Find research datasets worth reusing

opencc-zeroSep 2021View details →

Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of ex-situ and in-situ populations of B. insularis using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex-situ and in-situ populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the in-situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in-situ one, which is crucial for considering a reintroduction process into the island.

opencc-zeroSep 2021View details →

Data from: Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity

The long-term contribution of nitrification to nitrous oxide (N2O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2O, we test the relative importance of nitrification-derived N2O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2O fluxes was 13-17% in a conventionally fertilized annual cropping system, 27-42% in a low-input cover-cropped annual cropping system, and 52-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be less than 10% of these values because of low N2O yields in cultured nitrifiers (typically 0.04 to 8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2O was produced by ammonia oxidizing bacteria (AOB) rather than archaea (AOA), who appeared responsible for no more than 30% of nitrification-derived N2O production in all but one ecosystem. Although the proportion of nitrification-derived N2O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2O (higher Vmax) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2O in all ecosystems examined.

opencc-by-4.0Sep 2021View details →

Dataset (n=1671) of the publication "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes"

The excel file contains the replies of small-scale private forest owners in Lower Saxony, Germany, to certain questions of a survey analyzed within the following publication: "Small-scale private forest owners and the European Natura 2000 conservation network: Perceived ecosystem services, management practices, and nature conservation attitudes”. The questions included in this dataset cover their objectives, management activities, attitudes and forest stand structures. Further details can be found in the second sheet of the file called “Code explanation”. More information about the methods of data collection can be found in the before-mentioned publication.

opencc-by-4.0Oct 2021View details →

Tecolutla´s Solid waste management system surveys

The Tecolutla´s solid waste management system was evaluated thoughtout surveys aplied to diferent population sectors in three areas.

opencc-by-4.0Oct 2021View details →

Introduction to Research Data Management for Ecologists Distributed Graduate Seminar

This video was made to introduce students who had registered for the Spring 2021 Research Data Management for Ecologists distributed graduate seminar that was offered at Florida International University, University of New Mexico, and University of Wisconsin, Madison.

opencc-by-4.0Jun 2021View details →

Dependency Management Bots in Open-Source Systems - Prevalence and Adoption

This is a re-analysis package for the paper: Dependency Management Bots in Open-Source Systems - Prevalence and Adoption. The package includes scripts and processed data collected from GitHub about five investigated dependency management bots: Dependabot, Depfu, Greenkeeper, Pyup and Renovate.

Data for the article "Management of social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study"

Data for the paper "Social behaviour of domestic yaks in Manang, Nepal: an etho-ethnographic study". ANimated GIFs, GPS data, activity data and proximity data. Herdsmen use different techniques, as per varying geographies and cultures, to keep the cohesion within herds and avoid animals getting lost or predated. However, there is no study on the social behaviour of yaks and on herdsmen management practices. Therefore, this ethology study was initiated by ethnographic inquiries. We collected data from two herds living at the same settlement (Yak kharka, 4,100 m altitude, Nepal) by equipping them with loggers. One of the herdsman used the tether rope while other did not. Moreover, the Thaku herd had a more proactive shepherd than the Phurba one. In each herd, 17 animals were equipped with one actigraph wgt3x-BT to measure activity using accelerometer and spatial associations using proximity recorder. One of the herds was equipped with GPS (N=11) as well. Using GPS locations and activity, we showed that the two herds were cohesive and synchronised their activities but the herd with the tether rope was more cohesive.

Verification of the effects of a YouTube-based home-based (self-managed intervention) training system developed for frailty prevention―A pilot study ―

Background and Objectives: Resistance training is considered the most effective intervention for increasing older people’s muscle mass and strength. We devised a self-administered training system (squat + balance training, sukubara®) that incorporates a new low-load exercise. This study hypothesizes that introducing sukubara® affects skeletal muscle mass and physical function positively, and we first conducted a preliminary verification in healthy non-elderly participants. Materials and Methods: This study’s participants were non-elderly healthy hospital personnel. Applicants were randomly assigned to two groups, a resistance training group that performed an exercise program (sukubara®) and a control group that did not, and they received a 12-week intervention. This study’s primary endpoint was change in skeletal muscle mass; the secondary endpoints were knee extension strength and one-leg standing time with eyes closed. Results:  An analysis of Tthe 18 participants (10 in the resistance training group and 8 in the control group), who were 18 analyzed this study’s results was performed. The results of changes in variables between both groups during the intervention period were as follows: skeletal muscle mass, knee extension strength, and one-leg standing time were significantly improved or tended to be significantly higher in a resistance training group than in a control group. Conclusions: A self-administered training system (sukubara®) incorporating low-load exercise resulted in muscle hypertrophy and improvement in physical function.

