cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23641/asha.25016471
title: A new efficient and safe music exposure paradigm (Iliadou et al., 2024)

description: <b>Purpose:</b> The purpose of this study was to develop a time-efficient music exposure and testing paradigm that safely creates temporary cochlear dysfunction that could be used in future temporary threshold shift (TTS) studies.<b>Method:</b> A 30-min audio compilation of pop rock music tracks was created. Adult volunteers with normal hearing were then exposed to this music material monaurally through headphones for 30 min at 97 dBA or 15 min at 100 dBA. Levels were measured from the ear of a manikin and are considered to provide an equivalent daily noise dose based on a 3-dB exchange. We assessed the changes in their hearing, by means of distortion product otoacoustic emission (DPOAE) testing, and standard and extended high-frequency pure-tone audiometry before and after exposure. There were 17 volunteers in total. In the first trial, eight volunteers (four females; <i>Mdn</i><sub>age</sub> = 31 years [interquartile range, IQR = 4.25]) were included. Although TTS was observed in all eight participants for at least one frequency, a large variation in affected frequencies was observed. To address this issue, the audio material was further remastered to adjust levels across the different frequency bands. Fourteen adults (nine newly recruited and five from the first trial; seven females; <i>Mdn</i><sub>age</sub> = 31 years [IQR = 5]) were exposed to the new material.<b>Results:</b> All but two of 17 participants presented clinically significant TTS or decrease in DPOAE amplitude in at least one frequency. Statistically significant average TTS of 7.43 dB was observed at 6 kHz. There were statistically significant average DPOAE amplitude shifts of −2.55 dB at 4 kHz, −4.97 dB at 6 kHz, and −3.14 dB at 8 kHz. No participant presented permanent threshold shift.<b>Conclusions:</b> A monaural music paradigm was developed and shown to induce statistically significant TTS and DPOAE amplitude shifts, without evidence of permanent loss. This realistic and time-efficient paradigm may be considered a viable option for experimental studies of temporary music-induced hearing loss.<b>Supplemental Material S1.</b> TTS per frequency for the 17 participants of the pilot study.<b>Supplemental Material S2.</b> Ultimate PTA threshold shift per frequency for the first part of the experimental study.<b>Supplemental Material S3.</b> Ultimate PTA threshold shift per frequency for the second part of the experimental study.<b>Supplemental Material S4.</b> Distortion product otoacoustic emission data for Trials 1 and 2.Iliadou, E., Pastiadis, K., Dimitriadis, D., Plack, C. J., & Bibas, A. (2024). Development and validation of an efficient and safe loud music exposure paradigm. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 668–679. https://doi.org/10.1044/2023_JSLHR-23-00332
DOI: 10.6084/m9.figshare.19125841.v1
title: Estimation and model selection for nonparametric function-on-function regression

description: Regression models with a functional response and functional covariate have received significant attention recently. While various nonparametric and semiparametric models have been developed, there is an urgent need for model selection and diagnostic methods. In this article, we develop a unified framework for estimation and model selection in nonparametric function-on-function regression. We propose a general nonparametric functional regression model with the model space constructed through smoothing spline analysis of variance (SS ANOVA). The proposed model reduces to some of the existing models when selected components in the SS ANOVA decomposition are eliminated. We propose new estimation procedures under either <i>L</i><sub>1</sub> or <i>L</i><sub>2</sub> penalty and show that the combination of the SS ANOVA decomposition and <i>L</i><sub>1</sub> penalty provides powerful tools for model selection and diagnostics. We establish consistency and convergence rates for estimates of the regression function and each component in its decomposition under both the <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub> penalties. Simulation studies and real examples show that the proposed methods perform well. Technical details and additional simulation results are available in online supplementary materials.
DOI: 10.6084/m9.figshare.19126307
title: Additional file 2 of N6-methyladenosine-dependent modification of circGARS acts as a new player that promotes SLE progression through the NF-κB/A20 axis

description: Additional File 2: Table S2. Detailed information on the SLE patients.
DOI: 10.6084/m9.figshare.7591829
title: MOESM2 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 2: Table S2. Known miRNAs identified in HIST and NC libraries.
DOI: 10.6084/m9.figshare.8115659
title: Data File 2.csv

description: Data File 2 for measured parameters of the GC4.
DOI: 10.6084/m9.figshare.8115659.v1
title: Data File 2.csv

description: Data File 2 for measured parameters of the GC4.
DOI: 10.6084/m9.figshare.14931570.v1
title: Krüppel-like factor 5-induced overexpression of long non-coding RNA DANCR promotes the progression of cervical cancer via repressing microRNA-145-3p to target ZEB1

