cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7034792
title: CASP4/caspase-11 promotes autophagosome formation in response to bacterial infection

description: CASP4/caspase-11-dependent inflammasome activation is important for the clearance of various Gram-negative bacteria entering the host cytosol. Additionally, CASP4 modulates the actin cytoskeleton to promote the maturation of phagosomes harboring intracellular pathogens such as <i>Legionella pneumophila</i> but not those enclosing nonpathogenic bacteria. Nevertheless, this non-inflammatory role of CASP4 regarding the trafficking of vacuolar bacteria remains poorly understood. Macroautophagy/autophagy, a catabolic process within eukaryotic cells, is also implicated in the elimination of intracellular pathogens such as <i>Burkholderia cenocepacia</i>. Here we show that CASP4-deficient macrophages exhibit a defect in autophagosome formation in response to <i>B. cenocepacia</i> infection. The absence of CASP4 causes an accumulation of the small GTPase RAB7, reduced colocalization of <i>B. cenocepacia</i> with LC3 and acidic compartments accompanied by increased bacterial replication <i>in vitro</i> and <i>in vivo</i>. Together, our data reveal a novel role of CASP4 in regulating autophagy in response to <i>B. cenocepacia</i> infection.
DOI: 10.6084/m9.figshare.13324025.v1
title: Additional file 8 of Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

description: Additional file 8: Supplementary Data 8. Candidate regions and genes in these regions with KEGG and GO results for gradient zone.
DOI: 10.6084/m9.figshare.7559177.v1
title: Additional file 13: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Parameters of the random networks generated with the null model in XLSX format. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7559219
title: Additional file 4: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Disease to Treatment Network in GML format. (GML 30 kb)
DOI: 10.6084/m9.figshare.10184552
title: MOESM14 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 14: Table S9. List of the bHLH and MYB transcription factors detected in the â core transcriptomeâ and their expression fold change in group comparisons between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) during the fruit ripening stage. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7034792.v2
title: CASP4/caspase-11 promotes autophagosome formation in response to bacterial infection

description: CASP4/caspase-11-dependent inflammasome activation is important for the clearance of various Gram-negative bacteria entering the host cytosol. Additionally, CASP4 modulates the actin cytoskeleton to promote the maturation of phagosomes harboring intracellular pathogens such as <i>Legionella pneumophila</i> but not those enclosing nonpathogenic bacteria. Nevertheless, this non-inflammatory role of CASP4 regarding the trafficking of vacuolar bacteria remains poorly understood. Macroautophagy/autophagy, a catabolic process within eukaryotic cells, is also implicated in the elimination of intracellular pathogens such as <i>Burkholderia cenocepacia</i>. Here we show that CASP4-deficient macrophages exhibit a defect in autophagosome formation in response to <i>B. cenocepacia</i> infection. The absence of CASP4 causes an accumulation of the small GTPase RAB7, reduced colocalization of <i>B. cenocepacia</i> with LC3 and acidic compartments accompanied by increased bacterial replication <i>in vitro</i> and <i>in vivo</i>. Together, our data reveal a novel role of CASP4 in regulating autophagy in response to <i>B. cenocepacia</i> infection.
DOI: 10.6084/m9.figshare.10184552.v1
title: MOESM14 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 14: Table S9. List of the bHLH and MYB transcription factors detected in the â core transcriptomeâ and their expression fold change in group comparisons between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) during the fruit ripening stage. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7559210
title: Additional file 3: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Health to Disease Network in GML format. (GML 42 kb)
DOI: 10.6084/m9.figshare.7559531.v1
title: Additional file 12: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S5. Illumina-based microarray data is presented for the expression of Illumina-based microarray mean values and standard deviation for the genes FABP4, UCP1, ADIPOQ, CITED1, LIPASIN, MYH3, HOXA5, and DLX5 in fBAT, SAT, NP88, NP110, and nine new clonal isolates in the progenitor (Ctrl) state and after 14â days of differentiation in (BMP4, Rosi, T3, CL) in an effort to re-derive clonal progenitors to BAT. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7559534.v1
title: Additional file 1: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S1. Illumina-based microarray data on expression levels of FABP4, UCP1, ADIPOQ, CITED1, LIPASIN, and MYH3, from control cells and 20 random hES cell-derived clonal embryonic progenitor cell lines differentiated for 14â days in (BMP4, Rosi, T3, CL) used in support of Fig. 1. Values less than 130 RFU were considered to be background signal. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.13323740
title: Additional file 3 of Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

