cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh2033788.08fu
title: SH2033788.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1353558.08fu
title: SH1353558.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1353559.08fu
title: SH1353559.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2033789.08fu
title: SH2033789.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2033790.08fu
title: SH2033790.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1353560.08fu
title: SH1353560.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1353561.08fu
title: SH1353561.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2033791.08fu
title: SH2033791.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.13180570
title: YSIRK-G/S-directed translocation is required for <i>Streptococcus suis</i> to deliver diverse cell wall anchoring effectors contributing to bacterial pathogenicity

description: The <i>Streptococcus suis</i> serotype 2 (SS2) is a significant zoonotic pathogen that is responsible for various swine diseases, even causing cytokine storms of Streptococcal toxic shock-like syndromes amongst human. Cell wall anchoring proteins with a C-terminal LPxTG are considered to play vital roles during SS2 infection; however, their exporting mechanism across cytoplasmic membranes has remained vague. This study found that YSIRK-G/S was involved in the exportation of LPxTG-anchoring virulence factors MRP and SspA in virulent SS2 strain ZY05719. The whole-genome analysis indicated that diverse LPxTG proteins fused with an N-terminal YSIRK-G/S motif are encoded in strain ZY05719. Two novel LPxTG proteins SspB and YzpA were verified to be exported via a putative transport system that was dependent on the YSIRK-G/S directed translocation, and portrayed vital functions during the infection of SS2 strain ZY05719. Instead of exhibiting an inactivation of C5a peptidase in SspB, another LPxTG protein with an N-terminal YSIRK-G/S motif from <i>Streptococcus agalactiae</i> was depicted to cleave the C5a component of the host complement. The consequent domain-architecture retrieval determined more than 10,000 SspB/YzpA like proteins that are extensively distributed in the Gram-positive bacteria, and most of them harbor diverse glycosyl hydrolase or peptidase domains within their middle regions, thus presenting their capability to interact with host cells. The said findings provide compelling evidence that LPxTG proteins with an N-terminal YSIRK-G/S motif are polymorphic effectors secreted by Gram-positive bacteria, which can be further proposed to define as cell wall anchoring effectors in a new subset.
DOI: 10.6084/m9.figshare.13180570.v1
title: YSIRK-G/S-directed translocation is required for <i>Streptococcus suis</i> to deliver diverse cell wall anchoring effectors contributing to bacterial pathogenicity

description: The <i>Streptococcus suis</i> serotype 2 (SS2) is a significant zoonotic pathogen that is responsible for various swine diseases, even causing cytokine storms of Streptococcal toxic shock-like syndromes amongst human. Cell wall anchoring proteins with a C-terminal LPxTG are considered to play vital roles during SS2 infection; however, their exporting mechanism across cytoplasmic membranes has remained vague. This study found that YSIRK-G/S was involved in the exportation of LPxTG-anchoring virulence factors MRP and SspA in virulent SS2 strain ZY05719. The whole-genome analysis indicated that diverse LPxTG proteins fused with an N-terminal YSIRK-G/S motif are encoded in strain ZY05719. Two novel LPxTG proteins SspB and YzpA were verified to be exported via a putative transport system that was dependent on the YSIRK-G/S directed translocation, and portrayed vital functions during the infection of SS2 strain ZY05719. Instead of exhibiting an inactivation of C5a peptidase in SspB, another LPxTG protein with an N-terminal YSIRK-G/S motif from <i>Streptococcus agalactiae</i> was depicted to cleave the C5a component of the host complement. The consequent domain-architecture retrieval determined more than 10,000 SspB/YzpA like proteins that are extensively distributed in the Gram-positive bacteria, and most of them harbor diverse glycosyl hydrolase or peptidase domains within their middle regions, thus presenting their capability to interact with host cells. The said findings provide compelling evidence that LPxTG proteins with an N-terminal YSIRK-G/S motif are polymorphic effectors secreted by Gram-positive bacteria, which can be further proposed to define as cell wall anchoring effectors in a new subset.
DOI: 10.6084/m9.figshare.7937861.v3
title: RETRACTED ARTICLE: A novel Fas-binding outer membrane protein and lipopolysaccharide of <i>Leptospira interrogans</i> induce macrophage apoptosis through the Fas/FasL-caspase-8/-3 pathway