description: Long non-coding RNA (lncRNA) differentiation antagonizing non-protein coding RNA (DANCR) participates in the development of diverse cancers. Nevertheless, the impact of DANCR on cervical cancer (CC) remains largely unknown. This study aims to explore the effects of DANCR sponging microRNA-145-3p (miR-145-3p) on CC. Expression of KLF5, DANCR, miR-145-3p, and zinc finger E-box binding homeobox 1 (ZEB1) in CC and adjacent normal tissues was determined. Human CC cell lines were, respectively, treated with silenced DANCR or miR145-3p mimic/inhibitor. Then, the viability, migration, invasion, and apoptosis of CC cells were measured. The cell growth <i>in vivo</i> was observed as well. Chromatin immunoprecipitation assay was performed to analyze the binding of KLF5 and DANCR promoter. Interaction among DANCR, miR-145-3p, and ZEB1 was assessed. KLF5, DANCR, and ZEB1 were upregulated but miR-145-3p was downregulated in CC tissues. KLF5 activated DANCR expression and the high DANCR expression was related to tumor staging, infiltrating muscle depth and lymphatic metastasis of CC patients. Reduced DANCR or elevated miR-145-3p repressed malignant behaviors of CC cells. The tumor diameter and weight were also repressed by DANCR silencing or miR-145-3p elevation. The effect of DANCR knockdown on CC cells could be reversed by miR-145-3p inhibitor. MiR-145-3p was targeted by DANCR and ZEB1 was targeted by miR-145-3p. KLF5-induced overexpression of DANCR promotes CC progression via suppressing miR-145-3p to target ZEB1. This study may provide potential targets for CC treatment.
DOI: 10.6084/m9.figshare.7591427
title: Genetic variation of aggrecanase-2 (ADAMTS5) in susceptibility to osteoarthritis

description: Aggrecanase-2 (ADAMTS5) gene is responsible for aggrecan degradation that may contribute to cartilage destruction in a mouse osteoarthritis (OA) model. We aimed to investigate the effects of ADAMTS5 gene polymorphisms on OA risk in a Chinese population. A total of 300 OA patients and 300 controls were recruited and their genotypes for ADAMTS5 gene rs226794 and rs2830585 polymorphisms were determined using a custom-by-design 48-Plex single nucleotide polymorphism Scan™ kit. ADAMTS5-associated genes were identified by co-expression analysis and their functions were investigated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Bioinformatics analysis showed that ADAMTS5 was significantly related to the components, structural constituent, and organization of the extracellular matrix. The rs2830585 polymorphism, but not rs226794 polymorphism, was significantly associated with an increased risk of knee OA. Stratified analysis further confirmed this significant association in patients at age ≥55 years. In conclusion, the ADAMTS5 rs2830585 polymorphism may be involved in the development of knee OA by destroying the extracellular matrix, but this finding should be further confirmed by larger studies.
DOI: 10.6084/m9.figshare.19126307.v1
title: Additional file 2 of N6-methyladenosine-dependent modification of circGARS acts as a new player that promotes SLE progression through the NF-κB/A20 axis

description: Additional File 2: Table S2. Detailed information on the SLE patients.
DOI: 10.6084/m9.figshare.7591823
title: MOESM1 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 1: Table S1. The primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.23305124.v1
title: Additional file 3 of The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

description: Additional file 3: Table S13. The gene IDs of all mentioned genes in the manuscript.
DOI: 10.6084/m9.figshare.7591829.v1
title: MOESM2 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 2: Table S2. Known miRNAs identified in HIST and NC libraries.
DOI: 10.6084/m9.figshare.7591835.v1
title: MOESM3 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 3: Table S3. Novel candidate miRNAs identified from HIST and NC libraries.
DOI: 10.6084/m9.figshare.7591844.v1
title: MOESM5 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 5: Table S5. Target genes predicted for significantly differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.14931536.v1
title: Identification and validation of the miRNA–mRNA regulatory network in fetoplacental arterial endothelial cells of gestational diabetes mellitus

