cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17047242.v1
title: Additional file 3 of Explore association of genes in PDL1/PD1 pathway to radiotherapy survival benefit based on interaction model strategy

description: Additional file 3. Table S1: 73 genes in “PD-L1 expression and PD-1 checkpoint pathway in cancer”.
DOI: 10.6084/m9.figshare.17047244
title: Additional file 8 of Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

description: Additional file 8.
DOI: 10.6084/m9.figshare.17047244.v1
title: Additional file 8 of Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

description: Additional file 8.
DOI: 10.6084/m9.figshare.17047247
title: Additional file 9 of Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

description: Additional file 9.
DOI: 10.6084/m9.figshare.17047247.v1
title: Additional file 9 of Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.)

description: Additional file 9.
DOI: 10.6084/m9.figshare.17047251
title: Additional file 6 of Explore association of genes in PDL1/PD1 pathway to radiotherapy survival benefit based on interaction model strategy

description: Additional file 6. Table S4: RS genes of BRCA, HNSC, STAD and METABRIC data sets.
DOI: 10.6084/m9.figshare.17047251.v1
title: Additional file 6 of Explore association of genes in PDL1/PD1 pathway to radiotherapy survival benefit based on interaction model strategy

description: Additional file 6. Table S4: RS genes of BRCA, HNSC, STAD and METABRIC data sets.
DOI: 10.5281/zenodo.10660039
title: Dataset related to article "Bi-specific autoantigen-T cell engagers as targeted immunotherapy for autoreactive B cell depletion in autoimmune diseases"

description: The .xlsx file contains raw data related to the article "Bi-specific autoantigen-T cell engagers as targeted immunotherapy for autoreactive B cell depletion in autoimmune diseases". Front. Immunol. 07 Feb 2024. DOI: 10.3389/fimmu.2024.1335998, available at the following link.

 

Abstract

In autoimmune diseases, autoreactive B cells comprise only the 0.1-0.5% of total circulating B cells. However, current first-line treatments rely on non-specific and general suppression of the immune system, exposing patients to severe side effects. For this reason, identification of targeted therapies for autoimmune diseases is an unmet clinical need. Here, we designed a novel class of immunotherapeutic molecules, Bi-specific AutoAntigen-T cell Engagers (BiAATEs), as a potential approach for targeting the small subset of autoreactive B cells. To test this approach, we focused on a prototype autoimmune disease of the kidney, membranous nephropathy (MN), in which phospholipase A2 receptor (PLA2R) serves as primary nephritogenic antigen. Specifically, we developed a BiAATE consisting of the immunodominant Cysteine-Rich (CysR) domain of PLA2R and the single-chain variable fragment (scFv) of an antibody against the T cell antigen CD3, linked by a small flexible linker. As such, the BiAATE creates an immunological synapse between autoreactive B cells bearing an CysR-specific surface Ig + and T cells. Ex vivo, the BiAATE successfully induced T cell-dependent depletion of PLA2R-specific B cells isolated form MN patients, sparing normal B cells. Systemic administration of BiAATE to mice transgenic for human CD3 reduced anti-PLA2R antibody levels following active immunization with PLA2R. Should this approach be confirmed for other autoimmune diseases, BiAATEs could represent a promising offthe-shelf therapy for precision medicine in virtually all antibody-mediated autoimmune diseases for which the pathogenic autoantigen is known, leading to a paradigm shift in the treatment of these diseases.
description: Please send your request to biblioteca@marionegri.it
DOI: 10.5281/zenodo.10660040
title: Dataset related to article "Bi-specific autoantigen-T cell engagers as targeted immunotherapy for autoreactive B cell depletion in autoimmune diseases"

description: The .xlsx file contains raw data related to the article "Bi-specific autoantigen-T cell engagers as targeted immunotherapy for autoreactive B cell depletion in autoimmune diseases". Front. Immunol. 07 Feb 2024. DOI: 10.3389/fimmu.2024.1335998, available at the following link.

