cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/cjh584h5yg.1
title: Evaluation of triple negative breast cancer with heterogeneous immune infiltration

description: This research is the first one to measure differences in immune heterogeneity within the same patient, avoiding patients' inter-heterogeneity, for the study of potential casualties to the presence of infiltrating immune cells. This difference could be explained due to the tumor intrinsic characteristics (for example, their HLA -human leukocyte antigen- phenotype having different affinity for antigens). However, here we have shown that it may depend also on the tumor heterogeneity. Secretion of different proteins and enzymes, transcriptional alterations, and expression of different regulatory genes and oncogenes by the tumor cells can lead to immune recognition and infiltration in some areas but not in others. This observation is reflected in the differential expression analysis in each patient as well as in the gene set enrichment analysis, in which, on top of the upregulation of the immune pathways in the high TIL areas, there is an upregulation of other non-immune related pathways. We hypothesized that the differences in the gene expression between the two areas are due to intrinsic differences between the tumor cells of each area that evolve differently during tumor development. The team recommends future research with single cell sequencing in patients with the same characteristics.
DOI: 10.5281/zenodo.7844136
title: MUSES Fractional Vegetation Coverage (FVC) 8-Day Global 500m SIN Grid in 2011

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global FVC product at 500m spatial resolution and 8-day temporal resolution. The MUSES FVC product is provided on a Sinusoidal grid and spans from 2000 to 2018 (continuously updated). It was generated from the MUSES LAI product at 500m resolution and other ancillary information using the complement to unity of the transmittance of light through the entire canopy in the nadir viewing direction (Xiao <em>et al</em>., 2016). The MUSES FVC values are physically consistent with the corresponding MUSES LAI values. The MUSES FVC product is spatially complete and temporally continuous. This dataset is the MUSES FVC product in 2011. <em>Please <strong>click here</strong> to download the MUSES FVC product <strong>in 2010</strong></em>, and <em><strong>click here</strong> to download the MUSES FVC product <strong>in 2012</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2011 Spatial Resolution: 500m Temporal Resolution: 8 days Projection: Sinusoidal Data Format: HDF Scale: 0.004 Valid Range: 0 – 250 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et a</em>l. (2016). Estimating the Fractional Vegetation Cover from GLASS Leaf Area Index Product. <em>Remote Sensing</em>, 8, 337. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.5281/zenodo.7844135
title: MUSES Fractional Vegetation Coverage (FVC) 8-Day Global 500m SIN Grid in 2011

description: The MUltiscale Satellite remotE Sensing (MUSES) product suite includes products with different spatial and temporal resolutions for parameters such as Normalized Difference Vegetation Index (NDVI), Near-Infrared Reflectance of Vegetation (NIRv), Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), Fractional Vegetation Coverage (FVC), Gross Primary Production (GPP), Net Primary Production (NPP). For more information about the MUSES products, please refer to this website (https://muses.bnu.edu.cn/). This dataset is the MUSES global FVC product at 500m spatial resolution and 8-day temporal resolution. The MUSES FVC product is provided on a Sinusoidal grid and spans from 2000 to 2018 (continuously updated). It was generated from the MUSES LAI product at 500m resolution and other ancillary information using the complement to unity of the transmittance of light through the entire canopy in the nadir viewing direction (Xiao <em>et al</em>., 2016). The MUSES FVC values are physically consistent with the corresponding MUSES LAI values. The MUSES FVC product is spatially complete and temporally continuous. This dataset is the MUSES FVC product in 2011. <em>Please <strong>click here</strong> to download the MUSES FVC product <strong>in 2010</strong></em>, and <em><strong>click here</strong> to download the MUSES FVC product <strong>in 2012</strong></em>. <strong>Dataset Characteristics:</strong> Spatial Coverage: Global Temporal Coverage: 2011 Spatial Resolution: 500m Temporal Resolution: 8 days Projection: Sinusoidal Data Format: HDF Scale: 0.004 Valid Range: 0 – 250 <strong>Citation </strong>(Please cite this paper whenever these data are used)<strong>:</strong> Xiao Zhiqiang, <em>et a</em>l. (2016). Estimating the Fractional Vegetation Cover from GLASS Leaf Area Index Product. <em>Remote Sensing</em>, 8, 337. If you have any questions, please contact Prof. Zhiqiang Xiao (zhqxiao@bnu.edu.cn).
DOI: 10.17632/t969jsj3t7.1
title: PRC2.1 and PRC2.2 Specific Accessory Proteins Drive Recruitment of Different Forms of Canonical PRC1

description: PRC2.1 and PRC2.2 Specific Accessory Proteins Drive Recruitment of Different Forms of Canonical PRC1.

