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54 results for “pruning”
Code for: MHC Heterozygosity Prunes the Numbers of Different T Cell Receptors Expressed in CD4 T Cells
<p>Contains source data file and code for publication "MHC Heterozygosity Prunes the Numbers of Different T Cell Receptors Expressed in CD4 T Cells".<br>Associated FASTQ files are deposited on the NIH SRA under accession: PRJNA1106276</p>
Limited effect of thermal pruning on wild blueberry crop and its root-associated microbiota - Agricultural dataset
<p>These datasets contain all the agricultural data (soil chemistry, blueberry performance, weeds and diseases...) used in our study.</p>
Gajderowicz, B., Fisher, A., Mago, V.: (preperation) "Graph pruning for identifying COVID-19 misinformation dissemination patterns and indicators on Twitter/X"
<p>This dataset is for the repository <a href="https://github.com/bgajdero/social-graph-analysis-2024">https://github.com/bgajdero/social-graph-analysis-2024</a>.</p>
Effects of powdered cactus pear pruning amendment on the physical and hydraulic properties of two contrasting Mediterranean soils
<p>Full database.</p> <p>A production and consumption paradigm known as "circular economy" (CE) emphasizes sharing, renting, reusing, repairing, refurbishing, and, in particular, recycling materials as much as feasible. Traditional agriculture relied totally on the CE, progressively the search for maximization of yields has produced more and more by-products. Their recovery and reuse are possible with approaches that refer to the CE, for example, with the use of pruning biomasses. The cultivation of the cactus pear annually produces large quantities of pruning residues, which have been shown to be useful for the recovery and reuse of nutrients. This study investigates the hydraulic properties of benchmark soils in which this by-product is incorporated. Here we show that the amendment with powdered cactus pear pruning waste (PCPPW) positively affects soil water retention. However, observable benefits require very high amendment proportions, more than 20% by volume. These quantities make use in the open field unrealistic but offer perspectives in the horticultural and floricultural sectors. These results reveal agreement in direct comparison to what was thought to be the case previously, i.e., a decrease in soil bulk density, an increase in plant available water capacity and an increase in soil swelling. A few per cent application of PCPPW improves the drainable water capacity only in the case of not very clayey soils, where their use becomes useless. The principles of the CE are important, but they must not be pursued a priori. For example, in the use of soil amendments, the behavior in the different soils conditions the suitability of their use.</p>
Formatted Public GWAS Summary Statistics for 16 Traits and LD pruned SNP sets
<p>This data set includes 16 files with formatted GWAS summary statistic and a csv file gwas_info.csv. The csv provides the original download link and publication for each study. The data in this repository were created by downloading raw summary statistics for each study and processing them using Joe Marcus' GWAS pipeline (https://github.com/jhmarcus/gwass). The resulting data set have consistent allele orientation and column headers making them convenient for analysis. We use them in an MR analysis of pairs of GWAS traits described in Section 2.3 of Morrison et al (2019) (https://www.biorxiv.org/content/10.1101/682237v3) and here https://jean997.github.io/cause/gwas_pairs.html.</p> <p>New Sep 2022: I have added LD pruned SNP sets for each pair of traits.For each exposure/outcome pair, the set of snps in</p> <p>snps_<exposure>__<outcome>.txt</p> <p>were generated by LD pruning using LD estimated using LD Shrink (available https://zenodo.org/record/1464357/) at a threshold of r^2 < 0.1. LD pruning was performed using the ld_prune function in the cause R package (github.com/jean997/cause). These are the SNP sets used in the analysis in the paper</p>
Artifact for Paper Search-Space Pruning with Int-Splits for Faster QBF Solving
<p>This is the artifact for the paper "Search-Space Pruning with Int-Splits for Faster QBF Solving" submitted to the <a href="http://satisfiability.org/SAT23/">SAT2023</a> conference.</p>
Prunes for Gastrointestinal Function After Gynecologic Surgery
ClinicalTrials.gov study NCT03523715. IPD Sharing: NO. Countries: 1. Publications: 6.
