cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14597834.v1
title: Rice Ferredoxins localize to chloroplasts/plastids and may function in different tissues

description: Ferredoxins (Fds) play a unique and important role in photosynthetic electron transport. Recently, we characterized the function of Fd1 in rice (<i>Oryza sativa</i> L.), showing that Fd1 is the primary photosynthetic electron transport protein and that Fd1 participates in carbon assimilation. However, the subcellular localization and specific functions of other Fds in rice are not yet fully understood. Here, our subcellular localization analysis of the seven Fds in rice showed that they are located in the chloroplasts of photosynthetic tissues and the plastids of non-photosynthetic tissues. Moreover, qRT-PCR indicated that <i>Fd1</i> transcript levels were highest in photosynthetic tissues, while <i>Fd4</i> transcript levels were highest in non-photosynthetic tissues. Collectively, our results suggest that rice Fds are located in chloroplasts/plastids, but may function in different tissues, and Fd4 may be a non-photosynthetic type Fd.
DOI: 10.6084/m9.figshare.7257806
title: Additional file 16: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S10. Plastid associated differentially expressed proteins in rel1-D. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7257806.v1
title: Additional file 16: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S10. Plastid associated differentially expressed proteins in rel1-D. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7257815
title: Additional file 3: of Alternative polyadenylation factors link cell cycle to migration

description: Alternative isoform use with quiescence. (XLS 1401Â kb)
DOI: 10.6084/m9.figshare.7257815.v1
title: Additional file 3: of Alternative polyadenylation factors link cell cycle to migration

description: Alternative isoform use with quiescence. (XLS 1401Â kb)
DOI: 10.6084/m9.figshare.7257839
title: Additional file 5: of Alternative polyadenylation factors link cell cycle to migration

description: Alternative splicing with quiescence. (XLSX 136Â kb)
DOI: 10.6084/m9.figshare.7257839.v1
title: Additional file 5: of Alternative polyadenylation factors link cell cycle to migration

description: Alternative splicing with quiescence. (XLSX 136Â kb)
DOI: 10.6084/m9.figshare.7257848
title: Additional file 6: of Alternative polyadenylation factors link cell cycle to migration

description: Gene Ontology for alternative splicing. (XLSX 520Â kb)
DOI: 10.6084/m9.figshare.7257848.v1
title: Additional file 6: of Alternative polyadenylation factors link cell cycle to migration

description: Gene Ontology for alternative splicing. (XLSX 520Â kb)
DOI: 10.6084/m9.figshare.7257860
title: Additional file 7: of Alternative polyadenylation factors link cell cycle to migration

description: Polaydenylation site use with quiescence. (XLS 194Â kb)
DOI: 10.6084/m9.figshare.7257860.v1
title: Additional file 7: of Alternative polyadenylation factors link cell cycle to migration

description: Polaydenylation site use with quiescence. (XLS 194Â kb)
DOI: 10.6084/m9.figshare.9879305
title: T cells expressing CD26-specific chimeric antigen receptors exhibit extensive self-antigen-driven fratricide

description: <b>Background:</b> Immunotherapy utilizing T cells genetically modified to express chimeric antigen receptors (CARs) is rapidly emerging as a promising novel treatment for hematological and nonhematological malignancies. In order to target the TKI-insensitive leukemia stem cells (LSCs) in chronic myeloid leukemia (CML) by CAR T cells, we chose CD26 as a cell surface tumor-associated antigen due to preferentially expression on LSCs. Additionally, CD26 has also been suggested to be a multipurpose therapeutic target for other cancer. Therefore, developing the CD26-targeting CAR T cells may be a promising therapy for not only LSCs but also other CD26+ cancer cells. <b>Methods:</b> We designed the second-generation CD26-targeting CAR utilizing 4-1BB (CD137) as costimulatory domain, and transduced T cells with CD26-CAR containing lentiviral. Then we evaluated the transduction efficiency and expansion ability, and demonstrated the existence of self-antigen-driven fratricide by cytokine assay and cytotoxicity assay. <b>Results:</b> Anti-CD26-4-1BB-CAR T cells exhibited poor viability, multiple cytokine secretion, down-regulation of CD26 and direct cytotoxicity against themselves, indicating self-antigen-driven fratricide. <b>Conclusion:</b> Eradicating CML-LSCs via anti-CD26-4-1BB-CAR T cells is not applicable, and optimized design or alternative target is needed.
DOI: 10.6084/m9.figshare.9879305.v1
title: T cells expressing CD26-specific chimeric antigen receptors exhibit extensive self-antigen-driven fratricide

