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7,370 results for “supplementation”
Dataset S7: Oxfordiana motturii gen. et sp. nov. supplemental information (SRXMT data for slide BU 5266.30)
<p><strong>Dataset S7.</strong> SRXMT 8-bit BMP tomographic dataset of slide BU 5266.30. The dataset consists of 701 8-bit bitmap images compressed as a ZIP archive. Image brightness/contrast optimized and despeckling applied. Note that images from the tomographic stack beginning and end, without specimen data present, have not been included. [ZIP/BMP format 7.6 GB]</p>
Dataset S5: Oxfordiana motturii gen. et sp. nov. supplemental information (SRXMT data for BU 5265.3)
<p><strong>Dataset S5.</strong> SRXMT 8-bit BMP tomographic dataset of BU5265.3. The dataset consists of 1200 8-bit bitmap images compressed as a ZIP archive. Image brightness/contrast optimized and despeckling applied. Note that images from the tomographic stack beginning and end, without specimen data present, have not been included. [ZIP/BMP format 10.4 GB]</p>
Dataset supplementing Lichtenberg et al. (2017) Foraging traits modulate stingless bee community disassembly under forest loss. Journal of Animal Ecology
<p>This dataset contains data and scripts that supplement the publication</p> <p>Lichtenberg et al. (2017) Foraging traits modulate stingless bee community disassembly under forest loss. Journal of Animal Ecology. DOI 10.1111/1365-2656.12747.</p> <p> </p> <p>Please cite the above article if you use any of the included data or code.</p> <p> </p> <p>Files are described in README.md.</p>
Supplemental data for "The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma"
<div># List of files on Zenodo</div> <p> </p> <div>Data accompanying the manuscript have been uploaded on Zenodo (10.5281/zenodo.14185694). Here we</div> <div>present a brief description of each file and put them in meaningful groups.</div> <p> </p> <div>## referenced supplement</div> <p> </p> <div>(Cited) supplementary material from the manuscript. For more information, please refer to the figure/table legends and the supplementary file descriptions.</div> <p> </p> <div> <div>- add-file-01.pdf</div> <div>- add-file-02-table1-data_overview.tsv</div> <div>- add-file-03-table2-genome_progress.tsv</div> <div>- add-file-04-table3-Pycnognonum_microRNAs.tsv</div> <div>- add-file-05-table4-named_genes.tsv</div> <div>- add-file-06-table5-abdA.tsv</div> <div>- add-file-07-hox_tree.pdf</div> <div>- add-file-08-table6-r2_g3735-Alignment-HitTable.tsv</div> <div>- add-file-09-hro_tree.pdf</div> <div>- add-file-10-irx_tree.pdf</div> <div>- add-file-11-sine_tree.pdf</div> <div>- add-file-12-nk_tree.pdf</div> <div>- add-file-13-dbx.png</div> <div>- add-file-14-alignment.pdf</div> <div>- add-file-15-Plit_COI-alignment_distances.pdf</div> <div>- add-file-16-table7-isoseq.tsv</div> <div>- add-file-17-table8-chelicerate_repeat_content.tsv</div> <div>- add-file-18-table9-arthropod_genomes.tsv</div> <div>- add-file-19-table10-arthropod_repeat_content.tsv</div> <div>- add-file-20-table11-chelicerate_genomes.tsv</div> <div>- add-file-21-gene_analysis.zip</div> <div>- add-file-22-table12-self_synteny.tsv</div> </div> <p> </p> <div>## figures</div> <p> </p> <div>- figs.zip: archive of raw and processed figures for the manuscript in full resolution</div> <p> </p> <div>## analysis</div> <p> </p> <div>### genomic context</div> <p> </p> <div>The broader arthropod/chelicerate context for the _P. litorale_ genome assembly.</div> <p> </p> <div>- araneae.tsv: repeat makeup of published chelicerate assemblies</div> <div>- arthropoda.tsv: genome assembly statistics for arthropod genomes. From NCBI Genomes.</div> <div>- modern_taxids.txt: list of taxonomic IDs for species; made to be submitted to NCBI Taxonomy.