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Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker
<p>For more details see: http://iasreport.sanbi.org.za</p> <p>SANBI and CIB 2020. Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.3947799</p>
Data for: The impacts of bioenergy pine plantation management practices on bee communities
<p>1. Cultivation of bioenergy feedstocks is a growing land-use worldwide, yet we have a poor understanding of how bioenergy crop management practices affect biodiversity. This knowledge gap is particularly acute for candidate cellulosic bioenergy feedstocks, such as tree plantations, and for organisms that provide important ecosystem services, such as pollinators.</p> <p>2. We examined bee communities in 83 sites across three states in the southeastern USA—Alabama, Florida and Georgia. We compared bee abundance and diversity in 66 pine plantation sites that reflect management with and without potential bioenergy feedstock production. At least three bioenergy feedstock production methods have been proposed for this region: 1) converting conventional timber stands to short-rotation bioenergy plantations; 2) harvesting feedstock by thinning conventional plantations; and 3) harvesting of woody debris residues after plantations have been clear-cut.</p> <p>3. We found that bioenergy-associated management practices including younger plantations (relative to older) and woody debris removal (relative to debris unremoved) in clear-cut plantations were associated with reduced bee diversity. Removing ground debris in clear-cut plantations also drastically increased bee abundance, though this effect was largely driven by strong dominance of just two bee species. Clear-cut plantations had lower beta diversity than standing plantations.</p> <p>4. Synthesis and applications. Management practices associated with bioenergy feedstock production can have negative effects on bee community diversity. In particular, harvesting of debris in clear-cut plantations dramatically reduces bee diversity. Large-scale bioenergy feedstock production that increases the prevalence of young and clear-cut stands may cause landscape-level beta diversity to decline. Nevertheless, bioenergy pine plantations likely support higher bee diversity than corn fields, an alternative bioenergy feedstock.</p>
Data from: Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally-managed fields
<p>The structure and function of fungal communities in the coffee rhizosphere is shaped by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities in markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic or transitional management in two regions of Costa Rica. We amplified the ITS2 region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, more leaf litter, and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium than conventionally-managed fields, although differences between organic and conventionally-managed fields in shade, calcium and magnesium depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally-managed fields were also correlated with shade, soil acidity, nitrate, and copper. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse and plant pathogens were more abundant in organic than in conventionally-managed fields, while saprotroph-plant pathogens were more abundant in conventionally-managed fields. These differences reflected environmental differences and depended on region.</p> <p><b>IMPORTANCE</b></p> <p>Rhizosphere fungi play key roles in ecosystems, as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management shape rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but also maintains a greater richness of saprotrophic, plant pathogenic and mycoparasitic fungi that has implications for efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.</p>
Data from: Evaluating population viability and efficacy of conservation management using integrated population models
Predicting population responses to environmental conditions or management scenarios is a fundamental challenge for conservation. Proper consideration of demographic, environmental and parameter uncertainties is essential for projecting population trends and optimal conservation strategies. We developed a coupled integrated population model-Bayesian population viability analysis to assess the (1) impact of demographic rates (survival, fecundity, immigration) on past population dynamics; (2) population viability 10 years into the future; and (3) efficacy of possible management strategies for the federally endangered Great Lakes piping plover Charadrius melodus population. Our model synthesizes long-term population survey, nest monitoring and mark–resight data, while accounting for multiple sources of uncertainty. We incorporated latent abundance of eastern North American merlins Falco columbarius, a primary predator of adult plovers, as a covariate on adult survival via a parallel state-space model, accounting for the influence of an imperfectly observed process (i.e. predation pressure) on population viability. Mean plover abundance increased from 18 pairs in 1993 to 75 pairs in 2016, but annual population growth (math formula) was projected to be 0.95 (95% CI 0.72–1.12), suggesting a potential decline to 67 pairs within 10 years. Without accounting for an expanding merlin population, we would have concluded that the plover population was projected to increase (math formula = 1.02; 95% CI 0.94–1.09) to 91 pairs by 2026. We compared four conservation scenarios: (1) no proposed management; (2) increased control of chick predators (e.g. Corvidae, Laridae, mammals); (3) increased merlin control; and (4) simultaneous chick predator and merlin control. Compared to the null scenario, chick predator control reduced quasi-extinction probability from 11.9% to 8.7%, merlin control more than halved (3.5%) the probability and simultaneous control reduced quasi-extinction probability to 2.6%. Synthesis and applications. Piping plover recovery actions should consider systematic predator control, rather than current ad hoc protocols, especially given the predicted increase in regional merlin abundance. This approach of combining integrated population models with Bayesian population viability analysis to identify limiting components of the population cycle and evaluate alternative management strategies for conservation decision-making shows great utility for aiding recovery of threatened populations.
