cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4246139
title: Self and other body perception in anorexia nervosa: The role of posterior DMN nodes

description: <b>Objectives:</b> Body image distortion is a core symptom of anorexia nervosa (AN), which involves alterations in self- (and other’s) evaluative processes arising during body perception. At a neural level, self-related information is thought to rely on areas of the so-called default mode network (DMN), which, additionally, shows prominent synchronised activity at rest. <b>Methods:</b> Twenty female patients with AN and 20 matched healthy controls were scanned using magnetic resonance imaging when: (a) viewing video clips of their own body and another's body; (b) at rest. Between-group differences within the DMN during task performance were evaluated and further explored for task-related and resting-state-related functional connectivity alterations. <b>Results:</b> AN patients showed a hyperactivation of the dorsal posterior cingulate cortex during their own-body processing but a response failure to another’s body processing at the precuneus and ventral PCC. Increased task-related connectivity was found between dPCC–dorsal anterior cingulate cortex and precuneus–mid-temporal cortex. Further, AN patients showed decreased resting-state connectivity between the dPCC and the angular gyrus. <b>Conclusions:</b> The PCC and the precuneus are suggested as key components of a network supporting self–other-evaluative processes implicated in body distortion, while the existence of DMN alterations at rest might reflect a sustained, task-independent breakdown within this network in AN.
DOI: 10.6084/m9.figshare.4246139.v1
title: Self and other body perception in anorexia nervosa: The role of posterior DMN nodes

description: <b>Objectives:</b> Body image distortion is a core symptom of anorexia nervosa (AN), which involves alterations in self- (and other’s) evaluative processes arising during body perception. At a neural level, self-related information is thought to rely on areas of the so-called default mode network (DMN), which, additionally, shows prominent synchronised activity at rest. <b>Methods:</b> Twenty female patients with AN and 20 matched healthy controls were scanned using magnetic resonance imaging when: (a) viewing video clips of their own body and another's body; (b) at rest. Between-group differences within the DMN during task performance were evaluated and further explored for task-related and resting-state-related functional connectivity alterations. <b>Results:</b> AN patients showed a hyperactivation of the dorsal posterior cingulate cortex during their own-body processing but a response failure to another’s body processing at the precuneus and ventral PCC. Increased task-related connectivity was found between dPCC–dorsal anterior cingulate cortex and precuneus–mid-temporal cortex. Further, AN patients showed decreased resting-state connectivity between the dPCC and the angular gyrus. <b>Conclusions:</b> The PCC and the precuneus are suggested as key components of a network supporting self–other-evaluative processes implicated in body distortion, while the existence of DMN alterations at rest might reflect a sustained, task-independent breakdown within this network in AN.
DOI: 10.6084/m9.figshare.4252418
title: Comparative proteomics analysis of spermary and ovary in <i>Hyriopsis schlegelii</i>

description: We provide the first large-scale quantitative proteomics analysis in <i>Hyriopsis schlegelii</i>. To investigate the proteins expressed in the gonads, a quantitative proteomics approach has been utilized to analyze differentially expressed proteins between the spermary and ovary. In this study, we identified and quantified 2416 proteins in the gonads of <i>Hyriopsis schlegelii</i>. Of these, 559 proteins showed significantly different expression between the spermary and ovary. Some specific proteins expressed in either the spermary or ovary were identified in <i>Hyriopsis schlegelii</i>. In addition, a series of proteins related to gametogenesis were also identified. Compared with previous reports, many proteins in <i>Hyriopsis schlegelii</i> identified here have different expression patterns between the spermary and ovary. The special hermaphroditism in <i>Hyriopsis schlegelii</i> may contribute to these inconsistent results. The provided proteomics data could be considered as a starting point for subsequent studies focusing on the proteins involved in sexual gland development and maturity. The distribution of 2416 proteins based on the differential expression between spermary and ovary.
DOI: 10.6084/m9.figshare.4252418.v1
title: Comparative proteomics analysis of spermary and ovary in <i>Hyriopsis schlegelii</i>

