cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7706597.v1
title: Fed-batch high-cell-density fermentation strategies for <i>Pichia pastoris</i> growth and production

description: <i>Pichia pastoris</i> is extensively used to produce various heterologous proteins. Amounts of biopharmaceutical drugs and industrial enzymes have been successfully produced by fed-batch high-cell-density fermentation (HCDF) of this cell factory. High levels of cell mass in defined media can be easily achieved and therefore large quantities of recombinant proteins with enhanced activities and lower costs can be obtained through HCDF technology. A robust HCDF process makes a successful transition to commercial production. Recently, efforts have been made to increase the heterologous protein production and activity by the HCDF of <i>P. pastoris</i>. However, challenges around selecting a suitable HCDF strategy exist. The high-level expression of a specific protein in <i>P. pastoris</i> is still, at least in part, limited by optimizing the methanol feeding strategy. Here, we review the progress in developments and applications of <i>P. pastoris</i> HCDF strategies for enhanced expression of recombinant proteins. We focus on the methanol induction strategies for efficient fed-batch HCDF in bioreactors, mainly focusing on various stat-induction strategies, co-feeding, and the limited induction strategy. These processes control strategies have opened the door for expressing foreign proteins in <i>P. pastoris</i> and are expected to enhance the production of recombinant proteins.
DOI: 10.6084/m9.figshare.11376624
title: MOESM1 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 1: Table S1. Presence or absence of Bacillus cereus virulence-associated genes in each genome sequence as detected using BTyper version 2.3.0 [12]. The profiles of virulence-associated genes from Japanese B. cereus group isolates are shown.
DOI: 10.6084/m9.figshare.11376624.v1
title: MOESM1 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 1: Table S1. Presence or absence of Bacillus cereus virulence-associated genes in each genome sequence as detected using BTyper version 2.3.0 [12]. The profiles of virulence-associated genes from Japanese B. cereus group isolates are shown.
DOI: 10.6084/m9.figshare.11376636
title: MOESM3 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 3: Table S3. The 27 Bacillus cereus strains derived from countries other than Japan used in this study. The strain list for the B. cereus group isolates from countries other than Japan used in the present study is shown.
DOI: 10.6084/m9.figshare.11376636.v1
title: MOESM3 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 3: Table S3. The 27 Bacillus cereus strains derived from countries other than Japan used in this study. The strain list for the B. cereus group isolates from countries other than Japan used in the present study is shown.
DOI: 10.6084/m9.figshare.11376630
title: MOESM2 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 2: Table S2. List of isolates, corresponding metadata, and accession numbers. The strain list for the Japanese B. cereus group isolates used in the present study is shown.
DOI: 10.6084/m9.figshare.11376630.v1
title: MOESM2 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 2: Table S2. List of isolates, corresponding metadata, and accession numbers. The strain list for the Japanese B. cereus group isolates used in the present study is shown.
DOI: 10.6084/m9.figshare.11376645
title: MOESM4 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 4: Table S4. The capsule operon (capA, capB, capC, capD and capE) in three B. cereus group isolates genome. Total read count and average query coverage were calculated using “mapped reads to reference” option of CLC genomic workbench ver11.0.1 with default parameters. Total read count and query coverage of capsule operon are shown.
DOI: 10.6084/m9.figshare.11376645.v1
title: MOESM4 of Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

description: Additional file 4: Table S4. The capsule operon (capA, capB, capC, capD and capE) in three B. cereus group isolates genome. Total read count and average query coverage were calculated using “mapped reads to reference” option of CLC genomic workbench ver11.0.1 with default parameters. Total read count and query coverage of capsule operon are shown.
DOI: 10.6084/m9.figshare.11376642
title: MOESM1 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 1: Primer sequences and the results of DEGs
DOI: 10.6084/m9.figshare.11376648.v1
title: MOESM2 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 2: GO analysis in M1_vs_H1, M2_vs_H2, and M3_vs_H3.
DOI: 10.6084/m9.figshare.11376642.v1
title: MOESM1 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 1: Primer sequences and the results of DEGs
DOI: 10.6084/m9.figshare.11376654
title: MOESM3 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 3: GO and KEGG pathway enrichment analysis in TERM1 and TERM2.
DOI: 10.6084/m9.figshare.11376648
title: MOESM2 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 2: GO analysis in M1_vs_H1, M2_vs_H2, and M3_vs_H3.
DOI: 10.6084/m9.figshare.9803930
title: Dataset of 2019TC005516RR