</div> <div>- tax_report.txt: the full taxonomic report for each query species. Contains tax IDs for the entire lineage.</div> <div>- total_repeats.tsv: total repeat content of published chelicerate genomes.</div> <p> </p> <div>### Homeobox genes</div> <p> </p> <div>Files concerning the Homeobox gene cluster analysis. Each folder (hro, irx, nkx, sine) contains the</div> <div>candidate sequences from Aase-Remedios et al., the P. litorale sequences that matched, the multiple</div> <div>sequence alignment, the trimmed alignment, and the tree files.</div> <p> </p> <div>Additionally, the hox/ folder contains the analysis done for the AbdA gene, with searches performed</div> <div>against the de-novo assembled transcriptomes (.m8 files).</div> <p> </p> <div>Finally, the r2_g3735/ folder contains the analysis of the r2_3735 gene model, which is found in the</div> <div>Hox cluster area on the P. litorale genome. Sequence searches against NCBI nr and the developmental</div> <div>transcriptomes show that the gene has putative homologs in other taxa and is expressed throughout</div> <div>development.</div> <p> </p> <div>## processed (intermediate) data</div> <p> </p> <div>### 00-kmer-jellyfish.zip</div> <p> </p> <div>k-mer spectra analysis with GenomeScope and GenomeScope2.0</div> <p> </p> <div>### 00-seq-qc.zip</div> <p> </p> <div>quality control output for raw sequencing data (e.g. FastQC output)</div> <p> </p> <div>### 01-assembly</div> <p> </p> <div>- assembly_graph.gfa: Flye output</div> <div>- assembly_graph.gv: Flye output</div> <div>- assembly_info.txt: Flye output</div> <div>- assembly.fasta: Flye output</div> <div>- backmap.hifi.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped PacBio data</div> <div>- backmap.ont.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped ONT data</div> <div>- BUSCO.arthropoda_odb10.txt: BUSCO completeness report (arthropoda_odb10)</div> <div>- BUSCO.metazoa_odb10.txt: BUSCO completeness report (metazoa_odb10)</div> <div>- flye.log: Flye assembler log</div> <div>- quast_report.pdf: assembly QC</div> <p> </p> <div>### 02-scaffold</div> <p> </p> <div>`yahs` output files:</div> <p> </p> <div>- asm_hic.sorted.bam</div> <div>- flye-yahs.fa</div> <div>- yahs.out_scaffolds_final.agp</div> <div>- yahs.out_scaffolds_final.fa.hic</div> <div>- yahs.out_scaffolds_final.fa.assembly</div> <p> </p> <div>Juicebox (manual curating) results:</div> <p> </p> <div>- yahs.out_scaffolds_final.fa.review.assembly</div> <div>- 02-flye-yahs-juicebox.fa</div> <p> </p> <div>GAP `sort_scaffolds` pipeline outputs</div> <p> </p> <div>- 03-flye-yahs-juicebox-merge.fasta</div> <div>- plit_q_0_50000_0.5FracBest_unseen_scaffolds.txt</div> <div>- plit_q_0_50000_0.5FracBest_insertion_stats.tsv</div> <div>- plit_q_0_50000_0.5FracBest_appended_scaffolds.tsv</div> <div>- plit_q_0_50000_0.5FracBest_inserted_scaffolds.tsv</div> <p> </p> <div>### 03-contamination</div> <p> </p> <div>Refer to the [contamination analysis](https://github.com/galicae/plit-genome/blob/main/04-contam/README.md) for details.</div> <p> </p> <div>Decontaminating the draft genome from non-metazoan scaffolds:</div> <p> </p> <div>- plit_q_0_50000_0.5FracBest_output_filtered.fasta: input draft genome</div> <div>- contam_tax.m8: Alignment results of UniRef90 against draft genome (MMseqs2)</div> <div>- scaffolds_taxonomic_distribution.tsv: summary of contam_tax.m8; number of genes from each taxonomic level per scaffold.