Data for: Evaluating Golden-winged Warbler use of alder and aspen communities managed with shearing in the western Great Lakes

Best management practices are often written by researchers to guide land managers and landowners in the creation of habitat for wildlife species of interest. These documents are based on research evaluating the habitat needs of a species, but also describe tools and strategies managers can implement to create or restore desired conditions. Shrub and sapling shearing is a management practice often used to improve habitat for early-successional species, yet little monitoring or research has focused on wildlife response to shearing. The goal of this research was to formally evaluate the effect of shrub and sapling shearing as a best management strategy for Golden-winged Warbler (Vermivora chrysoptera) conservation at a regional scale. Specifically, we surveyed for male Golden-winged Warblers during the breeding season in sheared sites and untreated reference sites across portions of the western Great Lakes to assess the effects of 1) management status (i.e., sheared aspen or alder vs un-treated sites), and 2) the patch-level vegetation characteristics on male abundance. We found that male Golden-winged Warbler abundance was twice as high in sheared sites than in mature reference sites and peaked when sapling cover was ~40%. Male abundance was also negatively associated with percent cover of forbs and non-vegetated ground. These findings highlight the importance of patch-level heterogeneity when implementing shearing treatments for Golden-winged Warblers, and demonstrate the potential need for pre-treatment site assessments to help focus conservation efforts for this species. Ultimately, our results support the use of a site-specific, nuanced approach to shearing implementation to maximize cost efficiency and desired species outcomes.

Diagnostic algorithm for surgical management of limbal stem cell deficiency

Supplementary material (tables) for the article entitled "Diagnostic algorithm for surgical management of limbal stem cell deficiency".

Identity and density of parasite exposures alter the outcome of co-infections: Implications for management

1) Although research has focused on density-dependent responses of hosts to single-parasite infections, hosts are exposed to numerous parasites simultaneously under natural conditions and if these exposures lead to infections, they can threaten host populations and ecosystem stability. Moreover, spatiotemporal variation in abundance of co-occurring parasites might influence host infection intensity. If interactions are consistent between different co-infecting parasites, then these patterns could give managers another tool to control disease spread and even predict problematic disease emergences. 2) We investigated how parasite density and identity alter within-host co-infection dynamics. To test this, we simultaneously exposed Cuban treefrogs (Osteopilus septentrionalis) as a model amphibian species to all pairwise combinations of three problematic parasites that commonly co-infect amphibians: the fungus Batrachochytrium dendrobatidis (Bd), the nematode Aplectana hamatospicula, and Ranavirus. Hosts were exposed to one parasite at a fixed dose and another parasite at a range of five doses. 3) Higher doses of Bd decreased Ranaviral and A. hamatospicula loads, but Bd load was not influenced by the dose of either parasite. Ranaviral load was negatively associated with A. hamatospicula dose, but A. hamatospicula load was not affected by Ranaviral dose. We found that all the pairwise co-infections were dependent on parasite density and that pairwise interactions were highly asymmetric – strong in one direction and weak in the other – consistent with interactions dominating food webs. 4) Synthesis and applications: We also revealed that the exposure dose of A. hamatospicula was positively associated with host tolerance to Bd infection and negatively associated with Ranaviral load in hosts. Ranavirus and Bd cause mass die-offs in amphibians, but A. hamatospicula does not. Therefore, in systems where these parasites coexist, maintaining or increasing densities of A. hamatospicula could reduce the negative effects of Bd and Ranavirus infections. Additionally, if these asymmetric and density dependent patterns from community ecology are applicable to other amphibian co-infections or co-infections in other systems, this should allow conservation organizations and resource managers to predict outbreaks and manage host declines associated with deadly parasites by modifying the abundance of co-infecting parasites that might be easier to manage.