description: <b>Background:</b> Immunotherapy utilizing T cells genetically modified to express chimeric antigen receptors (CARs) is rapidly emerging as a promising novel treatment for hematological and nonhematological malignancies. In order to target the TKI-insensitive leukemia stem cells (LSCs) in chronic myeloid leukemia (CML) by CAR T cells, we chose CD26 as a cell surface tumor-associated antigen due to preferentially expression on LSCs. Additionally, CD26 has also been suggested to be a multipurpose therapeutic target for other cancer. Therefore, developing the CD26-targeting CAR T cells may be a promising therapy for not only LSCs but also other CD26+ cancer cells. <b>Methods:</b> We designed the second-generation CD26-targeting CAR utilizing 4-1BB (CD137) as costimulatory domain, and transduced T cells with CD26-CAR containing lentiviral. Then we evaluated the transduction efficiency and expansion ability, and demonstrated the existence of self-antigen-driven fratricide by cytokine assay and cytotoxicity assay. <b>Results:</b> Anti-CD26-4-1BB-CAR T cells exhibited poor viability, multiple cytokine secretion, down-regulation of CD26 and direct cytotoxicity against themselves, indicating self-antigen-driven fratricide. <b>Conclusion:</b> Eradicating CML-LSCs via anti-CD26-4-1BB-CAR T cells is not applicable, and optimized design or alternative target is needed.
DOI: 10.6084/m9.figshare.7257869
title: Additional file 8: of Alternative polyadenylation factors link cell cycle to migration

description: Polyadenylation site use with quiescence for genes with more than two polyadenylation sites. (XLSX 537Â kb)
DOI: 10.6084/m9.figshare.7257869.v1
title: Additional file 8: of Alternative polyadenylation factors link cell cycle to migration

description: Polyadenylation site use with quiescence for genes with more than two polyadenylation sites. (XLSX 537Â kb)
DOI: 10.6084/m9.figshare.7257872
title: Additional file 5: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S2. Differentially expressed genes in rel1-D mutant. (XLSX 190Â kb)
DOI: 10.6084/m9.figshare.7257872.v1
title: Additional file 5: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S2. Differentially expressed genes in rel1-D mutant. (XLSX 190Â kb)
DOI: 10.6084/m9.figshare.7257893
title: Additional file 9: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S4. GO enrichment (Molecular Function) of the up-regulated DEGs in rel1-D. (XLSX 121Â kb)
DOI: 10.6084/m9.figshare.7257893.v1
title: Additional file 9: of Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid

description: Table S4. GO enrichment (Molecular Function) of the up-regulated DEGs in rel1-D. (XLSX 121Â kb)
DOI: 10.6084/m9.figshare.13025090
title: Complete chloroplast genome sequence of Convolvulus arvensis

description: The complete chloroplast genome of <i>Convolvulus arvensis</i> was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 153,234 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 22,662 bp each, a large single-copy region (LSC) of 89,059 bp and a small single-copy region (SSC) of 19,651 bp .
DOI: 10.6084/m9.figshare.15122280
title: Additional file 3 of A scoping review of registry captured indicators for evaluating quality of critical care in ICU

description: Additional file 3. Supplementary File 2: List of articles included in the review.
DOI: 10.6084/m9.figshare.15122331
title: Additional file 2 of Relationship between tectonism and desertification inferred from provenance and lithofacies changes in the Cenozoic terrestrial sequence of the southwestern Tarim Basin

description: Additional file 2.
DOI: 10.6084/m9.figshare.15122280.v1
title: Additional file 3 of A scoping review of registry captured indicators for evaluating quality of critical care in ICU

description: Additional file 3. Supplementary File 2: List of articles included in the review.
DOI: 10.6084/m9.figshare.7782329
title: Additional file 4: of Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation

description: Table S5. Up specific common DEGs of the two high regeneration lines in 5 clusters; Table S6. Down specific common DEGs of the two high regeneration lines in 5 clusters; Table S7. Up specific common DEGs of the two low regeneration lines in 5 clusters; Table S8. Down specific common DEGs of the two low regeneration lines in 5 clusters.). (XLSX 195 kb)
DOI: 10.6084/m9.figshare.7782329.v1
title: Additional file 4: of Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation

description: Table S5. Up specific common DEGs of the two high regeneration lines in 5 clusters; Table S6. Down specific common DEGs of the two high regeneration lines in 5 clusters; Table S7. Up specific common DEGs of the two low regeneration lines in 5 clusters; Table S8. Down specific common DEGs of the two low regeneration lines in 5 clusters.). (XLSX 195 kb)
DOI: 10.5281/zenodo.10694024
title: Single-cell approach dissecting agr quorum sensing dynamics in Staphylococcus aureus

description: Training data for the two StarDist2D models and the DeLTA 2.0 2D tracking model used in the publication on bioarxiv. The trained stardist models are included in the respective zip files of the training data. mm: mother-machine; cc: connected chamber. Each of them contains two folders, img and seg_label. They contain matching pairs of phasecontrast images (img) and label images (seg_label). 

 

tracking_set_subset.zip contains the training data for the DeLTA tracking model following the default folder structure. We used custom weight functions to create the training weight maps in the folder wei. The folder wei_bck contains weights generated with the original function.

The unet_pads_tracking.hdf5 is the retrained tracking model used in the associated publication.

See associated GitHub repository for example code on how to use the models for segmentation and tracking.

The four numbered zip files contain the data used to create all figures displaying image analysis output.

Abstract:

Staphylococcus aureus both colonizes humans and causes severe virulent infections. Virulence is regulated by the agr quorum sensing system and its autoinducing peptide (AIP), with dynamics at the single-cell level across four agr-types – each defined by distinct AIP sequences and capable of cross-inhibition – remaining elusive. Employing microfluidics, time-lapse microscopy, and deep-learning image analysis, we uncovered significant differences in AIP sensitivity among agr-types. We observed bimodal agr activation, attributed to intergenerational phenotypic stability and influenced by AIP concentration. Upon AIP stimulation, agr‑III showed AIP insensitivity, while agr‑II exhibited increased sensitivity and prolonged generation time. Beyond expected cross-inhibition of agr‑I by heterologous AIP‑II and ‑III, the presumably cross-activating AIP‑IV also inhibited agr‑I. Community interactions across different agr-type pairings revealed four main patterns: stable or switched dominance, and delayed or stable dual activation, influenced by community characteristics. These insights underscore the potential of personalized treatment strategies considering virulence and genetic diversity.
DOI: 10.5281/zenodo.10694025
title: Single-cell approach dissecting agr quorum sensing dynamics in Staphylococcus aureus

description: Training data for the two StarDist2D models and the DeLTA 2.0 2D tracking model used in the publication. The trained stardist models are included in the respective zip files of the training data. mm: mother-machine; cc: connected chamber. Each of them contains two folders, img and seg_label. They contain matching pairs of phasecontrast images (img) and label images (seg_label). 

tracking_set_subset.zip contains the training data for the DeLTA tracking model following the default folder structure. We used custom weight functions to create the training weight maps in the folder wei. The folder wei_bck contains weights generated with the original function.

The unet_pads_tracking.hdf5 is the retrained tracking model used in the associated publication.

See associated GitHub repository for example code on how to use the models for segmentation and tracking.

Abstract:

Staphylococcus aureus both colonizes humans and causes severe virulent infections. Virulence is regulated by the agr quorum sensing system and its autoinducing peptide (AIP), with dynamics at the single-cell level across four agr-types – each defined by distinct AIP sequences and capable of cross-inhibition – remaining elusive. Employing microfluidics, time-lapse microscopy, and deep-learning image analysis, we uncovered significant differences in AIP sensitivity among agr-types. We observed bimodal agr activation, attributed to intergenerational phenotypic stability and influenced by AIP concentration. Upon AIP stimulation, agr‑III showed AIP insensitivity, while agr‑II exhibited increased sensitivity and prolonged generation time. Beyond expected cross-inhibition of agr‑I by heterologous AIP‑II and ‑III, the presumably cross-activating AIP‑IV also inhibited agr‑I. Community interactions across different agr-type pairings revealed four main patterns: stable or switched dominance, and delayed or stable dual activation, influenced by community characteristics. These insights underscore the potential of personalized treatment strategies considering virulence and genetic diversity.
DOI: 10.5281/zenodo.10720439
title: Single-cell approach dissecting agr quorum sensing dynamics in Staphylococcus aureus

description: Training data for the two StarDist2D models and the DeLTA 2.0 2D tracking model used in the publication on bioarxiv. The trained stardist models are included in the respective zip files of the training data. mm: mother-machine; cc: connected chamber. Each of them contains two folders, img and seg_label. They contain matching pairs of phasecontrast images (img) and label images (seg_label). 