Eleanor Glancy1*, Cheng Wang1*, Ellen Tuck1, Evan Healy1, Simona Amato2, Hannah K. Neikes3, Andrea Mariani2, Marlena Mucha1, Michiel Vermeulen3, Diego Pasini2,4, Adrian P. Bracken1,5.

1Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
2IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.
3Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands.
4University of Milan, Via A. di Rudini 8, Department of Health Sciences, 20142 Milan, Italy.
*These authors contributed equally.
5Lead Contact.

*Corresponding author: Adrian P. Bracken (adrian.bracken@tcd.ie).


Summary: 
Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition, which is believed to direct recruitment of canonical PRC1 (cPRC1) to promote stable repression of developmental genes. PRC2 forms two major subcomplexes, PRC2.1 and PRC2.2, but their specific roles remain unclear. Through genetic knockout and replacement of PRC2 subcomplex-specific accessory proteins, we discover that PRC2.1 and PRC2.2 function through distinct mechanisms. During the transition from naïve to primed pluripotency, PRC2.1 accumulates in sharp defined peak-like profiles at CpG islands, dependent on the DNA and histone modification binding activities of MTF2. In contrast, PRC2.2 is recruited in broader profiles, mirroring H2AK119ub1 accumulation, dependent on the ubiquitin-binding abilities of JARID2 and AEBP2. Surprisingly, we uncover distinct roles for PRC2.2 and PRC2.1 specific accessory proteins in specifically mediating the recruitment of either CBX7- or CBX2/4- containing canonical PRC1 (cPRC1), respectively. PRC2.1 mediates the majority of H3K27me3 deposition at Polycomb target genes, which is sufficient to promote recruitment  of CBX2/4-cPRC1, but not CBX7-cPRC1. Conversely, while PRC2.2 is poor at mediating H3K27me3 deposition, we find that JARID2 is essential for recruitment of CBX7-cPRC1 and its consequent 3D chromatin interactions at Polycomb target genes. We therefore define distinct contributions of PRC2.1 and PRC2.2 specific accessory proteins to Polycomb mediated repression and uncover distinct mechanisms for cPRC1 recruitment.

Highlights 
•	PRC2.1/PRC2.2 are co-recruited to promote de novo Polycomb target gene repression.
•	PRC2.1 binds in sharp peaks specialising in H3K27me3 deposition and CBX2/4-cPRC1 recruitment.
•	PRC2.2 binds in broader H2AK119ub1-like profiles and has weak H3K27me3 acivity.
•	PRC2.2 component JARID2 specifically recruits CBX7-cPRC1. 

Keywords: Polycomb, PRC2.1, PRC2.2, H3K27me3, JARID2, Polycomb-like protein, PRC1, CBX2, CBX4, CBX7.
DOI: 10.17632/cn7shfv6n9.3
title: Single-cell analysis of the postnatal dorsal V-SVZ reveals a role for Bmpr1a signaling in silencing pallial germinal activity

description: Single cell profiles of microdissected dorsal subventricular zone of postnatal day 2, 12 and 22 wild type mice. Samples were collected independently using the 10x Chromium Single Cell Controller and libraries were prepared according to 10x Genomics protocol.
DOI: 10.5281/zenodo.7848471
title: Singleton detection mode prevents habituation of the attentional capture by color singleton distractors

description: Datasets analysed during the study
DOI: 10.5281/zenodo.7848472
title: Singleton detection mode prevents habituation of the attentional capture by color singleton distractors

description: Datasets analysed during the study
DOI: 10.57745/u2kigu
title: Minc_v4_shac_genome.fasta

description: Contigs from M. incognita genome assembly
DOI: 10.57745/2vfh5n
title: Mjav_v4_genome.fasta

description: :unav
DOI: 10.57745/cwno5u
title: Mare_v4_genome.fasta

description: :unav
DOI: 10.57745/edadpd
title: MINC4c.20220722.recipeA.egnep_report.txt

description: Report of M. incognita Eugene annotation
DOI: 10.57745/7tct9e
title: MINC4c.20220722.recipeA_ncrna.fna

description: Predicted non-coding RNA sequences in FASTA format
DOI: 10.57745/7x3zf4
title: MINC4c.20220722.recipeA_prot.fna

description: Predicted protein sequences in FASTA format
DOI: 10.57745/pixowu
title: MINC4c.20220722.recipeA.general_statistics.xls

description: General statistics of Eugene M. incognita annotations
DOI: 10.57745/0jpcw7
title: MINC4c.20220722.recipeA.statistics_per_gene.xls