Data set for "Landscape-variability of the carbon balance across managed boreal forests"

This data set is a compilation of biometric- and chamber-based annual CO2 flux estimates obtained during the period 2016–2018. Data were collected in 50 main forest stands within the Krycklan Catchment Study (KCS, https://www.slu.se/Krycklan), a multi-scale long-term monitored boreal catchment spanning 68 km2 in northern Sweden. Seven additional old forest stands were also included with the aim to reconcile our CO2 flux estimates for the old age class. Selected forest stands encompassed different landscape attributes: 1) soil type (i.e., sediment and till), 2) dominant tree species (i.e., pine and spruce), and 3) stand age class (i.e., initiation, young, middle-aged, mature, and old stands). Annual CO2 fluxes included are the following: net ecosystem production (NEP), net primary production (NPP), net primary production of trees (NPPt), net primary production of understory (NPPu) as well as total heterotrophic respiration (RH) and its soil and dead wood components (RHs and RHdw, respectively). All component CO2 fluxes are presented as positive terms, whereas positive and negative NEP refers to net C sink and source, respectively. It also includes a set of potential abiotic and biotic drivers controlling NEP and its component fluxes at the landscape-scale. This data set is composed of three Microsoft Excel worksheets: readme, metadata, and data. More details can be found in Peichl et al. (2022) Landscape-variability of the carbon balance across managed boreal forests. Global Change Biology, 00, 1–14. https://doi.org/10.1111/gcb.16534. Contact information: Professor Matthias Peichl (<a href="mailto:matthias.peichl@slu.se">Matthias.Peichl@slu.se</a>) Ph.D. Eduardo Martínez García (<a href="mailto:eduardo.martinez@slu.se">Eduardo.Martinez@slu.se</a>, <a href="mailto:edu.martinez.garcia@gmail.com">edu.martinez.garcia@gmail.com</a>) Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd 17, SE-901 83, Umeå, Sweden

Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas

Tropical savannas are characterised by high primary productivity and high fire frequency, such that much of the carbon captured by vegetation is rapidly returned to the atmosphere. Hence, there have been suggestions that management-driven reductions in savanna fire frequency and/or severity could significantly reduce greenhouse gas emissions and sequester carbon in tree biomass. However, a key knowledge gap is the extent to which savanna tree biomass will respond to modest shifts in fire regimes due to plausible, large-scale management interventions. Here, we: (1) characterise relationships between the frequency and severity of fires and key demographic rates of savanna trees, based on long-term observations in vegetation monitoring plots across northern Australia; (2) use these relationships to develop a process-explicit demographic model describing the effects of fire on savanna tree populations; and (3) use the demographic model to address the question: to what extent is it feasible, through the strategic application of prescribed burning, to increase tree biomass in Australian tropical savannas? Our long-term tree monitoring dataset included observations of 12,344 tagged trees in 236 plots, monitored for between 3 and 24 years. Analysis of this dataset showed that frequent high-severity fires significantly reduced savanna tree recruitment, survival and growth. Our demographic model suggested that: (1) despite the negative effects of frequent high-severity fires on demographic rates, savanna tree biomass appears to be suppressed by only a relatively small amount by contemporary fire regimes, characterised by a mix of low- to high-severity fires; and (2) plausible, management-driven reductions in the frequency of high-severity fires are likely to lead to increases in tree biomass of about 11.0 t DM ha–1 (95% confidence interval: -1.2–20.8) over a century. Accounting for this increase in carbon storage could generate significant carbon credits, worth on average three times those generated annually by current greenhouse gas (methane and nitrous oxide) abatement projects, and has the potential to significantly increase the economic viability of fire/carbon projects, thereby promoting ecologically sustainable management of tropical savannas in Australia and elsewhere. This growing industry has the potential to bring much-needed economic activity to savanna landscapes, without compromising important natural and cultural values.

A Scalable Data Management System Data Model facilitating the integration of any inspection system and the automated data digitalization process.

In the context of the EU-funded project PILOTING (No. 871542), a scalable Data Management System (DMS) was deployed and facilitated the easy integration of nine different robotic systems and various payloads and the storing of all the data observations produced during the inspections. In particular, a three-phase methodology was adopted for the creation of the DMS Data Model (DMS-DM) in order to define the architectural design of the DMS.  The first phase was to semantically define the entities of the PILOTING ecosystem, identifying assets and activities that were important to the data providers, and including them in the data model design. The second phase was to identify relationships between the entities, focusing on information that must pre-exist for entities to be semantically accurate, hierarchies between entities, especially physical assets, and the data needed to form the inspection plan. For the third phase, the information collected by the previous two stages of the data model construction was used to create the overall data model, taking into consideration the possible integration with third parties and the needs of the I&M Visualization portal.  The constructed document is attempted to present the designed Entity-Relationship-Diagram (ERD) of the DMS-DM. Additional definitions of the existing entities and the relations between them are also depicted.

A Versatile and Secure Data Management System API facilitating the Interconnection of any software component and Easy Data Access.

