cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17283194
title: Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN Spinach Germplasm

description: White rust, caused by <i>Albugo occidentalis</i>, is one of the major yield-limiting diseases of spinach (<i>Spinacia oleracea</i>) in some major commercial production areas. The use of host resistance is the most economical and environment-friendly approach to manage white rust in spinach production. The objectives of this research were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction efficiency (PA). A GWAS panel of 346 USDA germplasm accessions was phenotyped for white rust resistance under field conditions and genotyped with 13,235 SNPs postulated from whole-genome resequencing (WGR). The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).
DOI: 10.6084/m9.figshare.17283194.v1
title: Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN Spinach Germplasm

description: White rust, caused by <i>Albugo occidentalis</i>, is one of the major yield-limiting diseases of spinach (<i>Spinacia oleracea</i>) in some major commercial production areas. The use of host resistance is the most economical and environment-friendly approach to manage white rust in spinach production. The objectives of this research were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction efficiency (PA). A GWAS panel of 346 USDA germplasm accessions was phenotyped for white rust resistance under field conditions and genotyped with 13,235 SNPs postulated from whole-genome resequencing (WGR). The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).
DOI: 10.6084/m9.figshare.17274938
title: Interview schedule in Malayalam with codes

description: Interview schedule with codes in Malayalam
DOI: 10.6084/m9.figshare.17283761
title: Full list of dyads & triads

description: Full list of dyads & triads
DOI: 10.6084/m9.figshare.17274791
title: Interview schedule in English with codes

description: Interview schedule with codes in English
DOI: 10.6084/m9.figshare.17277167
title: Dataset for the study

description: Dataset for the study
DOI: 10.5281/zenodo.5791192
title: Data associated with "Survival outcomes are associated with genomic instability in luminal breast cancers".

description: Data utilised in Survival outcomes are associated with genomic instability in luminal breast cancers.
DOI: 10.5281/zenodo.5791191
title: Data associated with "Survival outcomes are associated with genomic instability in luminal breast cancers".

description: Data utilised in Survival outcomes are associated with genomic instability in luminal breast cancers.
DOI: 10.6084/m9.figshare.14337772
title: Additional file 4 of Comprehensive identification of somatic nucleotide variants in human brain tissue

description: Additional file 4:. Table S6. List of primers and probes used in ddPCR validation experiments.
DOI: 10.6084/m9.figshare.14337772.v1
title: Additional file 4 of Comprehensive identification of somatic nucleotide variants in human brain tissue

description: Additional file 4:. Table S6. List of primers and probes used in ddPCR validation experiments.
DOI: 10.6084/m9.figshare.14337763
title: Additional file 2 of Comprehensive identification of somatic nucleotide variants in human brain tissue

description: Additional file 2:. Table S2. List of 400 candidate SNVs chosen for validation experiments.
DOI: 10.6084/m9.figshare.20099658
title: Additional file 2 of Gene expression variation explains maize seed germination heterosis

description: Additional file 2: Table S1. The inheritance classification and DEGs.
DOI: 10.6084/m9.figshare.20105293.v1
title: Increased expression of tribbles homolog 3 predicts poor prognosis and correlates with tumor immunity in clear cell renal cell carcinoma: a bioinformatics study

description: Tribbles homolog 3 (TRIB3), a pseudokinase that regulates multiple intracellular signaling pathways, has been reported to promote the growth of multiple tumors. However, its role in clear cell renal cell carcinoma (ccRCC) remains unelucidated. We evaluated the role of TRIB3 in ccRCC using publicly available data from The Cancer Genome Atlas and analyzed its relationship with the tumor microenvironment; moreover, we used gene knockout and overexpression techniques to detect the effects of TRIB3 on the biological behavior of ccRCC cells. RT-qPCR and western blotting were used to detect transfection efficiency, and the invasiveness of ccRCC cells was determined by Transwell migration assays. We found that TRIB3 overexpression was significantly associated with increased grade, stage, and distant metastasis, positively correlated with ccRCC invasiveness, and also an independent risk factor for overall survival (OS). In addition, 361 differentially expressed genes (DEGs) related to TRIB3 were identified. Functional enrichment analysis showed that DEGs were mainly enriched in humoral immune responses, collagen-containing extracellular matrix, and serine hydrolase activity. Immune landscape characterization revealed that TRIB3 expression was significantly and negatively associated with CD8<sup>+</sup> T and hematopoietic stem cells, whereas it was positively associated with NK T and macrophage M1 cells. Single-cell sequencing showed that localization and binding targets of TRIB3 mainly involved monocytes/macrophages and CD4<sup>+</sup> and CD8<sup>+</sup> T cells. Overall, our study revealed that elevated TRIB3 expression represents a promising prognostic marker for ccRCC patients and may play a key role in tumor microenvironment modulation.
DOI: 10.6084/m9.figshare.20105293
title: Increased expression of tribbles homolog 3 predicts poor prognosis and correlates with tumor immunity in clear cell renal cell carcinoma: a bioinformatics study