</div> <div>- scaffolds_taxonomic_distribution_collapsed_vir.tsv: scaffolds with predominantly viral hits</div> <div>- scaffolds_taxonomic_distribution_suspect.tsv: scaffolds whose genes are <90% metazoan</div> <p> </p> <div>Checking for widespread _Metridium_ contamination:</div> <p> </p> <div>- primary_mq30.txt: list of high-quality mapping reads (presumptive "metridial")</div> <div>- metridium_scaffolds.txt_summary: no. of presumptive _Metridium_ reads per draft scaffold</div> <div>- metridium_scaffolds.txt: filtered SAM file with all high-quality "_Metridium_" hits on draft scaffolds</div> <div>- metridium_contigs.sam_summary: no. of presumptive _Metridium_ reads per Flye contig</div> <p> </p> <div>### 04-annotation</div> <p> </p> <div>Repeat analysis with RepeatModeler/RepeatMasker:</div> <p> </p> <div>- draft.fasta.tbl: output of RepeatModeler in tabular form</div> <div>- pb.sam.flagstats: summary of mapping the repeat families to the PacBio data.</div> <div>- pycno-families.fa: output of RepeatModeler - the sequences of the _P. litorale_ repeat families</div> <div>- draft.fasta.out.gff: output of RepeatModeler - repeat locations on the draft genome</div> <p> </p> <div>Protein coding gene annotation:</div> <p> </p> <div>- annot-01-isoseq.gff: GFF file with the gene models proposed using Iso-seq isoforms</div> <div>- annot-01-braker.gff: GFF file with the gene models proposed from round 1 of BRAKER3 using developmental transcriptomes</div> <div>- annot-02-braker.gff3: GFF file with the gene models proposed from round 2 of BRAKER3, using developmental transcriptome reads that weren't used in round 1</div> <div>- annot-03-denovo.gff3: GFF file with the gene models proposed from the de novo transcriptomes</div> <div>- deep_denovo_assemblies.zip: the de-novo assembled transcriptomes from the deeply sequenced developmental time points. Also available on ENA.</div> <p> </p> <div>tRNAscan output</div> <p> </p> <div>- trnascan.bed</div> <div>- trnascan.out</div> <div>- trnascan.fasta</div> <div>- trnascan.stats</div> <p> </p> <div>MirMachine output</div> <p> </p> <div>- Pli_september.PRE.gff: MirMachine output with permissive threshold</div> <div>- Pli_september.PRE-1.gff: MirMachine output with strict threshold</div> <div>- Pli_september.PRE.fasta: predicted miRNA sequences</div> <p> </p> <div>## Results</div> <p> </p> <div>- draft_softmasked.fasta: draft genome with repetitive regions softmasked</div> <div>- draft.fasta: draft genome fasta</div> <div>- hox.gff3: the position of the Hox genes in GFF3 form.</div> <div>- merged_sorted_named_dedup_flagged.gff3: protein-coding gene models from all rounds of annotation after deduplication</div> <div>- transcripts.fa: TransDecoder-extracted putative transcripts</div> <div>- transcripts.fa.transdecoder.pep: TransDecoder predicted peptides</div> <div>- out.emapper.annotations: EggNOG-mapper functional annotation for the predicted peptides</div> <div>- out.emapper.best.annotations: filtered EggNOG-mapper annotation; best hit per gene kept</div> <div>- miRNA.fasta: FASTA sequences of predicted miRNAs</div> <div>- miRNA.lenient.gff: GFF of miRNA positions (permissive MirMachine cutoff)</div> <div>- miRNA.strict.gff: GFF of miRNA positions (strict MirMachine cutoff)</div>
Supplemental material and additionnal files
<p>5 files are available for the study "Ploidy determination and diploid phylogenetics from multiple targeted nuclear loci in circumpolar <i>Silene</i> sect. <i>Physolychnis </i>(Caryophyllaceae)":</p><p>-STACEY_42genes_56samples_genetreesremoved.xml to run STACEY analyses</p><p>-variants_count.sh a pyton script to calculate the genetic pairwise distance between phased haplotypes</p><p>-supplemental_material_Table_S1.xlsx includes voucher information and samples re-identification</p><p>-supplemental_material_TABLE_S2_Probes48loci_ExonPos.xlsx includes information about the probes and the exons-introns boundaries</p><p>-supplemental_material_TABLE_S3_metrics.xlsx includes information about the sequencing success</p><p> </p><p> </p>