Public opinion about management strategies for a low-profile Species across multiple jurisdictions: whitebark pine in the northern Rockies
<p>1. As public land managers seek to adopt and implement conservation measures aimed at reversing or slowing the negative effects of climate change, they are looking to understand public opinion regarding different management strategies.</p> <p>2. This study explores drivers of attitudes toward different management strategies (i.e., no management, protection, and restoration) for a low-profile but keystone tree species, the whitebark pine (<i>Pinus albicaulis</i>), in the Greater Yellowstone Ecosystem. Since the whitebark pine species has a range that traverses different federal land designations, we examine whether attitudes toward management strategies differ by jurisdiction (i.e., wilderness or federal lands more generally).</p> <p>3. We conducted a web and mail survey of residents from Montana, Idaho, and Wyoming, with 1,617 valid responses and a response rate of 16%. <a name="_Hlk36455244"></a></p> <p>4. We find that active management strategies have substantially higher levels of support than does no management, with relatively little differentiation across protection and restoration activities or across different land designations. We also find that support for management strategies is not influenced by values (political ideology) but is influenced by beliefs (about material vs. post-material environmental orientation, global climate change, and federal spending for public lands) and some measures of experience (e.g., knowledge of threats).</p> <p>5. This study helps land managers understand that support for active management of the whitebark pine species is considerable and nonpartisan and that beliefs and experience with whitebark pine trees are important for support</p>
African wild dog dispersal and implications for management
Successful conservation of species that roam and disperse over large areas requires detailed understanding of their movement patterns and connectivity between subpopulations. But empirical information on movement, space use, and connectivity is lacking for many species, and data acquisition is often hindered when study animals cross international borders. The African wild dog (Lycaon pictus) exemplifies such species that require vast undisturbed areas to support viable, self‐sustaining populations. To study wild dog dispersal and investigate potential barriers to movements and causes of mortality during dispersal, between 2016 and 2019 we followed the fate of 16 dispersing coalitions (i.e., same‐sex group of ≥1 dispersing African wild dogs) in northern Botswana through global positioning system (GPS)‐satellite telemetry. Dispersing wild dogs covered ≤54 km in 24 hours and traveled 150 km to Namibia and 360km to Zimbabwe within 10 days. Wild dogs were little hindered in their movements by natural landscape features, whereas medium to densely human‐populated landscapes represented obstacles to dispersal. Human‐caused mortality was responsible for >90% of the recorded deaths. Our results suggest that a holistic approach to the management and conservation of highly mobile species is necessary to develop effective research and evidence‐based conservation programs across transfrontier protected areas, including the need for coordinated research efforts through collaboration between national and international conservation authorities.
