cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13482381.v1
title: Biodegradation of <i>o</i>-dichlorobenzene by <i>Bacillus cereus</i> DL-1：kinetics, degradation pathway, biodegradability and performance in biotrickling filter

description: -Dichlorobenzene could be mineralized as the sole carbon and energy source by <i>Bacillus cereus</i> DL-1. In this work, Haldane–Andrews and pseudo-first-order models were used to simulate the growth and degradation abilities of the strain. Two possible degradation pathways were identified by GC/MS intermediate and open-loop analysis. The removal efficiency (RE) of biotrickling filter (BTF) could reach 57.86% at the start phase. At the steady phase, the effects of empty bed residence time (EBRT), inlet gas concentration and intake load rate (ILR) on the performance of BTF have highlighted the potential of strain DL-1 for the treatment of <i>o</i>-dichlorobenzene.
DOI: 10.6084/m9.figshare.16635354
title: Trace fossils, algae, invertebrate remains and new U-Pb detrital zircon geochronology from the lower Cambrian Torneträsk Formation, northern Sweden

description: Nineteen ichnotaxa, together with algal and invertebrate remains, and various pseudo-traces and sedimentary structures are described from the Torneträsk Formation exposed near Lake Torneträsk, Lapland, Sweden, representing a marked increase in the diversity of biotic traces recorded from this unit. The “lower siltstone” interval of the Torneträsk Formation contains mostly simple pascichnia, fodinichnia and domichnia burrows and trails of low-energy shoreface to intertidal settings. The assemblage has very few forms characteristic of high-energy, soft-sediment, foreshore or upper shoreface environments (representative of the <i>Skolithos</i> ichnofacies). Uranium-lead (U-Pb) LA-ICPMS analysis of zircon from a thin claystone layer within the “lower siltstone” interval yielded a maximum depositional age of 584 ± 13 Ma, mid-Ediacaran. Most of the zircon is represented by rounded detrital grains that yield dates between 3.3 and 1.0 Ga. Although the age of the basal sandstone-dominated interval of the Torneträsk Formation remains elusive owing to the absence of fossils, the ichnofossil suite from the overlying “lower siltstone” interval lacks deep arthropod trackways, such as <i>Rusophycus</i> and <i>Cruziana</i>, and is suggestive of a very early (Terreneuvian, possibly Fortunian) Cambrian age. The ichnofauna is otherwise similar to early Cambrian trace fossil assemblages from other parts of Baltica, regions further south in modern Europe, and from Greenland.
DOI: 10.6084/m9.figshare.19768061.v1
title: Additional file 3 of Microfluidic screening and genomic mutation identification for enhancing cellulase production in Pichia pastoris

description: Additional file 3: Dataset S2. Genomic variants in coding regions.
DOI: 10.6084/m9.figshare.18725859.v1
title: Bipolar system of sexual incompatibility and heterothallic life cycle in the basidiomycetes <i>Pachyma hoelen</i> Fr. (Fuling)

description: The sclerotia of <i>Pachyma hoelen</i> are one of the traditional Chinese medicines and foods that are widely used in East Asian countries. The strains used for cultivation showed bad performance in recent years, and breeding of superior strains has become increasingly important for this fungus. Nevertheless, the mating system and life cycle of <i>P. hoelen</i> were still ambiguous. In this study, the methods for distinguishing between homokaryotic offspring with different mating types were established, as well as confirmation of strain hybridization based on allelic polymorphism at a locus of the <i>rpb2</i> gene. The bipolar mating system was confirmed according to the mating results of homokaryotic SSIs. The fact that heterokaryotic parents produce homokaryotic meiospores proves that the life cycle is heterothallic. Combining scanning electron microscope observation and DAPI (4′,6-diamidino-2-phenylindole) fluorescent staining of hymenium and basidiospores <i>in situ</i> and <i>ex situ</i>, nuclear migration pattern from basidia to spores was revealed. The heterothallic life cycle was verified, revised, and supplemented step by step. This is the first report of systematic research on the mating system, life cycle, and outcrossing of homokaryotic offspring in <i>P. hoelen</i>. It will be helpful for the biological research, strain improvement, and development of the <i>P. hoelen</i> industry.
DOI: 10.6084/m9.figshare.19768061
title: Additional file 3 of Microfluidic screening and genomic mutation identification for enhancing cellulase production in Pichia pastoris