Effects of high dietary zinc supplementation timing on the biological responses of gestating sows and their piglets
<p class="MsoNormal">High dietary zinc (Zn) fed to gestating sows may have utility as a fetal imprinting strategy to decrease pre-weaning mortality of piglets. However, the biological action that Zn may work through is unknown. High Zn may modulate the microbiome of the sow and the microbial seeding of the offspring's gut microbiome. Additonally, high dietary Zn and piglet birth weight may alter gene expression in piglet whole blood. Sows (n = 267) were fed 1 of 3 dietary treatments: 1) Control: a corn-soybean meal-based diet containing 125 ppm total supplemental zinc, 2) Breed-to-Farrow: as Control + 141 ppm supplemental Zn as ZnSO<sub>4 </sub>fed from 5 days post-breeding to farrowing; and 3) Day 110-to-Farrow: as Control + 2,715 ppm supplemental Zn as ZnSO<sub>4 </sub>starting on day 110 of gestation until farrowing. A subset of third parity sows (n = 30) were selected to assess the microbiome of colostrum, milk, and rectal and vaginal surfaces of sows. At farrowing, 4 pigs per litter (n = 120) were selected based on birthweight (BiW), as 2 average BiW pigs and 2 pigs with BiW below the litter average were selected for assessing the piglet gut microbiome on the day of birth (day 0) and day 5 of age. 16S rRNA sequencing were implemented for milk and colostrum samples while all other sample types were sequenced using shotgun metagenomics to determine taxonomic and functional profiles. On a different subset of pigs, whole blood was collected from 9 LBW pigs per treatment and 8 ABW Control pigs for RNA-sequencing to evaluate differentially expressed genes (DEGs) and pathways. Only 2 to 3 genes were differentially expressed between Control LBW and LBW pigs born to sows fed high Zn. However, 262 DEGs were identified when comparing LBW and ABW pigs, mostly reflecting pathways associated with translation, ribosome biogenesis, and amino acid and protein synthesis. Measures of alpha diversity (richness and Shannon's H Index) and beta diversity (Bray-Curtis, PERMANOVA) were conducted along with indicator species analyses. Species with an indicator value of > 0.50 were confirmed with a generalized linear mixed model as each <em>P</em>-value was corrected for false discovery rate (FDR) to generate a Q-value. For piglet samples, the MaAsLin2 R package was used to determine multivariate associations between dietary treatment and piglet BiW. High dietary concentrations of Zn fed to gestating sows did not affect the colostrum, milk, or vaginal microbial diversity or populations of sows. Pathogenic bacteria such as <em>Shigella flexneri </em>and <em>Salmonella enterica</em> were less abundant in fecal samples from Breed-to-Farrow sows compared to Control sows. For piglets born to Breed-to-Farrow sows, their gut microbiome favored fiber fermenting, short chain fatty acid generating microbial species compared to Control pigs. Day 110-to-Farrow piglets demonstrated a lower abundance of SCFA producing bacteria compared to Control piglets. Gene families and pathways playing roles in central metabolic functions (starch, pyruvate, sucrose, amino acid metabolism) were more abundant in Breed-to-Farrow piglets compared to pigs born to Control sows. In conclusion, high Zn fed to gestating sows may influence SCFA-producing species and may reduce the abundance of potential pathogenic bacteria in the sow and piglet. Piglet birth weight may have greater effects on gene expression of neonatal pigs. </p>
Branch Policies in CI/CD: Categorization, Adoption, and Usage - Supplemental for replicability
Open the record for dataset details and reuse information.
