cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1271925.v2
title: First Round of DC+ and vaccine Sequest 3752 peptides

description: Proteomic data generated in DCs treated by CTB-INS
DOI: 10.6084/m9.figshare.1271926.v1
title: Second Round

description: Analysis of proteins modulated by CTB-INS in human DCs
DOI: 10.6084/m9.figshare.1271925.v1
title: Mass Spectometry data

description: Proteomic data generated in DCs treated by CTB-INS
DOI: 10.6084/m9.figshare.1271897
title: README.txt

description: README file for dataset
DOI: 10.6084/m9.figshare.1271896
title: Diversity of ageing trajectories plot data

description: These files provide the coordinates for the curves presented in Figure 1 of our 2014 Nature paper (reproduced here in low quality as LowResFigure.png). For further details please see the paper and its supplementary material. Jones, OR, et al. (2014) Diversity of ageing across the tree of life. Nature. 505, 169–173 (09 January 2014) doi:10.1038/nature12789
DOI: 10.6084/m9.figshare.1271820
title: Enrich0.2_config

description: Enrich config file used to analyze sequence reads.
DOI: 10.6084/m9.figshare.1271897.v1
title: README.txt

description: README file for dataset
DOI: 10.6084/m9.figshare.1271820.v1
title: Enrich0.2_config

description: Enrich config file used to analyze sequence reads.
DOI: 10.6084/m9.figshare.1271896.v2
title: Diversity of ageing trajectories plot data

description: These files provide the coordinates for the curves presented in Figure 1 of our 2014 Nature paper (reproduced here in low quality as LowResFigure.png). For further details please see the paper and its supplementary material. Jones, OR, et al. (2014) Diversity of ageing across the tree of life. Nature. 505, 169–173 (09 January 2014) doi:10.1038/nature12789
DOI: 10.6084/m9.figshare.1271808
title: MethodC_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271809
title: Method C_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271806
title: MethodA_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271809.v1
title: Method C_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271896.v1
title: Diversity of ageing trajectories

description: These files provide the coordinates for the curves presented in Figure 1 of our 2014 Nature paper (reproduced here in low quality as LowResFigure.png). For further details please see the paper and its supplementary material. Jones, OR, et al. (2014) Diversity of ageing across the tree of life. Nature. 505, 169–173 (09 January 2014) doi:10.1038/nature12789
DOI: 10.6084/m9.figshare.1271808.v1
title: MethodC_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271750
title: SPP_PG_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271804
title: MethodB_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271805
title: MethodB_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271806.v1
title: MethodA_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271750.v1
title: SPP_PG_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271805.v1
title: MethodB_R

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271742
title: SPP_PG_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271744
title: Are human peripheral nerves sensitive to x-ray imaging?

description: Diagnostic imaging techniques play an important role in assessing the exact location, cause, and extent of a nerve lesion, thus allowing clinicians to diagnose and manage more effectively a variety of pathological conditions such as entrapment syndromes, traumatic injuries, and space-occupying lesions. Ultrasound and nuclear magnetic resonance imaging are becoming useful methods for this purpose, but they still lack spatial resolution. In this regard, recent phase contrast x-ray imaging experiments of peripheral nerve allowed the visualization of each nerve fiber surrounded by its myelin sheath as clearly as optical microscopy. In the present study, we attempted to produce high-resolution x-ray phase contrast images of a human sciatic nerve by using synchrotron radiation propagation-based imaging. The images showed high contrast and high spatial resolution, allowing clear identification of each fascicle structure and surrounding connective tissue. The outstanding result is the detection of such structures by phase contrast x-ray tomography of a thick human sciatic nerve section. This may further enable the identification of diverse pathological patterns, such as Wallerian degeneration, hypertrophic neuropathy, inflammatory infiltration, leprosy neuropathy and amyloid deposits. To the best of our knowledge, this is the first successful phase contrast x-ray imaging experiment of a human peripheral nerve sample. Our long-term goal is to develop peripheral nerve imaging methods that could supersede biopsy procedures.
DOI: 10.6084/m9.figshare.1271804.v1
title: MethodB_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271741
title: High-Resolution Sequence-Function Mapping of Full-Length Proteins

description: Sequencing files to accompany High-Resolution Sequence-Function Mapping of Full-Length Proteins
DOI: 10.6084/m9.figshare.1271665
title: 2013 Publications

description: RPCC
DOI: 10.6084/m9.figshare.1271742.v1
title: SPP_PG_F

description: Sequencing file used for data analysis. See README.txt for more information.
DOI: 10.6084/m9.figshare.1271744.v1
title: Are human peripheral nerves sensitive to x-ray imaging?

