cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9771506.v1
title: A method for identifying allele-specific hydroxymethylation

description: We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin–dependent allele-specific methylation (pd-ASM), which causes parent-of-origin–dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin–dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of <i>Pax5</i> in strain-specific methylation and hydroxymethylation in exon 7 of <i>Pdgfrb</i>.
DOI: 10.6084/m9.figshare.9771443
title: Survey of ribose ring pucker of signaling nucleosides and nucleotides

description: The ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y<sub>1</sub> receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y<sub>12</sub> receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations.
DOI: 10.6084/m9.figshare.9771443.v2
title: Survey of ribose ring pucker of signaling nucleosides and nucleotides

description: The ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y<sub>1</sub> receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y<sub>12</sub> receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations.
DOI: 10.6084/m9.figshare.9771443.v1
title: Survey of ribose ring pucker of signaling nucleosides and nucleotides

description: The ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y<sub>1</sub> receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y<sub>12</sub> receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations.
DOI: 10.6084/m9.figshare.9771398
title: MOESM3 of Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural

description: Additional file 3: Table S9. Gene Ontology terms for biological processes with significantly over expressed genes upon exposure to furfural.
DOI: 10.6084/m9.figshare.9771395
title: Additional file 4: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: Excel module of the Rasch model for continuous responses. (XLSM 3009 kb)
DOI: 10.6084/m9.figshare.9771398.v1
title: MOESM3 of Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural

description: Additional file 3: Table S9. Gene Ontology terms for biological processes with significantly over expressed genes upon exposure to furfural.
DOI: 10.6084/m9.figshare.9771386
title: MOESM2 of Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural

description: Additional file 2: Table S1. Differentially expressed genes by RNA-seq in N. crassa, after exposure to 10Â mM furfural or 10Â mM HMF
DOI: 10.6084/m9.figshare.9771395.v1
title: Additional file 4: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: Excel module of the Rasch model for continuous responses. (XLSM 3009 kb)
DOI: 10.6084/m9.figshare.9771386.v1
title: MOESM2 of Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural

description: Additional file 2: Table S1. Differentially expressed genes by RNA-seq in N. crassa, after exposure to 10Â mM furfural or 10Â mM HMF
DOI: 10.6084/m9.figshare.9771380
title: Additional file 2: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: The demonstration of DRGs detection on website. http://www.healthup.org.tw/kpiall/quest2/drgdetect.htm . (TXT 125 bytes)
DOI: 10.6084/m9.figshare.9771368
title: Additional file 1: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: Study dataset. (XLSX 1030 kb)
DOI: 10.6084/m9.figshare.9771380.v1
title: Additional file 2: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: The demonstration of DRGs detection on website. http://www.healthup.org.tw/kpiall/quest2/drgdetect.htm . (TXT 125 bytes)
DOI: 10.6084/m9.figshare.9771368.v1
title: Additional file 1: of Detecting hospital behaviors of up-coding on DRGs using Rasch model of continuous variables and online cloud computing in Taiwan