description: Additional file 3. Gene Ontology enrichment of genes upregulated in EC (&gt;=1 fold change). Gene ontology classification results of genes that are upregulated at least 1FC in embryogenic callus when compared to nonembryogenic callus.
DOI: 10.6084/m9.figshare.10184561
title: MOESM15 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 15: Table S10. Overview of the metabolites detected and quantified in 3 fruit types of Prunus mira (PMHF, PMHR and PMHY) during 3 developmental stages (pit-hardening (A), cell enlargement (B) and fruit ripening (C)). Data are from 3 biological replicates and the mix01 to mix05 represent the mixture of sample extracts. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.10184561.v1
title: MOESM15 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 15: Table S10. Overview of the metabolites detected and quantified in 3 fruit types of Prunus mira (PMHF, PMHR and PMHY) during 3 developmental stages (pit-hardening (A), cell enlargement (B) and fruit ripening (C)). Data are from 3 biological replicates and the mix01 to mix05 represent the mixture of sample extracts. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.7559552.v1
title: Additional file 7: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S4. Illumina-based microarray data is presented for normalized data on all gene expression (sheet 1), the calculation of mean values and standard deviation (sheet 2), the data used in support of Fig. 4 (sheet 3), the data used in support of Fig. 5 (sheet 4),Â the data used in support of Fig. 6 (sheet 5), the data used in support of AdditionalÂ fileÂ 4: Figure S2 (sheet 6)Â and sugar transporter data (sheet 7). (XLSB 99804 kb)
DOI: 10.6084/m9.figshare.7559537
title: Additional file 2: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S2. Illumina-based microarray data on fBAT and SAT cells and the hES cell-derived clonal embryonic progenitor cell lines E85, E3, C4ELS5.1, C4ELS5.5, C4ELSR2, NP88, and NP110 in progenitor state (Ctrl) or differentiated for 14â days in (BMP4, Rosi, T3, CL). Calculation of mean RFUs in control (CTRL) and differentiated conditions for each line used in support of Fig. 2a (sheet 2) and Fig. 2b (sheet 3) are shown. Values less than 130 RFU were considered to be background signal. (XLSX 11511 kb)
DOI: 10.6084/m9.figshare.19093553
title: The minimal clinically important difference of the motricity index score

description: The Motricity Index (MI) can predict motor function after rehabilitation, but its minimal clinically important difference (MCID) has not been established. The primary study aim was to estimate the MCID value of the MI arm score. Between 2017 and 2018, 173 participants hospitalized with confirmed ischemic stroke were recruited into an observational rehabilitation study. Participants with motor weakness as measured by the Fugl-Meyer upper-extremity (FM-UE) and MI with complete baseline and follow-up assessments at 3 months were included in this analysis. The longitudinal recovery of the MI arm score was anchored to having a poor outcome based on the FM-UE recovery (&lt;9) longitudinally. Results reported include the area-under-curve (AUC), along with sensitivity, specificity, and optimal cut-points based on maximizing the Youden statistic. Sixty-nine patients (median [IQR] age 70 [18] years; 48% male; 54% white) were included in the final analysis. Mean ± standard deviation outcome scores at 3-months were: MI arm: 83.19 ± 22.80; FM-UE: 53.04 ± 17.26. For the primary results, the MI arm score optimal MCID cutoff for observed recovery was 13 points with a sensitivity of 80% (95% Confidence Interval (CI)(67.6%, 92.4%)) and a specificity of 69.0% (95% CI (52.1, 85.8%)), and the AUC was 0.8082 (0.7007, 0.9157). This was the first study to report the MCID of the MI arm score, as anchored to the FM-UE recovery between acute evaluation and 3-months. The estimated optimal MCID of improvement in the MI arm score was 13 points.
DOI: 10.6084/m9.figshare.19093578
title: Transcriptome profiling provides preliminary molecular insights into adventitious bud formation in herbaceous peony (<i>Paeonia ×</i> ‘Coral Charm’)

