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2,008 results for “presence”
Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation
<p><strong>Aims</strong>: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these plant communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime's CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what functional trade-offs they exhibit and how traits and functional diversity vary in response to bamboo presence/absence.</p> <p><strong>Methods</strong>: To characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. isolated woody plants in the grasslands community) . Then, we used Mann Whitney test, t-test and variation partitioning to determine the effects of inside vs outside tree island and bamboo presence on community weighted means, woody species diversity and functional diversity.</p> <p><strong>Results</strong>: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than in tree islands without bamboo.</p> <p><strong>Conclusions</strong>: The observed functional assembly hints towards large-scale environmental abiotic filtering shaping stress-tolerant community strategy, and small-scale biotic interactions driving small-scale trait variation. We recommend experimental studies with fire, facilitation treatments, eco-physiological and recruitment traits to elucidate on tree island expansion and communities response to climate change.</p>
Presence data for vascular plant, bryophyte and lichen species in 100 vegetation plots (each 1 m2) from 32 shell-beds at Akerøya, Hvaler, SE Norway
<p><strong>We present a data set consisting of abundance data for 106 vascular plant species, 36 bryophyte species and 13 lichen species from 100 vegetation plots, each 1 m2, distributed on 32 shell-beds at Akerøya, Hvaler municipality, former Østfold (in 2022 Viken) county. The plots were analysed with respect to species composition in June 1979. These data formed the basis for the publication: Halvorsen, R. 1980. Numerical analysis and successional relationships of shell-bed vegetation at Akerøya, Hvaler, SE Norway. Norw. J. Bot. Vol. 27 pp. 71-95. Oslo. ISSN 0300-1156.</strong></p>
Characteristics of the urban sewer system and rat presence in Seattle
<p>Rats are abundant and ubiquitous in urban environments. There has been increasing attention to the need for evidence-based, integrated rat management and surveillance approaches because rats can compromise public health and impose economic costs. Yet there are few studies that characterize rat distributions in sewers and there are no studies that incorporate the complexity of sewer networks that encompass multiple sewer lines, all comprised of their own unique characteristics. To address this knowledge gap, this study identifies sewer characteristics that are associated with rat presence in the city of Seattle's urban sewer system. We obtained sewer baiting data from 1752 geotagged manholes to monitor rat presence and constructed generalized additive models to account for spatial autocorrelation. Sewer rats were unevenly distributed across sampled manholes with clusters of higher rat presence at upper elevations, within sanitary pipes, narrower pipes, pipes at a shallower depth, and older pipes. These findings are important because identifying features of urban sewers that promote rat presence may allow municipalities to target areas for rat control activities and sewer maintenance. These findings suggest the need to evaluate additional characteristics of the surface environment and identify the factors driving rat movement within sewers, across the surface, and between the surface and the sewers. </p>
Outputs of molecular dynamics simulations of two NS1 ZIKV variants in the membrane presence
<p>Files corresponding to outputs obtained through Molecular Dynamics (MD) simulations of two Non-structural (NS) proteins 1 of the Zika virus from Uganda (ZIKV-UG) and Brazil (ZIKV-BR). Simulations were performed using GROMACS 5.1.5 or later versions. Systems were built based on atomistic models (https://zenodo.org/record/5608521#.YvDNZTlBzJw) and converted to a coarse-grained representation employing MARTINI 2.2p ElNeDyn. It was assumed to be NS1 systems in <em>apo</em> and <em>holo</em> forms (<em>i.e.</em>, in the absence and presence of a lipid bilayer, respectively). The membrane model tries to reproduce a lipid concentration of an endoplasmic reticulum lipid bilayer. <em>Holo</em> and <em>apo</em> systems were simulated until they reached 20 and 10 µs, respectively. Trajectories do not include water molecules. For the specific case of <em>holo</em> systems, frames were skipped every 5 frames, which means that processed trajectories are equivalent to simulations when it is recorded every 1000 ps. More details can be found at <a href="https://doi.org/10.1021/acs.jcim.2c01461">https://doi.org/10.1021/acs.jcim.2c01461</a></p> <p>Note: Some topology and index files important for MD analysis are also present.</p>
Increased water use by sugar maple trees in the presence of a dense beech understory layer