description: Additional file 3: Dataset S2. Genomic variants in coding regions.
DOI: 10.6084/m9.figshare.14531788
title: Hierarchical Total Variations and Doubly Penalized ANOVA Modeling for Multivariate Nonparametric Regression

description: For multivariate nonparametric regression, functional analysis of variance (ANOVA) modeling aims to capture the relationship between a response and covariates by decomposing the unknown function into various components, representing main effects, two-way interactions, etc. Such an approach has been pursued explicitly in smoothing spline ANOVA modeling and implicitly in various greedy methods such as MARS. We develop a new method for functional ANOVA modeling, based on doubly penalized estimation using total-variation and empirical-norm penalties, to achieve sparse selection of component functions and their basis functions. For this purpose, we formulate a new class of hierarchical total variations, which measures total variations at different levels including main effects and multi-way interactions, possibly after some order of differentiation. Furthermore, we derive suitable basis functions for multivariate splines such that the hierarchical total variation can be represented as a regular Lasso penalty, and hence we extend a previous backfitting algorithm to handle doubly penalized estimation for ANOVA modeling. We present extensive numerical experiments on simulations and real data to compare our method with existing methods including MARS, tree boosting, and random forest. The results are very encouraging and demonstrate notable gains from our method in prediction or classification accuracy and simplicity of the fitted functions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19768066
title: Additional file 11 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 11: Annotated differential ATAC, H3K4me1, H3K4me3, H3K27ac and H3K27ac peaks in microglia of KO-PBS versus WT-PBS, KO-LPS versus WT-LPS, WT-LPS versus WT-PBS and KO-LPS versus WT-PBS mice (related to Fig. 4A, 4B).
DOI: 10.6084/m9.figshare.19768069
title: Additional file 12 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 12: TFBS of differential ATAC peaks in microglia of WT-PBS versus KO-PBS and WT-LPS versus KO-LPS mice and classification of TFs based on correlation of TFBS peaks with TF target gene expression (related to Figs. 4D, 4E, 5C).
DOI: 10.6084/m9.figshare.19768072.v1
title: Additional file 13 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 13: Lists of genes uniquely or overlappingly enriched in acute, tolerized, primed and trained microglia (related to Fig. 5A).
DOI: 10.6084/m9.figshare.19768066.v1
title: Additional file 11 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 11: Annotated differential ATAC, H3K4me1, H3K4me3, H3K27ac and H3K27ac peaks in microglia of KO-PBS versus WT-PBS, KO-LPS versus WT-LPS, WT-LPS versus WT-PBS and KO-LPS versus WT-PBS mice (related to Fig. 4A, 4B).
DOI: 10.6084/m9.figshare.19768072
title: Additional file 13 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 13: Lists of genes uniquely or overlappingly enriched in acute, tolerized, primed and trained microglia (related to Fig. 5A).
DOI: 10.6084/m9.figshare.8240381.v1
title: Additional file 1: of Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

description: Table S1. primers. Primers for all the differentially expressed genes for quantitative real time PCR analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.19768063.v1
title: Additional file 10 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 10: TFBS of differential ATAC peaks in microglia of PP versus PL, LL versus PL and LP versus LL mice and classification of TFs based on correlation of TFBS peaks with TF target gene expression (related to Figs. 3D, 3E, 3F, 5C).
DOI: 10.6084/m9.figshare.19768069.v1
title: Additional file 12 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 12: TFBS of differential ATAC peaks in microglia of WT-PBS versus KO-PBS and WT-LPS versus KO-LPS mice and classification of TFs based on correlation of TFBS peaks with TF target gene expression (related to Figs. 4D, 4E, 5C).
DOI: 10.6084/m9.figshare.19768075.v1
title: Additional file 14 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 14: GO terms associated with genes uniquely or overlappingly enriched in acute, tolerized, primed and trained microglia (related to Fig. 5B).
DOI: 10.6084/m9.figshare.8240435.v1
title: Additional file 1: of Vaccination with synthetic long peptide formulated with CpG in an oil-in-water emulsion induces robust E7-specific CD8 T cell responses and TC-1 tumor eradication

description: Flow cytometry data presented in tabular form. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.8240096
title: Additional file 2: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S1. Gradient elution conditions. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8240237
title: Additional file 4: of TaAMT2;3a, a wheat AMT2-type ammonium transporter, facilitates the infection of stripe rust fungus on wheat