description: Study dataset. (XLSX 1030 kb)
DOI: 10.6084/m9.figshare.9771305
title: MOESM6 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 6: Script 2. RHS sub-algorithm that can be run directly in Fiji or ImageJ using ROI generated by RHS main algorithm.
DOI: 10.6084/m9.figshare.9771305.v2
title: MOESM6 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 6: Script 2. RHS sub-algorithm that can be run directly in Fiji or ImageJ using ROI generated by RHS main algorithm.
DOI: 10.6084/m9.figshare.9771287
title: MOESM4 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 4: Script 4. RHS main algorithm adapted for Arabidopsis thaliana roots.
DOI: 10.6084/m9.figshare.9771305.v1
title: MOESM6 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 6: Script 2. RHS sub-algorithm that can be run directly in Fiji or ImageJ using ROI generated by RHS main algorithm.
DOI: 10.6084/m9.figshare.9771278
title: MOESM3 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 3: Script 3. RHS main algorithm adapted for Brachypodium roots.
DOI: 10.6084/m9.figshare.9771287.v2
title: MOESM4 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 4: Script 4. RHS main algorithm adapted for Arabidopsis thaliana roots.
DOI: 10.6084/m9.figshare.9771287.v1
title: MOESM4 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 4: Script 4. RHS main algorithm adapted for Arabidopsis thaliana roots.
DOI: 10.6084/m9.figshare.9771263
title: MOESM1 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 1: Script 1. RHS main algorithm than can be run directly in Fiji or ImageJ.
DOI: 10.6084/m9.figshare.9771278.v2
title: MOESM3 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 3: Script 3. RHS main algorithm adapted for Brachypodium roots.
DOI: 10.6084/m9.figshare.9771263.v2
title: MOESM1 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 1: Script 1. RHS main algorithm than can be run directly in Fiji or ImageJ.
DOI: 10.6084/m9.figshare.9771278.v1
title: MOESM3 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 3: Script 3. RHS main algorithm adapted for Brachypodium roots.
DOI: 10.6084/m9.figshare.9771263.v1
title: MOESM1 of Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

description: Additional file 1: Script 1. RHS main algorithm than can be run directly in Fiji or ImageJ.
DOI: 10.6084/m9.figshare.9771137
title: Additional file 9: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S7. MapMan annotation of the JA-responsive candidate genes identified in the TENOR transcriptome database. (XLSX 384 kb)
DOI: 10.6084/m9.figshare.9771137.v1
title: Additional file 9: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S7. MapMan annotation of the JA-responsive candidate genes identified in the TENOR transcriptome database. (XLSX 384 kb)
DOI: 10.6084/m9.figshare.9771128
title: Additional file 8: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S6. Expression pattern of candidate genes in response to jasmonate in shoot and root using RNAseq dataset from TENOR. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9771122
title: Additional file 7: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S5. List of candidate genes found ±25 kb around the significant markers and MapMan and TFDB annotations. (XLSX 2416 kb)
DOI: 10.6084/m9.figshare.9771128.v1
title: Additional file 8: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S6. Expression pattern of candidate genes in response to jasmonate in shoot and root using RNAseq dataset from TENOR. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9771107
title: Additional file 5: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S4. List of signification markers of detected QTLs at p-value
DOI: 10.6084/m9.figshare.9771122.v1
title: Additional file 7: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S5. List of candidate genes found ±25 kb around the significant markers and MapMan and TFDB annotations. (XLSX 2416 kb)
DOI: 10.6084/m9.figshare.9771107.v1
title: Additional file 5: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S4. List of signification markers of detected QTLs at p-value
DOI: 10.6084/m9.figshare.9771092
title: Additional file 3: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S3. Effects of 5 μM JA on the phenotypic variation of the growth traits for 155 rice accessions. (CSV 12 kb)
DOI: 10.6084/m9.figshare.9771092.v1
title: Additional file 3: of Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

description: Table S3. Effects of 5 μM JA on the phenotypic variation of the growth traits for 155 rice accessions. (CSV 12 kb)
DOI: 10.6084/m9.figshare.9771071
title: Additional file 3: of The therapeutic effects of qigong in patients with chronic obstructive pulmonary disease in the stable stage: a meta-analysis

description: Details of excluded articles. The excluded articles in the stage of full text assessment. (XLS 25 kb)
DOI: 10.6084/m9.figshare.9771071.v1
title: Additional file 3: of The therapeutic effects of qigong in patients with chronic obstructive pulmonary disease in the stable stage: a meta-analysis

description: Details of excluded articles. The excluded articles in the stage of full text assessment. (XLS 25 kb)
DOI: 10.18112/openneuro.ds003095.v1.0.0
title: Polarization Dataset
DOI: 10.6084/m9.figshare.9770876.v2
title: High-Throughput Screening Platform for Solid Electrolytes Combining Hierarchical Ion-Transport Prediction Algorithms

