cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7592000.v1
title: Additional file 8: of Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

description: Expression annotation and functional annotation of unigenes shown in Fig. 7. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7591946
title: Additional file 1: of Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

description: Throughput and quality of apricot RNA-Seq data. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7591958
title: Additional file 2: of Homologous recombination-mediated targeted integration in monkey embryos using TALE nucleases

description: Table S1. List of putative off-target sites. The top 7 potential off-target sites (OTS1-OTS7) were selected for analysis. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7591958.v1
title: Additional file 2: of Homologous recombination-mediated targeted integration in monkey embryos using TALE nucleases

description: Table S1. List of putative off-target sites. The top 7 potential off-target sites (OTS1-OTS7) were selected for analysis. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7591961
title: Additional file 3: of Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

description: Statistics of assembly quality. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.23305154.v1
title: Additional file 7 of Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.23305157
title: Additional file 8 of Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.9164993.v2
title: Structures of Ag-Au and Cu-Au clusters from Theoretical study of the structures of bimetallic Ag–Au and Cu–Au clusters up to 108 atoms.

description: The Cartesian coordinates, energies, and successful rates for the putative stable structures of the investigated Ag-Au and Cu-Au clusters
DOI: 10.6084/m9.figshare.9164993.v1
title: Structures of Ag-Au and Cu-Au clusters from Theoretical study of the structures of bimetallic Ag–Au and Cu–Au clusters up to 108 atoms

description: The Cartesian coordinates, energies, and successful rates for the putative stable structures of the investigated Ag-Au and Cu-Au clusters
DOI: 10.6084/m9.figshare.23305151
title: Additional file 6 of Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

description: Supplementary Material 6
DOI: 10.23641/asha.25146338
title: Adaptive ECO-SiN (Miles et al., 2024)

description: <b>Purpose:</b> To investigate potential reasons for the mismatch between laboratory/clinic-based sentence-in-noise performance and real-world listening abilities, we recently developed a corpus of natural, spontaneously spoken speech with three vocal effort levels (Everyday Conversational Sentences in Noise [ECO-SiN]). Here, we examined the feasibility of using the ECO-SiN corpus for adaptive speech-in-noise testing, which might be a desirable format in certain situations (e.g., during a clinical visit).<b>Method:</b> Ten young, normal-hearing adults, along with 20 older adults with hearing loss participated in the study. Speech reception thresholds (SRTs) were obtained using ECO-SiN sentences, which were systematically compared to the SRTs obtained using traditional Bamford-Kowal-Bench–like sentences.<b>Results: </b>Results demonstrated the properties of the test compared favorably with those of a standard test based on scripted and clearly spoken sentences. Moreover, whereas normal-hearing listeners received a benefit from an increase in vocal effort, the participants with hearing loss showed a disbenefit that increased with increasing hearing loss.<b>Conclusion:</b> The adaptive version of the ECO-SiN test is feasible for research and clinical testing.<b>Supplemental Material S1. </b>Summary of the linear mixed effects model contrasts of the SRT data.Miles, K., Best, V., & Buchholz, J. M. (2024). Feasibility of an adaptive version of the Everyday Conversational Sentences in Noise Test. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 680–687. https://doi.org/10.1044/2023_JSLHR-23-00507
DOI: 10.23641/asha.25146338.v1
title: Adaptive ECO-SiN (Miles et al., 2024)

description: <b>Purpose:</b> To investigate potential reasons for the mismatch between laboratory/clinic-based sentence-in-noise performance and real-world listening abilities, we recently developed a corpus of natural, spontaneously spoken speech with three vocal effort levels (Everyday Conversational Sentences in Noise [ECO-SiN]). Here, we examined the feasibility of using the ECO-SiN corpus for adaptive speech-in-noise testing, which might be a desirable format in certain situations (e.g., during a clinical visit).<b>Method:</b> Ten young, normal-hearing adults, along with 20 older adults with hearing loss participated in the study. Speech reception thresholds (SRTs) were obtained using ECO-SiN sentences, which were systematically compared to the SRTs obtained using traditional Bamford-Kowal-Bench–like sentences.<b>Results: </b>Results demonstrated the properties of the test compared favorably with those of a standard test based on scripted and clearly spoken sentences. Moreover, whereas normal-hearing listeners received a benefit from an increase in vocal effort, the participants with hearing loss showed a disbenefit that increased with increasing hearing loss.<b>Conclusion:</b> The adaptive version of the ECO-SiN test is feasible for research and clinical testing.<b>Supplemental Material S1. </b>Summary of the linear mixed effects model contrasts of the SRT data.Miles, K., Best, V., & Buchholz, J. M. (2024). Feasibility of an adaptive version of the Everyday Conversational Sentences in Noise Test. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 680–687. https://doi.org/10.1044/2023_JSLHR-23-00507
DOI: 10.6084/m9.figshare.7591985.v1
title: Additional file 6: of Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

