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2,399 results for “fragmentation”
The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China
<p>Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.</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.
The comparative effects of landscape-level forest fragmentation, forest area and local habitat measures on Connecticut bird communities
<p>I studied how breeding and wintering forest bird communities across Connecticut responded to variation in habitat characteristics and particularly such landscape attributes as forest fragmentation. I surveyed birds at 1,815 points along 121 transects that traversed ca. 400 km of forest. I also made 12705 habitat measurements at survey points and computed areas of forest, non-forest, core forest and perimeter/area ratios of forest for 31,550 ha of study area. I computed sampled species richness and community density as well as individual species' population densities for each transect. Moreover, I classified species encountered as to their nest site selection, macrohabitat use, microhabitat use, migratory strategy and trophic affiliation. Based on observations of 36,702 summering individuals of 123 species and 13,742 wintering individuals of 63 species, declines in community density occurred with increasing fragmentation although species richness was often more closely associated with habitat measures. Among landscape measures, forest fragmentation had the closest association with summer community measures 67% of the time, strongly suggesting that fragmentation effects were the predominant driver of such community patterns. However, short-distance migrant density and richness, foraging generalist density and richness, edge/successional species density and richness, habitat generalist density, and Brown-headed Cowbird density showed little relationship to landscape measures. The effects of fragmentation appeared to predominate over those of simply forest extent in predicting summer and winter bird community characteristics even in the comparatively extensive forests of southern New England. Despite the importance of fragmentation effects, community and individual species measures often tended to be more closely associated with habitat measures than with those of fragmentation. In addition, few summer or winter community measures or species patterns showed any significant relationship to natural forest breaks. Winter community and species density patterns showed little relationship to any landscape measures, with particularly elevation appearing to be a principal driver of winter patterns.</p>
Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape
<p><em>Phrynosoma mcallii</em> (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.</p>
PENGWIN Task 2: Pelvic Fragment Segmentation on Synthetic X-ray Images
<p>The <a href="https://pengwin.grand-challenge.org/">PENGWIN segmentation challenge</a> is designed to advance the development of automated pelvic fracture segmentation techniques in both 3D CT scans (Task 1) and 2D X-ray images (Task 2), aiming to enhance their accuarcy and robustness. The full 3D dataset comprises CT scans from 150 patients scheduled for pelvic reduction surgery, collected from multiple institutions using a variety of scanning devices. This dataset represents a diverse range of patient cohorts and fracture types. Ground-truth segmentations for sacrum and hipbone fragments have been semi-automatically annotated and subsequently validated by medical experts, and are available <a href="https://doi.org/10.5281/zenodo.10927452">here</a>. From this 3D data, we have generated high-quality, realistic X-ray images and corresponding 2D labels from the CT data using <a href="https://github.com/arcadelab/deepdrr">DeepDRR</a>, incorporating a range of virtual C-arm camera positions and surgical tools. This dataset contains the training set for fragment segmentation in synthetic X-ray (task 2).</p> <p>The training set is derived from 100 CTs, with 500 images each, for a total of <strong>50,000 training images and segmentations</strong>. The C-arm geometry is randomly sampled for each CT within reasonable parameters for a full-size C-arm. The virtual patient is assumed to be in a head-first supine position. Imaging centers are randomly sampled within 50 mm of a fragment, ensuring good visibility. Viewing directions are sampled uniformly on the sphere within 45 degrees of vertical. Half of the images (IDs XXX_0250 - XXX_0500) contain up to 10 simulated K-wires and/or orthopaedic screws oriented randomly in the field of view.</p> <p>The input images are raw intensity images without any windowing or normalization applied. It is standard practice to first apply the negative log transformation and then window each image appropriately for feeding into a model. See the included augmentation pipeline in `pengwin_utils.py` for one approach. For viewing raw images, the <a href="https://imagej.net/software/fiji/">FIJI</a> image viewer is a viable option, but it is recommended to use the included visualization functions in `pengwin_utilities.py` to first apply CLAHE normalization and save to a universally readable PNG (see example usage below).</p> <p>Because X-ray images feature overlapping segmentation maks, the segmentations have been encoded as multi-label uint32 images, where each pixel should be treated as a binary vector with bits 1 - 10 for SA fragments, 11 - 20 for LI, and 21 - 30 for RI. <strong>Thus, the raw segmentation files are not viewable with standard image viewing software.