description: Tribbles homolog 3 (TRIB3), a pseudokinase that regulates multiple intracellular signaling pathways, has been reported to promote the growth of multiple tumors. However, its role in clear cell renal cell carcinoma (ccRCC) remains unelucidated. We evaluated the role of TRIB3 in ccRCC using publicly available data from The Cancer Genome Atlas and analyzed its relationship with the tumor microenvironment; moreover, we used gene knockout and overexpression techniques to detect the effects of TRIB3 on the biological behavior of ccRCC cells. RT-qPCR and western blotting were used to detect transfection efficiency, and the invasiveness of ccRCC cells was determined by Transwell migration assays. We found that TRIB3 overexpression was significantly associated with increased grade, stage, and distant metastasis, positively correlated with ccRCC invasiveness, and also an independent risk factor for overall survival (OS). In addition, 361 differentially expressed genes (DEGs) related to TRIB3 were identified. Functional enrichment analysis showed that DEGs were mainly enriched in humoral immune responses, collagen-containing extracellular matrix, and serine hydrolase activity. Immune landscape characterization revealed that TRIB3 expression was significantly and negatively associated with CD8<sup>+</sup> T and hematopoietic stem cells, whereas it was positively associated with NK T and macrophage M1 cells. Single-cell sequencing showed that localization and binding targets of TRIB3 mainly involved monocytes/macrophages and CD4<sup>+</sup> and CD8<sup>+</sup> T cells. Overall, our study revealed that elevated TRIB3 expression represents a promising prognostic marker for ccRCC patients and may play a key role in tumor microenvironment modulation.
DOI: 10.6084/m9.figshare.12853646.v1
title: Non-walled spherical <i>Acinetobacter baumannii</i> is an important type of persister upon <i>β</i>-lactam antibiotic treatment

description: Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in <i>Acinetobacter baumannii</i> survived from the treatment by three major classes of antibiotics (i.e. <i>β</i>-lactam, aminoglycoside, and fluoroquinolone) with microcopy and found that a fraction of enlarged spherical bacteria constitutes a major sub-population of bacterial survivors from <i>β</i>-lactam antibiotic treatment, whereas survivors from the treatment of aminoglycoside and fluoroquinolone were less changed morphologically. Further studies showed that these spherical bacteria had completely lost their cell wall structures but could survive without any osmoprotective reagent. The spherical bacteria were not the viable-but-non-culturable cells and they could revive upon the removal of <i>β</i>-lactam antibiotics. Importantly, these non-walled spherical bacteria also persisted during antibiotic therapy <i>in vivo</i> using <i>Galleria mellonella</i> as the infection model. Additionally, the combinational treatment on <i>A. baumannii</i> by <i>β</i>-lactam and membrane-targeting antibiotic significantly enhanced the killing efficacy. Our results indicate that in addition to the dormant, structure intact persisters, the non-wall spherical bacterium is another important type of persister in <i>A. baumannii.</i> The finding suggests that targeting the bacterial cell membrane during <i>β</i>-lactam chemotherapy could enhance therapeutic efficacy on <i>A. baumannii</i> infection, which might also help to reduce the resistance development of <i>A. baumannii</i>.
DOI: 10.6084/m9.figshare.19581503
title: An upper bound on the minimum rank of a symmetric Toeplitz matrix completion problem

description: We consider a symmetric Toeplitz matrix completion problem, of which the matrix possesses special row and column structures. It has wide applications in diverse areas and is well-known to be computationally NP-hard. This note presents an upper bound on the objective of minimizing the rank of the symmetric Toeplitz matrix in the completion problem based on conclusions from the trigonometric moment problem and the semi-infinite problem. We prove that the upper bound is less than twice the number of the active constraints of the associated semi-infinite problem. Moreover, it is less than twice the number of linear constraints of the problem.
DOI: 10.6084/m9.figshare.12853646.v3
title: Non-walled spherical <i>Acinetobacter baumannii</i> is an important type of persister upon <i>β</i>-lactam antibiotic treatment

