cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23736001
title: COVID-19 of differing severity: from bulk to single-cell expression data analysis

description: Coronavirus disease 2019 (COVID-19) is raging worldwide and causes an immense disease burden. Despite this, the biomarkers and targeting drugs of COVID-19 of differing severity remain largely unknown. Based on the GSE164805 dataset, we identified modules most critical for mild COVID-19 (mCOVID-19) and severe COVID-19 (sCOVID-19) through WGCNA, respectively. We subsequently constructed a protein–protein interaction network, and detected 16 hub genes for mCOVID-19 and 10 hub genes for sCOVID-19, followed by the prediction of upstream transcription factors (TFs) and kinases. The enrichment analysis then showed downregulation of TNFA signaling via NFKB for mCOVID-19, as well as downregulation of MYC targets V1 for sCOVID-19. Infiltration degrees of many immune cells, such as macrophages, were also sharply different between mCOVID-19 and sCOVID-19 samples. Predicted protein targeting drugs with the highest scores nearly all belong to naturally derived or synthetic glucocorticoids. For the two single-cell RNA-seq datasets, we explored the expression distribution of hub genes for mCOVID-19/sCOVID-19 in each cell type. The expression levels of PRKCA, MCM5, TYMS, RBBP4, BCL6, FLOT1, KDM6B, and TLR2 were found to be cell-type-specific. Furthermore, the expression levels of 10 hub genes for mCOVID-19 were significantly upregulated in PBMCs between eight healthy controls and eight mCOVID-19 patients at our institution. Collectively, we detected critical modules, pathways, TFs, kinases, immune cells, targeting drugs, hub genes, and their expression distributions in different cell types that may involve the pathogenesis of COVID-19 of differing severity, which may propel earlier diagnosis and more effective treatment of this intractable disease in the future.
DOI: 10.6084/m9.figshare.23736001.v1
title: COVID-19 of differing severity: from bulk to single-cell expression data analysis

description: Coronavirus disease 2019 (COVID-19) is raging worldwide and causes an immense disease burden. Despite this, the biomarkers and targeting drugs of COVID-19 of differing severity remain largely unknown. Based on the GSE164805 dataset, we identified modules most critical for mild COVID-19 (mCOVID-19) and severe COVID-19 (sCOVID-19) through WGCNA, respectively. We subsequently constructed a protein–protein interaction network, and detected 16 hub genes for mCOVID-19 and 10 hub genes for sCOVID-19, followed by the prediction of upstream transcription factors (TFs) and kinases. The enrichment analysis then showed downregulation of TNFA signaling via NFKB for mCOVID-19, as well as downregulation of MYC targets V1 for sCOVID-19. Infiltration degrees of many immune cells, such as macrophages, were also sharply different between mCOVID-19 and sCOVID-19 samples. Predicted protein targeting drugs with the highest scores nearly all belong to naturally derived or synthetic glucocorticoids. For the two single-cell RNA-seq datasets, we explored the expression distribution of hub genes for mCOVID-19/sCOVID-19 in each cell type. The expression levels of PRKCA, MCM5, TYMS, RBBP4, BCL6, FLOT1, KDM6B, and TLR2 were found to be cell-type-specific. Furthermore, the expression levels of 10 hub genes for mCOVID-19 were significantly upregulated in PBMCs between eight healthy controls and eight mCOVID-19 patients at our institution. Collectively, we detected critical modules, pathways, TFs, kinases, immune cells, targeting drugs, hub genes, and their expression distributions in different cell types that may involve the pathogenesis of COVID-19 of differing severity, which may propel earlier diagnosis and more effective treatment of this intractable disease in the future.
DOI: 10.6084/m9.figshare.23207835
title: Additional file 6 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.23207835.v1
title: Additional file 6 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.23207829
title: Additional file 4 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.23207832
title: Additional file 5 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.23207832.v1
title: Additional file 5 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.23207838.v1
title: Additional file 7 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.7479203
title: Additional file 11: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S9. The analysis of DEGs in FCd/SCd with an FPKM value ≥10 in at least one of four cDNA libraries and |log2 (FCd/SCd)| ≥ 3. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7479203.v1
title: Additional file 11: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S9. The analysis of DEGs in FCd/SCd with an FPKM value ≥10 in at least one of four cDNA libraries and |log2 (FCd/SCd)| ≥ 3. (XLSX 41 kb)
DOI: 10.5281/zenodo.10598390
title: Data: An experimental sound exposure study at sea: No spatial deterrence of free-ranging pelagic fish

description: Data abstract:

