cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11825973
title: Additional file 3 of Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

description: Additional file 3: Table S2. DNase-seq and H3K27ac sample annotation table for mouse and human.
DOI: 10.6084/m9.figshare.11825988.v1
title: Additional file 5 of Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

description: Additional file 5: Table S4. TF perturbation DNA microarray meta table for benchmarking the peak-RP and Lisa methods.
DOI: 10.6084/m9.figshare.11825982.v1
title: Additional file 4 of Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

description: Additional file 4: Table S3. Analysis of Lisa predictions of GR and ER regulated genes using data which does not match the specific cell type. The cell line and cell type of the highest ranked Lisa predicted target TR sample are shown in parentheses in each case.
DOI: 10.6084/m9.figshare.11825988
title: Additional file 5 of Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

description: Additional file 5: Table S4. TF perturbation DNA microarray meta table for benchmarking the peak-RP and Lisa methods.
DOI: 10.25549/one-ouc17559734
title: Mattachine Society, Los Angeles Area Council proposed bylaws and policies (1953-1954)

description: Mattachine Society; drafts for proposed bylaws and policies for the Los Angeles Area Council, also known as the Southern Area Council (1953-1954)
DOI: 10.6084/m9.figshare.19690184
title: GATA binding protein 1 recruits histone deacetylase 2 to the promoter region of nuclear receptor binding protein 2 to affect the tumor microenvironment and malignancy of thyroid carcinoma

description: The tumor microenvironment (TME) and activated angiogenesis in thyroid carcinoma (TC) are critical for tumor growth and metastasis. Nuclear receptor binding protein 2 (<i>NRBP2</i>) has been suggested as a tumor suppressor. This study examines the function of <i>NRBP2</i> in the progression of TC and the regulatory mechanism. By analyzing bioinformatic tools including GSE165724 dataset and the Cancer Genome Atlas system, we predicted <i>NRBP2</i> as a poorly expressed gene in TC. Decreased <i>NRBP2</i> expression was detected in TC tumor tissues and cells. Poor expression of <i>NRBP2</i> was linked to unfavorable prognosis of patients. GATA binding protein 1 (<i>GATA1</i>) was found as a negative regulator of <i>NRBP2</i>. It recruited histone deacetylase2 (<i>HDAC2</i>) to the <i>NRBP2</i> promoter to trigger histone deacetylation. <i>NRBP2</i> overexpression suppressed growth of TC cells, and it reduced expression of TME markers, M2 polarization of macrophages, and angiogenesis in TC. Similar results were reproduced <i>in vivo</i> in nude mice. However, the anti-oncogenic roles of <i>NRBP2</i> were blocked after further overexpression of <i>GATA1</i> or <i>HDAC2</i>. In summary, this study demonstrates that <i>GATA1</i> recruits <i>HDAC2</i> to the <i>NRBP2</i> promoter and enhances the TME and angiogenesis in TC cells.
DOI: 10.25549/one-ouc17552237
title: Mattachine Society, First Church of One Brotherhood (1956-1957)
DOI: 10.25549/one-ouc17559736
title: Los Angeles Mattachine Society, Inc., administrative records and promotional materials (1952-1964)

description: Los Angeles Mattachine Society, Inc.; bulletins, promotional materials, and administrative records, including the 1963 articles of incorporation; also includes photocopies of a notebook with notes documenting 1952 meetings of the Mattachine Society, also known as the Mattachine Foundation (1952-1964)
DOI: 10.6084/m9.figshare.19166125
title: MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation

description: Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid–liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations <i>in vitro</i> and <i>in vivo</i> to explore the mechanism of MeCP2-driven heterochromatin organization and dynamics. We show that MeCP2 alone forms liquid-like spherical droplets via multivalent electrostatic interactions and with isotropic mobility. Crowded environments and DNA promote MeCP2 LLPS and slow down MeCP2 mobility. DNA methylation, however, restricts the growth of heterochromatin compartments correlating with immobilization of MeCP2. Furthermore, MeCP2 self-interaction is required for LLPS and is disrupted by Rett syndrome mutations. In summary, we are able to model the heterochromatin compartmentalization as well as MeCP2 concentration and heterogeneous motion in the minimal <i>in vitro</i> system.
DOI: 10.6084/m9.figshare.19166125.v1
title: MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation

