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2,399 results for “fragmentation”
PanDDA analysis of PTP1B re-screened against fragment libraries at RT
<p>PTP1B re-screened against multiple fragment libraries with RT crystallography</p>
Tropical bat ectoparasitism in continuous versus fragmented forests: A gap analysis and preliminary meta-analysis
<p><span>Tropical regions are experiencing rapid rates of forest fragmentation, which can have several effects on wildlife, including altered parasite dynamics. Bats are a useful host group to consider these effects of fragmentation because they are abundant in the tropics, serve important ecological roles, and harbour many parasites. Nevertheless, research on the effects of fragmentation on bat ectoparasites is still limited. To help guide ongoing and future research efforts, this study had two objectives: (1) conduct a gap analysis to characterize the state of currently available research on fragmentation effects on bat ectoparasites, and (2) conduct a preliminary meta-analysis to identify current trends. We systematically highlighted several research gaps: studies comparing the effects of fragmented versus continuous forests on ectoparasites are limited and have primarily been conducted in the Neotropics, with a focus on bats in the superfamily Noctilionidea (especially frugivorous phyllostomids). Our preliminary meta-analysis suggested that ectoparasite prevalence (but not the mean or variance in intensity) was higher in fragments than in continuous forests. Moreover, prevalence increased with increasing roost duration, and mean intensity was higher for bats with higher wing aspect ratios. Intensity variance was affected by an interaction between forest type and wing aspect ratio, such that variance increased for bats with high wing aspect ratios in continuous forests but decreased in fragments. These results suggest that fragmentation can shape aspects of bat ectoparasitism and could have implications for the ecology, health, and conservation of bats in fragmented landscapes. However, existing research gaps could bias our current understanding of habitat change and bat health, and future research should thus investigate these effects in the Paleotropics and with other bat families. </span><span><br></span></p>
Figure 4 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit
Figure 4. Camponotus cillae recorded for the RPPN Botujuru: (A) front view; (B) dorsal view; (C) side view. regeneration of the older areas provides resources to Another important factor is the potential of conservation those species with more specialized habits. units to discover new species, mainly invertebrates (Liu We underscore the presence of two species, a pos- et al., 2022), a group that lacks inventory data. sible new species of Octostruma Forel, 1912, recorded They also emphasize the need to advance in the idenin the areas with an understory, and Camponotus cillae tification of recorded morphospecies, increase sampling Forel, 1912 (Fig. 4) recorded in Brazil only by the type se- efforts, use other collection techniques to better underries in the state of São Paulo (Botucatu) by Forel in 1912 stand the diversity of ants and other faunal and floristic (Forel, 1912). Data on their biology is scarce in the liter- groups in the RPPN. Moreover, these results also underature. This new record highlights the importance of new score the need for the creation of measures aiming at studies on biodiversity to our comprehension of the dis- preserving the area, given that the urbanization process tribution of species (Janicki et al., 2016). has been intense in the vicinity of the conservation unit. In addition, our results show the potential of RPPN Botujuru; the occurrence of C. cillae and the possible species of Octostruma in the Botujuru RPPN emphasizes the CONCLUSION importance of conservation units for threatened biomes. Fragments of Atlantic Forest found in conservation units The diversity of ants evaluated in this first work, carare important for the preservation of biodiversity, acting ried out with only one collection campaign, indicates as refuge areas for species that suffer from anthropo- that the natural regeneration process is having positive genic pressures such as deforestation and urban growth effects in abandoned areas. The fragments that compose (Gardner et al., 2009; Pardini et al., 2009; Lima et al., 2020), the RPPN Botujuru may prove to be very representative providing resources, even for those rarely collected. of the Alto Tietê region regarding the conservation of the
Figure 3 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit
Figure 3. Non-metric multidimensional scaling (NMDS) Bray-Curtis type for the areas with 1-4 years (grey), 7-12 years (light green), and 14 years (dark green). (Anosim = 0,0001).