description: Expression annotation and functional annotation of unigenes shown in Fig. 5. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.13359524
title: Comparative transcriptome analysis in three sorghum (<i>Sorghum bicolor</i>) cultivars reveal genomic basis of differential seed quality

description: Sorghum is a globally important C4 crop that serves both as staple food and as bio-fuel, and showed high phenotypic variation in grain quality. In this study, we performed RNA-seq in grains of three local <i>Sorghum</i> cultivars Z6, Z27 and HC4, which have differential agronomic traits especially in grain color. Our analysis revealed more than 3000 differentially expressed genes among the three cultivars. The differentially expressed genes were enriched in carbohydrate, amino acid and flavonoid metabolic pathways, which may affect the appearance and nutrition value of grains. We also identified new genes and SNPs in the three cultivars. Our results revealed the transcriptome variations among different <i>Sorghum</i> cultivars that correlates with grain nutrition, and provided valuable information for sorghum breeding.
DOI: 10.6084/m9.figshare.13359906.v3
title: Roles of the Hcp family proteins in the pathogenicity of <i>Salmonella typhimurium</i> 14028s

description: The type VI secretion system (T6SS) is a new secretion system that is widely distributed among Gram-negative bacteria. The core component hemolysin-coregulated protein (Hcp) can be used as both its structural protein and secretory protein or chaperone protein. Studies on Hcp are important to elucidate the overall virulence mechanism of T6SS. <i>Salmonella typhimurium</i> is an important foodborne pathogen. There are three copies of <i>hcp</i> genes identified in <i>S</i>. Typhimurium 14028s. This study aimed to characterize the functions of the three Hcp family proteins and to elucidate the interactions among them. The <i>hcp</i> gene deletion mutants were constructed by λ Red-based recombination system. Effects of <i>hcp</i> mutation on the pathogenicity of 14028s were studied by bacterial competition assays, <i>Dictyostelium discoideum</i> assays and mouse model. The three Hcp family proteins were found to play different roles. Hcp1 can affect the transcription of <i>rpoS</i> and type 2 flagellar gene and influence the motility of 14028s. It is also involved in the intracellular survival of 14028s in <i>Dictyostelium discoideum</i>; Hcp2 is involved in the early proliferative capacity of 14028s in mice and can prevent its excessive proliferation; Hcp3 did not show direct functions in these assays. Hcp1 can interact with Hcp2 and Hcp3. Deletion of one <i>hcp</i> gene can result in a transcription level variation in the other two <i>hcp</i> genes. Our findings elucidated the functions of the three Hcp family proteins in <i>S</i>.Typhimurium and illustrated that there are interactions between different Hcp proteins. This study will be helpful to fully understand how T6SS actions in an organism.
DOI: 10.6084/m9.figshare.9164993
title: Structures of Ag-Au and Cu-Au clusters from Theoretical study of the structures of bimetallic Ag–Au and Cu–Au clusters up to 108 atoms.

description: The Cartesian coordinates, energies, and successful rates for the putative stable structures of the investigated Ag-Au and Cu-Au clusters
DOI: 10.6084/m9.figshare.13359446
title: Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

description: The awnless trait is the favorite trait for wheat breeding in Qinghai, China, but the major gene underlying the trait is unknown. This study aimed to analyze a recombinant inbred line (RIL) population containing 112 lines by crossing common wheat varieties GY448 (awnless) and GY115 (awned) using genotyping-by-sequencing analysis. A total of 56.62 Gb of clean sequence data were generated. A major gene was identified for the awnless trait based on 101,275 single-nucleotide polymorphisms by quantitative trait locus (QTL)-seq analysis. The region from 685.50 to 709.77 Mb on chromosome 5AL contained 334 genes and 394 transcripts, including <i>B1</i>, the major gene controlling the awnless trait. A 25-bp indel located in the B1 promoter region has a diagnostic value for the awnless/awned genotypes in the RIL population. A total of 42 spring wheat cultivars in Qinghai, China, were analyzed. Further, 23 awnless cultivars had the alleles of the GY448 parent, while 19 awned cultivars had the alleles of the GY115 parent. <i>B1</i> is crucial in the awnless trait in wheat cultivars in Qinghai, China. The findings of this study might guide the breeding of new wheat cultivars in this region.
DOI: 10.6084/m9.figshare.20175802.v1
title: Additional file 2 of PITX2C increases the stemness features of hepatocellular carcinoma cells by up-regulating key developmental factors in liver progenitor