description: Herbaceous peony is a kind of perennial herbaceous flowering plant and most varieties are highly dependent on ramet propagation. Some varieties, such as <i>Paeonia ×</i> ‘Coral Charm’, have characteristics of relatively easy root cutting propagation. However, underlying adventitious buds of root cutting, the molecular mechanisms are still not completely understood. Here, we collected four key stages of adventitious bud formation of <i>P. ×</i> ‘Coral Charm’ for transcriptome sequencing, and assembled and annotated 326,139 transcripts. By carrying out weighted gene co-expression network analysis, three functional modules and several biological and metabolic pathways related to the adventitious bud formation were identified. Finally, we determined six transcription factors in the MYB, HD-ZIP, C2H2 and bZIP gene family that may play a key role in the adventitious bud formation. These results provided insights into the adventitious bud formation of herbaceous peony, and laid a theoretical foundation for the rapid propagation of <i>Paeonia</i>.
DOI: 10.6084/m9.figshare.7559231
title: Additional file 5: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Treatment to Health Network in GML format. (GML 42 kb)
DOI: 10.6084/m9.figshare.7559558
title: Additional file 9: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S6. A non-targeted relative quantitative liquid chromatographyâ tandem mass spectrometry RP and HILIC)/MS/MS platform was used to capture 624 cell metabolites and 406 metabolites in their respective media at time of harvest. Data is shown for fBAT and NP88 in undifferentiated and differentiated (in serum-free medium containing rosiglitazone, T3, and ITS for 14â days) cells. Data for other progenitor and adult cell lines is also presented in this table. (XLSX 474 kb)
DOI: 10.6084/m9.figshare.10184567
title: MOESM16 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 16: Table S11. List of the differential accumulated metabolites between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) representing the â core metabolomeâ and their expression fold change between group comparisons during the fruit ripening stage. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.13326398
title: Ultrastructure and development of acanthocytes, specialized cells in <i>Stropharia rugosoannulata</i>, revealed by scanning electron microscopy (SEM) and cryo-SEM

description: Acanthocytes are special cells with a distinct spiky shape produced exclusively by the fungi of <i>Stropharia</i> and can be used to defend against nematodes. In the present study, the ultrastructure and development of acanthocytes were revealed by scanning electron microscopy (SEM) and cryo-SEM in <i>S. rugosoannulata</i>, a popular cultivated mushroom both in China and Europe. The acanthocytes were abundant on the surface of rhizomorph, casing soils, and vegetative mycelia of homokaryotic and heterokaryotic strains in <i>S. rugosoannulata</i>. The development of the acanthocyte was investigated with cryo-SEM, which has distinct advantage for observation of the ultrastructure of live, hydrated structures. Three distinct stages, including formation of lateral branch that was covered with patches, spiky structure formation, and maturation of acanthocytes, were identified and described. The irregular patches deposited on the surface of lateral branches and the holes in the spiky branches of the acanthocytes were reported for the first time. The environmental nitrogen level showed impact on acanthocyte production, but it seemed not to be the indispensable factor. Acid medium could delay the initiation of the acanthocyte formation but did not affect the overall morphology and structure, indicating that the central deposit of acanthocytes should be acid soluble. Acanthocytes of <i>S. rugosoannulata</i> have similar hydrophobicity to mycelia. The observation of ultrastructure and development process of acanthocytes provides insights into the ecological function and evolution of this special structure.
DOI: 10.6084/m9.figshare.10184567.v1
title: MOESM16 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 16: Table S11. List of the differential accumulated metabolites between the 3 Prunus mira fruit types (PMHF, PMHR and PMHY) representing the â core metabolomeâ and their expression fold change between group comparisons during the fruit ripening stage. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.19093553.v1
title: The minimal clinically important difference of the motricity index score

description: The Motricity Index (MI) can predict motor function after rehabilitation, but its minimal clinically important difference (MCID) has not been established. The primary study aim was to estimate the MCID value of the MI arm score. Between 2017 and 2018, 173 participants hospitalized with confirmed ischemic stroke were recruited into an observational rehabilitation study. Participants with motor weakness as measured by the Fugl-Meyer upper-extremity (FM-UE) and MI with complete baseline and follow-up assessments at 3 months were included in this analysis. The longitudinal recovery of the MI arm score was anchored to having a poor outcome based on the FM-UE recovery (&lt;9) longitudinally. Results reported include the area-under-curve (AUC), along with sensitivity, specificity, and optimal cut-points based on maximizing the Youden statistic. Sixty-nine patients (median [IQR] age 70 [18] years; 48% male; 54% white) were included in the final analysis. Mean ± standard deviation outcome scores at 3-months were: MI arm: 83.19 ± 22.80; FM-UE: 53.04 ± 17.26. For the primary results, the MI arm score optimal MCID cutoff for observed recovery was 13 points with a sensitivity of 80% (95% Confidence Interval (CI)(67.6%, 92.4%)) and a specificity of 69.0% (95% CI (52.1, 85.8%)), and the AUC was 0.8082 (0.7007, 0.9157). This was the first study to report the MCID of the MI arm score, as anchored to the FM-UE recovery between acute evaluation and 3-months. The estimated optimal MCID of improvement in the MI arm score was 13 points.
DOI: 10.6084/m9.figshare.7559243.v1
title: Additional file 7: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Pathway enrichment (q-values) for each transition, in XLSX format. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.10184573
title: MOESM17 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 17: Table S12. List of genes showing a high correlation (R2â &gt;â 0.9) with the 5 anthocyanins detected as important molecules involved in the fruit flesh coloration in Prunus mira. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.13326398.v1
title: Ultrastructure and development of acanthocytes, specialized cells in <i>Stropharia rugosoannulata</i>, revealed by scanning electron microscopy (SEM) and cryo-SEM