Data from: Knowledge co-production with traditional herders on cattle grazing behaviour for better management of species-rich grasslands
The research gap between rangeland/livestock science and conservation biology/vegetation ecology has led to a lack of evidence needed for grazing-related conservation management. Connecting scientific understanding with traditional ecological knowledge of local livestock keepers could help bridge this research and knowledge gap. 1. We studied the grazing behaviour (plant selection and avoidance) of beef cattle (ca. 33 000 bites) on species-rich lowland pastures in Central Europe and traditional herding practices. We also did >450 outdoor interviews with traditional herders about livestock behaviour, herders' decisions to modify grazing behaviour, and effects of modified grazing on pasture vegetation. 2. We found that cattle grazing on species-rich pastures displayed at least 10 different behavioural elements as they encountered 117 forage species from highly desired to rejected. The small discrimination error suggests that cattle recognize all listed plants 'by species'. 3. We also found that herders had broad knowledge of grazing desire and they consciously aimed to modify desire by slowing, stopping or redirecting the herd. Modifications were aimed at increasing grazing intensity in less desired patches and decreasing grazing selectivity in heterogenous swards. 4. Synthesis and applications: These traditional herd management practices have significant conservation benefits, such as avoiding under- and overgrazing, and targeted removal of pasture weeds, litter and enchroaching bushes, tall competitive plants and invasive species. We argue that knowledge co-production with traditional herders who belong to another knowledge system could help connect isolated scientific disciplines especially if ecologists and rangeland scientists work closely with traditional herders, co-designing research projects and working together in data collection, analysis and interpretation. Stronger links between these disciplines could help develop evidence-based, specific conservation management practices while herders could contribute with their practical experiences and with real world testing of new management techniques.04-May-2020
Data from: Recognition of endophytic Trichoderma species by leaf-cutting ants and their potential in a Trojan-horse management strategy
Interactions between leaf-cutting ants, their fungal symbiont (Leucoagaricus) and the endophytic fungi within the vegetation they carry into their colonies are still poorly understood. If endophytes antagonistic to Leucoagaricus were found in plant material being carried by these ants, then this might indicate a potential mechanism for plants to defend themselves from leaf-cutter attack. In addition, it could offer possibilities for the management of these important Neotropical pests. Here, we show that, for Atta sexdens rubropilosa, there was a significantly greater incidence of Trichoderma species in the vegetation removed from the nests—and deposited around the entrances—than in that being transported into the nests. In a no-choice test, Trichoderma-infested rice was taken into the nest, with deleterious effects on both the fungal gardens and ant survival. The endophytic ability of selected strains of Trichoderma was also confirmed, following their inoculation and subsequent reisolation from seedlings of eucalyptus. These results indicate that endophytic fungi which pose a threat to ant fungal gardens through their antagonistic traits, such as Trichoderma, have the potential to act as bodyguards of their plant hosts and thus might be employed in a Trojan-horse strategy to mitigate the negative impact of leaf-cutting ants in both agriculture and silviculture in the Neotropics. We posit that the ants would detect and evict such 'malign' endophytes—artificially inoculated into vulnerable crops—during the quality-control process within the nest, and, moreover, that the foraging ants may then be deterred from further harvesting of 'Trichoderma-enriched' plants.
Data from: Plant demographic and functional responses to management intensification: a long-term study in a Mediterranean rangeland
1. Understanding how functional traits, which are key for plant functioning, relate to demographic parameters of populations is central to tackle pending issues in plant ecology such as the forecast of the fate of populations and communities in a changing world, the quantification of community assembly processes or the improvement of species distribution models. We addressed this question in the case of species from a Mediterranean rangeland of southern France. 2. Changes in species abundance in response to management intensification (fertilization and increased grazing pressure) were followed over a 28-year period. Probabilities of presence, and elasticities of the changes in the probability of space occupancy to colonization and survival, which are analogues of demographic parameters, were calculated for 53 species from the time series of abundance data using a space occupancy model. Nine quantitative traits pertaining to resource use, plant morphology, regeneration and phenology were measured on these species and related to demographic parameters. 3. The long-term dynamics of species in response to management intensification was associated with major changes in functional traits and strategies. Changes in the probability of occurrence – analogous to population growth rate - were correlated with traits describing the fast-slow continuum of leaf functioning. The elasticity of population growth rate to colonization was significantly related to reproductive plant height and seed mass, and to a lower extent, to leaf carbon isotopic ratio. 4. Synthesis. The functional response of species to management intensification corresponds to a shift along the second axis of a recently identified global spectrum of plant form and function, which maps, to some extent, onto the fast-slow continuum of life-history strategies. By contrast, the elasticity of colonization relates to the global spectrum axis capturing the size of organs. Seed mass contributes to this axis and is assumed to relate to one of the important traits structuring the reproductive strategy axis of life histories as well, namely net reproductive rate. While this mapping between functional and life-history traits is appealing, further tests in contrasting types of communities are required to assess its degree of generality.