description: We provide the first large-scale quantitative proteomics analysis in <i>Hyriopsis schlegelii</i>. To investigate the proteins expressed in the gonads, a quantitative proteomics approach has been utilized to analyze differentially expressed proteins between the spermary and ovary. In this study, we identified and quantified 2416 proteins in the gonads of <i>Hyriopsis schlegelii</i>. Of these, 559 proteins showed significantly different expression between the spermary and ovary. Some specific proteins expressed in either the spermary or ovary were identified in <i>Hyriopsis schlegelii</i>. In addition, a series of proteins related to gametogenesis were also identified. Compared with previous reports, many proteins in <i>Hyriopsis schlegelii</i> identified here have different expression patterns between the spermary and ovary. The special hermaphroditism in <i>Hyriopsis schlegelii</i> may contribute to these inconsistent results. The provided proteomics data could be considered as a starting point for subsequent studies focusing on the proteins involved in sexual gland development and maturity. The distribution of 2416 proteins based on the differential expression between spermary and ovary.
DOI: 10.6084/m9.figshare.4253888
title: Translation Repression by Maternal RNA Binding Protein Zar1 is Essential for Early Oogenesis in Zebrafish.rar

description: <br>Proteomic 
analysis with iTRAQ to 
compare <i>zar1</i> 
homozygous 
ovaries 
(homo) 
with 
<i>zar1</i> heterozygous ovaries 
(hetero). 
10 ovaries for each genotype were isolated 
at 33 dpf 
and analyzed with iTRAQ. 
Two replicates were performed for each genotype. 
The UniProt proteome sequences for Danio rerio were used for the database 
searching.
DOI: 10.6084/m9.figshare.4253888.v1
title: Translation Repression by Maternal RNA Binding Protein Zar1 is Essential for Early Oogenesis in Zebrafish.rar

description: <br>Proteomic 
analysis with iTRAQ to 
compare <i>zar1</i> 
homozygous 
ovaries 
(homo) 
with 
<i>zar1</i> heterozygous ovaries 
(hetero). 
10 ovaries for each genotype were isolated 
at 33 dpf 
and analyzed with iTRAQ. 
Two replicates were performed for each genotype. 
The UniProt proteome sequences for Danio rerio were used for the database 
searching.
DOI: 10.6084/m9.figshare.4263893
title: E2fl1 is a meiosis-specific transcription factor in the protist <i>Tetrahymena thermophila</i>

description: Members of the E2F family of transcription factors have been reported to regulate the expression of genes involved in cell cycle control, DNA replication, and DNA repair in multicellular eukaryotes. Here, <i>E2FL1</i>, a meiosis-specific E2F transcription factor gene, was identified in the model ciliate <i>Tetrahymena thermophila</i>. Loss of this gene resulted in meiotic arrest prior to anaphase I. The cytological experiments revealed that the meiotic homologous pairing was not affected in the absence of <i>E2FL1</i>, but the paired homologous chromosomes did not separate and assumed a peculiar tandem arrangement. This is the first time that an E2F family member has been shown to regulate meiotic events. Moreover, BrdU incorporation showed that DSB processing during meiosis was abnormal upon the deletion of <i>E2FL1</i>. Transcriptome sequencing analysis revealed that <i>E2FL1</i> knockout decreased the expression of genes involved in DNA replication and DNA repair in <i>T. thermophila</i>, suggesting that the function of E2F is highly conserved in eukaryotes. In addition, <i>E2FL1</i> deletion inhibited the expression of related homologous chromosome segregation genes in <i>T. thermophila</i>. The result may explain the meiotic arrest phenotype at anaphase I. Finally, by searching for E2F DNA-binding motifs in the entire <i>T. thermophila</i> genome, we identified 714 genes containing at least one E2F DNA-binding motif; of these, 235 downregulated represent putative <i>E2FL1</i> target genes.
DOI: 10.6084/m9.figshare.4263893.v1
title: E2fl1 is a meiosis-specific transcription factor in the protist <i>Tetrahymena thermophila</i>