description: Diagnostic imaging techniques play an important role in assessing the exact location, cause, and extent of a nerve lesion, thus allowing clinicians to diagnose and manage more effectively a variety of pathological conditions such as entrapment syndromes, traumatic injuries, and space-occupying lesions. Ultrasound and nuclear magnetic resonance imaging are becoming useful methods for this purpose, but they still lack spatial resolution. In this regard, recent phase contrast x-ray imaging experiments of peripheral nerve allowed the visualization of each nerve fiber surrounded by its myelin sheath as clearly as optical microscopy. In the present study, we attempted to produce high-resolution x-ray phase contrast images of a human sciatic nerve by using synchrotron radiation propagation-based imaging. The images showed high contrast and high spatial resolution, allowing clear identification of each fascicle structure and surrounding connective tissue. The outstanding result is the detection of such structures by phase contrast x-ray tomography of a thick human sciatic nerve section. This may further enable the identification of diverse pathological patterns, such as Wallerian degeneration, hypertrophic neuropathy, inflammatory infiltration, leprosy neuropathy and amyloid deposits. To the best of our knowledge, this is the first successful phase contrast x-ray imaging experiment of a human peripheral nerve sample. Our long-term goal is to develop peripheral nerve imaging methods that could supersede biopsy procedures.
DOI: 10.6084/m9.figshare.1271741.v1
title: High-Resolution Sequence-Function Mapping of Full-Length Proteins

description: Sequencing files to accompany High-Resolution Sequence-Function Mapping of Full-Length Proteins
DOI: 10.6084/m9.figshare.1271741.v2
title: High-Resolution Sequence-Function Mapping of Full-Length Proteins

description: Sequencing files to accompany High-Resolution Sequence-Function Mapping of Full-Length Proteins
DOI: 10.6084/m9.figshare.1279394.v145
title: Early ovariectomy reveals the non-somatic origin of murine anti-A-reactive IgM reflecting developmental malignancy.

description: The germline encoding of a non-immune immunoglobulin M molecule in mammals was experimentally documented for the first time as a result of the specifically timed ovariectomy of C57BL/10 mice. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when expressed in any non-developmental tissue. Although ovariectomy and castration result in uncontrolled and/or enhanced humoral and cellular immunity involving increased weights of the spleen and thymus with pronounced B and T cell production, the development of mercaptoethanol-sensitive, complement-binding, non-immune anti-A reactivity in murine plasma was not enhanced after an ovariectomy that was performed in C57BL/10 mice prior to the onset of puberty. This non-immune murine anti-A, which is complementary to the trans-species, syngeneic ovarian GalNAc-glycan-bearing glycolipids and distinct from the cross-reactive adaptive anti-A antibody, was strongly downregulated or did not appear in plasma of animals ovariectomized at the age of 20 days. Thus, contrary to our previous view, this reactivity is unlikely to originate from a somatic, primary immune or autoimmune response. All of the murine tissues expressed the species-specific Forssman<i> </i>reactivity, and further A-like structures were identified in the male and female reproductive and endodermal organs by reaction with innate human anti-A antibody, while the murine anti-A was exclusively inhibited by syngeneic ovarian glycolipids. Moreover, the early ovarian tissue, which represents a last evolutionary and/or developmental location, showed a developmental polymorphism characterized by reactivity to the lectin from <i>Dolichos biflorus</i> and the agglutinin from <i>Helix pomatia </i>indicating the functional involvement of the <i>O</i>-GalNAc-determined mucin-type A-like, Thomsen-Friedenreich (TF) epitope that signifies malignancy when expressed by non-developmental tissues.
DOI: 10.6084/m9.figshare.1271306
title: Mn<sup>II</sup> Complexes with a Novel Triacid as Ligand: Synthesis and Characterization