description: Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid–liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations <i>in vitro</i> and <i>in vivo</i> to explore the mechanism of MeCP2-driven heterochromatin organization and dynamics. We show that MeCP2 alone forms liquid-like spherical droplets via multivalent electrostatic interactions and with isotropic mobility. Crowded environments and DNA promote MeCP2 LLPS and slow down MeCP2 mobility. DNA methylation, however, restricts the growth of heterochromatin compartments correlating with immobilization of MeCP2. Furthermore, MeCP2 self-interaction is required for LLPS and is disrupted by Rett syndrome mutations. In summary, we are able to model the heterochromatin compartmentalization as well as MeCP2 concentration and heterogeneous motion in the minimal <i>in vitro</i> system.
DOI: 10.25549/one-ouc17559735
title: Los Angeles Mattachine Society, Inc., administrative records and promotional materials (1952-1964)

description: Los Angeles Mattachine Society, Inc.; bulletins, promotional materials, and administrative records, including the 1963 articles of incorporation; also includes photocopies of a notebook with notes documenting 1952 meetings of the Mattachine Society, also known as the Mattachine Foundation (1952-1964)
DOI: 10.6084/m9.figshare.17065960
title: Additional file 10 of Transcriptional landscape of highly lignified poplar stems at single-cell resolution

description: Additional file 10: Table S9. GO enrichment analysis for paralogs falling within the top10% of the Jaccard index distribution.
DOI: 10.25549/one-ouc17559737
title: Mattachine Society, Los Angeles Area Council proposed bylaws and policies (1953-1954)

description: Mattachine Society; drafts for proposed bylaws and policies for the Los Angeles Area Council, also known as the Southern Area Council (1953-1954)
DOI: 10.6084/m9.figshare.17065963.v1
title: Additional file 11 of Transcriptional landscape of highly lignified poplar stems at single-cell resolution

description: Additional file 11: Table S10. Primers used for RNA in situ hybridization in this study.
DOI: 10.6084/m9.figshare.17065960.v1
title: Additional file 10 of Transcriptional landscape of highly lignified poplar stems at single-cell resolution

description: Additional file 10: Table S9. GO enrichment analysis for paralogs falling within the top10% of the Jaccard index distribution.
DOI: 10.25549/one-ouc17559738
title: Mattachine Society, secretary general file (1954-1960)

description: Mattachine Society; file of the secretary general of the Mattachine Society, including administrative records from area councils; correspondence regarding Mattachine publications and financial donations; meeting minutes; membership information; and legal documents  (1954-1960)
DOI: 10.25549/one-ouc17555297
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.6084/m9.figshare.19687453
title: Additional file 2 of A prognostic model for oral squamous cell carcinoma using 7 genes related to tumor mutational burden

description: Additional file 2: Table S2. The full results of KEGG enrichment analysis.
DOI: 10.25549/one-ouc17555293
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.6084/m9.figshare.19687456
title: Additional file 3 of A prognostic model for oral squamous cell carcinoma using 7 genes related to tumor mutational burden

description: Additional file 3: Table S3. The fulfillment of proportional hazard’s assumption for all variables in multivariate Cox regression analysis.
DOI: 10.25549/one-ouc17555288
title: Mattachine Society, Tavern Guild (1964-1967)
DOI: 10.25549/one-ouc17555292
title: Mattachine Society, Wicker Research Studies, research project II (1959)
DOI: 10.6084/m9.figshare.11826312
title: Additional file 1 of Improving prediction performance of colon cancer prognosis based on the integration of clinical and multi-omics data

description: Additional file 1. List of prior knowledge. List of gene symbols for gene expression, gene symbols for DNA methylation and miRNA ids for miRNA expression used as prior knowledge.
DOI: 10.6084/m9.figshare.17065990
title: Additional file 7 of Transcriptional landscape of highly lignified poplar stems at single-cell resolution

description: Additional file 7: Table S6. Results of GO enrichment analysis for genes in Fig. 2D.
DOI: 10.25549/one-ouc17555294
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.5281/zenodo.10667112
title: replication package for the paper "The Relationship Between Different Python Argument-Passing Mechanisms and Fixes: An Empirical Study"

description: Abstract:

