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150 results for “data fusion”
Data from: Fusion or hypertrophy?: The unusual arms of the Petalocrinidae (Ordovician-Devonian; Crinoidea)
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Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm
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Data from: Similar but different: dynamic social network analysis highlights fundamental differences between the fission-fusion societies of two equid species, the onager and Grevy's zebra
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Data from: Post-embryonic development of Dalmanitina, and the evolution of facial suture fusion in Phacopina
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A 15-year full-coverage daily PM1 dataset across China based on a data-fusion model
<p>The long-term (2004-2018) full-coverage daily PM<sub>1</sub> dataset across China was developed based on a stacking decision tree model assimilating satellite data, meteorological variables, and other geographical covariates. The PM<sub>1</sub> dataset captured a strong prediction capability with a high cross-validation (CV) R<sup>2</sup> value (0.64), and the low root-mean-square error (RMSE: 18.60 μg/m<sup>3</sup>) and moderate absolute error (MAE: 11.96 μg/m<sup>3</sup>). The long-term PM<sub>1</sub> dataset obtained here provide a key scientific basis and data support for epidemiological research and air pollution mitigation.</p>
Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
The replication and segregation of the multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO (pKAL). During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a 'Kalilo' culture started significantly increased the maximum lifespan and variation in life span among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing.
Data from: Direct transfer of learned behaviour via cell fusion in non-neural organisms
Cell fusion is a fundamental phenomenon observed in all eukaryotes. Cells can exchange resources such as molecules or organelles during fusion. In this paper, we ask whether a cell can also transfer an adaptive response to a fusion partner. We addressed this question in the unicellular slime mould Physarum polycephalum, in which cell–cell fusion is extremely common. Slime moulds are capable of habituation, a simple form of learning, when repeatedly exposed to an innocuous repellent, despite lacking neurons and comprising only a single cell. In this paper, we present a set of experiments demonstrating that slime moulds habituated to a repellent can transfer this adaptive response by cell fusion to individuals that have never encountered the repellent. In addition, we show that a slime mould resulting from the fusion of a minority of habituated slime moulds and a majority of unhabituated ones still shows an adaptive response to the repellent. Finally, we further reveal that fusion must last a certain time to ensure an effective transfer of the behavioural adaptation between slime moulds. Our results provide strong experimental evidence that slime moulds exhibit transfer of learned behaviour during cell fusion and raise the possibility that similar phenomena may occur in other cell–cell fusion systems.
Data from: Clinical decision making in spinal fusion for chronic low back pain. Results of a nationwide survey among spine surgeons
OBJECTIVES: To assess the use of prognostic patient factors and predictive tests in clinical decision making for spinal fusion in patients with chronic low back pain. DESIGN AND SETTING: Nationwide survey among spine surgeons. PARTICIPANTS: Surgeon members of the Dutch Spine Society were questioned on their treatment strategy for chronic low back pain. PRIMARY AND SECONDARY OUTCOME MEASURES: The surgeons' opinion on the use of prognostic factors and tests for patient selection were addressed, and the degree of uniformity was assessed. In addition, the influence of surgeon specific factors, such as clinical experience and training, was determined. RESULTS: The comments from 62 surgeons (70% response rate) were analysed. Forty-four surgeons (71%) had extensive clinical experience. There was a statistically significant lack of uniformity of opinion in 7 of the 11 items on prognostic factors and 8 of the 11 items on predictive tests, respectively. Imaging was valued much higher than predictive tests, psychological screening, or patient preferences (all p<0.01). Apart from the use of discography and long multi-segment fusions, differences in training or clinical experience did not appear to be of significant influence on treatment strategy. CONCLUSIONS: The present survey showed a lack of consensus among spine surgeons on the use of predictive tests for patient selection. Prognostic patient factors were not consistently incorporated in their treatment strategy. Clinical decision making for spinal fusion to treat chronic low back pain does not have a uniform evidence base in practice. Future research should focus on identifying subgroups of patients for whom spinal fusion is an effective treatment. Only a reliable prediction of surgical outcome, combined with the implementation of individual patient factors, may enable the instalment of consensus guidelines in surgical decision making for chronic low back pain.
Data from: Extending phylogeography to account for lineage fusion
Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical framework—approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (400 bp) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.
Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels - additional data
<p>This repository stores additional data files for the article Rozenberg, Kaczmarczyk, Matzov, Vierock et al (2022) "<a href="https://doi.org/10.1038/s41594-022-00783-x">Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels</a>".</p> <p>The files included are as follows:</p> <ul> <li>Inputs.zip - all input files to <a href="https://github.com/BejaLab/RRB">the workflow</a> (also available there)</li> <li>Species phylogenies: <ul> <li>Chlorophyte_orthogroups.zip, Haptophyte_orthogroups.zip, Dinoflagellate_orthogroups.zip - zip files with the orthogroups used in species phylogeny. Each folder corresponds to an orthogroup (busco orthogroups for chlorophytes and dinoflagellate, proteinortho orthogroups for haptophytes): <ul> <li>mafft.faa - mafft alignment</li> <li>trimal.faa - trimal trimmed alignment</li> <li>iqtree.treefile and iqtree.log - iqtree tree and log file</li> <li>treeshrink.treefile - treeshrink pruned tree</li> </ul> </li> </ul> </li> <li>Structural_alignment.zip includes structural alignments of the bestrhodopsin's rhodopsin and bestrophin domains with reference sequences: <ul> <li>rhodopsins.aln and bestrophins.aln- raw alignments from t_coffee</li> <li>rhodopsins_modified.fasta and bestrophins_modified.fasta - curated alignments</li> <li>rhodopsins.gff and bestrophins.gff - secondary structure features for the sequences</li> </ul> </li> <li>Global phylogeny of bestrophins and rhodopsins: <ul> <li>Bestrophins_global_sequences.zip - sequence data for the bestrophin global phylogeny: <ul> <li>uniref50.txt - uniref50 tabular data matching bestrophins (Pfam PF01062)</li> <li>ur50_long.cdhit, ur50_long.cdhit.clstr - cdhit clustering (50% identity)</li> <li>ur50_trim.faa - filtered and trimmed alignment used as input to iqtree</li> </ul> </li> <li>Bestrophins_global_phylogeny.zip - global bestrophin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick ur50.treefile files.</li> <li>Rhodopsins_global_phylogeny.fasta, Rhodopsins_global_phylogeny.fasta.trimmed - alignment of rhodopsin sequences and its trimmed version as used for rhodopsin bestrophin phylogeny</li> <li>Rhodopsins_global_phylogeny.zip - global rhodopsin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick rhodopsins.treefile files</li> <li>Rhodopsins_global_phylogeny_interproscan.zip - results of interproscan analysis of the rhodopsin sequences used for global phylogeny</li> </ul> </li> </ul>
Experimental data used in the publication :" Investigation of the Effects of Various Severe Plastic Deformation Techniques on the Microstructure of Laser Powder Bed Fusion AlSi10Mg Alloy"
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Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression
The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.
Data from: Fusion pore regulation by cAMP/Epac2 controls cargo release during insulin exocytosis
Regulated exocytosis establishes a narrow fusion pore as initial aqueous connection to the extracellular space, through which small transmitter molecules such as ATP can exit. Co-release of polypeptides and hormones like insulin requires further expansion of the pore. There is evidence that pore expansion is regulated and can fail in diabetes and neurodegenerative disease. Here we report that the cAMP-sensor Epac2 (Rap-GEF4) controls fusion pore behavior by acutely recruiting two pore-restricting proteins, amisyn and dynamin-1, to the exocytosis site in insulin-secreting beta-cells. cAMP elevation restricts and slows fusion pore expansion and peptide release, but not when Epac2 is inactivated pharmacologically or in Epac2-/- (Rapgef4-/-) mice. Consistently, overexpression of Epac2 impedes pore expansion. Widely used antidiabetic drugs (GLP-1 receptor agonists and sulfonylureas) activate this pathway and thereby paradoxically restrict hormone release. We conclude that Epac2/cAMP controls fusion pore expansion and thus the balance of hormone and transmitter release during insulin granule exocytosis.
Retrospective/Prospective Data Collection on the LDR ROIC Interbody Fusion Device With VerteBRIDGE Plating
ClinicalTrials.gov study NCT02104167. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Deep Learning With MRI-based Multimodal-data Fusion Enhanced Postoperative Risk Stratification of Breast Cancer
ClinicalTrials.gov study NCT06546072. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Data from: Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition
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Data from: Alterations of gray and white matter networks in patients with obsessive-compulsive disorder: a multimodal fusion analysis of structural MRI and DTI using mCCA+jICA
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Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
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Data from: Fusion pore regulation by cAMP/Epac2 controls cargo release during insulin exocytosis
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Data from: Clinical decision making in spinal fusion for chronic low back pain. Results of a nationwide survey among spine surgeons
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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.