description: A novel aromatic tricarboxylic acid of 4,4′-(2-carboxypropane-1,3-diyl)dibenzoic acid (H<sub>3</sub>L) was used to prepare two Mn<sup>II</sup> complexes of [Mn<sub>3</sub>(L)<sub>2</sub>(bpy)<sub>2</sub>]<sub>n</sub> (<b>1</b>) and [Mn<sub>3</sub>(L)<sub>2</sub>(phen)<sub>2</sub>]<sub>n</sub> (<b>2</b>), where bpy = 2,2′-bipyridine and phen = 1,10-phenanthroline. The single crystal structures, thermal stability, and the magnetism of <b>1</b> and <b>2</b> were measured and discussed in this article. According to the magnetism measurements, the Curie constants and the Weiss constants should be 12.29 K·cm<sup>3</sup>·mol<sup>−1</sup> (g = 1.94, S = 5/2) and −9.80 K for <b>1</b> and 11.11 K·cm<sup>3</sup>·mol<sup>−1</sup> (g = 1.83, S = 5/2) and −9.26 K for <b>2</b>, respectively.
DOI: 10.6084/m9.figshare.1271305
title: Crystal Structure Analysis of Betti Base 1-((2-hydroxynaphthalen-1-yl)(2-hydroxyphenyl)methyl)urea•2DMF Solvate

description: A novel Betti base compound, 1-((2-hydroxynaphthalen-1-yl)(2-hydroxyphenyl)methyl)urea, UBB, was synthesized and characterized by spectral, structural and thermal studies. Single crystal X-ray diffraction studies reveal that the racemic mixture of the compound, when crystallized from DMF, yields R-isomer preferentially (prismatic crystals), whereas, when crystallized from 5:1 (v/v) mixture of DMF-THF, it yields S-isomer (rectangular shaped crystals) with two molecules of DMF, included in both the cases. The crystal structure is discussed in terms of supramolecular interactions and molecular modeling. Both R and S enantiomeric DMF solvate crystals are in their chiral triclinic <i>P1</i> space group.
DOI: 10.6084/m9.figshare.1279394.v146
title: Early ovariectomy reveals the non-somatic origin of murine anti-A-reactive IgM reflecting developmental malignancy.

description: The germline encoding of a non-immune immunoglobulin M molecule in mammals was experimentally documented for the first time as a result of the specifically timed ovariectomy of C57BL/10 mice. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when expressed in any non-developmental tissue. Although ovariectomy and castration result in uncontrolled and/or enhanced humoral and cellular immunity involving increased weights of the spleen and thymus with pronounced B and T cell production, the development of mercaptoethanol-sensitive, complement-binding, non-immune anti-A reactivity in murine plasma was not enhanced after an ovariectomy that was performed in C57BL/10 mice prior to the onset of puberty. This non-immune murine anti-A, which is complementary to the trans-species, syngeneic ovarian GalNAc-glycan-bearing glycolipids and distinct from the cross-reactive adaptive anti-A antibody, was strongly downregulated or did not appear in plasma of animals ovariectomized at the age of 20 days. Thus, contrary to our previous view, this reactivity is unlikely to originate from a somatic, primary immune or autoimmune response. All of the murine tissues expressed the species-specific Forssman<i> </i>reactivity, and further A-like structures were identified in the male and female reproductive and endodermal organs by reaction with innate human anti-A antibody, while the murine anti-A was exclusively inhibited by syngeneic ovarian glycolipids. Moreover, the early ovarian tissue, which represents a last evolutionary and/or developmental location, showed a developmental polymorphism characterized by reactivity to the lectin from <i>Dolichos biflorus</i> and the agglutinin from <i>Helix pomatia </i>indicating the functional involvement of the <i>O</i>-GalNAc-determined mucin-type A-like, Thomsen-Friedenreich (TF) epitope that signifies malignancy when expressed by non-developmental tissues.
DOI: 10.6084/m9.figshare.1271305.v1
title: Crystal Structure Analysis of Betti Base 1-((2-hydroxynaphthalen-1-yl)(2-hydroxyphenyl)methyl)urea•2DMF Solvate

description: A novel Betti base compound, 1-((2-hydroxynaphthalen-1-yl)(2-hydroxyphenyl)methyl)urea, UBB, was synthesized and characterized by spectral, structural and thermal studies. Single crystal X-ray diffraction studies reveal that the racemic mixture of the compound, when crystallized from DMF, yields R-isomer preferentially (prismatic crystals), whereas, when crystallized from 5:1 (v/v) mixture of DMF-THF, it yields S-isomer (rectangular shaped crystals) with two molecules of DMF, included in both the cases. The crystal structure is discussed in terms of supramolecular interactions and molecular modeling. Both R and S enantiomeric DMF solvate crystals are in their chiral triclinic <i>P1</i> space group.
DOI: 10.6084/m9.figshare.1270915
title: A gene expression atlas of a bicoid-depleted Drosophila embryo