 

Abstract

In autoimmune diseases, autoreactive B cells comprise only the 0.1-0.5% of total circulating B cells. However, current first-line treatments rely on non-specific and general suppression of the immune system, exposing patients to severe side effects. For this reason, identification of targeted therapies for autoimmune diseases is an unmet clinical need. Here, we designed a novel class of immunotherapeutic molecules, Bi-specific AutoAntigen-T cell Engagers (BiAATEs), as a potential approach for targeting the small subset of autoreactive B cells. To test this approach, we focused on a prototype autoimmune disease of the kidney, membranous nephropathy (MN), in which phospholipase A2 receptor (PLA2R) serves as primary nephritogenic antigen. Specifically, we developed a BiAATE consisting of the immunodominant Cysteine-Rich (CysR) domain of PLA2R and the single-chain variable fragment (scFv) of an antibody against the T cell antigen CD3, linked by a small flexible linker. As such, the BiAATE creates an immunological synapse between autoreactive B cells bearing an CysR-specific surface Ig + and T cells. Ex vivo, the BiAATE successfully induced T cell-dependent depletion of PLA2R-specific B cells isolated form MN patients, sparing normal B cells. Systemic administration of BiAATE to mice transgenic for human CD3 reduced anti-PLA2R antibody levels following active immunization with PLA2R. Should this approach be confirmed for other autoimmune diseases, BiAATEs could represent a promising offthe-shelf therapy for precision medicine in virtually all antibody-mediated autoimmune diseases for which the pathogenic autoantigen is known, leading to a paradigm shift in the treatment of these diseases.
description: Please send your request to biblioteca@marionegri.it
DOI: 10.6084/m9.figshare.12852972
title: Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose

description: Many phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (<i>β</i> = 0.0090 ± 0.0009 mM<sup>−1</sup>). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production. Acetosyringone inhibited xylanase activity in a reversible and non-competitive binding manner, which might be related to the disruption of tertiary structure of xylanase.
DOI: 10.6084/m9.figshare.12852972.v1
title: Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose

description: Many phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (<i>β</i> = 0.0090 ± 0.0009 mM<sup>−1</sup>). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production. Acetosyringone inhibited xylanase activity in a reversible and non-competitive binding manner, which might be related to the disruption of tertiary structure of xylanase.
DOI: 10.6084/m9.figshare.22290191
title: Test and Visualization of Covariance Properties for Multivariate Spatio-Temporal Random Fields

description: The prevalence of multivariate space-time data collected from monitoring networks and satellites, or generated from numerical models, has brought much attention to multivariate spatio-temporal statistical models, where the covariance function plays a key role in modeling, inference, and prediction. For multivariate space-time data, understanding the spatio-temporal variability, within and across variables, is essential in employing a realistic covariance model. Meanwhile, the complexity of generic covariances often makes model fitting very challenging, and simplified covariance structures, including symmetry and separability, can reduce the model complexity and facilitate the inference procedure. However, a careful examination of these properties is needed in real applications. In the work presented here, we formally define these properties for multivariate spatio-temporal random fields and use functional data analysis techniques to visualize them, hence, providing intuitive interpretations. We then propose a rigorous rank-based testing procedure to conclude whether the simplified properties of covariance are suitable for the underlying multivariate space-time data. The good performance of our method is illustrated through synthetic data, for which we know the true structure. We also investigate the covariance of bivariate wind speed, a key variable in renewable energy, over a coastal and an inland area in Saudi Arabia. The supplementary material is available online, including the R code for our developed methods.
DOI: 10.6084/m9.figshare.22290191.v1
title: Test and Visualization of Covariance Properties for Multivariate Spatio-Temporal Random Fields

description: The prevalence of multivariate space-time data collected from monitoring networks and satellites, or generated from numerical models, has brought much attention to multivariate spatio-temporal statistical models, where the covariance function plays a key role in modeling, inference, and prediction. For multivariate space-time data, understanding the spatio-temporal variability, within and across variables, is essential in employing a realistic covariance model. Meanwhile, the complexity of generic covariances often makes model fitting very challenging, and simplified covariance structures, including symmetry and separability, can reduce the model complexity and facilitate the inference procedure. However, a careful examination of these properties is needed in real applications. In the work presented here, we formally define these properties for multivariate spatio-temporal random fields and use functional data analysis techniques to visualize them, hence, providing intuitive interpretations. We then propose a rigorous rank-based testing procedure to conclude whether the simplified properties of covariance are suitable for the underlying multivariate space-time data. The good performance of our method is illustrated through synthetic data, for which we know the true structure. We also investigate the covariance of bivariate wind speed, a key variable in renewable energy, over a coastal and an inland area in Saudi Arabia. The supplementary material is available online, including the R code for our developed methods.
DOI: 10.6084/m9.figshare.12853062
title: <i>De novo</i> assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic <i>Euphorbia kansui</i>