description: Supporting data for manuscript entitled in "Cretaceous episodic extension in the South China Block, East Asia: Evidence from the Yuechengling Massif of central South China"
DOI: 10.6084/m9.figshare.16619738
title: Fitting Multilevel Vector Autoregressive Models in Stan, JAGS, and Mplus

description: The influx of intensive longitudinal data creates a pressing need for complex modeling tools that help enrich our understanding of how individuals change over time. Multilevel vector autoregressive (mlVAR) models allow for simultaneous evaluations of reciprocal linkages between dynamic processes and individual differences, and have gained increased recognition in recent years. High-dimensional and other complex variations of mlVAR models, though often computationally intractable in the frequentist framework, can be readily handled using Markov chain Monte Carlo techniques in a Bayesian framework. However, researchers in social science fields may be unfamiliar with ways to capitalize on recent developments in Bayesian software programs. In this paper, we provide step-by-step illustrations and comparisons of options to fit Bayesian mlVAR models using Stan, JAGS and Mplus, supplemented with a Monte Carlo simulation study. An empirical example is used to demonstrate the utility of mlVAR models in studying intra- and inter-individual variations in affective dynamics.
DOI: 10.6084/m9.figshare.11376657
title: MOESM4 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional file 4: Figure S1. Differences between mature HF and TYPE III MF. (A) Longitudinal section of HF. (B) Mature embryo sac in HF. (C) In Type III MF, embryo sac development stopped at the triad stage. (D) Longitudinal section of Type III MF. Sy, synergid; sn, secondary nucleus; hy, hypostase; ii, inner integument; oi, uter integument; mi, micropyle. Figure S2. Eight model profoles in TERM1 and TERM2, respectively. In TERM1, the expression patterns of 13,761 genes were analysed, eight model profiles were used to summarize, and five expression patterns of genes showed significant p-values (p &lt; 0.05) (coloured boxes). In TERM 2, the expression patterns of 16,130 genes were analysed, and eight model profiles were used to summarize. Three expression patterns of genes showed significant p-values (p &lt; 0.05) (coloured boxes). Each box represents a model expression profile with the model profile number and p-value. Colored boxes indicate that there are significant differences between floral stages. No color box means no difference. M1, M2 and M3 represent MF at stages 5, 6 and 10, respectively, while H1, H2 and H3 represent bisexual flowers at stages 5, 6 and 10, respectively. The meaning of the ‘significant p-value’ was a significant difference between floral stages. Figure S3. Numbers of differentially expressed genes. (A) TERM1 – trend all by gene number, trend all by P-value. In profile 3: 2364 gene (2.6e-19 P-value) had stable expression in floral stages 5 and 6, but decreased in expression in stage 10; in profile 4, 1664 genes (1.1e-11 P-value) had stable expression in floral stages 5 and 6, but increased in expression in stage 10; in profile 5, 2320 genes (3.7e-17 P-value) increased in expression in floral stages 5 and 6, but decreased in stage 10; in profile 6, 2170 genes (6.2e-06 P-value) had an increased expression in floral stages 5 and 6, but had stable expression in stage 10; in profile 7: 1471 genes (7.7e-18 P-value) had an increased expression in floral stages 5 to 10. (B) TERM2 – trend all by gene number, trend all by P-value. In profile 1, the expression of 2308 genes (3.6e-47 P-value) present the trend of first decline and then maintain stable from stage 5 to 10; profile 6: 3179 genes (1.2e-79 P-value) had an increased expression in floral stages 5 and 6, but had stable expression in stage 10; profile 7: 1839 genes (5.2e-39 P-value), the trend was always upward. (C) GO and KEGG pathway enrichment analysis in TERM1 and TERM2. The meaning of the ‘significant p-value’ was a significant difference between floral stages.
DOI: 10.6084/m9.figshare.11376654.v1
title: MOESM3 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional files 3: GO and KEGG pathway enrichment analysis in TERM1 and TERM2.
DOI: 10.6084/m9.figshare.8231207
title: Chemical composition, antioxidant activity and antitumor activity of tumorous stem mustard leaf and stem extracts