</strong> `pengwin_utilities.py` includes functions for converting to and from this format and for visualizing masks overlaid onto the original image (see below).</p> <p>To use the utilities, first install dependencies with `pip install -r requirement.txt`. Then, to visualize an image with its segmentation, you can do the following (assuming the training set has been downloaded and unzipped in the same folder):</p> <pre><code>import pengwin_utils from PIL import Image image_path = "train/input/images/x-ray/001_0000.tif" seg_path = "train/output/images/x-ray/001_0000.tif" # load image and masks image = pengwin_utils.load_image(image_path) # raw intensity image masks, category_ids, fragment_ids = pengwin_utils.load_masks(seg_path) # save visualization of image and masks # applies CLAHE normalization to the raw intensity image before overlaying segmentations. vis_image = pengwin_utils.visualize_sample(image, masks, category_ids, fragment_ids) vis_path = "vis_image.png" Image.fromarray(vis_image).save(vis_path) print(f"Wrote visualization to {vis_path}") # Obtain predicted masks, category_ids, and fragment_ids # Category IDs are {"SA": 1, "LI": 2, "RI": 3} # Fragment IDs are the integer labels from label_{category}.nii.gz, with 1 corresponding to the main fragment. pred_masks, pred_category_ids, pred_fragment_ids = masks, category_ids, fragment_ids # replace with your model # save the predicted masks for upload to the challenge # Note: cv2 does not work with uint32 images. It is recommended to use PIL or imageio.v3 pred_seg = pengwin_utils.masks_to_seg(pred_masks, pred_category_ids, pred_fragment_ids) pred_seg_path = "pred/train/output/images/x-ray/001_0000.tif" # ensure dir exists! Image.fromarray(pred_seg).save(pred_seg_path) print(f"Wrote segmentation to {pred_seg_path}")</code></pre> <p>The `pengwin_utils.Dataset` class is provided as an example of a Pytorch dataset, with strong domain randomization included to facilitate sim-to-real performance, but it is recommended to write your own as needed.</p>
Searching to improve connectivity in fragmented landscapes: Road verges as complementary habitats
<p><strong>Abstract</strong></p> <p><strong>Aims: </strong>Functional connectivity is crucial for conserving biodiversity and ecosystem services in fragmented landscapes. Linear landscape elements play an important role in providing refuge for plants and pollinators, as well as serving as biological corridors.<strong> </strong>The aim of this study was to assess the importance of road verges in maintaining the ecological connectivity of plant species assemblages in the Tandilia mountain system.</p> <p><strong>Location: </strong>South America. Southern Pampa region of Argentina. Tandilia mountain system.</p> <p><strong>Methods:</strong> Using graph theory, landscape connectivity was quantified both at landscape scale and at the patch scale using the probability connectivity index (PC<sub>num</sub>), taking into account the dispersal ability of observed species. The contribution of each landscape element to habitat availability and connectivity was evaluated using different fractions of the PC<sub>num</sub> metric. Likewise, the influence of connectivity variables in explaining species assemblages grouped by functional categories was investigated using canonical ordination techniques.</p> <p><strong>Results: </strong>The inclusion of road verges led to an 81% increase in overall connectivity at a threshold distance of 500 m. Connectivity significantly explained the assemblages of entomophilous plant species for all dispersal distances. Annual species assemblage variation was associated with intra-patch connectivity. Variation in perennial and shrub species assemblages was explained by intra-patch and inter-patch connectivity.</p> <p><strong>Conclusions: </strong>Preservation and restoration of these linear landscape elements play a pivotal role in transitioning towards more sustainable agroecosystems. This ecological and practical information may help prioritize plant species and the sites used to restore an essential but neglected ecosystem.</p> <p>This dataset includes: </p> <ol> <li>GPS coordinates for sampling sites.</li> <li>Data matrix includes sites x presence-absence of entomophilous plant species for the 54 sampling sites, 20 sierras and 34 rural road verges. The sierras are listed by name, while the road verges are identified by numbers.</li> </ol>
PanDDA analysis of fragment screen against the Nsp3 macrodomain of SARS-CoV-2 - P43 crystals at UCSF
<p>This deposition contains the X-ray diffraction data used for the PanDDA analysis of the fragment screen against the NSP3 macrodomain of SARS-CoV-2 described in Schuller et al. 2021 (DOI: 10.1126/sciadv.abf8711).</p> <p>A description of the files can be found in the "README" text file. </p> <p>The data in this deposition is from the fragment screen performed at UCSF using P43 crystals. The data from the fragment screen performed at UCSF using C2 crystals can be found here - https://zenodo.org/record/4716363 - in the zipped directory named "ucsf_nsp3_mac1_C2.zip". </p>
Fragmented sequences for mosquito-associated viruses and other viruses
<p>Fragmented fasta sequences associated with the manuscript Predicting novel mosquito-associated viruses from metatranscriptomic dark matter</p>
Fig. 3 in Reproductive success of Trypoxylon (Trypargilum) lactitarse (Hymenoptera: Crabronidae) in a fragmented landscape
Fig. 3. Example of the trap-nest blocks installed in the study areas in the state of Goiás, Brazil.