description: <i>Euphorbia kansui</i> Liou is an endemic and traditional medicinal plant in China. Despite its value, the genomic and transcriptomic information of <i>E. kansui</i> is limited. In the present study, a total of 43,211,690 high-quality reads were generated using Illumina paired-end sequencing technology. After assembly, 58,362 unigenes were recovered with an N50 length of 1,683 bp. 36,396 (62.36%) of these unigenes had at least one blast hit against the multiple public databases. Based on KEGG pathway analyses, unigenes were discovered to encode known enzymes that catalyze the formation of the terpenoid backone and diterpenoid. In addition, the unigenes related to casbene synthase, which catalyzes the formation of the major active constituents (diterpenoids) in <i>E. kansui,</i> were identified. For functional marker development, 7,016 candidate simple sequence repeats (SSR, microsatellites) were identified from 6,150 unigenes, and 40 SSR loci were selected randomly and amplified in two populations of <i>E. kansui</i>. A total of 28 loci were amplified successfully and 23 loci exhibited polymorphisms. The number of alleles of each locus ranged from 2 to 8 alleles and the mean number of alleles per locus was 3.391. The observed heterozygosity and expected heterozygosity varied from 0.100 to 1.000 and 0.099 to 0.809, respectively. The microsatellite markers developed here will be useful for studies on population genetics of this endemic species. Moreover, the information of the transcriptome will provide a useful resource for the future research on metabolism, regulation of the terpenoid biosynthesis, genetic and proteome studies of <i>E. kansui</i>.
DOI: 10.6084/m9.figshare.12853062.v1
title: <i>De novo</i> assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic <i>Euphorbia kansui</i>

description: <i>Euphorbia kansui</i> Liou is an endemic and traditional medicinal plant in China. Despite its value, the genomic and transcriptomic information of <i>E. kansui</i> is limited. In the present study, a total of 43,211,690 high-quality reads were generated using Illumina paired-end sequencing technology. After assembly, 58,362 unigenes were recovered with an N50 length of 1,683 bp. 36,396 (62.36%) of these unigenes had at least one blast hit against the multiple public databases. Based on KEGG pathway analyses, unigenes were discovered to encode known enzymes that catalyze the formation of the terpenoid backone and diterpenoid. In addition, the unigenes related to casbene synthase, which catalyzes the formation of the major active constituents (diterpenoids) in <i>E. kansui,</i> were identified. For functional marker development, 7,016 candidate simple sequence repeats (SSR, microsatellites) were identified from 6,150 unigenes, and 40 SSR loci were selected randomly and amplified in two populations of <i>E. kansui</i>. A total of 28 loci were amplified successfully and 23 loci exhibited polymorphisms. The number of alleles of each locus ranged from 2 to 8 alleles and the mean number of alleles per locus was 3.391. The observed heterozygosity and expected heterozygosity varied from 0.100 to 1.000 and 0.099 to 0.809, respectively. The microsatellite markers developed here will be useful for studies on population genetics of this endemic species. Moreover, the information of the transcriptome will provide a useful resource for the future research on metabolism, regulation of the terpenoid biosynthesis, genetic and proteome studies of <i>E. kansui</i>.
DOI: 10.6084/m9.figshare.12853077
title: SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China

description: The walnut is an excellent food product with abundant nutrients. However, the inference of its population structure has been hindered by the intricate phylogenetic relationships among <i>Juglans</i> species. In this study, RAD sequencing was conducted to investigate the genetic variation and population structure among 41 walnut cultivars from Southwestern Sichuan (SS, <i>n</i> = 10), Eastern Sichuan (ES, <i>n</i> = 26) and Northern China (NC, <i>n</i> = 5). The resulting 6357 single-nucleotide polymorphisms divided the 41 walnut cultivars into two major groups corresponding to the ES and SS gene pools, and NC was clustered with the ES1 subgroup. Additionally, two cultivars, WB01 and SMJ, were reclassified to correct their previous morphological classifications. The migration rate from ES to SS was greater than that in the reverse direction, and the genetic differentiation between the ES and SS populations was high. Moreover, the estimated expected heterozygosity (<i>H<sub>e</sub>
 </i> = 0.308) and polymorphism levels (<i>P<sub>i</sub>
 </i> (<i>π</i>) = 0.030) of the SS group were greater than those of the ES group. Similarly, the average genetic distance of the SS population (0.563) was higher than that of the ES population (0.522), and the rate of linkage disequilibrium decay in the SS population was faster. All the results indicate that the SS population has greater genetic diversity and is more primitive than the ES group. The present study provides a theoretical basis for the division, conservation, and utilization of walnut germplasm resources, and these findings can be applied in breeding programs to obtain high-quality cultivars of <i>Juglans</i>.
DOI: 10.6084/m9.figshare.12853077.v1
title: SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China