Supplemental data to AALE 2024 publication "Adaptive manufacturing: dynamic resource allocation using multi-agent reinforcement learning"
<p>Release as supplementary material for our contribution at AALE 2024: "Adaptive manufacturing: dynamic resource allocation using multi-agent reinforcement learning"<br><br>The evaluation datasets stored in this collection are used to compare the performance of multi-agent reinforcement learning. In addition, the performance of other methods such as (meta-) heuristic algorithms or single agent reinforcement learning algorithms or novel methods of search space reduction can also be compared.</p>
Supplement of "Algorithm for continual monitoring of fog life cycles based on geostationary satellite imagery as a basis for solar energy forecasting"
<p>The file uploaded here is an animation that visually illustrates the outputs of the a newly developed machine learning based FLS (<strong>F</strong>og and <strong>L</strong>ow <strong>S</strong>tratus) detection algorithm for the SEVIRI (<strong>S</strong>pinning <strong>E</strong>nhanced <strong>V</strong>isible and <strong>I</strong>nfra<strong>R</strong>ed <strong>I</strong>mager) instrument onboard the MSG (<strong>M</strong>eteosat <strong>S</strong>econd <strong>G</strong>eneration) geo-stationary satellites over the 24hr cycle of the day for the day of <strong>02/March/2021</strong> and compares them with the corresponding raw channel values observed by SEVIRI. The proposed algorithm classifies each SEVIRI pixel as "clear-sky", "FLS", or "non-FLS-cloud" (identified with Khaki, Red, and Blue in the animation) based on the SEVIRI pixel values of BT12.0, BT8.7 - BT12.0, BT10.8 - BT12.0, and BT12.0 - BT13.4 plus the standard deviation of each of these variables in a spatial window sized 3x3 pixels with the central pixel being the target pixel. </p><p><br>In this animation, the left-hand panel shows a false-color RGB image constructed based on the SEVIRI raw channel data with the red, green, and blue channels being BT12.0- BT13.4, BT8.7 - BT12.0, and BT10.8 - BT12.0, respectively. In this panel, the green color represents the high clouds, and the light and dark red colors represent the clear-sky and FLS, respectively. The right-hand panel of this animation also shows the outputs of the ML FLS detection algorithm developed in the present study.</p>
Supplemental Movie Files for "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by Chriss et al.
<p>This set of Supplemental Information contains two movies made from the simulations from the model developed in the manuscript "<strong>Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis</strong>" by A. Chriss, G. V. Börner, and S. D. Ryan. </p> <p> </p> <p>Supplemental Movie S1: <strong>WT Chromosome Trajectories during Prophase I. </strong>The first file "movie_WT..." contains the file for the results of simulations for the wild-type chromosomes and the exact parameter values can be found in Table 1 of the manuscript. The movie shows one realization of the agent-based model. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S2: <strong>WT Chromosome Trajectories during Prophase I with active dumbbell model. </strong> The second file "movie<em>WT</em>_activedumbbell..." contains the file for the results of the simulations for the modeling of chromosomes as active dumbbells (from polymers) to allow for the study of the effects of elongation, orientation, and flexibility. The movie shows one realization of the agent-based active dumbbell model which is closer to modeling a chromosome as a polymer. The simulation movie covers the homology search process from <em>t = 3h </em>to <em>t = 9h</em>. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii, but are allowed to change in time as the two beads expand and contract. The radius represents the attractive and non-homologous repulsive region.</p> <p> </p> <p>Supplemental Movie S3: <strong><em>spo11</em> hypomorph (30% WT DSB levels) Chromosome Trajectories during Prophase I (parameters from Fig 7B)</strong>. The third file "movie_spo11..." contains the file for the results of the simulations for the spo-11 hypomorph and the associated parameter values can be found in Table 1 of the manuscript. The movie depicts one realization of the agent-based model for the {\it spo11} hypomorphic mutant. The simulation movie covers the homology search process from <em>t = 3h</em> to <em>t = 9h</em> where mutant <em>spo11</em> is associated with a weaker attractive and repulsive force (e.g., reduction to 77% of WT values). True chromosome lengths are incorporated and scale the relevant interaction radii. Matching colors correspond to homologous pairs. The radii represent the homologous attractive and the non-homologous repulsive region. Note that the reduction in interaction strength delays homologous pairing consistent with experimental observations in [13]. </p> <p> </p> <p> </p> <p>The codes that generated these movies were written in Matlab and freely available via GitHub: <a href="https://github.com/sdryan/ChromosomeDynamicsProphase1">https://github.com/sdryan/ChromosomeDynamicsProphase1</a></p> <p> </p> <p>For questions please contact the corresponding authors: G. Valentin Börner <a href="mailto:g.boerner@csuohio.edu">g.boerner@csuohio.edu</a> (Biology) or Shawn D. Ryan <a href="mailto:s.d.ryan@csuohio.edu">s.d.ryan@csuohio.edu</a> (Math).</p>