description: Gestational diabetes mellitus (GDM) increases the risk of fetal heart malformations, though little is known about the mechanism of hyperglycemia-induced heart malformations. Thus, we aimed to reveal the global landscape of miRNAs and mRNAs in GDM-exposed fetoplacental arterial endothelial cells (dAECs) and establish regulatory networks for exploring the pathophysiological mechanism of fetal heart malformations in maternal hyperglycemia. Gene Expression Omnibus (GEO) datasets were used, and identification of differentially expressed miRNAs (DEMs) and genes (DEGs) in GDM was based on a previous sequencing analysis of dAECs. A miRNA-mRNA network containing 20 DEMs and 65 DEGs was established using DEMs altered in opposite directions to DEGs. In an in vivo study, we established a streptozotocin-induced pregestational diabetes mellitus (PGDM) mouse model and found the fetal cardiac wall thickness in different regions to be dramatically increased in the PGDM grouValidation of DEMs and DEGs in the fetal heart showed significantly upregulated expression of let-7e-5p, miR-139-5p and miR-195-5p and downregulated expression of SGOL1, RRM2, RGS5, CDK1 and CENPA. In summary, we reveal the miRNA-mRNA regulatory network related to fetal cardiac development disorders in offspring, which may shed light on the potential molecular mechanisms of fetal cardiac development disorders during maternal hyperglycemia.
DOI: 10.6084/m9.figshare.7591946.v1
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: 10.25386/genetics.11786094
title: Supplemental Material for Chen et al., 2020

description: Supplemental files, movies, and tables for Wenjun Chen et al., 2020
DOI: 10.6084/m9.figshare.13359446.v1
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.7592258.v1
title: Additional file 1: of Tumor microenvironment modulation enhances immunologic benefit of chemoradiotherapy

description: Figure S1. The combination of CTX / L-NIL reverses the cold tumor microenvironment. Figure S2. CTX / L-NIL activates the immune microenvironment of CRT treated tumors. Figure S3. CTX/L-NIL improves CRT treatment effects in established HPV-negative tumors. Figure S4. Gating strategy for myeloid sub-types and inflammatory monocyte phenotyping. Figure S5. Systemic myeloid effects induced by CRT+CTX/L-NIL. Figure S6. Gating strategy for lymphocyte sub-types. Figure S7. Systemic lymphoid effects induced by CRT+CTX/L-NIL. Figure S8. CD8+ T cell phenotype in tumors. Table S1. Flow cytometry antibodies used for myeloid subset analysis. Table S2. Flow cytometry antibodies used for lymphocyte and CD8+ T cell subset analysis. Table S3. Immune pathway signature gene list used in gene expression analysis. Table S4. Immune cell type signature gene list used in gene expression analysis [68â 70]. (ZIP 12061 kb)
DOI: 10.6084/m9.figshare.13359524.v1
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.23305118
title: Additional file 2 of The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

description: Additional file 2: Table S12. Biomass of V. sp. H4302, V. stellata, and N. oculata in 18 days cultivations with 1 mM or 2 mM initial nitrogen concentrations of sodium cyanateand sodium nitrateas sole nitrogen resource, respectively.
DOI: 10.6084/m9.figshare.23305118.v1
title: Additional file 2 of The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

description: Additional file 2: Table S12. Biomass of V. sp. H4302, V. stellata, and N. oculata in 18 days cultivations with 1 mM or 2 mM initial nitrogen concentrations of sodium cyanateand sodium nitrateas sole nitrogen resource, respectively.
DOI: 10.6084/m9.figshare.23305124
title: Additional file 3 of The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

description: Additional file 3: Table S13. The gene IDs of all mentioned genes in the manuscript.
DOI: 10.6084/m9.figshare.7592258
title: Additional file 1: of Tumor microenvironment modulation enhances immunologic benefit of chemoradiotherapy

description: Figure S1. The combination of CTX / L-NIL reverses the cold tumor microenvironment. Figure S2. CTX / L-NIL activates the immune microenvironment of CRT treated tumors. Figure S3. CTX/L-NIL improves CRT treatment effects in established HPV-negative tumors. Figure S4. Gating strategy for myeloid sub-types and inflammatory monocyte phenotyping. Figure S5. Systemic myeloid effects induced by CRT+CTX/L-NIL. Figure S6. Gating strategy for lymphocyte sub-types. Figure S7. Systemic lymphoid effects induced by CRT+CTX/L-NIL. Figure S8. CD8+ T cell phenotype in tumors. Table S1. Flow cytometry antibodies used for myeloid subset analysis. Table S2. Flow cytometry antibodies used for lymphocyte and CD8+ T cell subset analysis. Table S3. Immune pathway signature gene list used in gene expression analysis. Table S4. Immune cell type signature gene list used in gene expression analysis [68â 70]. (ZIP 12061 kb)
DOI: 10.25386/genetics.11786094.v3
title: Supplemental Material for Chen et al., 2020