Pre-trained DNN model data for pruning example code
<p>Pre-trained DNN model datasets for example codes of neural network pruning.</p> <p>Example pruning codes are published in "https://github.com/FujitsuLaboratories/CAC/tree/main/cac/pruning".</p>
Pre-trained neural network model for pruning example code
<p>Pre-trained neural network models for example codes of neural network pruning.</p> <p>Example pruning codes are published in "https://github.com/FujitsuResearch/automatic_pruning".</p>
text-fig. 54. Reduced consensus tree of the pruned data matrix after the deletion of Shuvosaurus, Segisaurus, and Poekilopleuron. Named nodes: 1, Saurischia; 4, Herrerasauridae; 5, Neotheropoda; 6, Coelophysoidea; 8, Coelophysidae; 9, Liliensternus', 12, Ceratosauria; 13, Abelisauroidea; 14, etanurae; 16, Camosauria; 17, Spinosauroidea; 20, Allosauroidea; 24, Coelurosauria; 26, Coeluridae; 27, Compsognathinae; 30, Tyrannosauroidea; 34, Maniraptora; 37, Deinonychosauria. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 54. Reduced consensus tree of the pruned data matrix after the deletion of Shuvosaurus, Segisaurus, and Poekilopleuron. Named nodes: 1, Saurischia; 4, Herrerasauridae; 5, Neotheropoda; 6, Coelophysoidea; 8, Coelophysidae; 9, Liliensternus', 12, Ceratosauria; 13, Abelisauroidea; 14, etanurae; 16, Camosauria; 17, Spinosauroidea; 20, Allosauroidea; 24, Coelurosauria; 26, Coeluridae; 27, Compsognathinae; 30, Tyrannosauroidea; 34, Maniraptora; 37, Deinonychosauria.
text-fig. 53. Strict consensus tree resulting from the analysis of the pruned data matrix with 51 taxa. Numbers at the nodes indicate bootstrap support values in branches that have more than 50 per cent support. The consensus tree is based on 5544 trees of 652 steps (CI 0-42, RI 0-748, RCI 0-314). in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 53. Strict consensus tree resulting from the analysis of the pruned data matrix with 51 taxa. Numbers at the nodes indicate bootstrap support values in branches that have more than 50 per cent support. The consensus tree is based on 5544 trees of 652 steps (CI 0-42, RI 0-748, RCI 0-314).
Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
Figure 14. Pruned maximum credibility Bayesian trees. Dataset C in Redescription of the skull of the Australian flatback sea turtle, Natator depressus, provides new morphological evidence for phylogenetic relationships among sea turtles (Chelonioidea)
Figure 14. Pruned maximum credibility Bayesian trees. Dataset C based on the matrix from Evers & Benson (2019). Dataset D based on matrix from Evers & Benson (2019) with added characters found in this study. Colours at nodes represent base of clades. Numbers at the node show posterior probability value of node.
Prune Consumption and Bone Health in Young Women Using Hormonal Contraceptives
ClinicalTrials.gov study NCT04785131. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Kiwifruit, Prunes, & Fiber for Abdominal and Bowel Symptoms in US Patients With Chronic Constipation
ClinicalTrials.gov study NCT03569527. IPD Sharing: NO. Countries: 1. Publications: 2.
Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Open the record for dataset details and reuse information.
Local externalization of phosphatidylserine mediates developmental synaptic pruning by microglia
<p>Neuronal circuit assembly requires the fine balance between synapse formation and elimination. Microglia, through the elimination of supernumerary synapses, have an established role in this process. While the microglial receptor TREM2 and the soluble complement proteins C1q and C3 are recognized as key players, the neuronal molecular components that specify synapses to be eliminated are still undefined. Here, we show that exposed phosphatidylserine (PS) represents a neuronal "eat-me" signal involved in microglial-mediated pruning. In hippocampal neuron and microglia co-cultures, synapse elimination can be partially prevented by blocking accessibility of exposed PS using Annexin V or through microglial loss of TREM2. In vivo, PS exposure at both hippocampal and retinogeniculate synapses and engulfment of PS-labeled material by microglia occurs during established developmental periods of microglial-mediated synapse elimination. Mice deficient in C1q, which fail to properly refine retinogeniculate connections, have elevated presynaptic PS exposure and reduced PS engulfment by microglia. These data provide mechanistic insight into microglial-mediated synapse pruning and identify a novel role of developmentally regulated neuronal PS exposure that is common among developing brain structures.</p>
Data from: Supertrees based on the subtree prune-and-regraft distance
Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of simulated benchmark datasets, we show that SPR supertrees are more similar to correct species histories under plausible rates of LGT than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera; a small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT.
Data from: Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice
The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive web-service implementing this algorithm. Compared to our previous method, the new algorithm is up to four orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world datasets, we show that, our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116,334 taxa each. Using simulated datasets we show that, when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum likelihood trees that are topologically closer to the respective true trees.
Pruned DNN model data for pruning example code
<p>Pruned DNN model datasets for example codes of neural network pruning.</p> <p>Example pruning codes are published in "https://github.com/FujitsuLaboratories/CAC/tree/main/cac/pruning".</p>
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International Brain Laboratory public data
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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.