Contributors: Jing Gao
... 16S rRNA gene sequencing is performed to analyze the changes in composition of raw milk microbiota of mastitis dairy cows supplemented with different probiotics.
Model and output for Vadsaria et al, "Development of a sequential tool LMDZ-NEMO-med-V1 for global to regional past climate simulation over the Mediterranean basin: an early Holocene case study", GMD publication
Contributors: Vadsaria, Tristan, Li, Laurent, Ramstein, Gilles, Dutay, Jean-Claude
... These files are related to the publication: "Development of a sequential tool LMDZ-NEMO-med-V1 for global to regional past climate simulation over the Mediterranean basin: an early Holocene case study" (currently under review). Description of the files as in "README.txt": "vadsaria_et_al_LMDZ-NEMO-med_model.tar.gz" contains the LMDZ-nemo-med-v1 model (three components: atmospheric global model, atmospheric regional model and oceanic regional model). It includes starting files and codes to run the model. "output-for-vadsaria-et-al-gmd.tar.gz" contains the model output presented in the main article. It also provides python scripts to compute the overturning function, the freshwater budget and the stratification index as well.
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Transcriptomic profiling of Purple Broccoli reveal light-induced anthocyanin biosynthetic signaling and structural genes
Contributors: Liu, Chunqing, Yao, Xueqin, Li, Guangqing, Huang, Lei, Xie, Zhujie
... Figure S1: GO enrichment analysis for down-regulated DEGs in A53WJ-vs-B53CK. Figure S2: GO enrichment analysis for down-regulated DEGs in B53WJ-vs-B53CK. Figure S3: Patterns of gene expressions across three time points under head-shaded condition. Figure S4: Patterns of gene expressions across three time points under normal light condition. Table S1: GO enrichment analysis for down-regulated DEGs in A53WJ-vs-B53CK. Table S2: GO enrichment analysis for down-regulated DEGs in B53WJ-vs-B53CK. Table S3: Reads Mapping stats. Table S4: de novo assembly and annotation. Table S5: assemble unigenes FPKM value. Table S6: specially expressed DEGs in cluster 8 under head shading condition. Table S7: specially expressed DEGs in cluster 8 under normal light condition. Table S8: co-expressed DEGs in cluster 8.
Contributors: Mariano, Benjamin, Reese, Josh, Xu, Siyuan, Nguyen, ThanhVu, Qiu, Xiaokang, Foster, Jeffrey S., Armando Solar-Lezama
... JLibSketch tool for specifying Java library behavior via rewrite rules.
Original Data of Paper: Novel lncRNA-panel as biomarkers for prognosis in breast cancer via Ce-RNA Network analysis
Contributors: Yizhou Bai
... Paper title: Novel lncRNA-panel as biomarkers for prognosis in breast cancer via Ce-RNA Network analysis. Our paper was submitted to PeerJ recently. This data file is the original data of this study which contains all the original data involved in this work.
Contributors: Leslie, Matthew S., Peredo, Carlos M., Pyenson Nicholas D
... Supplemental dataset for Leslie et al. (2019) The data included in this Zenodo archive are primarily the derived 3D models (STL or PLY files) for the main osteological elements of USNM 10300: the skull, the left and right periotics, and the right tympanic bulla. One DICOM data file includes all CT data for right tympanic bulla and both periotics. The files in this archive include materials published with the original article in PeerJ (Leslie et al., 2019). The type specimen itself (USNM 10300) is housed in the Department of Paleobiology at the Smithsonian Institution's National Museum of Natural History in Washington, D.C. Skull: - 3D model created from 3D laser scan data. (PLY, 138.9 MB) right tympanic bulla: - 3D model created from CT scan data. (STL, 31 MB) - within DICOM data set. (578.1 MB) right periotic - 3D model created from CT scan data. (STL, 17.5 MB) - within DICOM data set. (578.1 MB) left periotic - 3D model created from CT scan data. (STL, 19.1 MB) - within DICOM data set. (578.1 MB)
Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages.
Contributors: Sullivan, Amy L., Benner, Christopher, Heinz, Sven, Huang, Wendy, Lan, Xie, Miano, Joseph M., Glass, Christopher K.
