or proprietary restrictions. We would like researchers to cite this paper if the associated database is used to find studies of interest for analysis.