description: The swollen succulent stem of tumorous stem mustard (<i>Brassica juncea</i> var. <i>tumida</i> Tsen et Lee) is the raw material in the processing of Chinese <i>Fuling</i> zhàcài. We found that total polyphenols and flavonoids contents of tumorous stem mustard leaf extracts (TSMLE) were significant higher than that of tumorous stem mustard stem extracts (TSMSE). The percentage of isorhamnetin 5-O-hexoside, methyl quercetin O-hexoside, and luteolin O-hexosyl-O-hexosyl-O-hexoside in TSMLE were 170, 230 and 694 times higher than that in TSMSE. TSMLE presented stronger antioxidant capacity against 2,2'-Azino-bis[3-ethylbenzothiazoline]-6-sulfonic acid cationic free radical (ABTS<sup>+</sup>) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radicals, and it also showed higher reducing power and ferric reducing antioxidant power. Both TSMLE and TSMSE inhibited lung carcinoma cell growth in a dose-dependent manner, while TSMLE was more effective against A549 cells than TSMSE. This is the first report indicates that tumorous stem mustard, especially its leaf, is a potential diet source in preventing of oxidative stress and cancer.
DOI: 10.6084/m9.figshare.8231207.v1
title: Chemical composition, antioxidant activity and antitumor activity of tumorous stem mustard leaf and stem extracts

description: The swollen succulent stem of tumorous stem mustard (<i>Brassica juncea</i> var. <i>tumida</i> Tsen et Lee) is the raw material in the processing of Chinese <i>Fuling</i> zhàcài. We found that total polyphenols and flavonoids contents of tumorous stem mustard leaf extracts (TSMLE) were significant higher than that of tumorous stem mustard stem extracts (TSMSE). The percentage of isorhamnetin 5-O-hexoside, methyl quercetin O-hexoside, and luteolin O-hexosyl-O-hexosyl-O-hexoside in TSMLE were 170, 230 and 694 times higher than that in TSMSE. TSMLE presented stronger antioxidant capacity against 2,2'-Azino-bis[3-ethylbenzothiazoline]-6-sulfonic acid cationic free radical (ABTS<sup>+</sup>) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radicals, and it also showed higher reducing power and ferric reducing antioxidant power. Both TSMLE and TSMSE inhibited lung carcinoma cell growth in a dose-dependent manner, while TSMLE was more effective against A549 cells than TSMSE. This is the first report indicates that tumorous stem mustard, especially its leaf, is a potential diet source in preventing of oxidative stress and cancer.
DOI: 10.6084/m9.figshare.12949510.v1
title: Additional file 16 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 16. Metabolite company information.
DOI: 10.6084/m9.figshare.11376657.v1
title: MOESM4 of Anatomy and RNA-Seq reveal important gene pathways regulating sex differentiation in a functionally Androdioecious tree, Tapiscia sinensis