description: Data accompanying Staller et al. Development, in press (open access link will be included when available) and used in Staller et al., PNAS, in press (open access link will be included when available). These data were generated in the DePace Lab at Harvard Medical School, using protocols developed by the Berkeley Drosophila Transcription Network Project (BDTNP) and the DePace Lab. Files include: bcdrnai_20140807_v1.1.vpc : a cellular resolution gene expression atlas of an average Drosophila melanogaster embryo depleted of the maternal transcription factor bicoid. Contains expression patterns for 13 genes <em>(caudal (cad), Krüppel (Kr), knirps (kni), giant (gt), hunchback (hb), fork head ( fkh), huckebein (hkb), tailless (tll), Dichaete (D), runt (run), hairy (h), even-skipped (eve)</em> and<em> fushi-tarazu ( ftz))</em> and 6 enhancer reporter constructs <em>(hb posterior, gt posterior, eve stripe3+7, eve stripe5,</em> two <em>eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Dmel_reporters_20141211.vpc : a cellular resolution gene expression atlas of eve enhancer reporter constructs in wild type Drosophila melanogaster embryos. The enhancers are: <em>(eve stripe1, eve stripe2, eve stripe2+7 eve stripe3+7, eve stripe5,</em> two<em> eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Deml_snahb_20141223.vpc : a cellular gene expression atlas of <em>eve</em> enhancer reporters in embryos carrying 2 copies of an activated <em>snail::hunchback</em> transgene. EveFtzPCS_forDistributions.zip : individual point cloud files for embryos co-stained for <em>even-skipped (eve)</em> and<em> fushi tarazu (ftz)</em>. Data from additional genes is available upon request. Data can be analyzed using the BDTNP PointCloudToolBox and visualized using the BDTNP PointCloudXplore program which are both freely available (links below). Please contact the DePace lab with any additional questions (link below).
DOI: 10.6084/m9.figshare.1271306.v1
title: Mn<sup>II</sup> Complexes with a Novel Triacid as Ligand: Synthesis and Characterization

description: A novel aromatic tricarboxylic acid of 4,4′-(2-carboxypropane-1,3-diyl)dibenzoic acid (H<sub>3</sub>L) was used to prepare two Mn<sup>II</sup> complexes of [Mn<sub>3</sub>(L)<sub>2</sub>(bpy)<sub>2</sub>]<sub>n</sub> (<b>1</b>) and [Mn<sub>3</sub>(L)<sub>2</sub>(phen)<sub>2</sub>]<sub>n</sub> (<b>2</b>), where bpy = 2,2′-bipyridine and phen = 1,10-phenanthroline. The single crystal structures, thermal stability, and the magnetism of <b>1</b> and <b>2</b> were measured and discussed in this article. According to the magnetism measurements, the Curie constants and the Weiss constants should be 12.29 K·cm<sup>3</sup>·mol<sup>−1</sup> (g = 1.94, S = 5/2) and −9.80 K for <b>1</b> and 11.11 K·cm<sup>3</sup>·mol<sup>−1</sup> (g = 1.83, S = 5/2) and −9.26 K for <b>2</b>, respectively.
DOI: 10.6084/m9.figshare.1270915.v3
title: A gene expression atlas of a bicoid-depleted Drosophila embryo