Device Management Cycle
<p>While the IT sector is rocketing to yield piles of dollars for the corporates, it also faces threats which can doom the entire effort in a fraction of second. Yes! It is called security breach or data loss protection. Tech-savvy business people use their personal devices for work, employees are concerned that if they lose their device or if it gets stolen, company will wipe it clean to protect any sensitive company data. However, it's not sure whether personal things will stay intact. Now, it's not the job of a mobile device management (MDM) to see if a few personal pictures are lost, but it is also necessary to realize that end users do care, and as a result might attempt to circumvent the MDM to keep their personal contacts, photos, and other information safe.</p> <p>MDM suppliers are looking to secure smart devices from the application layer because of this shift in mentality to keep personal and corporate information separate. It’s a double-edged sword, because employers want an unobtrusive tool that doesn’t contain a lot of oversight but also allows IT to stay up-to-date on their organization’s security requirements.</p>
Training for RD Management: Comparative European Approaches, Raw data & Tidied Data
<p>Raw and tidied data of responses to the Knowledge Exchange survey around Training for Research Data management. The data accompanies the Knowledge Exchange report 'Training for RD Management: Comparative European Approaches' DOI: 10.5281/zenodo.50068</p> <p> </p>
Infusion Manager
<p>The oracle - a judge of the correctness of the system under test (SUT) - is a major component of the testing process. Specifying test oracles is challenging for some domains, such as real-time embedded systems, where small changes in timing or sensory input may cause large behavioral differences. Models of such systems, often built for analysis and simulation, are appealing for reuse as oracles. These models, however, typically represent an idealized system, abstracting away certain issues such as non-deterministic timing behavior and sensor noise. Thus, even with the same inputs, the model’s behavior may fail to match an acceptable behavior of the SUT, leading to many false positives reported by the oracle.</p> <p>We propose an automated steering framework that can adjust the behavior of the model to better match the behavior of the SUT to reduce the rate of false positives. This model steering is limited by a set of constraints (defining acceptable differences in behavior) and is based on a search process attempting to minimize a dissimilarity metric. This framework allows non-deterministic, but bounded, behavior differences, while preventing future mismatches, by guiding the oracle-within limits-to match the execution of the SUT. Results show that steering significantly increases SUT-oracle conformance with minimal masking of real faults and, thus, has significant potential for reducing false positives and, consequently, development costs.</p>
Research Data Management: The Numbers
<p>Infographic illustrating the numbers associated with research data management. In particular the associated costs, the value and the volume of data</p>
Experimental results of "Managing variant calling datasets the big data way"
<p>Tomatula was demonstrated for retrieving the allele frequencies for a given region in the data from Aflitos et al (2014). We developed scripts to retrieve allele frequencies, either from the VCF file storage or Apache Parquet. We executed a series of experiments, querying for a region of 2000 bases in the file of chromosome 6, that corresponds to the approximate length of a gene. We compared both storage formats (VCF files and Parquet), two input sizes (104 and 1144 individuals), different cluster sizes varying between 2 and 150 executor nodes, and HDFS replication factor was set to 3, 5, 7, and 9, in order to examine four main factors that<br> can affect the performance of a Big Data cluster: (a) the storage format, (b) the size of the input files, (c) the number of computing nodes of the cluster, and (d) the replication factor of HDFS. The block size of the HDFS was kept at the default value of 128MB. All experiments were executed five times and the detailed results are provided here, along with a script that produces the corresponding figures.</p>
Patterns in the appropriation of a learning management system by instructors based on Q-methodology: Dataset