Modern programming languages (such as Python, but not only) have introduced a variety of constructs and syntactical elements to make software development more efficient and concise. Examples include lambda functions, comprehension collections, of mechanisms to facilitate the passing of arguments to a function. While many of such constructs may, in principle, be beneficial for developers, recent studies have shown that certain programming constructs introduce atoms of confusion, and may therefore affect program understanding. Moreover, recent work has shown that changes to some constructs, namely functional constructs of Python, induce more fixes than other changes. This paper studies the effect of different Python argument-passing mechanisms to investigate their relationship with code proneness to be fixed. Specifically, we study the fix-proneness for what concerns the function definition, as well as its invocation. This is done by analyzing the evolutionary history of 200 Python projects, for a total of about 3M functions and 12M call sites. While there are varying effects for what concerns parameter declaration mechanisms, we found evidence that keyword-based argument passing is less defect prone than positional argument passing, and this is not affected by size-related confounding factors.
DOI: 10.5281/zenodo.10667113
title: replication package for the paper "The Relationship Between Different Python Argument-Passing Mechanisms and Fixes: An Empirical Study"

description: Abstract:

Modern programming languages (such as Python, but not only) have introduced a variety of constructs and syntactical elements to make software development more efficient and concise. Examples include lambda functions, comprehension collections, of mechanisms to facilitate the passing of arguments to a function. While many of such constructs may, in principle, be beneficial for developers, recent studies have shown that certain programming constructs introduce atoms of confusion, and may therefore affect program understanding. Moreover, recent work has shown that changes to some constructs, namely functional constructs of Python, induce more fixes than other changes. This paper studies the effect of different Python argument-passing mechanisms to investigate their relationship with code proneness to be fixed. Specifically, we study the fix-proneness for what concerns the function definition, as well as its invocation. This is done by analyzing the evolutionary history of 200 Python projects, for a total of about 3M functions and 12M call sites. While there are varying effects for what concerns parameter declaration mechanisms, we found evidence that keyword-based argument passing is less defect prone than positional argument passing, and this is not affected by size-related confounding factors.
DOI: 10.5281/zenodo.7482556
title: Datasets and Model for "Age-Independent Oceanic Plate Thickness and Asthenosphere Melting from SS Precursor Imaging"

description: The Earth’s asthenosphere is a mechanically weak layer characterized by low seismic velocity and high attenuation. The nature of this layer has been strongly debated. In this study, we process twelve years of seismic data recorded at the global seismological network (GSN) stations to investigate SS waves reflected at the upper and lower boundaries of this layer in global oceanic regions. We observe strong reflections from both the top and the bottom of the asthenosphere, dispersive across all major oceans. The average depths of the two discontinuities are 120 km and 255 km, respectively. The SS waves reflected at the lithosphere and asthenosphere boundary are characterized by anomalously large amplitudes, which require ∼12.5% reduction in seismic velocity across the interface. This large velocity drop can not be explained by a thermal cooling model but indicates 1.5%-2% localized melt in the oceanic asthenosphere. The depths of the two discontinuities show large variations, indicating that the asthenosphere is far from a homogeneous layer but likely associated with strong and heterogeneous small-scale convections in the oceanic mantle. The average depths of the two boundaries are largely constant across different age bands. In contrast to the half space cooling model, this observation supports the existence of a constant-thickness plate in oceanic regions with a complex and heterogeneous origin. This repository contains four datasets and one reference earth model from this study.
DOI: 10.5281/zenodo.7482557
title: Datasets and Model for "Age-Independent Oceanic Plate Thickness and Asthenosphere Melting from SS Precursor Imaging"