description: Members of the E2F family of transcription factors have been reported to regulate the expression of genes involved in cell cycle control, DNA replication, and DNA repair in multicellular eukaryotes. Here, <i>E2FL1</i>, a meiosis-specific E2F transcription factor gene, was identified in the model ciliate <i>Tetrahymena thermophila</i>. Loss of this gene resulted in meiotic arrest prior to anaphase I. The cytological experiments revealed that the meiotic homologous pairing was not affected in the absence of <i>E2FL1</i>, but the paired homologous chromosomes did not separate and assumed a peculiar tandem arrangement. This is the first time that an E2F family member has been shown to regulate meiotic events. Moreover, BrdU incorporation showed that DSB processing during meiosis was abnormal upon the deletion of <i>E2FL1</i>. Transcriptome sequencing analysis revealed that <i>E2FL1</i> knockout decreased the expression of genes involved in DNA replication and DNA repair in <i>T. thermophila</i>, suggesting that the function of E2F is highly conserved in eukaryotes. In addition, <i>E2FL1</i> deletion inhibited the expression of related homologous chromosome segregation genes in <i>T. thermophila</i>. The result may explain the meiotic arrest phenotype at anaphase I. Finally, by searching for E2F DNA-binding motifs in the entire <i>T. thermophila</i> genome, we identified 714 genes containing at least one E2F DNA-binding motif; of these, 235 downregulated represent putative <i>E2FL1</i> target genes.
DOI: 10.6084/m9.figshare.4282631
title: Biocathode MCL Curated Metagenome

description: This file contains the curated metagenome assembled from a combination of eight biological replicates of Illumina short read sequencing data, two closed genomes and one plasmid sequence derived from PacBio RSII sequencing of DNA isolated from two pure cultures, and one closed genome with a plasmid assembled from PacBio metagenomic data.  The genome bins and unbinned contigs matching the three complete genome sequences and two plasmids were removed from the short read metagenome assembly and replaced by the closed sequences.  Raw data, parent metagenome assembly, and isolate sequences are linked through NCBI Bioproject PRJNA244670 at https://www.ncbi.nlm.nih.gov/
DOI: 10.6084/m9.figshare.4282631.v1
title: Biocathode MCL Curated Metagenome

description: This file contains the curated metagenome assembled from a combination of eight biological replicates of Illumina short read sequencing data, two closed genomes and one plasmid sequence derived from PacBio RSII sequencing of DNA isolated from two pure cultures, and one closed genome with a plasmid assembled from PacBio metagenomic data.  The genome bins and unbinned contigs matching the three complete genome sequences and two plasmids were removed from the short read metagenome assembly and replaced by the closed sequences.  Raw data, parent metagenome assembly, and isolate sequences are linked through NCBI Bioproject PRJNA244670 at https://www.ncbi.nlm.nih.gov/
DOI: 10.6084/m9.figshare.4286369.v1
title: A functional nanocarrier that copenetrates extracellular matrix and multiple layers of tumor cells for sequential and deep tumor autophagy inhibitor and chemotherapeutic delivery

description: To further enhance the intensity of deep tumor drug delivery and integrate a combined therapy, we herein report on a core-shell nanocarrier that could simultaneously overcome the double barriers of the extracellular matrix (ECM) and multiple layers of tumor cells (MLTC). A pH-triggered reversible swelling-shrinking core and an MMP2 (matrix metallopeptidase 2) degradable shell were developed to encapsulate chemotherapeutics and macroautophagy/autophagy inhibitors, respectively. MMP2 degraded the shell, which was followed by the autophagy inhibitors' release. The exposed core could diffuse along the pore within the ECM to deliver chemotherapeutics into deep tumors, and it was able to swell in lysosomes and shrink back in the cytoplasm or ECM. The swelling of the core resulted in the rapid release of chemotherapeutics to kill autophagy-inhibited cells. After leaving the dead cells, the shrinking core could act on neighboring cells that were closer to the center of the tumor. The core thus could also cross MLTC layer by layer to deliver chemotherapeutics into the deep tumor.
DOI: 10.6084/m9.figshare.4286369
title: A functional nanocarrier that copenetrates extracellular matrix and multiple layers of tumor cells for sequential and deep tumor autophagy inhibitor and chemotherapeutic delivery