description: EuGene statistics per gene
DOI: 10.57745/szfnop
title: MINC4c.20220722.recipeA_mrna.fna

description: Predicted messenger RNAs in FASTA format
DOI: 10.57745/ekl8ul
title: MINC4c.20220722.recipeA_gene.fna

description: Predicted genes inFASTA format
DOI: 10.57745/x6cm0g
title: MINC4c.20220722.recipeA.gff3

description: Eugene annotatin of the M. incognita genome in GFF3 format
DOI: 10.57745/knw7vw
title: MINC4c.20220722.recipeA_cds.fna

description: Predicted coding sequences in FASTA format
DOI: 10.57745/iaaehj
title: MJAV.20220802.recipeA.general_statistics.xls

description: :unav
DOI: 10.57745/p7gw4d
title: MJAV.20220802.recipeA.gff3

description: :unav
DOI: 10.57745/x3onpf
title: MJAV.20220802.recipeA.egnep_report.txt

description: :unav
DOI: 10.57745/0swstx
title: MJAV.20220802.recipeA_ncrna.fna

description: :unav
DOI: 10.57745/noxtkm
title: MJAV.20220802.recipeA_prot.fna

description: :unav
DOI: 10.57745/aijbe3
title: MJAV.20220802.recipeA_mrna.fna

description: :unav
DOI: 10.57745/2ighqy
title: MJAV.20220802.recipeA.statistics_per_gene.xls

description: :unav
DOI: 10.57745/aivgkx
title: MJAV.20220802.recipeA_cds.fna

description: :unav
DOI: 10.57745/xqybb3
title: MJAV.20220802.recipeA_gene.fna

description: :unav
DOI: 10.57745/wbmkss
title: MARE.20220802.recipeA.statistics_per_gene.xls

description: :unav
DOI: 10.57745/zmny28
title: MARE.20220802.recipeA_prot.fna

description: :unav
DOI: 10.57745/wypkoq
title: MARE.20220802.recipeA.general_statistics.xls

description: :unav
DOI: 10.57745/xlmiz3
title: MARE.20220802.recipeA_gene.fna

description: :unav
DOI: 10.57745/xla6dl
title: MARE.20220802.recipeA.gff3

description: :unav
DOI: 10.57745/tdnhqt
title: MARE.20220802.recipeA.egnep_report.txt

description: :unav
DOI: 10.57745/y5zvue
title: MARE.20220802.recipeA

description: :unav
DOI: 10.57745/ichod0
title: MARE.20220802.recipeA_ncrna.fna

description: :unav
DOI: 10.57745/22zv9x
title: MARE.20220802.recipeA_cds.fna

description: :unav
DOI: 10.57745/cocyf7
title: MARE.20220802.recipeA_mrna.fna

description: :unav
DOI: 10.57745/c1pdyq
title: MLUCI.20210421.recipeA_ncrna.fna

description: :unav
DOI: 10.57745/3osw11
title: MLUCI.20210421.recipeA_prot.fna

description: :unav
DOI: 10.57745/tbmljk
title: MLUCI.20210421.recipeA.general_statistics.xls

description: :unav
DOI: 10.57745/hmo1e9
title: MLUCI.20210421.recipeA.statistics_per_gene.xls

description: :unav
DOI: 10.57745/rybh8y
title: MLUCI.20210421.recipeA_cds.fna

description: :unav
DOI: 10.57745/q9fusp
title: MLUCI.20210421.recipeA.gff3

description: :unav
DOI: 10.57745/sevhuh
title: MLUCI.20210421.recipeA_mrna.fna

description: :unav
DOI: 10.57745/bw0kvm
title: MLUCI.20210421.recipeA.egnep_report.txt

description: :unav
DOI: 10.57745/vg8veb
title: MLUCI.20210421.recipeA_gene.fna

description: :unav
DOI: 10.6084/m9.figshare.22664446
title: Supplementary Material for: Prognostic Value of SSTR-derived Volumetric Parameters from a Hybrid Standardized Uptake Value Thresholding Method in Patients with 68Ga-DOTATATE-avid Stage IV Neuroendocrine Neoplasms: A preliminary study