Data supplement for "Drops on polymer brushes – advances in thin-film modelling of adaptive substrates"
<p>This dataset contains supplementary data for the following publication:</p> <p>Hartmann, S., Diekmann, J., Greve, D., and & Thiele, U.<br>Drops on polymer brushes – advances in thin-film modelling of adaptive substrates<br><span><em>Langmuir</em></span> <span>2024</span><span>, 40</span><span>, 8</span><span>, 4001–4021</span></p> <p>We provide the source files and data for figures 3-15.</p>
Supplemental Data for: Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum
<p><strong><span>Premise:</span></strong><span> <em>Polypodium pellucidum</em>, a fern endemic to the Hawaiian Islands, encompasses a broad spectrum of morphological and ecological variation, suggesting a complex history involving divergence and hybridization. In contrast to angiosperm systems, spore dispersal in ferns presents a unique opportunity to study how highly dispersible organisms diversify in the dynamic landscape of the archipelago.</span></p> <p><strong><span>Key Results: </span></strong><span>We infer <em>P. pellucidum</em> is monophyletic, dispersing to the Hawaiian archipelago 11.53 to 7.77 Mya, with diversification into extant clades 5.66 to 4.73 Mya. We identify four non-hybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidate several intraspecific hybrid combinations and evidence for undiscovered or extinct 'ghost' lineages contributing to extant hybrids populations. </span></p> <p><strong><span>Conclusions:</span></strong><span> We provide a roadmap for revising the taxonomy of <em>P. pellucidum</em> to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific divergent clades within <em>P. pellucidum, </em>with intraspecific hybrids arising as a result of ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawaii's diverse fern flora and allows for better conservation efforts that are often complicated by the presence of cryptic taxa and hybridization.</span></p>
Supplemental data files for: A potential mode of the lithospheric growth and delamination of orogenic belts: Evidence from high-resolution magnetotelluric data
<p>Data files for a 2-D electrical resistivity model in the Greater Xing'an Range, including the observed MT data, the data fitting, the preferred resistivity model, and the raw data in impedance format.</p>
Supplemental information for: Inhibition of CSF1R and KIT with pexidartinib reduces inflammatory signaling and cell viability in endometriosis
<p>Endometriosis is a common and debilitating disease, affecting ~170 million women worldwide. Affected patients have limited therapeutic options such as hormonal suppression or surgical excision of the lesions, though therapies are often not completely curative. Targeting receptor tyrosine-kinases (RTKs) could provide a nonhormonal treatment option for endometriosis. We determined that two RTKs, Macrophage colony stimulating factor receptor (CSF1R) and Mast/stem cell growth factor receptor KIT (KIT), are overexpressed in endometriotic lesions and could be novel nonhormonal therapeutic targets for endometriosis. The kinase activity of CSF1R and KIT is suppressed by pexidartinib, a small molecule inhibitor that was recently approved by the US Food and Drug Administration (FDA). Using immunohistochemistry, we detected CSF1R and KIT in endometriotic tissues obtained from peritoneal lesions, colorectal lesions, and endometriomas. Specifically, we show that KIT is localized to the epithelium of the lesions, while CSF1R is expressed in the stroma and macrophages of the endometriotic lesions. Given the high epithelial expression of CSF1R and KIT, 12Z endometriotic epithelial cells were used to evaluate the efficacy of dual CSF1R and KIT inhibition with pexidartinib. We found that pexidartinib suppressed activation in 12Z cells of JNK, STAT3 and AKT signaling pathways, which control key pro-inflammatory and survival networks within the cell. Using quantitative real time PCR, we determined that pexidartinib suppressed interleukin 8 (<em>IL8) </em>and cyclin D1 (<em>CCND1) </em>expression<em>.</em> Lastly, we demonstrated that pexidartinib decreased cell growth and viability.<em> </em>Overall, these results indicate that pexidartinib-mediated CSF1R and KIT inhibition reduces pro-inflammatory signaling and cell viability in endometriosis.</p>
Supplement to the article "Simulation of marine stratocumulus using the super-droplet method: Numerical convergence and comparison to a double-moment bulk scheme"