description: To further enhance the intensity of deep tumor drug delivery and integrate a combined therapy, we herein report on a core-shell nanocarrier that could simultaneously overcome the double barriers of the extracellular matrix (ECM) and multiple layers of tumor cells (MLTC). A pH-triggered reversible swelling-shrinking core and an MMP2 (matrix metallopeptidase 2) degradable shell were developed to encapsulate chemotherapeutics and macroautophagy/autophagy inhibitors, respectively. MMP2 degraded the shell, which was followed by the autophagy inhibitors' release. The exposed core could diffuse along the pore within the ECM to deliver chemotherapeutics into deep tumors, and it was able to swell in lysosomes and shrink back in the cytoplasm or ECM. The swelling of the core resulted in the rapid release of chemotherapeutics to kill autophagy-inhibited cells. After leaving the dead cells, the shrinking core could act on neighboring cells that were closer to the center of the tumor. The core thus could also cross MLTC layer by layer to deliver chemotherapeutics into the deep tumor.
DOI: 10.6084/m9.figshare.4287668
title: Example input files

description: Example input files can be downloaded from here. Note that the attached input and output example files are not real data but have the same format with them. Required input files for each step are described in instructions.<br>Data Sets : The glioblastoma (GBM) data sets including the expression data of mRNA, protein, miRNA used in this paper were collected from TCGA. The information about GBM-related miRNAs was collected from Human miRNA & Disease Database v2.0 (HMDD v2.0). Protein-protein interaction data sets were collected from the Human Protein Reference Database (HPRD) (Prasad et al.,2009).<br>
DOI: 10.6084/m9.figshare.4287668.v1
title: Example input files

description: Example input files can be downloaded from here. Note that the attached input and output example files are not real data but have the same format with them. Required input files for each step are described in instructions.<br>Data Sets : The glioblastoma (GBM) data sets including the expression data of mRNA, protein, miRNA used in this paper were collected from TCGA. The information about GBM-related miRNAs was collected from Human miRNA & Disease Database v2.0 (HMDD v2.0). Protein-protein interaction data sets were collected from the Human Protein Reference Database (HPRD) (Prasad et al.,2009).<br>
DOI: 10.6084/m9.figshare.4287677
title: Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNA

description: News: 2016/09/27: Source codes and data sets are updated.<br>Paper: Jiyoun Seo, Daeyong Jin, Chan-Hun Choi and Hyunju Lee* (2016) Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PLoS One, In Press.<br>Introduction: This study explores two approaches for the investigation of gene-miRNA relationships by integrating mRNA expression and protein expression data. This study presents ranked miRNAs lists according to their effects on cancer development and constructed modules containing mRNAs, proteins, and miRNAs, in which these three molecular types are highly correlated.<br><br><br>Description: Source codes were implemented in r and are available here. Instructions and example input files for running source codes can be downloaded from here. Note that the attached input and output example files are not real data but have the same format with them. Required input files for each step are described in instructions.<br>Data sets: <b>The glioblastoma (GBM) data sets including the expression data of mRNA, protein, miRNA used in this paper were collected from TCGA. The information about GBM-related miRNAs was collected from Human miRNA & Disease Database v2.0 (HMDD v2.0). Protein-protein interaction data sets were collected from the Human Protein Reference Database (HPRD) (Prasad et al.,2009).</b>
DOI: 10.6084/m9.figshare.4288385
title: Isotope fractionation of sandy-soil water during evaporation – an experimental study

description: Soil samples containing water with known stable isotopic compositions were prepared. The soil water was recovered by using vacuum/heat distillation. The experiments were held under different conditions to control rates of water evaporation and water recovery. Recoveries, δ<sup>18</sup>O and δ<sup>2</sup>H values of the soil water were determined. Analyses of the data using a Rayleigh distillation model indicate that under the experimental conditions only loosely bound water is extractable in cases where the recovery is smaller than 100 %. Due to isotopic exchange between vapour and remaining water in the micro channels or capillaries of the soil matrix, isotopic fractionation may take place under near-equilibrium conditions. This causes the observed relationship between δ<sup>2</sup>H and δ<sup>18</sup>O of the extracted water samples to have a slope close to 8. The results of this study may indicate that, in arid zones when soil that initially contains water dries out, the slope of the relationship between δ<sup>2</sup>H and δ<sup>18</sup>O values should be close to 8. Thus, a smaller slope, as observed by some groundwater and soil water samples in arid zones, may be caused by evaporation of water before the water has entered the unsaturated zone.
DOI: 10.6084/m9.figshare.4288385.v1
title: Isotope fractionation of sandy-soil water during evaporation – an experimental study