description: Introduction: The ability of PET/CT imaging to delineate neuroendocrine neoplasms (NENs) and predict prognosis in affected patients is often compromised by substantial uptake heterogeneity. We hereby proposed a hybrid standardized uptake value (SUV) thresholding algorithm to extract volumetric parameters from somatostatin receptor (SSTR) PET/CT imaging, and investigate their prognostic performance in patients with 68Ga-DOTATATE-avid stage IV NENs. Methods: For 38 retrospectively enrolled patients, we used either fixed SUV thresholding of normal liver parenchyma (method A), 41% of the SUVmax for each lesion (method B), or a hybrid method (method A for liver metastases; fixed SUV threshold of normal bone for bone metastases; method B for primary tumors and other metastases) to quantify the whole-body SSTR-expressing tumor volume (SRETVwb) and total lesion SSTR expression (TLSREwb). Patient survival was also recorded and analyzed. Results: PET/CT images revealed heterogeneous uptake of 68Ga-DOTATATE at primary and metastatic sites. Progression-free (PFS) and overall survival (OS) were negatively correlated with the extent of liver or bone metastases (P &lt; 0.05), but not significantly correlated with tumor grade or 18F-FDG PET/CT positivity. By the hybrid method, PFS was significantly shorter in patients with high SRETVwb, and OS was significantly shorter in those with high SRETVwb and TLSREwb (P &lt; 0.05). However, when derived from method A or method B, neither SRETVwb nor TLSREwb could predict patient outcomes. Conclusion: Compared with other methods used in 68Ga-DOTATATE-avid stage IV NENs, our hybrid SUV thresholding method demonstrated robustness, with greater precision, reliability, and prognostic power.
DOI: 10.6084/m9.figshare.22664446.v1
title: Supplementary Material for: Prognostic Value of SSTR-derived Volumetric Parameters from a Hybrid Standardized Uptake Value Thresholding Method in Patients with 68Ga-DOTATATE-avid Stage IV Neuroendocrine Neoplasms: A preliminary study

description: Introduction: The ability of PET/CT imaging to delineate neuroendocrine neoplasms (NENs) and predict prognosis in affected patients is often compromised by substantial uptake heterogeneity. We hereby proposed a hybrid standardized uptake value (SUV) thresholding algorithm to extract volumetric parameters from somatostatin receptor (SSTR) PET/CT imaging, and investigate their prognostic performance in patients with 68Ga-DOTATATE-avid stage IV NENs. Methods: For 38 retrospectively enrolled patients, we used either fixed SUV thresholding of normal liver parenchyma (method A), 41% of the SUVmax for each lesion (method B), or a hybrid method (method A for liver metastases; fixed SUV threshold of normal bone for bone metastases; method B for primary tumors and other metastases) to quantify the whole-body SSTR-expressing tumor volume (SRETVwb) and total lesion SSTR expression (TLSREwb). Patient survival was also recorded and analyzed. Results: PET/CT images revealed heterogeneous uptake of 68Ga-DOTATATE at primary and metastatic sites. Progression-free (PFS) and overall survival (OS) were negatively correlated with the extent of liver or bone metastases (P &lt; 0.05), but not significantly correlated with tumor grade or 18F-FDG PET/CT positivity. By the hybrid method, PFS was significantly shorter in patients with high SRETVwb, and OS was significantly shorter in those with high SRETVwb and TLSREwb (P &lt; 0.05). However, when derived from method A or method B, neither SRETVwb nor TLSREwb could predict patient outcomes. Conclusion: Compared with other methods used in 68Ga-DOTATATE-avid stage IV NENs, our hybrid SUV thresholding method demonstrated robustness, with greater precision, reliability, and prognostic power.
DOI: 10.5519/qd.uzyobga3
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.17909/dr7t-g194
title: Atmospheric Characterisation of A Disintegrating Planet in the Hot Neptune Desert

description: HST WFC3 G102 and G141 transit time-series observations.
DOI: 10.57745/tivls8
title: Trinity_J3.fna

description: Assembled transcriptome of the mixed late J2,J3-J4 endophytic stages
DOI: 10.57745/6ggkqw
title: Trinity_w.fna

description: Assembled transcriptome of the egg stage
DOI: 10.57745/yaw6c4
title: Trinity_fem.fna

description: Assembled transcriptome of the adult female stage
DOI: 10.57745/dvjzjs
title: Trinity_J2.fna

description: Assembled transcriptome of the infective juvenile J2 stage
DOI: 10.4121/19074482
title: Data underlying the Research on the Identification of potential biomarkers of septic shock based on pathway analysis and immune-related transcriptome analysis

description: This study selected several immune-related biomarkers of septic shock, and validated their expression on clinical samples (six septic shock patients and six healthy controls) using qRT-PCR and Western blot.
DOI: 10.4121/19074482.v5
title: Data underlying the Research on the Identification of potential biomarkers of septic shock based on pathway analysis and immune-related transcriptome analysis

