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Benchmark maps of 33 years of secondary forest age for Brazil
<p><strong>Title: </strong>Benchmark maps of 33 years of secondary forest age for Brazil</p> <p><strong>Contact:</strong> Celso H. L. Silva Junior (celsohlsj@gmail.com)</p> <p> </p> <p><strong>Data:</strong> Increment (Product 1), Extent (Product 2), Loss (Product 3), and Age (Product 4) of Brazilian Secondary Vegetation</p> <p><strong>Coverage:</strong> Brazil land</p> <p><strong>Period:</strong> 1986 to 2018 (1987 to 2018 for secondary forest loss)</p> <p><strong>Spatial resolution:</strong> 30-meters</p> <p><strong>Temporal resolution:</strong> Annual</p> <p><strong>Coordinate reference system:</strong> Geographic Coordinate System with Datum WGS84</p> <p><strong>File format:</strong> 131 zip files per year (being 33 for increment, 33 for extent, 33 for age and 32 for loss). Each zip file containing eight tiles in compressed TIFF format.</p> <p><strong>Code:</strong> <a href="https://github.com/celsohlsj/gee_brazil_sv">https://github.com/celsohlsj/gee_brazil_sv</a></p> <p><strong>Dataset usage</strong>: It is free to use, but if you use this dataset in your work, please make sure to cite the repository and our paper properly. We also welcome users to invite us for collaboration.</p> <p><strong>For the use of this dataset, please cite: </strong>Silva Junior, C.H.L., Heinrich, V.H.A., Freire, A.T.G., Broggio, I.S., Rosan, T.M., Doblas, J., Anderson, L.O., Rousseau, G.X., Shimabukuro, Y.E., Silva, C.A., House, J.I., Aragão, L.E.O.C. Benchmark maps of 33 years of secondary forest age for Brazil. Scientific Data (2020). <a href="https://doi.org/10.1038/s41597-020-00600-4">https://doi.org/10.1038/s41597-020-00600-4</a></p>
Data from: An Early Devonian actinostelic euphyllophyte with secondary growth from the Emsian of Gaspé (Canada) and the importance of tracheid wall thickening patterns in early euphyllophyte systematics
<p>Secondary growth is a tracheophyte structural feature whose earliest known occurrence dates to the late Pragian-early Emsian. <i>Armoricaphyton</i>, <i>Franhueberia</i> and an unnamed plant from eastern Canada represent the only instances of secondary growth documented to date for the Early Devonian. Here, we describe a new Early Devonian euphyllophyte exhibiting secondary growth, from the Emsian (c. 400-395 Ma) Battery Point Formation (Québec, Canada): <i>Gmujij</i> <i>tetraxylopteroides</i> gen. et sp. nov. is characterized by a mesarch actinostele with <i>Psilophyton</i>-type (P-type) tracheid wall thickenings and exhibits a new type of anatomical organization among Early Devonian wood-producing euphyllophytes. <i>Gmujij</i> differs from coeval euphyllophytes, but lack of data on branching patterns, reproductive structures and other traditional diagnostic features preclude classification among previously recognized euphyllophyte groups. We experiment with a numerical approach to tracheid size distributions, to compare <i>Gmujij</i> with younger euphyllophytes exhibiting secondary growth. Comparisons show similarity between <i>Gmujij</i> and aneurophytalean progymnosperms, such as <i>Tetraxylopteris</i>. However, its plesiomorphic P-type tracheids set apart<i> Gmujij</i> from younger actinostelic euphyllophytes, raising questions on the importance of tracheid thickening patterns as diagnostic characters separating major lineages. Answers to this question hinge on whether transitions between wall thickening patterns require simple or complex changes in developmental regulation, a matter that requires improved understanding of regulatory programs that determine tracheid thickening patterns. Irrespective of these, <i>Gmujij</i> adds a new component to the diversity of anatomically preserved plants known in the Early Devonian, an incompletely explored interval of tracheophyte anatomical diversification, contributing information that will help understanding of the evolutionary origins of secondary growth.</p>
Data from - Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal
<p>Data from "Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal" published in <em>Ecology </em>in 2020. doi.org/10.1002/ecy.3192</p>
Predicted secondary structures (2-D representation of this self-folding) of the terminal untranslated regions (UTR) of FvMV1 and FaMV1-162
<p>Schemes (a) and (c) represent the 5`-UTR and 3`-UTR of FvMV1 with dG = -82.52 and dG = -29.55, respectively. Schemes (b) and (d) represent the 5`-UTR and 3`-UTR of FaMV1-162 with dG = -73.96 and dG = -13.93, respectively. The +ssRNA molecules were folded, and the free energy was calculated with the RNA Folding Form V 2.3 Energies (MFOLD) program. For these calculations, the following conditions were sectioned: 25ºC, 1M NaCl and 0M divalent ions. The rendering of the structures has been defined with natural angles and annotated using colored base characters, based on p-num information. Colors are ranged from red to black representing the probability as well-determined (1) to poorly determined (0), respectively.</p>