description: Soil samples containing water with known stable isotopic compositions were prepared. The soil water was recovered by using vacuum/heat distillation. The experiments were held under different conditions to control rates of water evaporation and water recovery. Recoveries, δ<sup>18</sup>O and δ<sup>2</sup>H values of the soil water were determined. Analyses of the data using a Rayleigh distillation model indicate that under the experimental conditions only loosely bound water is extractable in cases where the recovery is smaller than 100 %. Due to isotopic exchange between vapour and remaining water in the micro channels or capillaries of the soil matrix, isotopic fractionation may take place under near-equilibrium conditions. This causes the observed relationship between δ<sup>2</sup>H and δ<sup>18</sup>O of the extracted water samples to have a slope close to 8. The results of this study may indicate that, in arid zones when soil that initially contains water dries out, the slope of the relationship between δ<sup>2</sup>H and δ<sup>18</sup>O values should be close to 8. Thus, a smaller slope, as observed by some groundwater and soil water samples in arid zones, may be caused by evaporation of water before the water has entered the unsaturated zone.
DOI: 10.6084/m9.figshare.4288406
title: Comprehensive mapping of 5-hydroxymethylcytosine epigenetic dynamics in axon regeneration

description: In contrast to central nervous system neurons, dorsal root ganglia (DRG) neurons can switch to a regenerative state after peripheral axotomy. In a screen for chromatin regulators of the regenerative responses in this conditioning lesion paradigm, we identified Tet methylcytosine dioxygenase 3 (Tet3) as upregulated in DRG neurons, along with increased 5-hydroxymethylcytosine (5hmC). We generated genome-wide 5hmC maps in adult DRG, which revealed that peripheral and central axotomy (leading to no regenerative effect) triggered differential 5hmC changes that are associated with distinct signaling pathways. 5hmC was altered in a large set of regeneration-associated genes (RAGs), including well-known RAGs, such as <i>Atf3, Bdnf</i>, and <i>Smad1</i>, that regulate axon growth potential of DRG neurons, thus supporting its role for RAG regulation. Our analyses also predicted HIF-1, STAT, and IRF as potential transcription factors that may collaborate with Tet3 for 5hmC modifications. Intriguingly, central axotomy resulted in widespread 5hmC modifications that had little overlap with those of peripheral axotomy, thus potentially constituting a roadblock for regeneration. Our study revealed 5hmC dynamics as a previously unrecognized epigenetic mechanism underlying the divergent responses after axonal injury.
DOI: 10.6084/m9.figshare.4288406.v1
title: Comprehensive mapping of 5-hydroxymethylcytosine epigenetic dynamics in axon regeneration

description: In contrast to central nervous system neurons, dorsal root ganglia (DRG) neurons can switch to a regenerative state after peripheral axotomy. In a screen for chromatin regulators of the regenerative responses in this conditioning lesion paradigm, we identified Tet methylcytosine dioxygenase 3 (Tet3) as upregulated in DRG neurons, along with increased 5-hydroxymethylcytosine (5 hmC). We generated genome-wide 5 hmC maps in adult DRG, which revealed that peripheral and central axotomy (leading to no regenerative effect) triggered differential 5 hmC changes that are associated with distinct signaling pathways. 5 hmC was altered in a large set of regeneration-associated genes (RAGs), including well-known RAGs, such as <i>Atf3, Bdnf</i>, and <i>Smad1</i>, that regulate axon growth potential of DRG neurons, thus supporting its role for RAG regulation. Our analyses also predicted HIF-1, STAT, and IRF as potential transcription factors that may collaborate with Tet3 for 5 hmC modifications. Intriguingly, central axotomy resulted in widespread 5 hmC modifications that had little overlap with those of peripheral axotomy, thus potentially constituting a roadblock for regeneration. Our study revealed 5 hmC dynamics as a previously unrecognized epigenetic mechanism underlying the divergent responses after axonal injury.