description: The combination of a materials database with high-throughput ion-transport calculations is an effective approach to screen for promising solid electrolytes. However, automating the complicated preprocessing involved in currently widely used ion-transport characterization algorithms, such as the first-principles nudged elastic band (FP-NEB) method, remains challenging. Here, we report on high-throughput screening platform for solid electrolytes (SPSE) that integrates a materials database with hierarchical ion-transport calculations realized by implementing empirical algorithms to assist in FP-NEB calculation. We first preliminarily screen candidates and determine the approximate ion-transport paths using empirical geometric analysis and bond valence method. A chain of images is then automatically generated along these paths for accurate FP-NEB calculation. In addition, an open web interface is actualized to enable access to the SPSE database, thereby facilitating machine learning. This interactive platform provides a workflow toward high-throughput screening for future discovery and design of promising solid electrolytes and the SPSE database is based on the FAIR principles for the benefit of the broad research community.<br>
DOI: 10.6084/m9.figshare.9770876.v1
title: High-Throughput Screening Platform for Solid Electrolytes Combining Hierarchical Ion-Transport Prediction Algorithms

description: The combination of a materials database with high-throughput ion-transport calculations is an effective approach to screen for promising solid electrolytes. However, automating the complicated preprocessing involved in currently widely used ion-transport characterization algorithms, such as the first-principles nudged elastic band (FP-NEB) method, remains challenging. Here, we report on high-throughput screening platform for solid electrolytes (SPSE) that integrates a materials database with hierarchical ion-transport calculations realized by implementing empirical algorithms to assist in FP-NEB calculation. We first preliminarily screen candidates and determine the approximate ion-transport paths using empirical geometric analysis and bond valence method. A chain of images is then automatically generated along these paths for accurate FP-NEB calculation. In addition, an open web interface is actualized to enable access to the SPSE database, thereby facilitating machine learning. This interactive platform provides a workflow toward high-throughput screening for future discovery and design of promising solid electrolytes and the SPSE database is based on the FAIR principles for the benefit of the broad research community.<br>
DOI: 10.6084/m9.figshare.9770807
title: Twitter Sentiment Analysis Data

description: This excel work book includes NRC sentiment analysis for all hashtags, #pride tweets, #lesbian tweets, #pride NRC scores, # lesbian NRC scores, all sentiment scores in the syuzhet package for #pride and lesbian, lexicon comparison, #lesbian subsamples and #pride subsamples.
DOI: 10.6084/m9.figshare.9770792
title: 50 most mixed tweets with #pride and #lesbian

description: 50 most mixed tweets with #pride and #lesbian
DOI: 10.6084/m9.figshare.9770792.v2
title: 50 most mixed tweets with #pride and #lesbian

description: 50 most mixed tweets with #pride and #lesbian
DOI: 10.6084/m9.figshare.9770807.v1
title: Twitter Sentiment Analysis Data

description: This Excel work book includes NRC sentiment analysis for all hashtags, #pride tweets, #lesbian tweets, #pride NRC scores, # lesbian NRC scores, all sentiment scores in the syuzhet package and comparison for #pride and lesbian, lexicon comparison, etc
DOI: 10.6084/m9.figshare.9770792.v1
title: 50 most mixed tweets with #pride and #lesbian

description: 50 most mixed tweets with #pride and #lesbian
DOI: 10.6084/m9.figshare.9770765
title: The role of microRNA-210-3p in hepatitis B virus-related hepatocellular carcinoma

description: <b>Supplementary Figure 1.</b> List of the normalized expression intensities for the 879 miRNA probes that were used for the analysis.
DOI: 10.6084/m9.figshare.9770687
title: Metadata record for: De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal

description: This dataset contains key characteristics about the data described in the Data Descriptor De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format 3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br><br>
DOI: 10.6084/m9.figshare.9770690
title: Pose and pressure mat data of participants adopting various poses while supine on a robotic bed.