description: Additional file 4: Figure S1. Differences between mature HF and TYPE III MF. (A) Longitudinal section of HF. (B) Mature embryo sac in HF. (C) In Type III MF, embryo sac development stopped at the triad stage. (D) Longitudinal section of Type III MF. Sy, synergid; sn, secondary nucleus; hy, hypostase; ii, inner integument; oi, uter integument; mi, micropyle. Figure S2. Eight model profoles in TERM1 and TERM2, respectively. In TERM1, the expression patterns of 13,761 genes were analysed, eight model profiles were used to summarize, and five expression patterns of genes showed significant p-values (p &lt; 0.05) (coloured boxes). In TERM 2, the expression patterns of 16,130 genes were analysed, and eight model profiles were used to summarize. Three expression patterns of genes showed significant p-values (p &lt; 0.05) (coloured boxes). Each box represents a model expression profile with the model profile number and p-value. Colored boxes indicate that there are significant differences between floral stages. No color box means no difference. M1, M2 and M3 represent MF at stages 5, 6 and 10, respectively, while H1, H2 and H3 represent bisexual flowers at stages 5, 6 and 10, respectively. The meaning of the ‘significant p-value’ was a significant difference between floral stages. Figure S3. Numbers of differentially expressed genes. (A) TERM1 – trend all by gene number, trend all by P-value. In profile 3: 2364 gene (2.6e-19 P-value) had stable expression in floral stages 5 and 6, but decreased in expression in stage 10; in profile 4, 1664 genes (1.1e-11 P-value) had stable expression in floral stages 5 and 6, but increased in expression in stage 10; in profile 5, 2320 genes (3.7e-17 P-value) increased in expression in floral stages 5 and 6, but decreased in stage 10; in profile 6, 2170 genes (6.2e-06 P-value) had an increased expression in floral stages 5 and 6, but had stable expression in stage 10; in profile 7: 1471 genes (7.7e-18 P-value) had an increased expression in floral stages 5 to 10. (B) TERM2 – trend all by gene number, trend all by P-value. In profile 1, the expression of 2308 genes (3.6e-47 P-value) present the trend of first decline and then maintain stable from stage 5 to 10; profile 6: 3179 genes (1.2e-79 P-value) had an increased expression in floral stages 5 and 6, but had stable expression in stage 10; profile 7: 1839 genes (5.2e-39 P-value), the trend was always upward. (C) GO and KEGG pathway enrichment analysis in TERM1 and TERM2. The meaning of the ‘significant p-value’ was a significant difference between floral stages.
DOI: 10.6084/m9.figshare.12949492
title: Additional file 10 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 10. Cross-kingdom correlations representing the MGS-ITS correlation network. Correlations are listed for each time point.
DOI: 10.6084/m9.figshare.12949504
title: Additional file 14 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 14. Patient information.
DOI: 10.6084/m9.figshare.12949507
title: Additional file 15 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 15. List of published genome assemblies available on NCBI. A subset of these were used to infer strain information on several MGS clusters.
DOI: 10.6084/m9.figshare.12949522
title: Additional file 3 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 3. Statistical results for differences in fungal relative abundance between time points at species level.
DOI: 10.6084/m9.figshare.12949510
title: Additional file 16 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 16. Metabolite company information.
DOI: 10.6084/m9.figshare.12949498
title: Additional file 12 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 12. Statistical results for differences in node degree between time points in RNA-MetaCyc network. Results are given for the entire network as well as differences based on funcational categories.
DOI: 10.6084/m9.figshare.12949507.v1
title: Additional file 15 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 15. List of published genome assemblies available on NCBI. A subset of these were used to infer strain information on several MGS clusters.
DOI: 10.6084/m9.figshare.12949513.v1
title: Additional file 17 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 17. Dilution series of metabolites for which we tested their effect on Candida albicans growth, morphology, and host cell damage.
DOI: 10.6084/m9.figshare.12949519
title: Additional file 2 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 2. Statistical results for differences in fungal relative abundance between time points at genus level.
DOI: 10.6084/m9.figshare.12949519.v1
title: Additional file 2 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 2. Statistical results for differences in fungal relative abundance between time points at genus level.
DOI: 10.6084/m9.figshare.12949525
title: Additional file 4 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 4. Fungal network properties and statistical results for differences in node degree between time points.
DOI: 10.6084/m9.figshare.12949522.v1
title: Additional file 3 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 3. Statistical results for differences in fungal relative abundance between time points at species level.
DOI: 10.6084/m9.figshare.12949531.v1
title: Additional file 6 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 6. Statistical results for differences between group-centroids between different time points using distance-based redundancy analysis.
DOI: 10.6084/m9.figshare.12949531
title: Additional file 6 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 6. Statistical results for differences between group-centroids between different time points using distance-based redundancy analysis.
DOI: 10.6084/m9.figshare.12949537
title: Additional file 8 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 8. Statistical results for differences in MGS relative abundance between time points.
DOI: 10.6084/m9.figshare.12949537.v1
title: Additional file 8 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 8. Statistical results for differences in MGS relative abundance between time points.
DOI: 10.6084/m9.figshare.12949540.v1
title: Additional file 9 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 9. MGS network properties and statistical results for differences in node degree between time points.
DOI: 10.6084/m9.figshare.12949525.v1
title: Additional file 4 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 4. Fungal network properties and statistical results for differences in node degree between time points.
DOI: 10.6084/m9.figshare.12949528.v1
title: Additional file 5 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 5. Growth rate indices of bacterial strains per sample as estimated by GRiD. GRiD values of 1 imply no growth.
DOI: 10.5281/zenodo.10624617
title: Model data of the physical-biogeochemical state of the Mediterranean Sea during the Last Glacial Maximum

description: Model data  (NetCDF) and python notebooks for visualization used in  "Modeling Mediterranean ocean biogeochemistry of the Last Glacial Maximum" by  Katharina D. Six et al. submitted to Climate of the Past.
DOI: 10.6084/m9.figshare.11376801
title: MOESM1 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 1: Table S1. Table representing strain identification codes (Key), MLVA-8 data, MLVA-11 data, biovars, and year of isolation for 40 Brucella isolates.
DOI: 10.6084/m9.figshare.11376819.v1
title: MOESM2 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 2: Table S2. 340 Chinese Brucella strains were used to construct the MST (strains in this study are indicated with yellow circles).