<p>The formation of a recalcitrant understory vegetation layer is a phenomenon observed in various forests around the world, which can limit tree regeneration and in the long term, modify the composition, succession process and water balance of forests. In temperate forests of southern Quebec (Canada), the proliferation of American beech (<em>Fagus grandifolia</em>) in stands dominated by sugar maple (<em>Acer saccharum</em>) can be related to the recalcitrant vegetation phenomenon. With a projected increase in the severity and duration of droughts, a better understanding of its effect on water fluxes is crucial to understand the trajectory of impacted forests. The objective of this study was to understand how recalcitrant-type vegetation, in this case beech proliferation in sugar maple stands, influence tree water use. We compared transpiration i) by overstory trees (i.e. sugar maples) and ii) by understory saplings (i.e. American beech) in sites with and without beech understory dominance. At each of the six sites, we measured sap flux density (F<sub>d</sub>) of two sugar maple trees (diameter at breast height > 9 cm) and one beech sapling (1 cm < diameter at breat height ≤ 9 cm) with thermal dissipation sensors during the growing season. At tree level, F<sub>d</sub> of sugar maple trees was significantly larger in beech-dominated sites compared to control ones, indicating greater water consumption by sugar maple when understory is dominated by beech. At stand scale, total transpiration varied between 140 and 296 mm for the study period, with no significant difference between beech-dominated and control sites. We provide two hypotheses to explain our results at tree scale: i) reduced cover by forest floor vegetation would limit transpiration through this layer, thus allowing increased availability of water resources to supply tree transpiration or ii) increased tree transpiration rate would be a mechanism to satisfy nutrient requirements in beech-dominated stands often associated with lower soil fertility. Further research is needed to better understand the mechanisms explaining tree water use given beech proliferation.</p>
Spring-Summer cumulated water presence of "Marais Breton nord" calculated with the WIW
<p>The WIW was calculated for all SENTINEL 2 cloudless images available within the period from May to September from 2017 to 2022. All WIW rasters were then added to provide the cumulated water presence ranging from 1 to 39 corresponding to the number of dates related to available cloudless images at that period in the Marais Breton Nord. The table provides the dates of the images used. EPSG 3857</p>
Winter cumulated water presence of "Loire-Atlantique et abord" calculated with the WIW
<p>4 rasters cover the "Loire-Atlantique et abord" study area. The WIW was calculated for all SENTINEL 2 cloudless images available within the period from January to April from 2017 to 2023. All WIW rasters were then added to provide the cumulated water presence ranging from 1 to 15 corresponding to the number of dates related to available cloudless images at that period. The table provides the dates of the images used. EPSG 3857.</p>
Spring-Summer cumulated water presence of "Loire-Atlantique et abord" calculated with the WIW
<p>4 rasters cover the "Loire-Atlantique et abord" study area. The WIW was calculated for all SENTINEL 2 cloudless images available within the period from May to September from 2017 to 2023. All WIW rasters were then added to provide the cumulated water presence ranging from 1 to 24 corresponding to the number of dates related to available cloudless images at that period. The table provides the dates of the images used. EPSG 3857.</p>
Fig. 1 in SHORT COMMUNICATION Confirming the presence of Clelia equatoriana Amaral, 1924 (Squamata: Dipsadidae) in Peru
Fig. 1. Map of Isthmian Central America and northwestern South America showing the locality records of Clelia equatoriana (circles). Black circles are records by Zaher (1996), red circle is Quebrada Molletón and blue circle is El Sauce.
Fig. 2 in SHORT COMMUNICATION Confirming the presence of Clelia equatoriana Amaral, 1924 (Squamata: Dipsadidae) in Peru
Fig. 2. Individuals of Clelia equatoriana from Quebrada Molletón, Piura, Peru: CORBIDI 14869 (A) and 14875 (B).
Dataset for publication: "Exploring ORCID adoption and metadata presence in Spain's research landscape"
<p>This dataset is for the publication "<em>Exploring ORCID adoption and metadata presence in Spain's research landscape</em>" and is composed of the following files:</p> <ul> <li><strong>norm_aff.tsv</strong> (2795x5) - Curated list of role titles</li> <li><strong>openalex_all_spanish.csv</strong> (811062x4) - List of Spanish authors retrieved from OpenAlex</li> <li><strong>orcid_affiliation.csv</strong> (377377x23) - Activity employment affiliation of Spanish ORCID records</li> <li><strong>orcid_full_maps.csv</strong> (15182292x6)- Topic classification of Spanish ORCID records</li> <li><strong>orcid_metrics.csv</strong> (226512x39) - Metadata availability in Spanish ORCID records</li> </ul>
APPENDIX 3 in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 3. — Automatic Barcode Gap Discovery (ABGD) results and distribution of pairwise distances for the marker 5P-COI. A, ABGD results showing the number of groups (primary partitions) obtained for a range of prior maximum divergence of intraspecific diversity; B, bar chart showing the proportion of pairwise comparisons of 5P-COI gene at each range of sequence divergence (K2P distance). Intraspecific divergences are represented in grey bars and divergences belonging to different species are represented in yellow bars.
APPENDIX 4. — Ultrametric Bayesian tree reconstructed with the 5P in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 4. — Ultrametric Bayesian tree reconstructed with the 5P-COI marker. The dotted vertical red line indicates the maximum likelihood transition point of the switch in branching rates, as estimated by a General Mixed Yule-Coalescent (GMYC) model. The GMYC analysis was performed using a single threshold. Haplotype code as in Appendix 5.