description: Pose and pressure mat data of participants adopting various poses while supine on a robotic bed. The bed had a pressure-sensing mat on which the participants lay. The room was fitted with motion tracking cameras from which ground-truth pose was found.This data is used in several papers including "Estimating 3D Human Pose on a Configurable Bed from a Single Pressure Image." Clever, Henry M., Ariel Kapusta, Daehyung Park, Zackory Erickson, Yash Chitalia, and Charles C. Kemp. arXiv preprint arXiv:1804.07873 (2018).
DOI: 10.6084/m9.figshare.9770711
title: Dataset for: Karyopherin MoKap119-mediated nuclear import of cyclin dependent kinase regulator MoCks1 is essential for Magnaporthe oryzae pathogenicity

description: Nuclear import of proteins relies on nuclear import receptors called importins/karyopherins (Kaps), whose functions were reported in yeasts, fungi, plants and animal cells, including cell cycle control, morphogenesis, stress sensing/response, and also fungal pathogenecity. However, limited is known about the physiological function and regulatory mechanism of protein import in the rice-blast fungus Magnaporthe oryzae. Here, we identified an ortholog of β-importin in M. oryzae encoded by an ortholog of KAP119 gene. Functional characterization of this gene via reverse genetics revealed that it is required for vegetative growth, conidiation, melanin pigmentation and pathogenicity of M. oryzae. The mokap119 mutant was also defective in formation of appressorium-like structure from hyphal tips. By affinity assay and LC-MS/MS, we identified potential MoKap119-interacting proteins, and we further verified that MoKap119 interacts with the cyclin dependent kinase subunit MoCks1 and mediates its nuclear import. Transcriptional profiling indicated that MoKap119 may regulate transcription of infection-related genes via MoCks1-regulation of MoSom1. Overall, our findings provide a novel insight into the regulatory mechanism of M. oryzae pathogenesis likely by MoKap119-mediated nuclear import of the cyclin dependent kinase subunit MoCks1.
DOI: 10.6084/m9.figshare.9770711.v1
title: Dataset for: Karyopherin MoKap119-mediated nuclear import of cyclin dependent kinase regulator MoCks1 is essential for Magnaporthe oryzae pathogenicity

description: Nuclear import of proteins relies on nuclear import receptors called importins/karyopherins (Kaps), whose functions were reported in yeasts, fungi, plants and animal cells, including cell cycle control, morphogenesis, stress sensing/response, and also fungal pathogenecity. However, limited is known about the physiological function and regulatory mechanism of protein import in the rice-blast fungus Magnaporthe oryzae. Here, we identified an ortholog of β-importin in M. oryzae encoded by an ortholog of KAP119 gene. Functional characterization of this gene via reverse genetics revealed that it is required for vegetative growth, conidiation, melanin pigmentation and pathogenicity of M. oryzae. The mokap119 mutant was also defective in formation of appressorium-like structure from hyphal tips. By affinity assay and LC-MS/MS, we identified potential MoKap119-interacting proteins, and we further verified that MoKap119 interacts with the cyclin dependent kinase subunit MoCks1 and mediates its nuclear import. Transcriptional profiling indicated that MoKap119 may regulate transcription of infection-related genes via MoCks1-regulation of MoSom1. Overall, our findings provide a novel insight into the regulatory mechanism of M. oryzae pathogenesis likely by MoKap119-mediated nuclear import of the cyclin dependent kinase subunit MoCks1.
DOI: 10.6084/m9.figshare.9770444
title: Rectal Tumor Targeted Sequencing

description: These data are aligned sequencing data (BAM) of pre- and post-treatment samples of rectal cancer tumors. Data were generated from custom Agilent SureSelect XT panel libraries, capturing regions surrounding somatic variants identified by lower-coverage exome-seq. Data were generated on an Illumina HiSeq4000 instrument, and are paired-150bp reads. Reads were adapter-trimmed and mapped to the UCSC hg19 human reference genome using the Burrows-Wheeler Aligner (BWA mem v0.7.8). <br>
DOI: 10.6084/m9.figshare.9770441
title: Matlab.rar

description: These Matlab codes can find the best geometry for minimizing the side lobe level of 8-element antenna array