description: Additional file 2: Table S2. The gene ontology (GO) analysis of PITX2C ChIP-seq.
DOI: 10.6084/m9.figshare.13698119
title: Additional file 3 of Insight of transcriptional regulators reveals the tolerance mechanism of carpet-grass (Axonopus compressus) against drought

description: Additional file 3.
DOI: 10.6084/m9.figshare.13698119.v1
title: Additional file 3 of Insight of transcriptional regulators reveals the tolerance mechanism of carpet-grass (Axonopus compressus) against drought

description: Additional file 3.
DOI: 10.6084/m9.figshare.20175570.v1
title: Additional file 2 of Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations

description: Additional File 2: Supplementary Tables S1-S7.
DOI: 10.6084/m9.figshare.13359562.v1
title: Molecular characteristics of <i>eae</i>-positive clinical Shiga toxin-producing <i>Escherichia coli</i> in Sweden

description: Shiga toxin (Stx)-producing <i>Escherichia coli</i> (STEC) can cause a wide range of symptoms from asymptomatic carriage, mild diarrhea to bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Intimin, encoded by the <i>eae</i> gene, also plays a critical role in STEC pathogenesis. Herein, we investigated the prevalence and genetic diversity of <i>eae</i> among clinical STEC isolates from patients with diarrhea, BD, HUS as well as from asymptomatic STEC-positive individuals in Sweden with whole-genome sequencing. We found that 173 out of 239 (72.4%) of clinical STEC strains were <i>eae</i> positive. Six <i>eae</i> subtypes (<i>ϵ</i>1, <i>γ</i>1, <i>β</i>3, <i>θ</i>, <i>ζ</i> and <i>ρ</i>) were identified <i>eae</i> and its subtype <i>γ</i>1 were significantly overrepresented in O157:H7 strains isolated from BD and HUS patients. <i>ϵ</i>1 was associated with O121:H19 and O103:H2 strains, and <i>β</i>3 to O26:H11 strains. The combination of <i>eae</i> subtype <i>γ</i>1 and <i>stx</i> subtype (<i>stx</i><sub>2</sub> or <i>stx</i><sub>1</sub>+<i>stx</i><sub>2</sub>) is more likely to cause severe disease, suggesting the possibility of using <i>eae</i> genotypes in risk assessment of STEC infection. In summary, this study demonstrated a high prevalence of <i>eae</i> in clinical STEC strains and considerable genetic diversity of <i>eae</i> in STEC strains in Sweden from 1994 through 2018, and revealed association between <i>eae</i> subtypes and disease severity.
DOI: 10.6084/m9.figshare.13359694.v1
title: <i>Toxoplasma gondii</i> infection in white spoonbills (<i>Platalea leucorodia</i>) from Henan Province, China

description: <i>Toxoplasma gondii</i> oocysts in the environment are a threat to humans and animals. This study is aimed to evaluate the prevalence of <i>T. gondii</i> in white spoonbills and isolate viable <i>T. gondii</i> from white spoonbills. In 28.6% (2/7) of white spoonbills, <i>T. gondii</i> antibodies were found in heart juice by the modified agglutination test (cut-off: 1:4). <i>T. gondii</i> DNA was detected in tissues of 42.9% (3/7) white spoonbills. One viable <i>T. gondii</i> strain, named TgSpoonbillCHn1, was isolated from the myocardium of a white spoonbill by bioassay in mice. DNA extracted from TgSpoonbillCHn1 tachyzoites was characterized by PCR-restriction fragment length polymorphism with ten markers and the virulence genes ROP5 and ROP18. The results revealed that it was ToxoDB#2 (Type III). The ROP18/ROP5 genotype combination predicts that this strain is avirulent for mice, which is supported by the infection experiments in mice. This is the first report of the isolation of viable <i>T. gondii</i> strain from white spoonbil. The prevalence of <i>T. gondii</i> in white spoonbills may be indicative of environmental contamination of oocysts. This report provides direct evidence of white spoonbill as an intermediate host of <i>T. gondii</i>.
DOI: 10.6084/m9.figshare.20175570
title: Additional file 2 of Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations

description: Additional File 2: Supplementary Tables S1-S7.
DOI: 10.6084/m9.figshare.13359906.v2
title: Roles of the Hcp family proteins in the pathogenicity of <i>Salmonella typhimurium</i> 14028s

description: The type VI secretion system (T6SS) is a new secretion system that is widely distributed among Gram-negative bacteria. The core component hemolysin-coregulated protein (Hcp) can be used as both its structural protein and secretory protein or chaperone protein. Studies on Hcp are important to elucidate the overall virulence mechanism of T6SS. <i>Salmonella typhimurium</i> is an important foodborne pathogen. There are three copies of <i>hcp</i> genes identified in <i>S</i>. Typhimurium 14028s. This study aimed to characterize the functions of the three Hcp family proteins and to elucidate the interactions among them. The <i>hcp</i> gene deletion mutants were constructed by λ Red-based recombination system. Effects of <i>hcp</i> mutation on the pathogenicity of 14028s were studied by bacterial competition assays, <i>Dictyostelium discoideum</i> assays and mouse model. The three Hcp family proteins were found to play different roles. Hcp1 can affect the transcription of <i>rpoS</i> and type 2 flagellar gene and influence the motility of 14028s. It is also involved in the intracellular survival of 14028s in <i>Dictyostelium discoideum</i>; Hcp2 is involved in the early proliferative capacity of 14028s in mice and can prevent its excessive proliferation; Hcp3 did not show direct functions in these assays. Hcp1 can interact with Hcp2 and Hcp3. Deletion of one <i>hcp</i> gene can result in a transcription level variation in the other two <i>hcp</i> genes. Our findings elucidated the functions of the three Hcp family proteins in <i>S</i>.Typhimurium and illustrated that there are interactions between different Hcp proteins. This study will be helpful to fully understand how T6SS actions in an organism.
DOI: 10.6084/m9.figshare.19126397.v1
title: Additional file 1 of FCER1G positively relates to macrophage infiltration in clear cell renal cell carcinoma and contributes to unfavorable prognosis by regulating tumor immunity

description: Additional file 1. Detail information of TMA-30.
DOI: 10.6084/m9.figshare.19126403.v1
title: Additional file 3 of FCER1G positively relates to macrophage infiltration in clear cell renal cell carcinoma and contributes to unfavorable prognosis by regulating tumor immunity

description: Additional file 3. Differentially expressed genes correlated with macrophage markers.
DOI: 10.6084/m9.figshare.20175859
title: Additional file 13 of Cleavage of tropomodulin-3 by asparagine endopeptidase promotes cancer malignancy by actin remodeling and SND1/RhoA signaling

description: Additional file 13: Supplementary Table 3. Tissue microarry and Tmod3 staining.
DOI: 10.6084/m9.figshare.13359906
title: Roles of the Hcp family proteins in the pathogenicity of <i>Salmonella typhimurium</i> 14028s

description: The type VI secretion system (T6SS) is a new secretion system that is widely distributed among Gram-negative bacteria. The core component hemolysin-coregulated protein (Hcp) can be used as both its structural protein and secretory protein or chaperone protein. Studies on Hcp are important to elucidate the overall virulence mechanism of T6SS. <i>Salmonella typhimurium</i> is an important foodborne pathogen. There are three copies of <i>hcp</i> genes identified in <i>S</i>. Typhimurium 14028s. This study aimed to characterize the functions of the three Hcp family proteins and to elucidate the interactions among them. The <i>hcp</i> gene deletion mutants were constructed by λ Red-based recombination system. Effects of <i>hcp</i> mutation on the pathogenicity of 14028s were studied by bacterial competition assays, <i>Dictyostelium discoideum</i> assays and mouse model. The three Hcp family proteins were found to play different roles. Hcp1 can affect the transcription of <i>rpoS</i> and type 2 flagellar gene and influence the motility of 14028s. It is also involved in the intracellular survival of 14028s in <i>Dictyostelium discoideum</i>; Hcp2 is involved in the early proliferative capacity of 14028s in mice and can prevent its excessive proliferation; Hcp3 did not show direct functions in these assays. Hcp1 can interact with Hcp2 and Hcp3. Deletion of one <i>hcp</i> gene can result in a transcription level variation in the other two <i>hcp</i> genes. Our findings elucidated the functions of the three Hcp family proteins in <i>S</i>.Typhimurium and illustrated that there are interactions between different Hcp proteins. This study will be helpful to fully understand how T6SS actions in an organism.
DOI: 10.6084/m9.figshare.13359906.v1
title: Roles of the Hcp family proteins in the pathogenicity of <i>Salmonella typhimurium</i> 14028s