description: The Earth’s asthenosphere is a mechanically weak layer characterized by low seismic velocity and high attenuation. The nature of this layer has been strongly debated. In this study, we process twelve years of seismic data recorded at the global seismological network (GSN) stations to investigate SS waves reflected at the upper and lower boundaries of this layer in global oceanic regions. We observe strong reflections from both the top and the bottom of the asthenosphere, dispersive across all major oceans. The average depths of the two discontinuities are 120 km and 255 km, respectively. The SS waves reflected at the lithosphere and asthenosphere boundary are characterized by anomalously large amplitudes, which require ∼12.5% reduction in seismic velocity across the interface. This large velocity drop can not be explained by a thermal cooling model but indicates 1.5%-2% localized melt in the oceanic asthenosphere. The depths of the two discontinuities show large variations, indicating that the asthenosphere is far from a homogeneous layer but likely associated with strong and heterogeneous small-scale convections in the oceanic mantle. The average depths of the two boundaries are largely constant across different age bands. In contrast to the half space cooling model, this observation supports the existence of a constant-thickness plate in oceanic regions with a complex and heterogeneous origin. This repository contains four datasets and one reference earth model from this study.
DOI: 10.6084/m9.figshare.11826336.v1
title: Additional file 3 of Improving prediction performance of colon cancer prognosis based on the integration of clinical and multi-omics data

description: Additional file 3. Differentially expressed genes identified based on cluster labels of gene expression. Differentially expressed genes identified based on cluster labels of gene expression.
DOI: 10.25549/one-ouc17555360
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.25549/one-ouc17552253
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.6084/m9.figshare.12874926.v1
title: Additional file 2 of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file 2: siRNAs used in the present study. Supplementary Table 2 containing details of the siRNAs used in the present study. (XLS 22 KB)
DOI: 10.25549/one-ouc17555304
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.6084/m9.figshare.11826207
title: Additional file 4 of MiR-612 regulates invadopodia of hepatocellular carcinoma by HADHA-mediated lipid reprogramming

description: Additional file 4. Exel file. The original data of mir-612-targeted genes available via RNA immunoprecipitation which up- or down-regulated significantly.
DOI: 10.6084/m9.figshare.11826312.v1
title: Additional file 1 of Improving prediction performance of colon cancer prognosis based on the integration of clinical and multi-omics data

description: Additional file 1. List of prior knowledge. List of gene symbols for gene expression, gene symbols for DNA methylation and miRNA ids for miRNA expression used as prior knowledge.
DOI: 10.25549/one-ouc17555362
title: Mattachine Society, Long Beach (Harbor) Area Council correspondence and memoranda (1953-1956)
DOI: 10.6084/m9.figshare.11826207.v1
title: Additional file 4 of MiR-612 regulates invadopodia of hepatocellular carcinoma by HADHA-mediated lipid reprogramming

description: Additional file 4. Exel file. The original data of mir-612-targeted genes available via RNA immunoprecipitation which up- or down-regulated significantly.
DOI: 10.25549/one-ouc17555307
title: Mattachine Society, Long Beach (Harbor) area council constitution and bylaws (1953-1954)
DOI: 10.6084/m9.figshare.12874890.v13
title: Additional file of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file of Exploring the link between MORF4L1 and risk of breast cancer
DOI: 10.6084/m9.figshare.11826195.v1
title: Additional file 1 of Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)

description: Additional file 1: Figure S1. Size distribution of unigenes. Figure S2. E-value distribution of the Blastx hits against the nr protein database with an E-value cutoff of 1E− 5. Figure S3. Pie chart representation of seashore paspalum’s transcriptome GO annotation on level 2. Figure S4. Species distribution of unigenes. Table S1. Summary of transcriptome sequencing and de novo assembly. Table S2. Summary of annotation statistics of seashore paspalum’s transcriptome. Table S3. BUSCO analysis for the assessment of transcriptome completeness. Table S4. Transcription factors of different families in seashore paspalum’s transcriptome. Table S6. Summary of possible transcription factors that are commonly regulated by Supreme and Parish under salt-treated conditions. Table S7A. DEGs involved in “oxidation-reduction process” in salt-treated Supreme. Table S8A. DEGs with “nucleic acid binding activity” in salt-treated Supreme
DOI: 10.6084/m9.figshare.12874830
title: Additional file 1 of A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