description: Data accompanying Staller et al. Development, in press (open access link will be included when available) and used in Staller et al., PNAS, in press (open access link will be included when available). These data were generated in the DePace Lab at Harvard Medical School, using protocols developed by the Berkeley Drosophila Transcription Network Project (BDTNP) and the DePace Lab. Files include: bcdrnai_20140807_v1.1.vpc : a cellular resolution gene expression atlas of an average Drosophila melanogaster embryo depleted of the maternal transcription factor bicoid. Contains expression patterns for 13 genes <em>(caudal (cad), Krüppel (Kr), knirps (kni), giant (gt), hunchback (hb), fork head ( fkh), huckebein (hkb), tailless (tll), Dichaete (D), runt (run), hairy (h), even-skipped (eve)</em> and<em> fushi-tarazu ( ftz))</em> and 6 enhancer reporter constructs <em>(hb posterior, gt posterior, eve stripe3+7, eve stripe5,</em> two <em>eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Dmel_reporters_20141211.vpc : a cellular resolution gene expression atlas of eve enhancer reporter constructs in wild type Drosophila melanogaster embryos. The enhancers are: <em>(eve stripe1, eve stripe2, eve stripe2+7 eve stripe3+7, eve stripe5,</em> two<em> eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Deml_snahb_20141223.vpc : a cellular gene expression atlas of <em>eve</em> enhancer reporters in embryos carrying 2 copies of an activated <em>snail::hunchback</em> transgene. EveFtzPCS_forDistributions.zip : individual point cloud files for embryos co-stained for <em>even-skipped (eve)</em> and<em> fushi tarazu (ftz)</em>. Data from additional genes is available upon request. Data can be analyzed using the BDTNP PointCloudToolBox and visualized using the BDTNP PointCloudXplore program which are both freely available (links below). Please contact the DePace lab with any additional questions (link below).
DOI: 10.6084/m9.figshare.1270915.v2
title: A gene expression atlas of a bicoid-depleted Drosophila embryo

description: Data accompanying Staller et al. Development, in press (open access link will be included when available) and used in Staller et al., PNAS, in press (open access link will be included when available). These data were generated in the DePace Lab at Harvard Medical School, using protocols developed by the Berkeley Drosophila Transcription Network Project (BDTNP) and the DePace Lab. Files include: bcdrnai_20140807_v1.1.vpc : a cellular resolution gene expression atlas of an average Drosophila melanogaster embryo depleted of the maternal transcription factor bicoid. Contains expression patterns for 13 genes <em>(caudal (cad), Krüppel (Kr), knirps (kni), giant (gt), hunchback (hb), fork head ( fkh), huckebein (hkb), tailless (tll), Dichaete (D), runt (run), hairy (h), even-skipped (eve)</em> and<em> fushi-tarazu ( ftz))</em> and 6 enhancer reporter constructs <em>(hb posterior, gt posterior, eve stripe3+7, eve stripe5,</em> two <em>eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Dmel_reporters_20141211.vpc : a cellular resolution gene expression atlas of eve enhancer reporter constructs in wild type Drosophila melanogaster embryos. The enhancers are: <em>(eve stripe1, eve stripe2, eve stripe2+7 eve stripe3+7, eve stripe5,</em> two<em> eve stripe4+6</em> enhancers, and a whole locus <em>eve</em> reporter). Deml_snahb_20141223.vpc : a cellular gene expression atlas of <em>eve</em> enhancer reporters in embryos carrying 2 copies of an activated <em>snail::hunchback</em> transgene. EveFtzPCS_forDistributions.zip : individual point cloud files for embryos co-stained for <em>even-skipped (eve)</em> and<em> fushi tarazu (ftz)</em>. Data from additional genes is available upon request. Data can be analyzed using the BDTNP PointCloudToolBox and visualized using the BDTNP PointCloudXplore program which are both freely available (links below). Please contact the DePace lab with any additional questions (link below).
DOI: 10.6084/m9.figshare.1270900
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.
DOI: 10.6084/m9.figshare.1270900.v1
title: 1000homes

description: Mapping file, OTU tables with taxonomic information for each OTU, and representative sequences for each OTU.
DOI: 10.6084/m9.figshare.1270900.v2
title: 1000homes

description: Mapping file, OTU tables with taxonomic information for each OTU, and representative sequences for each OTU.
DOI: 10.6084/m9.figshare.1270900.v3
title: 1000homes

description: Mapping file, OTU tables with taxonomic information for each OTU, and representative sequences for each OTU.
DOI: 10.6084/m9.figshare.1270900.v4
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.
DOI: 10.6084/m9.figshare.1270900.v5
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.
DOI: 10.6084/m9.figshare.1270900.v6
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.
DOI: 10.6084/m9.figshare.1270900.v7
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.
DOI: 10.6084/m9.figshare.1270900.v8
title: Homes_USA

description: Information on how to get the raw sequencing data. Also OTU tables with taxonomic information, fasta files with representative sequences for each OTU, and metadata file.