description: <i>Leptospira interrogans</i> is the major causative agent of leptospirosis, an emerging, globally spreading zoonotic infectious disease. The pathogen induces macrophage apoptosis, but the molecular basis and mechanism remain unknown. In the present study, we found that <i>L. interrogans</i> caused apoptosis of phagocytosis-inhibited macrophages, and the product of the <i>L. interrogans</i> LB047 gene (Lep-OMP047) was the unique protein captured by mouse and human Fas proteins. The recombinant expressed Lep-OMP047 (rLep-OMP047) strongly bound mouse and human Fas proteins with equilibrium association constant (<i>K</i><sub>D</sub>) values of 5.20 × 10<sup>−6</sup> to 2.84 × 10<sup>−9</sup> M according to surface plasmon resonance measurement and isothermal titration calorimetry. Flow-cytometric examination showed that 5 μg rLep-OMP047 or 1 μg lipopolysaccharide of <i>L. interrogans</i> (Lep-LPS) caused 43.70% or 21.90% early apoptosis in mouse J774A.1 macrophages and 28.41% or 15.80% for PMA-differentiated human THP-1 macrophages, respectively, but the apoptosis was blocked by Fas-antagonizing IgGs, Fas siRNAs, and caspase-8/-3 inhibitors. Moreover, Lep-OMP047 was significantly upregulated during infection of macrophages. Lep-LPS promoted the expression and cytomembrane translocation of Fas and FasL in macrophages. The JNK and p38 MAPK but not ERK signaling pathways, as well as the transcription factors c-Jun and ATF2 but not CHOP, mediated Lep-LPS-induced Fas/FasL expression and translocation. TLR2 but not TLR4 mediated Lep-LPS-induced JNK/p38 MAPK activation. Therefore, we demonstrated that a novel Fas-binding OMP and LPS of <i>L. interrogans</i> induce macrophage apoptosis through the Fas/FasL-caspase-8/-3 pathway.
DOI: 10.6084/m9.figshare.11608971
title: PREPARATION AND SIMULATION OF THE ON-LINE SiO2/S COATING FOR COKING INHIBITION IN THE INDUSTRIAL CRACKING FURNACE

description: Abstract Coke formation inside radiant coils is one of the main problems during thermal cracking of hydrocarbons. The on-line preparation of the coating for coking inhibition is a promising technology because it provides more flexibility to the operators on site. The SiO2/S coating was prepared on the inner surface of coils in an 8-year-served GK-VI industrial cracking furnace. The effects of the coating preparation process on the operation of TLE were studied. The coking rates of the tube with and without coating preparation were evaluated by the trend change of tube metal temperature. Simulations of the coating deposition process were further carried out using the computational fluid dynamics approach. The results showed that a significant temperature increase at the outlets of TLEs during coating preparation were due to the accumulation of SiO2 and S in a loose form under the TLE operating conditions when the concentration of coating precursors was 7500 ppm (wt. %). In the three tests, coating precursors were mainly completely consumed in tubes and TLEs. For the coated tube, the run time was extended by 4-7 days because the catalytic coking was decreased. No significant changes in the distribution of products and molar yields of main products were observed. In the simulations, it was found that increasing the inlet flow rate led to a more uniform thickness and improved the mass content of sulfur in the coating. In the tube bend section, circumferential nonuniformities for the deposition were due to circumferential differences in the temperatures and mass fractions. The mass fraction of S in the coating was within the range of 0.02%-0.1%. The control step for the SiO2/S coating deposition was kinetic. Based on the simulation results, the optimized coating preparation parameters were determined, i.e., the inlet flow rate of 15t/h, the outlet temperature of 1093K and the inlet mass concentration of 3000 ppm (wt. %).
DOI: 10.6084/m9.figshare.11608971.v1
title: PREPARATION AND SIMULATION OF THE ON-LINE SiO2/S COATING FOR COKING INHIBITION IN THE INDUSTRIAL CRACKING FURNACE