<p>Anonymized dataset</p>
Data from: Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas
<div> <em>Culex quinquefasciatus</em> is mosquito species of significant public health importance due to its ability to transmit multiple pathogens that can cause mosquito-borne diseases, such as West Nile fever and St. Louis encephalitis. In Harris County, Texas, <em>Cx. quinquefasciatus</em> is a common vector species and is subjected to insecticide-based management by the Harris County Public Health Department. However, insecticide resistance in mosquitoes has increased rapidly worldwide and raises concerns about maintaining the effectiveness of vector control approaches. This concern is highly relevant in Texas, with its humid subtropical climate along the Gulf Coast that provides suitable habitat for <em>Cx. quinquefasciatus</em> and other mosquito species that are known disease vectors. Therefore, there is an urgent and ongoing need to monitor the effectiveness of current vector control programs. In this study, we evaluated the impact of vector control approaches by estimating the effective population size of <em>Cx. quinquefasciatus</em> in Harris County. We applied Approximate Bayesian Computation to microsatellite data to estimate effective population size. We collected <em>Cx. quinquefasciatus</em> samples from two mosquito control operation areas, 415 and 802, during routine vector monitoring in 2016 and 2017. No county mosquito control operations were applied at area 415 in 2016 and 2017, whereas extensive adulticide spraying operations were in effect at area 802 during the summer of 2016. We collected data for eighteen microsatellite markers for 713 and 723 mosquitoes at eight timepoints from 2016 to 2017 in areas 415 and 802, respectively. We also investigated the impact of Hurricane Harvey's landfall in the Houston area in August of 2017 on <em>Cx. quinquefasciatus</em> population fluctuation. Although we did not detect significant effects of vector control interventions, we found considerable influences of the winter season and a major hurricane on the effective population size of <em>Cx. quinquefasciatus</em>. The fluctuations in effective population size in both areas showed a significant seasonal pattern. Additionally, the significant population expansion following Hurricane Harvey in 2017 supports the necessity for post-hurricane vector-control interventions.</div>
Data Management Plan preliminary version (D1.3)
<p>First version of the Data Management Plan, to be updated twice in the project</p>
BBN designed to develop future land-use scenarios for the Sierra Nevada under different environmental and management conditions
<p>Land-use change (deforestation for crops and pastures, reforestation, firewood removal, etc.) constitutes one of the primary drivers of global change, since human activity is to a greater or lesser degree altering the vegetation cover of the planet. The combined effects of climate change and shifts in land use determine the distribution and structure of the vegetation of the Sierra Nevada, and the associated ecosystem services. The surface cover of tree formations in Sierra Nevada has expanded from 15% to 51.23% over the last 60 years. Similarly, a densification of the scattered tree cover and the natural forests and a decline in the surface area occupied by cultivated fields (from 17.8% to 4.72%) has occurred in the last six decades (Zamora, et al, 2016). Therefore, it is important to ascertain future land use change and its effects on the vegetation cover. </p><p>The main purpose of this model is to facilitate the land-use management of Protected Areas (PAs) based on ecosystem services (ES). A BBN is being designed to develop future land-use scenarios for the Sierra Nevada under different environmental and management conditions. Afterwards, we will implement these scenarios in other ES assessment models. The analysis of ES trade-offs in several scenarios will help managers to predict the state of ES and their relations in the future.</p>
Study of the overwintering ecology of the hazelnut pest, Palomena prasina (Hemiptera: Pentatomidae) in a perspective of Integrated Pest Management