FEater dataset: A molecular fragment dataset to benchmark the robustness of 3D flexible object recognition
<p>This dataset is associated with the work: Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models</p> <pre><code># Original FEater-Single and FEater_Dual dataset. FEater_Single ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 FEater_Dual ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 # Non-redundant baseline dataset FEater_Baseline ├── TestSet_Dual.h5 ├── TestSet_Single.h5 ├── TrainingSet_Dual.h5 └── TrainingSet_Single.h5 # FEater-Single and FEater_Dual in different sample size FEater_Mini200 ├── Mini200_Dual.h5 └── Mini200_Single.h5 FEater_Mini400 ├── Mini400_Dual.h5 └── Mini400_Single.h5 FEater_Mini800 ├── Mini800_Dual.h5 └── Mini800_Single.h5</code></pre> <p>For further details of the usage, please visit the original GitHub repository: <a title="FEater_repo" href="https://github.com/miemiemmmm/FEater" target="_blank" rel="noopener">https://github.com/miemiemmmm/FEater</a></p>
DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway
<p><span>A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). <em>In vitro</em> biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of <em>E. coli</em> with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the <em>APP<sup>lon</sup></em> mutation in Alzheimer’s disease without disrupting the <em>APP<sup>wt</sup></em> locus. It is worth mentioning that the <em>APP<sup>lon</sup></em> sequence has only one base difference from that of <em>APP<sup>wt</sup></em>. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.</span></p>
Habitat fragmentation induces rapid phenotypic divergence of migratory and isolated sticklebacks
<p>The adaptive capacity of many organisms is seriously challenged by human-imposed environmental change, which currently happens at unprecedented rates and magnitudes. For migratory fish, habitat fragmentation is a major challenge that can compromise their survival and reproduction. Therefore, it is important to study if fish populations can adapt to such modifications of their habitat. Here, we study whether originally anadromous three-spined stickleback populations (Gasterosteus aculeatus; 'migrants') changed in behavior and morphology in response to human-induced isolation. We made use of a natural field-experiment, where the construction of pumping stations and sluices in the 1970s unintendedly created replicates of land-locked stickleback populations ('resident') in the Netherlands. For two years, we systematically tested populations of residents and migrants for differences in morphology and behavioral traits (activity, aggressiveness, exploration, boldness and shoaling) in lab-based assays. We detected differences between migrant and resident populations in virtually all phenotypic traits studied: compared to the ancestral migrants, residents were smaller in size, had fewer and smaller plates and were significantly more active, aggressive, exploratory and bolder and shoaled less. Despite large ecological differences between 2018 and 2019, results were largely consistent across the two years. Our study shows that human-induced environmental change has led to the rapid and consistent morphological and behavioral divergence of stickleback populations in about 50 generations. Such changes may be adaptive but this remains to be tested.</p>
Rapid morphological change in a small mammal species after habitat fragmentation over the past half-century
<p><b>Study Aim:</b> To compare the rapid shifts in body size of mainland and island populations of a native rodent and examine the mechanisms underlying these changes.</p> <p><b>Location:</b> Thousand Island Lake, China, which was created in 1959 when the Xin'anjiang Dam was constructed for generating hydroelectricity.</p> <p><b>Taxon:</b> The Chinese white-bellied rat, <i>Niviventer confucianus</i>.</p> <p><b>Methods</b>: Field surveys were conducted from 2015 to 2018 to collect data on body size of the rodents from a set of islands and nearby mainland sites. We constructed multiple linear models to examine the relationships between body size (length and mass) of rodents and biological variables (predators, interspecific and intraspecific competitors, and food availability). We also conducted structural equation modeling (SEM) by constructing models via confirmatory path analysis.</p> <p><b>Results: </b>All island populations of <i>N. confucianus</i> had significantly larger body size (both body mass and body length) than their mainland counterparts. Moreover, populations on small and more isolated islands had larger body size than their relatives on big islands. The relative absence of predators (large-bodied mammals, snakes, and raptors) on islands was most strongly associated with shifts in the body size of rodents. The documented changes occurred after only a half-century of fragmentation.</p> <p><b>Main conclusions: </b>The observed rapid body enlargement of rodents after habitat fragmentation is consistent with a release from predation pressure. SEM indicated that island area, rather than island isolation, had positive effects on the richness of predators, interspecific competitors and food resources, which then had an indirect impact on body size of the rodents. In this study, we report a remarkably rapid case of mammal morphological shifts in a small mammal in response to habitat fragmentation. Given the omnipresence of dams and other anthropogenic disturbances, our findings suggest that a wave of rapid phenotypic shifts in terrestrial vertebrates is taking place in the Anthropocene.</p>
Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves
<p><i>Chalcophaps</i> is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of <i>Chalcophaps</i>. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized <i>Chalcophaps </i>species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies <i>C. longirostris timorensis, </i>raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the <i>Chalcophaps</i> doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.</p>
Nanopore MinION Run Metrics and genomic DNA fragment size analysis data from automated phenol-chloroform extractions (RBI LabDroid Maholo)
<p>Nanopore MinION run MinKNOW statistical metrics output, Agilent Femto Pulse and Tape Station gDNA fragment size analysis reports of genomic DNA isolated from automated RBI LabDroid Maholo organic extractions.</p>
Benchmark set inputs for absolute binding free energy calculations of fragment optimisations
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Provided here are the various scripts, input files, and results necessary to reproduce the outcomes of the above mentioned publication. Please see the provided README.md files for further information on the contents of this dataset.</p>
Data from: Survival of polycyclic aromatic hydrocarbon knockout fragments in the interstellar medium
<p>Original and published data for the paper "Survival of polycyclic aromatic hydrocarbon knockout fragments in the interstellar medium", published in Nature Communications, from measurements at the DESIREE facility. See original publication for experimental details.</p> <p> </p> <p><strong>Folder structure:</strong></p> <p><em>Raw_Data</em> contains the raw particle-detector data obtained from the measurements as csv-files in two separate subdirectories. The <em>Beam_Dump</em> folder contains measurements where the ion beam is dumped onto a detector after a different time delays. The <em>Spontaneous_Decay</em> folder contains measurements of neutral particle counts as a function of ion storage time. Metadata is present in the included json-files.</p> <p>Figure_Data contains the processed data presented in the figures of the original publication as csv-files. Metadata is present in the included json-file.</p>
From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation
<p>Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management.</p> <p>We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modeling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density).</p> <p>In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes.</p> <p>When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner.</p> <p><em>Synthesis and applications</em>: Matrix improvement and connectivity modeling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.</p>
ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries
<p>This dataset contains the library produced by the ProtNAff tool for the paper.</p> <p>The files are in the numpy format matrix.</p> <p>There are files for the reduced and the all atoms fragments.</p>
Parasitization of bats by bat flies (Streblidae) in fragmented habitats
Parasites represent a large fraction of the world's biodiversity. They control host population sizes and contribute to ecosystem functioning. However, surveys on species diversity rarely include parasitic species. Bats often present traits favoring parasite diversity, such as large home ranges, long life spans, and large colonies. The most conspicuous bat parasites are the highly host specific, blood-sucking bat flies (Diptera: Streblidae, Nycteribiidae). Recent studies have found a direct effect of habitat alteration on the abundance of bat species. We expected, therefore, that changes in the host community in response to anthropogenic habitat modification will also result in changes in the associated parasite community. We captured bats in three different habitats in Central Panama between 2013 and 2015. We recorded information on prevalence and intensity of bat fly parasitization of the seven most commonly captured bat species. Prevalence and intensity were both significantly influenced by roost type, abundance, and host sex and age. We found that habitat variables and matrix type significantly influenced the prevalence and intensity of parasitization, while the direction of the responses were host species- and parasite species-specific. In general, roosting conditions and behavior of host bats appear to be fundamental in explaining changes in prevalence and intensity of parasitization between different habitat types, as bat flies are bound to the roost during their reproductive cycle. Habitat alterations affects next to the host community composition also the availability of possible roost structures as well as microclimatic conditions, which all three reflect in parasitization.
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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.