3D metabolic profiles acquired by a Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)
<p>Dataset for "Spatially resolved 3D metabolomic profiling in tissues"</p> <p>The Dataset has 6 subdata of TOF-SIMS signal raw data:<br> * Inside germinal center dataset separate into 2<br> * Outside germinal center dataset<br> * Border germinal center dataset<br> * Unlabeled dataset separate into 2<br> * Labeled tonsil tissue dataset<br> * Unlabeled tonsil tissue dataset</p> <p>1 processed data for python numpy version: 3D metabolites npy Data.zip</p> <p>Each dataset is a folder that has 191 txt files corresponding to the signal of 189 mass channels, the sum of all signals and the rest of signals not captured. <br> In each folder, the signal corresponding to a channel is named: name - molecular compound<br> </p>
video tutorials for inkscape in secondary school
<p>Video tutorials designed for the experimental phase of the study published in </p> <p>Sáez-LacaveA., Rodriguez-LopezA., Serrano-MuñozS., & Perez-FariñasR. (2020). Changing the Spanish arts curriculum for secondary school: the case for digital geometry and screencasting. <em>Research in Learning Technology</em>, <em>28</em>. https://doi.org/10.25304/rlt.v28.2342</p> <p> </p>
Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
<p><strong>Background </strong>The dieback epidemic decimating common ash (<em>Fraxinus excelsior</em>) in Europe is caused by the invasive fungus <em>Hymenoscyphus fraxineus</em>. In this study we analyzed the genomes of <em>H. fraxineus</em> and <em>H. albidus</em>, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of <em>Helotiales</em>. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of <em>H. fraxineus</em> and displacement of <em>H. albidus</em>.</p> <p><strong>Results</strong> The genomes of <em>H. fraxineus</em> and <em>H. albidus </em>showed a high level of synteny and identity. The assembly of <em>H. fraxineus </em>is 13 Mb longer than that of <em>H. albidus’, </em>most of this difference can be attributed to higher dispersed repeat content ((i.e transposable elements [TEs]) in <em>H. fraxineus</em>. In general, TE families in <em>H. fraxineus</em>showed more signals of repeat-induced point mutations (RIP) than in <em>H. albidus</em>, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those that did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the <em>H. fraxineus-</em>specific, <em>hymenosetin </em>biosynthetic gene cluster (BGC).</p> <p><strong>C</strong><strong>onclusion </strong>The genomes of <em>H. fraxineus</em> and <em>H. albidus</em> show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that <em>H. albidus</em> may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. </p> <p><strong>Data included</strong></p> <p>This post contains the alternate structural and functional annotations of the genomes of Helotealean fungi used in the study.</p>
Supplementary Data for Secondary structure and DNA binding domain prediction
<p><strong>This project contains the following extended data:</strong></p> <ul> <li><strong>Supplementary Table 1: </strong>Summary table of DNA binding domains (DBD), the counts of target regions within the genome and statistical analysis. (DNA_BINDING_DOMAINS_ID.tsv)</li> <li><strong>Sequence</strong>: ecCEBPα secondary structure prediction with RNAplfold at a pairing probability cut off of 0.1. N represents all sequences with pairing probability greater than 0.1. (predicted_secondary_structure_of_ecCEBPA.fa)</li> </ul>
Genetic variation in an ephemeral mudflat species: the role of the soil seed bank and dispersal in river and secondary anthropogenic habitats
<p>Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near-natural river habitats and anthropogenic habitats created by traditional fish farming practices using <i>Cyperus fuscus</i> as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above-ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short-term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harboured significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe and Anatolia (high values) to northern, especially north-western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.</p>
Figure 8 in A new species of the genus Lasioseius (Acari: Blattisociidae) inhabiting litter of secondary rainforest in Sumatra, Indonesia
Figure 8 Lasioseius orangrimbaen. sp., adult male: Ventral idiosoma.
Figure 6 in A new species of the genus Lasioseius (Acari: Blattisociidae) inhabiting litter of secondary rainforest in Sumatra, Indonesia
Figure 6 Lasioseius orangrimbaen. sp., adult female: spermathecal apparatus.