description: Additional file 1:Details of the 507 sequence-based markers on the RCZ16_DH map, and information relating to anchored scaffolds using the RCZ16_DH map and the other three publicly available genetic linkage maps. (XLS 154 KB)
DOI: 10.6084/m9.figshare.12874940.v1
title: SACF vs GAC BWC from Sisal xylem fibre-based activated carbon fibres for fuel adsorption: effect of thermal stabilization of diammonium phosphate

description: Butane Working Capacity of SACF and GAC
DOI: 10.25549/one-ouc17552254
title: Mattachine Society, American Civil Liberties Union (1956-1958)
DOI: 10.6084/m9.figshare.11826195
title: Additional file 1 of Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum)

description: Additional file 1: Figure S1. Size distribution of unigenes. Figure S2. E-value distribution of the Blastx hits against the nr protein database with an E-value cutoff of 1E− 5. Figure S3. Pie chart representation of seashore paspalum’s transcriptome GO annotation on level 2. Figure S4. Species distribution of unigenes. Table S1. Summary of transcriptome sequencing and de novo assembly. Table S2. Summary of annotation statistics of seashore paspalum’s transcriptome. Table S3. BUSCO analysis for the assessment of transcriptome completeness. Table S4. Transcription factors of different families in seashore paspalum’s transcriptome. Table S6. Summary of possible transcription factors that are commonly regulated by Supreme and Parish under salt-treated conditions. Table S7A. DEGs involved in “oxidation-reduction process” in salt-treated Supreme. Table S8A. DEGs with “nucleic acid binding activity” in salt-treated Supreme
DOI: 10.6084/m9.figshare.12874830.v1
title: Additional file 1 of A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

description: Additional file 1:Details of the 507 sequence-based markers on the RCZ16_DH map, and information relating to anchored scaffolds using the RCZ16_DH map and the other three publicly available genetic linkage maps. (XLS 154 KB)
DOI: 10.6084/m9.figshare.17065978
title: Additional file 3 of Transcriptional landscape of highly lignified poplar stems at single-cell resolution

description: Additional file 3: Table S2. List of the cluster-enriched genes.
DOI: 10.25549/one-ouc17555306
title: Mattachine Society, Long Beach (Harbor) area council meeting minutes (1954-1955)
DOI: 10.6084/m9.figshare.12874890.v14
title: Additional file of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file of Exploring the link between MORF4L1 and risk of breast cancer
DOI: 10.6084/m9.figshare.12874923
title: Additional file 1 of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file 1: Y2H baits for 12 proteins in the FA/BrCa signaling pathway. Supplementary Table 1 containing details of the design of Y2H baits for 12 proteins in the FA/BrCa signaling pathway. (XLS 28 KB)
DOI: 10.25549/one-ouc17552257
title: Mattachine Society, First Church of One Brotherhood (1956-1957)
DOI: 10.6084/m9.figshare.12874923.v1
title: Additional file 1 of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file 1: Y2H baits for 12 proteins in the FA/BrCa signaling pathway. Supplementary Table 1 containing details of the design of Y2H baits for 12 proteins in the FA/BrCa signaling pathway. (XLS 28 KB)
DOI: 10.6084/m9.figshare.12874890.v11
title: Additional file of Exploring the link between MORF4L1 and risk of breast cancer

description: Additional file of Exploring the link between MORF4L1 and risk of breast cancer
DOI: 10.25549/one-ouc17555305
title: Mattachine Society, Tavern Guild (1964-1967)
DOI: 10.6084/m9.figshare.12874946.v1
title: SACF-DAP0(ASAP2460) from Sisal xylem fibre-based activated carbon fibres for fuel adsorption: effect of thermal stabilization of diammonium phosphate

description: Pore characteristics of SACF-DAP0 by ASAP2460