 

tracking_set_subset.zip contains the training data for the DeLTA tracking model following the default folder structure. We used custom weight functions to create the training weight maps in the folder wei. The folder wei_bck contains weights generated with the original function.

The unet_pads_tracking.hdf5 is the retrained tracking model used in the associated publication.

See associated GitHub repository for example code on how to use the models for segmentation and tracking.

The four numbered zip files contain the data used to create all figures displaying image analysis output.

Abstract:

Staphylococcus aureus both colonizes humans and causes severe virulent infections. Virulence is regulated by the agr quorum sensing system and its autoinducing peptide (AIP), with dynamics at the single-cell level across four agr-types – each defined by distinct AIP sequences and capable of cross-inhibition – remaining elusive. Employing microfluidics, time-lapse microscopy, and deep-learning image analysis, we uncovered significant differences in AIP sensitivity among agr-types. We observed bimodal agr activation, attributed to intergenerational phenotypic stability and influenced by AIP concentration. Upon AIP stimulation, agr‑III showed AIP insensitivity, while agr‑II exhibited increased sensitivity and prolonged generation time. Beyond expected cross-inhibition of agr‑I by heterologous AIP‑II and ‑III, the presumably cross-activating AIP‑IV also inhibited agr‑I. Community interactions across different agr-type pairings revealed four main patterns: stable or switched dominance, and delayed or stable dual activation, influenced by community characteristics. These insights underscore the potential of personalized treatment strategies considering virulence and genetic diversity.
DOI: 10.6084/m9.figshare.19316700
title: Characterization and distribution of HIV-infected cells in semen

description: Semen is a known vector for both human immunodeficiency virus (HIV) infection and transmission. However, the distribution and characteristics of HIV-infected cells in semen remain unclear. Investigating the possibility of transmission through the spermatozoon in semen is of great clinical significance to improve the strategies for exposure prevention and assisted reproduction for HIV-infected partners. Twenty-six HIV-infected patients, including twelve treatment-naïve (TN) patients and fourteen antiretroviral treated (ART) patients, were enrolled in this study. HIV p24 protein in spermatozoa was detected using imaging flow cytometry and immunohistochemistry, and HIV RNA was identified using next-generation RNAscope <i>in situ</i> hybridization. Additionally, we described the rates of HIV-positive spermatozoon and CD4<sup>+</sup> T lymphocytes in semen, and found that p24<sup>+</sup> spermatozoon were mainly CD4 negative regardless of whether the patients received ART. Of note, p24-positive cells in semen are predominantly spermatozoa, and we confirmed that motile spermatozoa carried HIV into peripheral blood mononuclear cells of healthy men <i>in vitro</i>. Our findings provide evidence regarding the risk of HIV-infected spermatozoa.
DOI: 10.6084/m9.figshare.15122331.v1
title: Additional file 2 of Relationship between tectonism and desertification inferred from provenance and lithofacies changes in the Cenozoic terrestrial sequence of the southwestern Tarim Basin

description: Additional file 2.
DOI: 10.6084/m9.figshare.19316700.v2
title: Characterization and distribution of HIV-infected cells in semen