description: Abstract Coke formation inside radiant coils is one of the main problems during thermal cracking of hydrocarbons. The on-line preparation of the coating for coking inhibition is a promising technology because it provides more flexibility to the operators on site. The SiO2/S coating was prepared on the inner surface of coils in an 8-year-served GK-VI industrial cracking furnace. The effects of the coating preparation process on the operation of TLE were studied. The coking rates of the tube with and without coating preparation were evaluated by the trend change of tube metal temperature. Simulations of the coating deposition process were further carried out using the computational fluid dynamics approach. The results showed that a significant temperature increase at the outlets of TLEs during coating preparation were due to the accumulation of SiO2 and S in a loose form under the TLE operating conditions when the concentration of coating precursors was 7500 ppm (wt. %). In the three tests, coating precursors were mainly completely consumed in tubes and TLEs. For the coated tube, the run time was extended by 4-7 days because the catalytic coking was decreased. No significant changes in the distribution of products and molar yields of main products were observed. In the simulations, it was found that increasing the inlet flow rate led to a more uniform thickness and improved the mass content of sulfur in the coating. In the tube bend section, circumferential nonuniformities for the deposition were due to circumferential differences in the temperatures and mass fractions. The mass fraction of S in the coating was within the range of 0.02%-0.1%. The control step for the SiO2/S coating deposition was kinetic. Based on the simulation results, the optimized coating preparation parameters were determined, i.e., the inlet flow rate of 15t/h, the outlet temperature of 1093K and the inlet mass concentration of 3000 ppm (wt. %).
DOI: 10.6084/m9.figshare.10036112
title: Additional file 17: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S7. Genome-wide association between chromatin modification and transcriptional change. Based on the chromatin modification at each genomic region, transcripts are separated into up-regulated, down- regulated, and non-significant (Additional file 7). The chromatin-up and -down transcripts are correlated with transcripts that show expression change using Fisherâ s exact test. This generates four combinations ('s' = chromatin modification, 'e' = expression change): s.up.e.up; s.up.e.down; s.down.e.up; s.down.e.down. The P-values were adjusted using the BH [78] method and a FDR cutoff of &lt;10% was used to select mark-region combinations. The analysis was first done with the enhancer regions included and then repeated with the enhancers removed. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.10036112.v1
title: Additional file 17: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S7. Genome-wide association between chromatin modification and transcriptional change. Based on the chromatin modification at each genomic region, transcripts are separated into up-regulated, down- regulated, and non-significant (Additional file 7). The chromatin-up and -down transcripts are correlated with transcripts that show expression change using Fisherâ s exact test. This generates four combinations ('s' = chromatin modification, 'e' = expression change): s.up.e.up; s.up.e.down; s.down.e.up; s.down.e.down. The P-values were adjusted using the BH [78] method and a FDR cutoff of &lt;10% was used to select mark-region combinations. The analysis was first done with the enhancer regions included and then repeated with the enhancers removed. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.10036115
title: Additional file 22: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S9. A2BP1 and H3K4me3 overlapping genes that are also cocaine-regulated. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.10036115.v1
title: Additional file 22: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S9. A2BP1 and H3K4me3 overlapping genes that are also cocaine-regulated. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.10036118
title: Additional file 2: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S1. RNA-seq quality control metrics for acute and chronic data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.10036118.v1
title: Additional file 2: of Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

description: Table S1. RNA-seq quality control metrics for acute and chronic data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7414847.v1
title: Additional file 5: of Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L]Merr)

description: GmCHS transcript abundance in soybean tissues. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.11609172
title: Seismic resistance performance of a utility tunnel in saline soil foundation based on new cementitious composite materials

description: Abstract Because soluble salt in saline soil dissolves with water, utility tunnels built in saline soil foundation are more likely to damage due to by groundwater and earthquake. In this study, new cementitious composite materials were developed by using slag, building gypsum, quicklime, and magnesia. The unconfined compressive strengths of the saline soil solidified by new cementitious composite materials and cement are investigated, and the optimum proportion of the different components of the new cementitious composite materials is determined. We found from microscopic characteristics of the saline soil solidified by the new cementitious composite materials and cement that the new materials could better absorb chloride ions. Finally, the new cementitious composite materials were applied to saline soil foundation reinforcement of a utility tunnel. By using the finite element method (FEM) and shaking table tests, it can be seen that the displacement, acceleration and extent of damage of the utility tunnel after saline soil foundation reinforcement using new cementitious composite materials significantly decreased; therefore, the new cementitious composite materials can improve the seismic behaviour of the utility tunnel and shows potential future engineering application value.