Figure 2 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit
Figure 2. The number of occurrences of trophic guilds along the regeneration gradient in areas of Eucalyptus sp.: 1-4 years (no understory), located in the buffer zone of RPPN Botujuru – Serra do Itapety; 7-12 years (with an understory composed of shrubby vegetation), and 14 years (with an understory displaying both shrubby and arboreal vegetation).
Data from: Habitat heterogeneity determines species richness on small habitat islands in a fragmented landscape
<p><span><strong>Aim</strong>:</span><span> The small-island effect (SIE), as an exception to the species-area relationship, has received much attention in true island systems. However, the prevalence and related patterns of the SIE have not been well evaluated in habitat island systems. Here, we aimed to identify the existence of SIE for habitat islands in fragmented landscapes and determine the key factors influencing species richness on small habitat islands.</span></p> <p><span><strong>Location</strong>:</span><span> Inner Mongolia Autonomous Region, China.</span></p> <p><span><strong>Taxon</strong>:</span><span> Vascular plants.</span></p> <p><strong><span>Methods</span></strong><span>: Based on 78 grassland fragments in fragmented landscapes of the agro-pastoral ecotone of northern China, we used piecewise regression, path analysis, and null models to investigate the SIE of the species-area relationship. We then used a multi-model selection to evaluate the impacts of four influencing factors (instability, isolation, habitat heterogeneity, and surrounding productivity) on species richness (including habitat specialists and generalists) on small habitat islands within the range of SIE. </span></p> <p><span><strong>Results</strong>:</span><span> We found an obvious threshold of 5.1 ha in the species-area relationship,</span> <span>below which habitat island area had no direct and indirect effects on species richness.</span><span> Small habitat islands (< 5.1 ha) host a lower percentage of habitat specialists and a higher percentage of generalists. On small habitat islands, species richness was positively affected by habitat heterogeneity while negatively affected by instability and isolation. Habitat heterogeneity had the strongest effect on species richness, positively affecting specialist richness while negatively affecting generalist richness.</span></p> <p><strong><span>Main conclusions</span></strong><span>: There is a SIE in fragmented landscapes of the agro-pastoral ecotone of northern China, which should be considered in biodiversity conservation. Habitat heterogeneity had a key role in determining the pattern of species richness, especially for small islands. Habitat specialists and generalists had different SIE-related patterns. Our study highlights the importance of considering different ecological groups of species to improve our understanding of the SIE in fragmented habitats.</span></p>
Dataset for: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area.
<p>Dataset for: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area. (Pending publication in Wildlife Biology as of 02/24/2023)</p>
Ultra-Accurate Correlation Between Precursor and Fragment Ions in Two-lDimensional Mass Spectrometry: Acetylated vs. Trimethylated Histone Peptides
<p>Two-dimensional mass spectrometry (2D MS) is a method<br> for tandem<br> mass spectrometry in which precursor and fragment ions are correlated<br> by manipulating ion radii rather than by ion isolation. A 2D mass<br> spectrum contains the fragmentation patterns of all analytes in a<br> sample, acquired in parallel. We report ultrahigh-resolution narrowband<br> 2D mass spectra of a mixture of two histone peptides with the same<br> sequence, one of which carries an acetylation and the other a trimethylation<br> (m/z 0.006 difference). We reduced<br> the distance between data points in the precursor ion dimension and<br> compared the accuracy of the precursor-fragment correlation with the<br> resolving power. We manage to perform label-free quantification on<br> the histone peptide mixture and show that precursor and fragment ions<br> can be accurately correlated even though the precursor ions are not<br> resolved. Finally, we show that increasing the resolution of a 2D<br> mass spectrum in the precursor ion dimension too far can lead to a<br> decline in the signal-to-noise ratio.</p>
Data from: Evolution of Large Aβ16-22 Aggregates at Atomic Details and Potential of Mean force Associated to Peptide Unbinding and Fragmentation Events