APPENDIX 1 in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 1. — Maximum likelihood (ML) phylogram of the genus Plocamium Lamouroux based on rbcL sequences. ML bootstrap (BS)/Bayesian posterior probability (PP) values are shown above or close to each branch and only values superior to 75 and 0.75, respectively, are given. Colors correspond to oceans where individuals sequenced where sampled. Outgroup corresponds to Sarcodia ciliata Zanardini (GenBank accession: KM360040).
FIG. 3. — A in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
FIG. 3. — A, ML tree (left) and Neighbour joining (NJ) network (right) inferred from 5P-COI sequences dataset of Plocamium specimens from the present study. In the tree, numbers above the branches are support values as inferred from ML analysis, only values superior to 75 are given. In the NJ networks, haplotypes are represented by open circles with size proportional to frequency within each genetic species (see upper left corner for correspondence between number of sequences and circle size). For haplotypes separated by more than one mutational step, black bars indicate the additional number of steps; B, Plocamium Lamouroux species distribution; the number (N) of individuals sequenced is indicated for each sampling locality. Code for each locality as in Table 1; haplotype code as in Appendix 5. Dashed line represents the biogeographic transition zone located at 42°S.
FIG. 1 in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
FIG. 1. — Maximum likelihood (ML) phylogram of the genus Plocamium Lamouroux based on 5P-COI sequences. ML bootstrap (BS)/Bayesian posterior probability (PP) values are shown above each branch and only values superior to 75 and 0.75, respectively, are given. Colors correspond to oceans where individuals sequenced where sampled. Species names, as reported in GenBank, are given on the right. Outgroup corresponds to Asparagopsis armata Harvey (GenBank accession: KJ960344).
FIGURE 4 in The presence of Wilfredomys oenax (Rodentia: Cricetidae: Sigmodontinae) in São Paulo state, southeastern Brazil: a locally extinct species?
FIGURE 4: Map of the range distribution of Wilfredomys oenax. Numbered points correspond to known southeastern records from: (1) Ubatuba, São Paulo (Present work), (2) Abismo Iguatemi, Apiaí city, São Paulo (Castro & Langer, 2011), (3) Curitiba, Paraná (ÁvilaPires, 1960). Dotted circles represent data from live caught specimens and cross represents fossil records. The gray shaded area is the geographic distribution of the species suggested by IUCN (adapted from Vieira & Christoff, 2008), been considered extinct at Curitiba (heavy gray shaded area). Full solid lines indicate Brazilian Federal state boundaries; solid light gray lines indicate major rivers.
FIGURE 3 in The presence of Wilfredomys oenax (Rodentia: Cricetidae: Sigmodontinae) in São Paulo state, southeastern Brazil: a locally extinct species?
FIGURE 3: Detailed views of morphology of the skull (A-E and I), mandible (F) and upper (G) and lower (H) left molars of Wilfredomys oenax (based on MZUSP 6281, from Ubatuba, SP). Labeled structures and region includes: auditory bulla (ab), anteroflexus (af), anteroloph (al), angular notch (an), angular process (ap), anterolabial conule (aac), anterolingual conule (alc), anteromedium flexus (amf), buccinator-masticatory foramen (bmf), condyloid process (cp), capsular process of the lower incisor alveolus (cap), coronoid process (crp), incisive foramina (if), frontal (fr), foramen ovale accessorius (foa), mesopterygoid fossa (ms), nasal (na), parapterygoid fossa (pt), palatal pits (plt), sigmoid notch (sn), zygomatic notch (zn), zygomatic plate (zp), anterocone (AR), paracone (PA), protocone (PT). White arrow indicate shallow depression along the frontals. Black bars indicate comparatives width (C) and alignment (D) between structures. Note the confluence between bmf and foa as a result of the absence of bony strut on the alisphenoid (see Voss, 1991: fig. 12), and that main molar cups are typed in upper case letters with two letter abbreviation.
FIGURE 2 in The presence of Wilfredomys oenax (Rodentia: Cricetidae: Sigmodontinae) in São Paulo state, southeastern Brazil: a locally extinct species?
FIGURE 2: Dorsal and ventral views of the skin of Wilfredomys oenax (MZUSP 6281) from Ubatuba, São Paulo. This skin was erroneously given a tag with the number MZUSP 7501, but note a second tag with 6281 on it, which corresponds to the skull MZUSP 6281. Scale 15 mm.
FIGURE 1 in The presence of Wilfredomys oenax (Rodentia: Cricetidae: Sigmodontinae) in São Paulo state, southeastern Brazil: a locally extinct species?
FIGURE 1: Dorsal, ventral, and lateral views of the cranium and lateral and dorsal views of the mandible of Wilfredomys oenax (MZUSP 6281) from Ubatuba, São Paulo. Scale 10 mm.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.