<p>This is a supplement to the article "Simulation of marine stratocumulus using the super-droplet method: Numerical convergence and comparison to a double-moment bulk scheme".</p> <p>The time evolution of horizontal distribution of LWP:</p> <ul> <li>SDM_lwp_2d_sdm.mp4: from nine SDM runs with different grid resolutions.</li> <li>SN14_lwp_2d_sn14.mp4: from nine SN14 runs with different grid resolutions.</li> </ul> <p>The time evolution of vertical profiles:</p> <ul> <li>sdm_profile_t.mp4: from nine SDM runs with different grid resolutions.</li> <li>sn14_profile_t.mp4: from nine SN14 runs with different grid resolutions.</li> <li>sdm_incloud_t.mp4: vertical profiles in cloudy areas and cloud holes in SDM runs.</li> <li>sn14_incloud_t.mp4: vertical profiles in cloudy areas and cloud holes in SN14 runs.</li> <li>sdm_50x5_incloud_t.mp4: comparison between original SDM and SDM without sedimentation.</li> </ul>
Supplemental data and figures behind: Atom scale element and isotopic investigation of 25Mg-rich stardust from a H-burning supernova
<p>We have discovered a presolar olivine from ALH 77307 with the highest <sup>25</sup>Mg isotopic composition measured in a silicate to date (δ<sup>25</sup>Mg = 3025.1‰ ± 38.3‰).<strong> </strong>Its isotopic compositions challenge current stellar models, with modelling of Mg, Si and O showing a closest match to formation in a supernova where hydrogen ingestion occurred in the pre-supernova phase. Presolar grains within primitive astromaterials retain records of processes and environmental changes throughout stellar evolution. However, accessing these records has proved challenging due to the average grain size (~150 nm) of presolar silicates, their sensitivity to extraction agents and instrumental restrictions, limiting the range of isotopic and chemical signatures which can be studied per grain volume. Here, we present the first known detailed, geochemical study of a presolar silicate from a H-burning supernova, studied in 3D without contributions to the analysis volume and at unprecedented spatial resolutions (< 1 nm), essential for constraining physical and chemical processes occurring within this recently proposed stellar environment. From our results, we infer either; [1] condensation within an environment depleted of heavy elements compatible with the olivine lattice under the pressure and temperature conditions during condensation. [2] during periods of limited mixing either near the end of the pre-supernova phase or from a collapse so rapid localised pockets of different gas compositions formed.</p>
Supplemental Files for manuscript "Prenatal Transmission of Bacteriophage DNA in Humans"
<p>This repository includes the following files:</p> <p>1) Maternal_UCB_Phage_Analysis.RMD<br>This is an R markdown file to reproduce the analysis in the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”. It depends on the following files:</p> <p>2) BLAST_Processing.R<br>R script used for the processing of BLAST outputs. The outputs of this analysis for our two cohorts and negative controls with each phage database are provided as R objects. <br> a. POPE_AllPhage_Stats.RDS<br> b. POPE_GPD_Stats.RDS<br> c. Witt_AllPhage_Stats.RDS<br> d. Witt_GPD_Stats.RDS<br> e. Neg_AllPhage_Stats.RDS<br> f. Neg_GPD_Stats.RDS</p> <p>3) Clean_Data_Structures.R<br>This script includes 3 sections to generate the data structures used in subsequent analyses. </p> <p>4) Phage_Plots_Tables.R<br>This script includes 3 sections to reproduce the figures and tables from the manuscript “Prenatal Transmission of Bacteriophage DNA in Humans”. </p> <p>5) POPE_index.csv<br>This CSV file contains the metadata for the POPE cohort.</p> <p>6) SummaryMetaData.csv<br>This CSV file contains the metadata for the Witt cohort as relayed by the study authors from the original publication of this dataset.</p> <p>7) README.txt which summarizes the above as well as provides links to other relevant data.</p> <p>These scripts can be used to re-process our sequencing data or to process and interpret additional datasets.</p>
Supplemental Material to Doctoral Thesis "Engineering approach for predicting tunneling crack initiation in trailing-edge adhesive joints of wind turbine blades under mechanical fatigue and thermal residual stresses"
<p>This set supplements the figure data to the doctoral thesis "Engineering approach for predicting tunneling crack initiation in trailing-edge adhesive joints of wind turbine blades under mechanical fatigue and thermal residual stresses", DOI: <a href="https://doi.org/10.14279/depositonce-19144">10.14279/depositonce-19144</a></p>
Productivity-Susceptibility Analysis for Top 250 Marine Aquarium Fish Supplemental Information
<p>Data storage for supplemental information, containting the full dataset, a summarized dataset, and comparing vulnerability scores between FishBase and our Productivity-Susceptibility Analysis. </p>
Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway
<p>This is Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway.</p>
ScienceDex guides
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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.