Data from: Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds
Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as site-averaged noise, using a well-established field experimental system in northwestern New Mexico. We hypothesized that high levels of noise, both at the nest site and in the environment, would decrease nest box occupancy. We set up nest boxes using a geospatially paired control and experimental site design and analyzed four years of occupancy data from four secondary cavity-nesting birds common to the Colorado Plateau. We found different effects of noise and landscape features depending on species, with strong effects of noise observed in breeding habitat selection of Myiarchus cinerascens, the Ash-throated Flycatcher, and Sialia currucoides, the Mountain Bluebird. In contrast, the amount of forest cover less frequently explained habitat selection for those species or had a smaller standardized effect than the acoustic environment. Although forest cover characterization and management is commonly employed by natural resource managers, our results show that characterizing and managing the acoustic environment should be an important tool in protected area management.
Data from: Plant community responses to stand-level nutrient fertilization in a secondary tropical dry forest
The size of the terrestrial carbon (C) sink is mediated by the availability of nutrients that limit plant growth. However, nutrient controls on primary productivity are poorly understood in the geographically extensive yet understudied tropical dry forest biome. To examine how nutrients influence above‐ and belowground biomass production in a secondary, seasonally dry tropical forest, we conducted a replicated, fully factorial nitrogen (N) and phosphorus (P) fertilization experiment at the stand scale in Guanacaste, Costa Rica. The production of leaves, wood, and fine roots was monitored through time; root colonization by mycorrhizal fungi and the abundance of N‐fixing root nodules were also quantified. In this seasonal forest, interannual variation in rainfall had the largest influence on stand‐level productivity, with lower biomass growth under drought. By contrast, aboveground productivity was generally not increased by nutrient addition, although fertilization enhanced growth of individual tree stems in a wet year. However, root growth increased markedly and consistently under P addition, significantly altering patterns of stand‐level biomass allocation to above‐ vs. belowground compartments. Although nutrients did not stimulate total biomass production at the community scale, N‐fixing legumes exhibited a twofold increase in woody growth in response to added P, accompanied by a dramatic increase in the abundance of root nodules. These data suggest that the relationship between nutrient availability and primary production in tropical dry forest is contingent on both water availability and plant functional diversity.
Data from: Attract or defend? Pollen and vegetative secondary chemistry of three pollen-rewarding lupines
PREMISE OF THE STUDY: Optimal Defense Theory predicts that selection should drive plants to differentially allocate resources for herbivore defense to tissues with high fitness values. As pollen's primary role is the transport of gametes, plants may be expected to defend it from herbivory. However, for many animal-pollinated plants, pollen serves a secondary role as a pollinator reward. This may present a conflict between selection to defend pollen from herbivores and selection to reward pollinators. Here, we investigate whether pollen secondary chemistry in three pollen-rewarding Lupinus species better reflects the need to defend pollen or reward pollinators. METHODS: Lupinus (Fabaceae) species are nectarless, pollen-rewarding, and produce defensive quinolizidine and/or piperidine alkaloids throughout their tissues. We used gas chromatography to identify and quantitate the alkaloids in four above-ground tissues (pollen, flower, leaf, stem) of three western North American lupines: L. argenteus, L. bakeri, and L. sulphureus, and compared alkaloid concentrations and composition among tissues within individuals. KEY RESULTS: Pollen alkaloid concentrations were 11-35% of those concentrations in other tissues in L. argenteus and L. sulphureus. We detected no alkaloids in L. bakeri pollen, though they were present in other tissues. Alkaloid concentrations were not strongly correlated among tissues within individuals. We detected fewer alkaloids in pollen compared to other tissues and pollen contained no unique alkaloids. CONCLUSIONS: Our results are consistent with the hypothesis that, in these pollen-rewarding species, pollen secondary chemistry may reflect the need to attract and reward pollinators more than the need to defend pollen from herbivory.
Data from: The ephemerality of secondary forests in southern Costa Rica
Secondary forests are increasingly recognized for conserving biodiversity and mitigating global climate change, but these and other desired outcomes can only be achieved after decades of regeneration, and secondary forests are frequently recleared before they recover to predisturbance conditions. We used a time series of aerial photographs (1947-2014) to evaluate multidecadal persistence of secondary forests across a 320 sq. km landscape in southern Costa Rica. Secondary forests had relatively short lifespans, with 50% recleared within 20 years and 85% recleared within 54 years of when they were first observed. Larger forest fragments and forests near rivers had a lower reclearance hazard, but forest persistence did not differ over time, indicating that regional forest regeneration may be generally ephemeral. Costa Rica has made an international commitment to restore 1 million ha of degraded land by 2020. Depending on how this is achieved, only half that target may remain forested by 2040.
Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks
<p>Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (<i>Anas platyrhynchos</i>) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (<i>A. rubripes</i>) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.</p>
Improving phonetic alignment by handling secondary sequence structures
<p>Supplementary material accompanying the paper "Improving phonetic alignment by handling secondary sequence structures".</p> <p>The data consists of 5 files:</p> <ul> <li>gold_standard.psa : the gold standard used in the analysis in PSA format</li> <li> sca-secondary.psa : the output of the algorithm with the secondary extension</li> <li>sca-traditional.psa : the output of the traditional algorithm</li> <li>sca-secondary-diff.psa : the differences of the secondary extension compared to the GS</li> <li>sca-traditional-diff.psa : the differences of the traditional algorithm compared to the GS</li> </ul> <p>For a description of the file-format used in this dataset, please refer to the LingPy tutorial under http://lingpy.org.</p>
Raw data for SELDI-TOF high range from article: Free serum haemoglobin is associated with brain atrophy in secondary progressive multiple sclerosis
<p>Raw normalised data from SELDI-TOF at high range following Expression Difference Mapping (ProteinChip Data Manager. Bio-Rad). Columns contain sample name, sample group (corresponds to longitudinal measurements for each patients at 1,3,4 and 5), peak number (all peaks detected at high range at each time point), peak intensity and mass/charge ratio.</p>
Assessing the Nature and Quality of Emergency Obstetric Care for Preventing Maternal and Perinatal Mortality in 8 Secondary and Tertiary Hospitals in Nigeria: Results of a Formative Research Study
<p>Nigeria suffers some of the highest rates of maternal and perinatal mortality in the world. Poor quality of obstetric care is a key factor, and although not quantified at a national level, local studies suggest that high rates of maternal and perinatal deaths are due to clinical management errors in hospitals. This project therefore explored the nature of existing practices and quality of clinical management of three leading causes of maternal and perinatal deaths (primary postpartum haemorrhage, eclampsia, and obstructed labour); implement an intervention package aimed at improving the quality of clinical management of these causes of deaths; and test the effectiveness of this package on quality of care indicators and maternal and perinatal outcomes. </p> <p>The study follows a quasi-experimental research design, using interrupted time series analysis for assessment over a three year period. Six public secondary care hospitals and two public tertiary care hospitals in both north and south of Nigeria were selected randomly. Formative research was conducted in all eight hospitals, and thereafter the intervention will be carried out in four hospitals, with the remaining four hospitals functioning as control sites. </p> <p>Clinical outcomes will be compared between intervention and control sites in a total of 2334 cases of PPH, preeclampsia/eclampsia and obstructed labour (based on an anticipated 50% reduction in case fatality rates, significance level of 0.05 and 80% power). This will consist of 1167 cases in the intervention sites and 1167 in the control sites. Maternal and perinatal mortality rates will serve as primary outcome measures. Secondary outcomes involve quality of care drawn from United Nations process indicators, skilled attendance index and data derived from this formative audit phase of the project.</p> <p>The results will enable the identification of a system-wide quality of care framework for improving the delivery of emergency obstetric care for the prevention of maternal and perinatal morbidity and mortality in Nigeria.</p>
Assessing the Nature and Quality of Emergency Obstetric Care for Preventing Maternal and Perinatal Mortality in 8 Secondary and Tertiary Hospitals in Nigeria: Results of a Formative Research Study
<p>Nigeria suffers some of the highest rates of maternal and perinatal mortality in the world. Poor quality of obstetric care is a key factor, and although not quantified at a national level, local studies suggest that high rates of maternal and perinatal deaths are due to clinical management errors in hospitals. This project therefore explored the nature of existing practices and quality of clinical management of three leading causes of maternal and perinatal deaths (primary postpartum haemorrhage, eclampsia, and obstructed labour); implement an intervention package aimed at improving the quality of clinical management of these causes of deaths; and test the effectiveness of this package on quality of care indicators and maternal and perinatal outcomes. </p> <p>The study follows a quasi-experimental research design, using interrupted time series analysis for assessment over a three year period. Six public secondary care hospitals and two public tertiary care hospitals in both north and south of Nigeria were selected randomly. Formative research was conducted in all eight hospitals, and thereafter the intervention will be carried out in four hospitals, with the remaining four hospitals functioning as control sites.</p> <p>Clinical outcomes will be compared between intervention and control sites in a total of 2334 cases of PPH, preeclampsia/eclampsia and obstructed labour (based on an anticipated 50% reduction in case fatality rates, significance level of 0.05 and 80% power). This will consist of 1167 cases in the intervention sites and 1167 in the control sites. Maternal and perinatal mortality rates will serve as primary outcome measures. Secondary outcomes involve quality of care drawn from United Nations process indicators, skilled attendance index and data derived from this formative audit phase of the project.</p> <p>The results will enable the identification of a system-wide quality of care framework for improving the delivery of emergency obstetric care for the prevention of maternal and perinatal morbidity and mortality in Nigeria</p>
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OpenNeuro
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