description: Table S2 Information of primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8240096.v1
title: Additional file 2: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S1. Gradient elution conditions. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8240486.v1
title: Additional file 10: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S7. The PRM results of 16 key proteins. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240498
title: Additional file 1: of A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

description: Table S1. Statistics of sequencing data for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S2. Statistics of reads of insert (ROI) for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S3. Statistics of full-length reads for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S4. Statistics of iterative clustering for error correction (ICE) for all isoforms by PacBio SMRT analysis. Table S5. The gene structure optimization information by PacBio SMRT sequencing. Table S6. The annotated information of 21,122 novel genes. Table S7. Detailed information on 250 fusion genes. Table S8. The list of 1356 TF genes. Table S9. Statistics of sequencing data for strains 349 and 1115 at three time points (7 DAF, 14 DAF and 21 DAF) by Illumina RNA sequencing. Table S10. Comparison of transcriptome sequencing reads with genome references by Illumina RNA sequencing. Table S11. The primers for quantitative real-time PCR in this study. (ZIP 1535 kb)
DOI: 10.6084/m9.figshare.8240501
title: Additional file 3: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S2. The detail information of the DAPs during fruit ripening. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.14531788.v1
title: Hierarchical Total Variations and Doubly Penalized ANOVA Modeling for Multivariate Nonparametric Regression

description: For multivariate nonparametric regression, functional analysis of variance (ANOVA) modeling aims to capture the relationship between a response and covariates by decomposing the unknown function into various components, representing main effects, two-way interactions, etc. Such an approach has been pursued explicitly in smoothing spline ANOVA modeling and implicitly in various greedy methods such as MARS. We develop a new method for functional ANOVA modeling, based on doubly penalized estimation using total-variation and empirical-norm penalties, to achieve sparse selection of component functions and their basis functions. For this purpose, we formulate a new class of hierarchical total variations, which measures total variations at different levels including main effects and multi-way interactions, possibly after some order of differentiation. Furthermore, we derive suitable basis functions for multivariate splines such that the hierarchical total variation can be represented as a regular Lasso penalty, and hence we extend a previous backfitting algorithm to handle doubly penalized estimation for ANOVA modeling. We present extensive numerical experiments on simulations and real data to compare our method with existing methods including MARS, tree boosting, and random forest. The results are very encouraging and demonstrate notable gains from our method in prediction or classification accuracy and simplicity of the fitted functions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8240117.v1
title: Additional file 4: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S3. Candidate unigenes involved in anthocyanin biosynthesis. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240390
title: Additional file 2: of Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

description: Table S2. Tumor type-related genes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8240399
title: Additional file 4: of Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

description: Table S4. The 201 downregulated genes in breast cancer tissues. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8240504.v1
title: Additional file 2: of A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

description: Figure S1. Correlation thermograms between 18 samples from Illumina RNA sequencing. Figure S2. ROI read length distribution of each size (1–2 k, 2-3 k and 3-6 k) of bins in the cDNA database. Figure S3. GO classification according to cellular component, molecular function and biological process of differentially expressed genes. Strain 349 vs. strain 1115 at 7 DAF (A), 14 DAF (B), and 21 DAF (C). Figure S4. KEGG classification and Pathway enrichment statistics of differentially expressed genes. (A) KEGG classification between strains 349 and 1115 at 7 DAF. (B) KEGG classification between 349 and 1115 at 14 DAF. (C) KEGG classification between 349 and 1115 at 21 DAF. (D) Pathway enrichment statistics between 349 and 1115 at 7 DAF. (E) Pathway enrichment statistics between 349 and 1115 at 14 DAF. (F) Pathway enrichment statistics between 349 and 1115 at 14 DAF. Figure S5. COG function classification of differentially expressed genes. (A) 349 vs. 1115 at 7 DAF. (B) 349 vs. 1115 at 14 DAF. (C) 349 vs. 1115 at 21 DAF. (ZIP 29130 kb)
DOI: 10.6084/m9.figshare.8240108
title: Additional file 3: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S2. Most enriched pathway terms of Differentially Expressed Genes (DEGs). GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240117
title: Additional file 4: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S3. Candidate unigenes involved in anthocyanin biosynthesis. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240528
title: Additional file 7: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S4. The detail information of the pathogen defense-related proteins. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8240126.v1
title: Additional file 5: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S4. Candidate unigenes involved in chlorophyll metabolism. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8240126
title: Additional file 5: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S4. Candidate unigenes involved in chlorophyll metabolism. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8240237.v1
title: Additional file 4: of TaAMT2;3a, a wheat AMT2-type ammonium transporter, facilitates the infection of stripe rust fungus on wheat