description: Semen is a known vector for both human immunodeficiency virus (HIV) infection and transmission. However, the distribution and characteristics of HIV-infected cells in semen remain unclear. Investigating the possibility of transmission through the spermatozoon in semen is of great clinical significance to improve the strategies for exposure prevention and assisted reproduction for HIV-infected partners. Twenty-six HIV-infected patients, including twelve treatment-naïve (TN) patients and fourteen antiretroviral treated (ART) patients, were enrolled in this study. HIV p24 protein in spermatozoa was detected using imaging flow cytometry and immunohistochemistry, and HIV RNA was identified using next-generation RNAscope <i>in situ</i> hybridization. Additionally, we described the rates of HIV-positive spermatozoon and CD4<sup>+</sup> T lymphocytes in semen, and found that p24<sup>+</sup> spermatozoon were mainly CD4 negative regardless of whether the patients received ART. Of note, p24-positive cells in semen are predominantly spermatozoa, and we confirmed that motile spermatozoa carried HIV into peripheral blood mononuclear cells of healthy men <i>in vitro</i>. Our findings provide evidence regarding the risk of HIV-infected spermatozoa.
DOI: 10.6084/m9.figshare.11452410
title: The traditional Chinese medicine formulation Ruanjian Sanjie Decoction regulates the tumor matrix and improves the anti-tumor efficacy of TP-PEG-LPs

description: The Ruanjian Sanjie Decoction (RSD) is a traditional Chinese medicine (TCM) formulation consisting of Spica Prunellae, Pseudobulbus Cremastrae Seu Pleiones, Concha Ostreae and Semen Coicis, and widely used as an adjuvant in anti-cancer therapy. The aim of this study was to determine the effects of RSD on the extracellular matrix (ECM) of tumors, and on the efficacy of anti-cancer nano-formulations in a tumor-bearing mouse model. The mice were treated with triptolide encapsulated in PEG-modified liposomes (TP-PEG-LPs), either alone or in combination with RSD. The combination treatment significantly retarded tumor growth relative to the untreated controls, indicating the potent adjuvant effect of RSD in targeted anti-cancer therapy. In addition, RSD also reduced the amount of total collagen and collagen I and increased that of collagen III in the tumor ECM, along with decreasing the expression of the pro-angiogenic VEGF. Finally, even high doses of RSD did not significantly affect the liver and kidney function or body weight, indicating low toxicity.
DOI: 10.6084/m9.figshare.11452410.v1
title: The traditional Chinese medicine formulation Ruanjian Sanjie Decoction regulates the tumor matrix and improves the anti-tumor efficacy of TP-PEG-LPs

description: The Ruanjian Sanjie Decoction (RSD) is a traditional Chinese medicine (TCM) formulation consisting of Spica Prunellae, Pseudobulbus Cremastrae Seu Pleiones, Concha Ostreae and Semen Coicis, and widely used as an adjuvant in anti-cancer therapy. The aim of this study was to determine the effects of RSD on the extracellular matrix (ECM) of tumors, and on the efficacy of anti-cancer nano-formulations in a tumor-bearing mouse model. The mice were treated with triptolide encapsulated in PEG-modified liposomes (TP-PEG-LPs), either alone or in combination with RSD. The combination treatment significantly retarded tumor growth relative to the untreated controls, indicating the potent adjuvant effect of RSD in targeted anti-cancer therapy. In addition, RSD also reduced the amount of total collagen and collagen I and increased that of collagen III in the tumor ECM, along with decreasing the expression of the pro-angiogenic VEGF. Finally, even high doses of RSD did not significantly affect the liver and kidney function or body weight, indicating low toxicity.
DOI: 10.6084/m9.figshare.14073984
title: Identification and validation of a new gene signature predicting prognosis of hepatocellular carcinoma patients by network analysis of stemness indices

description: <b>Background</b>: Stem cells play an important role in hepatocellular carcinoma (HCC). However, their precise effect on HCC tumorigenesis and progression remains unclear. The present study aimed to characterize stem cell-related gene expression in HCC. <b>Methods</b>: The mRNA expression-based stemness index (mRNAsi) was used to analyze the clinical characteristics and prognosis of HCC patients. The weighted gene co-expression network analysis (WGCNA) was used to construct a gene co-expression network of 374 HCC patients. Finally, six genes were used to construct the prognosis signature. <b>Results</b>: HCC patients had a higher mRNAsi score than healthy people, suggesting poor prognosis. Two gene modules highly related to mRNAsi were identified. Multivariate Cox analysis was carried out to establish a Cox proportional risk regression model. The risk score for each patient was the sum of the product of each gene expression and its coefficient. Survival analysis suggested that the low-risk group had a significantly better prognosis. <b>Conclusions</b>: The established six-gene signature was able to predict patient prognosis accurately. This new signature should be verified in prospective studies in order to determine patient prognosis in clinical decision-making.