In the context of the EU-funded project PILOTING (No. 871542), a versatile Data Management System (DMS) was deployed and facilitated the easy integration of nine different robotic systems and various payloads and the storing of all the data observations produced during the inspections. The DMS is designed under the DMS-Data Model (DMS-DM) and operates on top of a representational state transfer (REST) application programming interface (API) that provides a simplified way to exchange data through HTTP(S) requests from a client to the server. One of its key advantages is that it provides a great deal of flexibility so the model could accommodate extensions if needed. Data is not tied to resources or methods, so REST can handle multiple types of calls, return different data formats and even change structurally with the correct implementation of hypermedia.  It supports CRUD operations via GET, POST, PUT, PATCH, and DELETE HTTP methods and stores the data on a PostgreSQL object-relational database system. The REST API has been created with Python's Django (web framework) and Django REST Framework, a powerful and flexible toolkit for building Web APIs.  The constructed document presents the communication endpoints (DMS API’s Uniform Resource Identifiers (URIs)) under which an authorized user can have access to the DMS API and subsequently to the collected data.

Green Space Management - Urban Green as perceived by citizens

This dataset contains the results, as csv file, of the monitoring surveys of green space management as perceived by citizens. The resources will be 1) results from first survey (summer 2021) and 2) results from the 2nd survey (TBD). Some of the most interesting columns in the results Column 9 ("Quartiere") is the residential area of the citizen. Column 10 ("Indirizzo"), when available, is the street where the citizen lives Column 11, ("Freq_parco"), when available, is the frequency with which the citizen visit a green area/park in the town Column 18, ("Distanza_parco"), when available, is the distance in minutes to reach a park

Data for: A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism's genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact of this issue and provide a common starting place for new research. Genotyping-in-thousands (GTSeq) is one approach used to create standardized marker panels for non-model organisms. Here we describe the development, optimization, and early assessments of a new GTSeq panel for use with walleye (Sander vitreus) from the Great Lakes region of North America. High genome-coverage sequencing conducted using RAD-capture provided genotypes for thousands of single nucleotide polymorphisms (SNPs). From these markers, SNP and microhaplotype markers were chosen that were informative for genetic stock identification (GSI) and kinship analysis. The final GTSeq panel contained 500 markers, including 197 microhaplotypes and 303 SNPs. Leave-one-out GSI simulations indicated that GSI accuracy should be greater than 80% in most jurisdictions. The false positive rates of parent-offspring and full-sibling kinship identification was found to be low. Finally, genotypes could be consistently scored among separate sequencing runs >94% of the time. Results indicate that the GTSeq panel that we developed should perform well for multijurisdictional walleye research throughout the Great Lakes region.

opencc-zeroDec 2022View details →

Data for: The role of landscape in shaping bird community and implications for landscape management at Nanjing Lukou International Airport

Understanding the patterns of bird diversity and its driving force is necessary for bird strike prevention. In this study, we investigated the effects of landscape attributes on phylogenetic and functional diversity of bird communities at Nanjing Lukou International Airport (NLIA). Bird identifications and counting of individuals were carried out from November 2017 to October 2019. Based on the land cover data, the landscape was divided into four main types, including farmlands, woodlands, wetlands and urban areas. Bird phylogenetic and functional diversity were strongly affected by landscape matrix types. Bird species, phylogenetic and functional richness were highest in woodlands, while phylogenetic and functional structure were most complex in wetlands. We found that related carnivorous birds occupied most niches at the NLIA. Moreover, bird assemblages exhibited phylogenetic and functional clustering in all landscape matrix types, which meant environmental filtering governed community assembly. Landscape attributes of different matrix types influenced phylogenetic and functional diversity of bird communities. Landscape diversity affected bird functional structure positively, and the mean of patch area in the landscape had the strongest explanatory effects. To prevent bird strikes, we suggest that more small-area woodlands with low levels of aggregation can be considered and farmlands should be patchier and more regular. At landscape level, the number of patches can be adjusted to reduce the frequency of bird activities.

opencc-zeroDec 2022View details →

Evaluating livestock farmers' knowledge, beliefs, and management of arboviral diseases in Kenya

Globally, arthropod-borne virus (arbovirus) infections continue to pose substantial threats to public health and economic development, especially in developing countries. In Kenya, although arboviral diseases (ADs) are largely endemic, little is known about the factors influencing livestock farmers' knowledge, beliefs, and management (KBM) of the three major ADs: Rift Valley fever (RVF), dengue fever and chikungunya fever. This study evaluates the drivers of livestock farmers' KBM of ADs from a sample of 629 respondents selected using a three-stage sampling procedure in Kenya's three hotspot counties of Baringo, Kwale, and Kilifi.