<p>This data accompanies the paper entitled <em>Evolution of Large Aβ16-22 Aggregates at Atomic Details and Potential of Mean force Associated to Peptide Unbinding and Fragmentation Events</em></p> <p>The zip archive contains the results of molecular dynamics simulations of the 2 systems investigated in the paper: the first one with 139 <em>Aβ16-22 </em><em>peptides, the second one with 106 peptides.</em><em> </em>Each system has been simulated at 300 K. Starting configurations of the peptides are provided for all the systems in GRO Gromos87 format. Trajectories with the positions of the peptides every 100 ps are provided for all the systems in XTC gromacs format. For system 1 we also provide XTC trajectories for all the replicas of the REST2 simulation.</p>
Unraveling the decarboxylation dynamics of the fluorescein dianion with fragment action spectroscopy
<p>The raw action spectra of Fl<sup>2-</sup> recorded by monitoring the yields of electrons, Fl<sup>-</sup> and Fl-CO<sub>2</sub><sup>-</sup>, as well as the photoelectron image of Fl<sup>2-</sup> at 320 nm.</p>
Data from: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area
<p>Coyotes (<em>Canis latrans</em>) in urban landscapes provide important food web functions and ecological services but can also trigger human-wildlife conflict when their diet includes anthropogenic resources or domestic pets. As adaptable omnivores, coyotes adjust their diet to their environment, routinely switching among food items to accommodate spatial and seasonal differences in availability. To evaluate coyotes' potential impacts within the food web of urban Long Beach, California where human-wildlife conflict involving coyotes may occur, we analyzed 115 scat samples collected once every two weeks from two open space fragments inside the urban matrix. We hypothesized that differences in scat composition would correlate with seasonal and site differences, with greater use of anthropogenic resources during the dry season supplementing lower prey availability, and greater consumption of wild mammal prey during the wet season when rabbits and small mammals reproduce. We found coyote diet was predominately composed of natural prey and vegetation year-round. Mammals made up more of the coyote diet in the wet season than the dry, while arthropods and vegetation occurred more in dry season scats. Coyotes relied on rabbits as their main prey year-round across all sites. Domestic cats (<em>Felis catus</em>) were the third most common individual prey species found in coyote scats; we did not find evidence of domestic dog (<em>Canis lupus familiaris</em>) consumption. The overall frequency of mammalian remains did not differ across sites but did differ across sites for other prey types. While there is a potential for human-wildlife conflict in coyote's consumption of feral or domestic cats, coyotes may also be providing an ecological service by reducing cats in natural habitat fragments.</p>
Lesser prairie-chicken habitat selection and survival relative to a wind energy facility located in a fragmented landscape
<p>The overlap of renewable wind energy with the range of lesser prairie-chickens (<em>Tympanuchus</em> <em>pallidicinctus</em>) raises concern of population declines and habitat loss. Lesser prairie-chickens are adversely affected by landscape change, however, it is unclear how this species may respond to wind energy development. Therefore, managers and wind energy developers are currently tasked with making management or siting recommendations of future wind energy facilities based on lesser prairie-chicken behavioral responses to other forms of anthropogenic development or responses of other grouse species to wind energy development. The current strategy of siting wind turbines in cultivated cropland within lesser prairie-chicken range has not been evaluated for its effectiveness at minimizing potential adverse impacts. We captured 60 female and 66 male lesser prairie-chicken from leks located along a gradient from wind turbines in southern Kansas, USA, from 2017–2021. Over the study period, we collected lesser prairie-chicken location data and demographic information to evaluate resource selection, movements, and demography relative to environmental predictors and metrics associated with the wind energy facility. Lesser prairie-chickens used habitats in close proximity to wind turbines, provided that turbine density was low; however, avoidance associated with cultivated cropland appeared to be more predictive than the presence of wind turbines. We observed movement between turbines suggesting that wind turbines did not act as a barrier to local movements. We did not detect an influence of wind turbines on nest success or individual survival during breeding or non-breeding periods, a relationship that is consistent among multiple grouse species using habitats near wind energy infrastructure. Additional research is necessary to evaluate impacts associated with wind energy development in intact lesser prairie-chicken habitats, but placing wind turbines in cultivated croplands or other fragmented landscapes appears to be an important siting measure when considering wind energy facility siting across the lesser prairie-chicken range.</p>
Supplemetary Data for the article: Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons
<p>This is a set of Supplementary materials for the article 'Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons', by Meng et al.</p> <p>Supplementary_Data_I.pdf contains an extensive table spanning 36 pages that lists the top-10 molecular fragments accountable for the spectral bands between 2.761 and 1172.745 μm. To access this table, hyperlinks within the document can be used for navigation.</p> <p>Supplementary_Data_II.pdf comprises a large table that encompasses 10,691 pages, including the top-100 molecular fragments responsible for the spectral bands between 2.761 and 1172.745 μm. Navigation through the hyperlinks enables access to this table.</p> <p>Supplementary_Data_III.csv encompasses the chemical formulas, number of unpaired valence electrons, spin multiplicities, xyz data, and SMILES strings of the PAHs carrying the additional spectra.</p> <p>Supplementary_data_IV.zip includes the input and output datasets along with the ML code. The code script is written in Python 3.7, and is supported by the following libraries: sklearn, json, numpy, and pandas.</p> <p>Supplementary_Information.pdf contains the evidence supporting the choice of the cutoff radius, as well as the figures of the count of the molecules in the dataset, the FI with changing datasets and hyperparameters, of cross-validation, and of UIE bands and emission features of four SH PAHs. Importance of three carbon skeleton fragments for bands in different intervals is also demonstrated.</p>
APPENDIX 13 in Detangling the effects of patch attributes on bryophyte diversity in fragmented subtropical secondary forests - a case study of land-bridge islands
APPENDIX 13. — Islands with multi-long branched appearance in the Thousand Island Lake, China.
Validating NISAR's cropland mapping approach and the USDA/NASS Cropland Data Layer against ground truth data in a fragmented urban agricultural region
<p>Field data used in manuscript:</p> <p>1 shapefile containing the ROI outline for which Sentinel-1 data was cropped</p> <p>1 shapefile containing the 93 fields investigated with their names, types and sizes as attributes </p> <p>8 annual csv data for active fields, consisting of 3 harvest dates and 5 planting dates. This list is after translating data from Farmlogic Report (not conducive to analysis in the format) and filtering for fields greater 1 acre. The study lateron further screened to use only fields greater than 2 acreas (0.81 hectares). </p> <p> </p>
RNA 3D structure modeling by fragment assembly with Small Angle X-ray Scattering restraints
<p>Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the Small Angle X-ray Scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts and Small Angle X-ray Scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.</p>
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
<p>Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides"</p> <p>The database directory contains the FASTA files of the four protein sequence databases used in the analysis of the paper.</p> <p>The data directory contains exports with lists of all peptide-to-spectrum matches obtained from the analysis.</p> <p>More information and scripts to reproduce the post-processing steps are available at: https://github.com/ProGenNo/VariantPeptideIdentification</p>
Habitat area and edges affect the length of trophic chains in a fragmented forest
<p class="MsoNormal">We built plant-leaf miner-parasitoid food webs in 19 remnants of a fragmented Chaco forest in central Argentina. We constructed food webs on each remnant from different locations at the forest interior and edges. For each food web, we registered the abundance of species, the species richness of each trophic level, estimated the connectivity of their networks, and the average food chain length. We used structural equation models to evaluate the direct and indirect effects of habitat area and edge/interior location on food chain length mediated by species richness, abundance, and connectivity. </p>
Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region
<p class="MsoNormal"><span>Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole <em>Myodes rufocanus </em>was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35–20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16–24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. Genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.</span></p>
Data and code for: Trapped DNA fragments in marine sponge specimens unveil north Atlantic deep-sea fish diversity
<p>Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80–1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples – as well as the specimens already stored in museums and other research collections – represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring.</p>
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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.