description: Acanthocytes are special cells with a distinct spiky shape produced exclusively by the fungi of <i>Stropharia</i> and can be used to defend against nematodes. In the present study, the ultrastructure and development of acanthocytes were revealed by scanning electron microscopy (SEM) and cryo-SEM in <i>S. rugosoannulata</i>, a popular cultivated mushroom both in China and Europe. The acanthocytes were abundant on the surface of rhizomorph, casing soils, and vegetative mycelia of homokaryotic and heterokaryotic strains in <i>S. rugosoannulata</i>. The development of the acanthocyte was investigated with cryo-SEM, which has distinct advantage for observation of the ultrastructure of live, hydrated structures. Three distinct stages, including formation of lateral branch that was covered with patches, spiky structure formation, and maturation of acanthocytes, were identified and described. The irregular patches deposited on the surface of lateral branches and the holes in the spiky branches of the acanthocytes were reported for the first time. The environmental nitrogen level showed impact on acanthocyte production, but it seemed not to be the indispensable factor. Acid medium could delay the initiation of the acanthocyte formation but did not affect the overall morphology and structure, indicating that the central deposit of acanthocytes should be acid soluble. Acanthocytes of <i>S. rugosoannulata</i> have similar hydrophobicity to mycelia. The observation of ultrastructure and development process of acanthocytes provides insights into the ecological function and evolution of this special structure.
DOI: 10.6084/m9.figshare.10184573.v1
title: MOESM17 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 17: Table S12. List of genes showing a high correlation (R2â &gt;â 0.9) with the 5 anthocyanins detected as important molecules involved in the fruit flesh coloration in Prunus mira. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.10184579
title: MOESM18 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 18: Table S13. The primer sequences for real time PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10184579.v1
title: MOESM18 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 18: Table S13. The primer sequences for real time PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10184582
title: MOESM1 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 1: Table S1. Overview of the transcriptome sequencing dataset and quality check in 3 Prunus mira fruit types (PMHF, PMHR and PMHY) during 3 developmental stages (pit-hardening (A), cell enlargement (B) and fruit ripening (C)). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.10184582.v1
title: MOESM1 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 1: Table S1. Overview of the transcriptome sequencing dataset and quality check in 3 Prunus mira fruit types (PMHF, PMHR and PMHY) during 3 developmental stages (pit-hardening (A), cell enlargement (B) and fruit ripening (C)). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.10184585
title: MOESM2 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 2: Table S2. Full list of the unique genes detected in Prunus mira fruit transcriptome and their functional annotation. (XLSX 2092 kb)
DOI: 10.6084/m9.figshare.10184585.v1
title: MOESM2 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 2: Table S2. Full list of the unique genes detected in Prunus mira fruit transcriptome and their functional annotation. (XLSX 2092 kb)
DOI: 10.6084/m9.figshare.10184591
title: MOESM3 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 3: Table S3. List of the novel genes specific to Prunus mira detected from fruit transcriptome and their functional annotation. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7559558.v1
title: Additional file 9: of Clonal derivation of white and brown adipocyte progenitor cell lines from human pluripotent stem cells

description: Table S6. A non-targeted relative quantitative liquid chromatographyâ tandem mass spectrometry RP and HILIC)/MS/MS platform was used to capture 624 cell metabolites and 406 metabolites in their respective media at time of harvest. Data is shown for fBAT and NP88 in undifferentiated and differentiated (in serum-free medium containing rosiglitazone, T3, and ITS for 14â days) cells. Data for other progenitor and adult cell lines is also presented in this table. (XLSX 474 kb)
DOI: 10.6084/m9.figshare.10184591.v1
title: MOESM3 of Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species

description: Additional file 3: Table S3. List of the novel genes specific to Prunus mira detected from fruit transcriptome and their functional annotation. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7559243
title: Additional file 7: of Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

description: Pathway enrichment (q-values) for each transition, in XLSX format. (XLSX 13 kb)