description: Table S2 Information of primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8240135
title: Additional file 6: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S5. Candidate unigenes involved in carotenoid metabolism. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8240534
title: Additional file 8: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S5. The information of the fatty acid metabolism-related proteins. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.18725859
title: Bipolar system of sexual incompatibility and heterothallic life cycle in the basidiomycetes <i>Pachyma hoelen</i> Fr. (Fuling)

description: The sclerotia of <i>Pachyma hoelen</i> are one of the traditional Chinese medicines and foods that are widely used in East Asian countries. The strains used for cultivation showed bad performance in recent years, and breeding of superior strains has become increasingly important for this fungus. Nevertheless, the mating system and life cycle of <i>P. hoelen</i> were still ambiguous. In this study, the methods for distinguishing between homokaryotic offspring with different mating types were established, as well as confirmation of strain hybridization based on allelic polymorphism at a locus of the <i>rpb2</i> gene. The bipolar mating system was confirmed according to the mating results of homokaryotic SSIs. The fact that heterokaryotic parents produce homokaryotic meiospores proves that the life cycle is heterothallic. Combining scanning electron microscope observation and DAPI (4′,6-diamidino-2-phenylindole) fluorescent staining of hymenium and basidiospores <i>in situ</i> and <i>ex situ</i>, nuclear migration pattern from basidia to spores was revealed. The heterothallic life cycle was verified, revised, and supplemented step by step. This is the first report of systematic research on the mating system, life cycle, and outcrossing of homokaryotic offspring in <i>P. hoelen</i>. It will be helpful for the biological research, strain improvement, and development of the <i>P. hoelen</i> industry.
DOI: 10.6084/m9.figshare.8240381
title: Additional file 1: of Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

description: Table S1. primers. Primers for all the differentially expressed genes for quantitative real time PCR analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240540
title: Additional file 9: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S6. The information of the proteins involved in the cell-related process. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8240108.v1
title: Additional file 3: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S2. Most enriched pathway terms of Differentially Expressed Genes (DEGs). GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.19768099
title: Additional file 8 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 8: Genes and associated gene ontology terms for each cluster identified in the priming mouse model (related to Figs. 2 and S3).
DOI: 10.6084/m9.figshare.8240135.v1
title: Additional file 6: of Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum

description: Table S5. Candidate unigenes involved in carotenoid metabolism. GL, green leaves; RL, red leaves; YL, yellow leaves. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8240390.v1
title: Additional file 2: of Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer

description: Table S2. Tumor type-related genes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8240501.v1
title: Additional file 3: of Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

description: Table S2. The detail information of the DAPs during fruit ripening. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.19768093
title: Additional file 6 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 6: Count table and differentially expressed genes for all comparisons in the primed mouse model (related to Figs. 1 and 4).
DOI: 10.6084/m9.figshare.19768096
title: Additional file 7 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 7: Genes and associated gene ontology terms for each cluster identified in the tolerance model (related to Figs. 2 and S3).
DOI: 10.6084/m9.figshare.19768058.v1
title: Additional file 2 of Microfluidic screening and genomic mutation identification for enhancing cellulase production in Pichia pastoris

description: Additional file 2: Dataset S1. Genomic variants in mutant strains obtained from five rounds of ARTP mutagenesis of cellulase-producing P. pastoris.
DOI: 10.6084/m9.figshare.19768102.v1
title: Additional file 9 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 9: Annotated differential ATAC, H3K4me3 and H3K27ac peaks in microglia of PL versus PP, PL versus LL and LL versus LP mice (related to Fig. 3A, 3B, 3C).
DOI: 10.6084/m9.figshare.19768090.v1
title: Additional file 5 of Epigenetic regulation of innate immune memory in microglia

description: Additional file 5: Count table and differentially expressed genes for all comparisons in the tolerance mouse model (related to Figs. 1 and 3).
DOI: 10.5281/zenodo.13381984
title: A multimodal and fully automated system for prediction of pathological complete response to neoadjuvant chemotherapy in breast cancer