<p class="MsoNormal"><em>Palomena prasina</em>, the green shield bug (GSB), is widely distributed in the Eurosiberian region. In the Southwest of France it is considered a serious pest of hazelnuts, its feeding punctures lead to blank hazelnuts and kernel necrosis, causing heavy losses in commercial orchards. To date, no Integrated Pest Management strategy is available to control <em>P. prasina</em>.</p> <p class="MsoNormal">Control strategies often focus on the pests' spring-summer ecology, when they are in the field or in the vicinity of crops. However, the abundance of pest populations in crops is also related to their autumn-winter ecology. The present work focussed on the autumn-winter ecology of <em>P. prasina</em> to identify new opportunities for this pest suppression. We investigate (i) where <em>P. prasina</em> overwinters, (ii) if it aggregates in its overwintering sites, and (iii) if it mates while overwintering. Samples were collected over a two-year period in different ecosystems (forests, hedges, orchards), in human-made structures, and habitats (litter, bushes/trees, dead trees). The reproductive status of GBS individuals was monitored in winter, and in spring when they emerged from overwintering sites.</p> <p class="MsoNormal">Our results show that 97% <em>P. prasina</em> adults overwinter in the leaf litter of orchards and natural ecosystems and that 70% overwinter individually. The abundance of GSB in those sites is negatively correlated with litter temperature and positively correlated with humidity levels. Furthermore, adults only mate after leaving their overwintering site. Finally, there was an important number of overwintering adults hosting endoparasitoids (32%).</p> <p class="MsoNormal">The fact that GSB overwinters alone in the leaf litter means controlling its populations by destroying the overwintering sites is not a solution. All the same, our results do open new perspectives for the control of <em>P. prasina</em>. First, the emergence traps, in particular the cone traps, proved efficient for collecting emerging adults and could be used for monitoring. Moreover, our observations point out the existence of long-range mating signals that could be exploited for trapping. Last but not least, the important number of overwintering parasitised adults is a promising biocontrol avenue.</p>
[VERSION 2] Data set and analytic codes supporting "How do management decisions impact butterfly assemblages in smallholding oil palm plantations in Peninsular Malaysia?"
<p>This is <strong>VERSION 2</strong> of data set and analytic codes (with a meta data [see the meta data from VERSION 1]) supporting "How do management decisions impact butterfly assemblages in smallholding oil palm plantations in Peninsular Malaysia?". We investigated the impacts of replanting and alternative replanting decisions (replanting with monoculture versus polyculture oil palm plantations) on within-plantation environmental conditions and butterfly assemblages (diversity, density, and composition). We also assessed the effects of habitat structure and complexity within plantations on butterfly assemblages. Apart from "BantingButterflies_ButterflyData", other data are the same as in VERSION 1.</p><p><strong>## List of changes:</strong></p><p># 1. <i>Tirumala septentrionis </i>was not included in the analyses because it should have been <i>Ideopsis vulgaris</i> (had been corrected),</p><p># 2. PC5 and PC6 (from PCA) were considered as predictors for the GLMs,</p><p># 3. The Mantel test was added.</p><p><strong>## Other notes:</strong></p><p># 1. Older version of ggiNEXT could work with facet.var = "site", now it needs to be "Assemblage"</p><p># 2. Older version of ggiNEXT could work with facet.var = "order", now it needs to be "Order.q"</p><p># 3. "set.seed(42)" function was used before running "iNEXT", ANOSIM, and the Mantel test to get reproducible outputs (exactly the same outputs every time each function is run).</p><p><strong>Funding and research permission:</strong> Jardine Foundation, the Cambridge Trust, and Tim Whitmore Fund provided funding for MFH, the Biotechnology and Biological Sciences Research Council (BBSRC) funded JS (USN: 304338625), and BBSRC (BB/T012366/1) provided funding for the establishment of the plots and surveys of environmental parameters. Research permission was provided by the Economic Planning Unit (EPU) of Malaysia's Prime Minister's Department for MFH (Ref: EPU 40/200/19/3727) and JS (Ref: MEA 40/200/19/3705).</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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