description: The walnut is an excellent food product with abundant nutrients. However, the inference of its population structure has been hindered by the intricate phylogenetic relationships among <i>Juglans</i> species. In this study, RAD sequencing was conducted to investigate the genetic variation and population structure among 41 walnut cultivars from Southwestern Sichuan (SS, <i>n</i> = 10), Eastern Sichuan (ES, <i>n</i> = 26) and Northern China (NC, <i>n</i> = 5). The resulting 6357 single-nucleotide polymorphisms divided the 41 walnut cultivars into two major groups corresponding to the ES and SS gene pools, and NC was clustered with the ES1 subgroup. Additionally, two cultivars, WB01 and SMJ, were reclassified to correct their previous morphological classifications. The migration rate from ES to SS was greater than that in the reverse direction, and the genetic differentiation between the ES and SS populations was high. Moreover, the estimated expected heterozygosity (<i>H<sub>e</sub>
 </i> = 0.308) and polymorphism levels (<i>P<sub>i</sub>
 </i> (<i>π</i>) = 0.030) of the SS group were greater than those of the ES group. Similarly, the average genetic distance of the SS population (0.563) was higher than that of the ES population (0.522), and the rate of linkage disequilibrium decay in the SS population was faster. All the results indicate that the SS population has greater genetic diversity and is more primitive than the ES group. The present study provides a theoretical basis for the division, conservation, and utilization of walnut germplasm resources, and these findings can be applied in breeding programs to obtain high-quality cultivars of <i>Juglans</i>.
DOI: 10.6084/m9.figshare.12853089
title: New insights into the evolution of the SBP-box family and expression analysis of genes in the growth and development of <i>Brassica juncea</i>

description: The SQUAMOSA promoter binding protein (SBP)-box consists of a family of transcription factors unique to plants and mediates important roles in plant growth and development. We identified 57 SBP genes in the <i>Brassica juncea</i> (swollen-stem mustard) genome, and analyzed the structural characteristics, evolutionary relationships, as well as their involvement in regulation and response to environmental stress. By the help of phylogenetic analysis, the SBP genes were divided into seven subgroups (G1-G7). Interestingly, most members of the same group shared conserved gene structure and motifs as well as gene duplications. This suggests that their functions are redundant highlighting evolutionary relatedness. Identification of the <i>cis</i>-acting elements of the promoter revealed multiple regulatory elements that responded to phytohormone or abiotic stresses. In addition, data from GO annotation indicated that <i>BjuSBPs</i> play a role in biological processes. Further interrogation of the expression of <i>BjuSBPs</i> in different stages of swollen-stem mustard showed spatiotemporal expression patterns. On the other hand, quantitative real-time polymerase chain reaction (qRT-PCR) showed that the expression levels of SBP genes at the development stage correlated with their transcriptome data but treatment with phytohormones affected their expression levels. Our study showed that the SBP-box responds to phytohormone signals and the genes might confer different functions in the development of the mustard plant. Our data lay the foundation for further studies evaluating the regulatory mechanisms of SBP-box family of genes.
DOI: 10.6084/m9.figshare.12853089.v1
title: New insights into the evolution of the SBP-box family and expression analysis of genes in the growth and development of <i>Brassica juncea</i>

description: The SQUAMOSA promoter binding protein (SBP)-box consists of a family of transcription factors unique to plants and mediates important roles in plant growth and development. We identified 57 SBP genes in the <i>Brassica juncea</i> (swollen-stem mustard) genome, and analyzed the structural characteristics, evolutionary relationships, as well as their involvement in regulation and response to environmental stress. By the help of phylogenetic analysis, the SBP genes were divided into seven subgroups (G1-G7). Interestingly, most members of the same group shared conserved gene structure and motifs as well as gene duplications. This suggests that their functions are redundant highlighting evolutionary relatedness. Identification of the <i>cis</i>-acting elements of the promoter revealed multiple regulatory elements that responded to phytohormone or abiotic stresses. In addition, data from GO annotation indicated that <i>BjuSBPs</i> play a role in biological processes. Further interrogation of the expression of <i>BjuSBPs</i> in different stages of swollen-stem mustard showed spatiotemporal expression patterns. On the other hand, quantitative real-time polymerase chain reaction (qRT-PCR) showed that the expression levels of SBP genes at the development stage correlated with their transcriptome data but treatment with phytohormones affected their expression levels. Our study showed that the SBP-box responds to phytohormone signals and the genes might confer different functions in the development of the mustard plant. Our data lay the foundation for further studies evaluating the regulatory mechanisms of SBP-box family of genes.