description: Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in <i>Acinetobacter baumannii</i> survived from the treatment by three major classes of antibiotics (i.e. <i>β</i>-lactam, aminoglycoside, and fluoroquinolone) with microcopy and found that a fraction of enlarged spherical bacteria constitutes a major sub-population of bacterial survivors from <i>β</i>-lactam antibiotic treatment, whereas survivors from the treatment of aminoglycoside and fluoroquinolone were less changed morphologically. Further studies showed that these spherical bacteria had completely lost their cell wall structures but could survive without any osmoprotective reagent. The spherical bacteria were not the viable-but-non-culturable cells and they could revive upon the removal of <i>β</i>-lactam antibiotics. Importantly, these non-walled spherical bacteria also persisted during antibiotic therapy <i>in vivo</i> using <i>Galleria mellonella</i> as the infection model. Additionally, the combinational treatment on <i>A. baumannii</i> by <i>β</i>-lactam and membrane-targeting antibiotic significantly enhanced the killing efficacy. Our results indicate that in addition to the dormant, structure intact persisters, the non-wall spherical bacterium is another important type of persister in <i>A. baumannii.</i> The finding suggests that targeting the bacterial cell membrane during <i>β</i>-lactam chemotherapy could enhance therapeutic efficacy on <i>A. baumannii</i> infection, which might also help to reduce the resistance development of <i>A. baumannii</i>.
DOI: 10.6084/m9.figshare.12853637
title: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon

description: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon
DOI: 10.6084/m9.figshare.22721405.v1
title: Additional file 1 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.5956285
title: A novel scoring system to predict the outcomes of adult patients with hypoxic-ischemic encephalopathy

description: <b>Background:</b> Adult patients with hypoxic-ischemic encephalopathy (HIE) often incur large costs, but their outcomes are poor. Currently, there is lack of a comprehensive quantitative approach to predict patient prognoses. <b>Methods</b>: A total of 73 adult patients with HIE participated in this prospective, observational study. Clinical assessments, laboratory tests, and electrophysiological examinations were conducted within 3 days after HIE occurred. Logistic regression model was used to identify independent factors associated with patient outcomes. <b>Results</b>: After a 6-month follow-up, 44 (61.1%) patients survived, 28 (38.9%) patients died, and one patient was lost to follow-up. The level of blood calcium and lactate, the presence of electroencephalography reactivity, and Glasgow Coma Scale (GCS) score were significantly associated with the patient’s outcome. Based on the regression coefficients from logistic regression analysis, we constructed a scoring system (CEGL; C: calcium, E: EEG reactivity, G: GCS, L: lactate) to predict the possibility of a patient’s death. The area under the receiver operating characteristic curve was 0.91 (P &lt; 0.001, 95% CI [0.87–0.95]) with a specificity of 97.7% and a positive predictive value of 97.4%. <b>Conclusion:</b> CEGL score can provide clinicians useful information for assessment of patient prognosis within 6 months after HIE.
DOI: 10.6084/m9.figshare.21153778.v1
title: Additional file 2 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 2. Clinical Information of the Subjects.
DOI: 10.6084/m9.figshare.21153781.v1
title: Additional file 3 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 3. Specimen Information and Sequencing Methods.
DOI: 10.6084/m9.figshare.21153787
title: Additional file 5 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 5. Statistical Analysis Conducted in this Study.
DOI: 10.6084/m9.figshare.12853637.v1
title: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon

description: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon
DOI: 10.6084/m9.figshare.12853637.v2
title: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon

description: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon
DOI: 10.6084/m9.figshare.12853637.v3
title: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon

description: Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon
DOI: 10.6084/m9.figshare.21153778
title: Additional file 2 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 2. Clinical Information of the Subjects.
DOI: 10.6084/m9.figshare.21153781
title: Additional file 3 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 3. Specimen Information and Sequencing Methods.
DOI: 10.6084/m9.figshare.21153784.v1
title: Additional file 4 of Gene mutations in sporadic lymphangioleiomyomatosis and genotype–phenotype correlation analysis

description: Additional file 4. Mutation Content Detected in this Study.
DOI: 10.6084/m9.figshare.12853646
title: Non-walled spherical <i>Acinetobacter baumannii</i> is an important type of persister upon <i>β</i>-lactam antibiotic treatment