description: The type VI secretion system (T6SS) is a new secretion system that is widely distributed among Gram-negative bacteria. The core component hemolysin-coregulated protein (Hcp) can be used as both its structural protein and secretory protein or chaperone protein. Studies on Hcp are important to elucidate the overall virulence mechanism of T6SS. <i>Salmonella typhimurium</i> is an important foodborne pathogen. There are three copies of <i>hcp</i> genes identified in <i>S</i>. Typhimurium 14028s. This study aimed to characterize the functions of the three Hcp family proteins and to elucidate the interactions among them. The <i>hcp</i> gene deletion mutants were constructed by λ Red-based recombination system. Effects of <i>hcp</i> mutation on the pathogenicity of 14028s were studied by bacterial competition assays, <i>Dictyostelium discoideum</i> assays and mouse model. The three Hcp family proteins were found to play different roles. Hcp1 can affect the transcription of <i>rpoS</i> and type 2 flagellar gene and influence the motility of 14028s. It is also involved in the intracellular survival of 14028s in <i>Dictyostelium discoideum</i>; Hcp2 is involved in the early proliferative capacity of 14028s in mice and can prevent its excessive proliferation; Hcp3 did not show direct functions in these assays. Hcp1 can interact with Hcp2 and Hcp3. Deletion of one <i>hcp</i> gene can result in a transcription level variation in the other two <i>hcp</i> genes. Our findings elucidated the functions of the three Hcp family proteins in <i>S</i>.Typhimurium and illustrated that there are interactions between different Hcp proteins. This study will be helpful to fully understand how T6SS actions in an organism.
DOI: 10.6084/m9.figshare.19126403
title: Additional file 3 of FCER1G positively relates to macrophage infiltration in clear cell renal cell carcinoma and contributes to unfavorable prognosis by regulating tumor immunity

description: Additional file 3. Differentially expressed genes correlated with macrophage markers.
DOI: 10.6084/m9.figshare.11787006
title: Additional file 4 of A positive feedback loop between EZH2 and NOX4 regulates nucleus pulposus cell senescence in age-related intervertebral disc degeneration

description: Additional file 4: Table S1. Original data of PCR array analysis.
DOI: 10.6084/m9.figshare.13359694
title: <i>Toxoplasma gondii</i> infection in white spoonbills (<i>Platalea leucorodia</i>) from Henan Province, China

description: <i>Toxoplasma gondii</i> oocysts in the environment are a threat to humans and animals. This study is aimed to evaluate the prevalence of <i>T. gondii</i> in white spoonbills and isolate viable <i>T. gondii</i> from white spoonbills. In 28.6% (2/7) of white spoonbills, <i>T. gondii</i> antibodies were found in heart juice by the modified agglutination test (cut-off: 1:4). <i>T. gondii</i> DNA was detected in tissues of 42.9% (3/7) white spoonbills. One viable <i>T. gondii</i> strain, named TgSpoonbillCHn1, was isolated from the myocardium of a white spoonbill by bioassay in mice. DNA extracted from TgSpoonbillCHn1 tachyzoites was characterized by PCR-restriction fragment length polymorphism with ten markers and the virulence genes ROP5 and ROP18. The results revealed that it was ToxoDB#2 (Type III). The ROP18/ROP5 genotype combination predicts that this strain is avirulent for mice, which is supported by the infection experiments in mice. This is the first report of the isolation of viable <i>T. gondii</i> strain from white spoonbil. The prevalence of <i>T. gondii</i> in white spoonbills may be indicative of environmental contamination of oocysts. This report provides direct evidence of white spoonbill as an intermediate host of <i>T. gondii</i>.
DOI: 10.6084/m9.figshare.20175859.v1
title: Additional file 13 of Cleavage of tropomodulin-3 by asparagine endopeptidase promotes cancer malignancy by actin remodeling and SND1/RhoA signaling

description: Additional file 13: Supplementary Table 3. Tissue microarry and Tmod3 staining.