... Cells of the monocyte/macrophage lineage play essential roles in tissue homeostasis and immune responses, but mechanisms underlying the coordinated expression of cytoskeletal genes required for specialized functions of these cells, such as directed migration and phagocytosis, remain unknown. Here, using genetic and genomic approaches, we provide evidence that serum response factor (SRF) regulates both general and cell type-restricted components of the cytoskeletal gene expression program in macrophages. Genome-wide location analysis of SRF in macrophages demonstrates enrichment of SRF binding at ubiquitously expressed target gene promoters, as expected, but also reveals that the majority of SRF binding sites associated with cell type-restricted target genes are at distal inter- and intragenic locations. Most of these distal SRF binding sites are established by the prior binding of the macrophage- and the B cell-specific transcription factor PU.1 and exhibit histone modifications characteristic of enhancers. Consistent with this, representative cytoskeletal target genes associated with these elements require both SRF and PU.1 for full expression. These findings suggest that SRF uses two distinct molecular strategies to regulate programs of cytoskeletal gene expression: a promoter-based strategy for ubiquitously expressed target genes and an enhancer-based strategy at target genes that exhibit cell type-restricted patterns of expression.
Contributors: Goldmann, Lutz
... The purpose of this dataset is to develop and evaluate layout analysis techniques. More specifically it is focused on the classification of indiviual words and the detection of semantic regions described by boxes.
Contributors: Will Handley
... Paper references: Will Handley. Primordial power spectra for curved inflating universes. arXiv, 1907.08524, Jul 2019. W. J. Handley, A. N. Lasenby, and M. P. Hobson. Novel quantum initial conditions for inflation. PRD, 94(2):024041, Jul 2016. W. J. Handley, A. N. Lasenby, and M. P. Hobson. The Runge-Kutta-Wentzel-Kramers-Brillouin Method. arXiv, 1612.02288, Dec 2016. F. Agocs, W. Handley, A. Lasenby, and M. Hobson. An efficient method for solving highly oscillatory ordinary differential equations. arXiv, 1906.01421, May 2019. Jamie Bamber and Will Handley. Beyond the Runge-Kutta-Wentzel-Kramers-Brillouin method. arXiv, 1907.11638, Jul 2019. W. I. J. Haddadin and W. J. Handley. Rapid numerical solutions for the Mukhanov-Sazaki equation. arXiv, 1809.11095, Sep 2018. W. J. Handley, S. D. Brechet, A. N. Lasenby, and M. P. Hobson. Kinetic initial conditions for inflation. PRD, 89(6):063505, Mar 2014. Will Handley, Anthony Lasenby, and Mike Hobson. Logolinear series expansions with applications to primordial cosmology. PRD, 99(12):123512, Jun 2019. L. T. Hergt, W. J. Handley, M. P. Hobson, and A. N. Lasenby. A case for kinetically dominated initial conditions for inflation. PRD, 100(2):023502, Jul 2019. L. T. Hergt, W. J. Handley, M. P. Hobson, and A. N. Lasenby. Constraining the kinetically dominated universe. PRD, 100(2):023501, Jul 2019. W. J. Handley, A. N. Lasenby, H. V. Peiris, and M. P. Hobson. Bayesian inflationary reconstructions from Planck 2018 data. arXiv, 1908.00906, Aug 2019. W. J. Handley, M. P. Hobson, and A. N. Lasenby. POLYCHORD: next-generation nested sampling. MNRAS, 453(4):4384\u20134398, Nov 2015. Will Handley. fgivenx: A Python package for functional posterior plotting. JOSS, 3(28):849, Aug 2018. Will Handley. Curvature tension: evidence for a closed universe. arXiv, 1908.09139, Aug 2019. Will Handley. anesthetic: nested sampling visualisation. JOSS, 4:1414, May 2019. Will Handley and Pablo Lemos. Quantifying tensions in cosmological parameters: Interpreting the DES evidence ratio. PRD, 100(4):043504, Aug 2019. Will Handley and Pablo Lemos. Quantifying dimensionality: Bayesian cosmological model complexities. PRD, 100(2):023512, Jul 2019