description: Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in <i>Acinetobacter baumannii</i> survived from the treatment by three major classes of antibiotics (i.e. <i>β</i>-lactam, aminoglycoside, and fluoroquinolone) with microcopy and found that a fraction of enlarged spherical bacteria constitutes a major sub-population of bacterial survivors from <i>β</i>-lactam antibiotic treatment, whereas survivors from the treatment of aminoglycoside and fluoroquinolone were less changed morphologically. Further studies showed that these spherical bacteria had completely lost their cell wall structures but could survive without any osmoprotective reagent. The spherical bacteria were not the viable-but-non-culturable cells and they could revive upon the removal of <i>β</i>-lactam antibiotics. Importantly, these non-walled spherical bacteria also persisted during antibiotic therapy <i>in vivo</i> using <i>Galleria mellonella</i> as the infection model. Additionally, the combinational treatment on <i>A. baumannii</i> by <i>β</i>-lactam and membrane-targeting antibiotic significantly enhanced the killing efficacy. Our results indicate that in addition to the dormant, structure intact persisters, the non-wall spherical bacterium is another important type of persister in <i>A. baumannii.</i> The finding suggests that targeting the bacterial cell membrane during <i>β</i>-lactam chemotherapy could enhance therapeutic efficacy on <i>A. baumannii</i> infection, which might also help to reduce the resistance development of <i>A. baumannii</i>.
DOI: 10.6084/m9.figshare.12853646.v2
title: Non-walled spherical <i>Acinetobacter baumannii</i> is an important type of persister upon <i>β</i>-lactam antibiotic treatment

description: Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in <i>Acinetobacter baumannii</i> survived from the treatment by three major classes of antibiotics (i.e. <i>β</i>-lactam, aminoglycoside, and fluoroquinolone) with microcopy and found that a fraction of enlarged spherical bacteria constitutes a major sub-population of bacterial survivors from <i>β</i>-lactam antibiotic treatment, whereas survivors from the treatment of aminoglycoside and fluoroquinolone were less changed morphologically. Further studies showed that these spherical bacteria had completely lost their cell wall structures but could survive without any osmoprotective reagent. The spherical bacteria were not the viable-but-non-culturable cells and they could revive upon the removal of <i>β</i>-lactam antibiotics. Importantly, these non-walled spherical bacteria also persisted during antibiotic therapy <i>in vivo</i> using <i>Galleria mellonella</i> as the infection model. Additionally, the combinational treatment on <i>A. baumannii</i> by <i>β</i>-lactam and membrane-targeting antibiotic significantly enhanced the killing efficacy. Our results indicate that in addition to the dormant, structure intact persisters, the non-wall spherical bacterium is another important type of persister in <i>A. baumannii.</i> The finding suggests that targeting the bacterial cell membrane during <i>β</i>-lactam chemotherapy could enhance therapeutic efficacy on <i>A. baumannii</i> infection, which might also help to reduce the resistance development of <i>A. baumannii</i>.
DOI: 10.5281/zenodo.10630039
title: Supplementary dataset for: Carbonate Clumped Isotope Constraints on Early Triassic NeoTethyan Seawater Oxygen Isotope Compositions and Temperatures

description: The dataset includes data generated for the study titled: Carbonate Clumped Isotope Constraints on Early Triassic NeoTethyan Seawater Oxygen Isotope Compositions and Temperatures

The Excel file includes 



Clumped isotope data for analyzed brachiopod calcites, bulk rock micrite, as well as analytical standards (Tables S1 and S2).

Rare Earth element concentration data for brachiopod samples analyzed (Table S3)

Element/Ca ratios for analyzed samples (Table S4).
DOI: 10.5281/zenodo.10653115
title: Supplementary dataset for: Carbonate Clumped Isotope Constraints on Early Triassic NeoTethyan Seawater Oxygen Isotope Compositions and Temperatures

description: The dataset includes data generated for the study titled: Carbonate Clumped Isotope Constraints on Early Triassic NeoTethyan Seawater Oxygen Isotope Compositions and Temperatures

The Excel file includes 



Clumped isotope data for analyzed brachiopod calcites, bulk rock micrite, as well as analytical standards (Tables S1 and S2).

Rare Earth element concentration data for brachiopod samples analyzed (Table S3)

Element/Ca ratios for analyzed samples (Table S4).