description: This study selected several immune-related biomarkers of septic shock, and validated their expression on clinical samples (six septic shock patients and six healthy controls) using qRT-PCR and Western blot.
DOI: 10.25345/c5ww7791m
title: MassIVE MSV000091753 - Hepatic Mcpip1 regulates adaptation to food restriction in mice
title: Monocyte-chemoattractant protein-induced protein 1 (Mcpip1, or Regnase-1) is an endoribonuclease that degrades translationally active mRNA molecules. Mcpip1 is mostly known by its anti-inflammatory actions, but it is also an important regulator of adipogenesis and lipid metabolism. In this study, genetic deletion of Zc3h12a was used to characterize the role of Mcpip1 in the murine adaptation to 24-hour food restriction. We found that Mcpip1 deficiency in the liver epithelial cells (Mcpip1fl/flAlbCre mice) led to better adaptation to fasting, manifested by higher serum glucose concentration in comparison to Mcpip1fl/fl counterparts. Hepatic proteome analysis showed 26 down-regulated and 117 up-regulated proteins in Mcpip1fl/flAlbCre animals, that were involved in cellular adhesion, extracellular matrix and metabolic processes. In conclusion, our studies provide new insight into the hepatic function of Mcpip1 and its involvement in metabolic control.
DOI: 10.5281/zenodo.7848530
title: SPELLFLICT survey questionnaire results

description: File formats: SPSS Number of files: 4 Number of respondents: 2000 Country of origin of respondents: Bosnia and Herzegovina, Croatia, Montenegro, Serbia
DOI: 10.5281/zenodo.7848529
title: SPELLFLICT survey questionnaire results

description: File formats: SPSS Number of files: 4 Number of respondents: 2000 Country of origin of respondents: Bosnia and Herzegovina, Croatia, Montenegro, Serbia
DOI: 10.5281/zenodo.6678861
title: Relative velocity variations curves

description: These are the relative velocity variations curves used in the scientific article titled "Spatio-temporal velocity variations observed during the pre-eruptive episode of La Palma 2021 eruption inferred from ambient noise interferometry."
DOI: 10.5281/zenodo.6678301
title: Relative velocity variations curves

description: These are the relative velocity variations curves used in the scientific article titled "Spatio-temporal velocity variations observed during the pre-eruptive episode of La Palma 2021 eruption inferred from ambient noise interferometry."
DOI: 10.57745/9dqouo
title: Supplementary_table_9_IsoSeq.tab

description: Results of ISO-seq data mapping on the M. incogntia genome and presence of telomeric motifs
DOI: 10.57745/mnyl39
title: Data_MS-mulipop_DOI.tab

description: :unav
DOI: 10.5517/ccdc.csd.cc29jlct
title: CCDC 2131106: Experimental Crystal Structure Determination

description: Related Article: Yunlu Chen, Bingyi Zhang, Xide Xie, Yue Sun, Lian Duan, Jie Li|2023|J.Lumin.|259|119819|doi:10.1016/j.jlumin.2023.119819
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29xdvh
title: CCDC 2142467: Experimental Crystal Structure Determination

description: Related Article: Yunlu Chen, Bingyi Zhang, Xide Xie, Yue Sun, Lian Duan, Jie Li|2023|J.Lumin.|259|119819|doi:10.1016/j.jlumin.2023.119819
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29xdwj
title: CCDC 2142468: Experimental Crystal Structure Determination

description: Related Article: Yunlu Chen, Bingyi Zhang, Xide Xie, Yue Sun, Lian Duan, Jie Li|2023|J.Lumin.|259|119819|doi:10.1016/j.jlumin.2023.119819
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.57745/hyln4d
title: Motifs-trinitry-transcripts.tab

description: Minc assembled transcripts containing the telomeric motif
DOI: 10.6084/m9.figshare.22664437
title: Untitled Item

description: UFS documents
DOI: 10.6084/m9.figshare.22664437.v1
title: Untitled Item

description: UFS documents
DOI: 10.57745/dfevfa
title: Mluci-Minc-repeat-blast.xlsx

description: Matches of Minc repeat on Mluci contigs
DOI: 10.6084/m9.figshare.22664623
title: DMP_Checklist_2013.pdf

description: RHC 400 students UP
DOI: 10.6084/m9.figshare.22664623.v1
title: DMP_Checklist_2013.pdf

description: RHC 400 students UP
DOI: 10.5522/04/22567615
title: An experimental imaging method to study the evolution of bubble size distributions for different breaking wave crest geometries

description: Data for submitted paper. Data derived as part from a PhD program that measured breaking wave crests and bubble size evolution in laboratory. Readme file has more info. Bubble size distributions, bubble volume and wave crest profiles time series.