description: Supplemental files, movies, and tables for Wenjun Chen et al., 2020
DOI: 10.25386/genetics.11786094.v2
title: Supplemental Material for Chen et al., 2020

description: Supplemental files, movies, and tables for Wenjun Chen et al., 2020
DOI: 10.6084/m9.figshare.23305166.v1
title: Additional file 11 of Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

description: Supplementary Material 11
DOI: 10.25386/genetics.11786094.v1
title: Supplemental Material for Chen et al., 2020

description: Supplemental files, movies, and tables for Wenjun Chen et al., 2020
DOI: 10.6084/m9.figshare.12033768.v1
title: Synthesis, characterization, X-ray crystal structures, and antibacterial property of oxidovanadium(V) complexes with halide-containing hydrazones

description: Two oxidovanadium(V) complexes, [VOL<sup>1</sup>(OMe)(MeOH)] (<b>1</b>) and [VOL<sup>2</sup>(OEt)(EtOH)] (<b>2</b>), where H<sub>2</sub>L<sup>1</sup> = 4-bromo-<i>N’</i>-(3,5-dibromo-2-hydroxybenzylidene)benzohydrazide and H<sub>2</sub>L<sup>2</sup> = 4-bromo-<i>N’</i>-(3,5-dichloro-2-hydroxybenzylidene)benzohydrazide, have been synthesized by reaction of VO(acac)<sub>2</sub> with the hydrazone ligands and characterized by elemental analyses, IR, UV-Vis, molar conductivity, and X-ray single-crystal structural determination. The hydrazone ligands coordinate to the V atoms through phenolate oxygen, imino nitrogen, and enolate oxygen atoms. The V atoms are in octahedral coordination, with the other three sites furnished by one methanol or ethanol oxygen, one deprotonated methanol or ethanol oxygen, and one oxido group. The antibacterial property of the complexes and the hydrazones against the bacteria <i>Bacillus subtilis</i>, <i>Escherichia coli</i>, <i>Pseudomonas putida</i>, and <i>Staphylococcus aureus</i> were studied. Both complexes exhibit remarkable antibacterial properties on <i>B. subtilis</i> and <i>S. aureus</i> comparable to Penicillin.
DOI: 10.6084/m9.figshare.13359562
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.23305157.v1
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.12033768
title: Synthesis, characterization, X-ray crystal structures, and antibacterial property of oxidovanadium(V) complexes with halide-containing hydrazones

description: Two oxidovanadium(V) complexes, [VOL<sup>1</sup>(OMe)(MeOH)] (<b>1</b>) and [VOL<sup>2</sup>(OEt)(EtOH)] (<b>2</b>), where H<sub>2</sub>L<sup>1</sup> = 4-bromo-<i>N’</i>-(3,5-dibromo-2-hydroxybenzylidene)benzohydrazide and H<sub>2</sub>L<sup>2</sup> = 4-bromo-<i>N’</i>-(3,5-dichloro-2-hydroxybenzylidene)benzohydrazide, have been synthesized by reaction of VO(acac)<sub>2</sub> with the hydrazone ligands and characterized by elemental analyses, IR, UV-Vis, molar conductivity, and X-ray single-crystal structural determination. The hydrazone ligands coordinate to the V atoms through phenolate oxygen, imino nitrogen, and enolate oxygen atoms. The V atoms are in octahedral coordination, with the other three sites furnished by one methanol or ethanol oxygen, one deprotonated methanol or ethanol oxygen, and one oxido group. The antibacterial property of the complexes and the hydrazones against the bacteria <i>Bacillus subtilis</i>, <i>Escherichia coli</i>, <i>Pseudomonas putida</i>, and <i>Staphylococcus aureus</i> were studied. Both complexes exhibit remarkable antibacterial properties on <i>B. subtilis</i> and <i>S. aureus</i> comparable to Penicillin.
DOI: 10.6084/m9.figshare.7592033.v1
title: Additional file 2: of OCT4 maintains self-renewal and reverses senescence in human hair follicle mesenchymal stem cells through the downregulation of p21 by DNA methyltransferases

description: The details of the DEGs. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.7591823.v1
title: MOESM1 of Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

description: Additional file 1: Table S1. The primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.7592033
title: Additional file 2: of OCT4 maintains self-renewal and reverses senescence in human hair follicle mesenchymal stem cells through the downregulation of p21 by DNA methyltransferases

description: The details of the DEGs. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.7591997
title: Additional file 6: of Homologous recombination-mediated targeted integration in monkey embryos using TALE nucleases

description: Table S2. Primers used for off-target analysis. (XLSX 13 kb)