All data and scripts to replicate all plots and statistical results of the paper mentioned below. The data are sound recordings and processed echosounder data (raw echosounder data is available on request but > 100 GB in size and require specialized software).

 

Paper reference:

Jeroen Hubert, Jozefien M. Demuynck, M. Rafa Remmelzwaal, Carlota Muñiz, Elisabeth Debusschere, Benoit Berges, Hans Slabbekoorn; An experimental sound exposure study at sea: No spatial deterrence of free-ranging pelagic fish. J. Acoust. Soc. Am. 1 February 2024; 155 (2): 1151–1161. https://doi.org/10.1121/10.0024720

 

Paper abstract:

Acoustic deterrent devices are used to guide aquatic animals from danger or toward migration paths. At sea, moderate sounds can potentially be used to deter fish to prevent injury or death due to acoustic overexposure. In sound exposure studies, acoustic features can be compared to improve deterrence efficacy. In this study, we played 200–1600 Hz pulse trains from a drifting vessel and investigated changes in pelagic fish abundance and behavior by utilizing echosounders and hydrophones mounted to a transect of bottom-moored frames. We monitored fish presence and tracked individual fish. This revealed no changes in fish abundance or behavior, including swimming speed and direction of individuals, in response to the sound exposure. We did find significant changes in swimming depth of individually tracked fish, but this could not be linked to the sound exposures. Overall, the results clearly show that pelagic fish did not flee from the current sound exposures, and we found no clear changes in behavior due to the sound exposure. We cannot rule out that different sounds at higher levels elicit a deterrence response; however, it may be that pelagic fish are just more likely to respond to sound with (short-lasting) changes in school formation.
DOI: 10.5281/zenodo.10598391
title: Data: An experimental sound exposure study at sea: No spatial deterrence of free-ranging pelagic fish

description: Data abstract:

All data and scripts to replicate all plots and statistical results of the paper mentioned below. The data are sound recordings and processed echosounder data (raw echosounder data is available on request but > 100 GB in size and require specialized software).

 

Paper reference:

Jeroen Hubert, Jozefien M. Demuynck, M. Rafa Remmelzwaal, Carlota Muñiz, Elisabeth Debusschere, Benoit Berges, Hans Slabbekoorn; An experimental sound exposure study at sea: No spatial deterrence of free-ranging pelagic fish. J. Acoust. Soc. Am. 1 February 2024; 155 (2): 1151–1161. https://doi.org/10.1121/10.0024720

 

Paper abstract:

Acoustic deterrent devices are used to guide aquatic animals from danger or toward migration paths. At sea, moderate sounds can potentially be used to deter fish to prevent injury or death due to acoustic overexposure. In sound exposure studies, acoustic features can be compared to improve deterrence efficacy. In this study, we played 200–1600 Hz pulse trains from a drifting vessel and investigated changes in pelagic fish abundance and behavior by utilizing echosounders and hydrophones mounted to a transect of bottom-moored frames. We monitored fish presence and tracked individual fish. This revealed no changes in fish abundance or behavior, including swimming speed and direction of individuals, in response to the sound exposure. We did find significant changes in swimming depth of individually tracked fish, but this could not be linked to the sound exposures. Overall, the results clearly show that pelagic fish did not flee from the current sound exposures, and we found no clear changes in behavior due to the sound exposure. We cannot rule out that different sounds at higher levels elicit a deterrence response; however, it may be that pelagic fish are just more likely to respond to sound with (short-lasting) changes in school formation.
DOI: 10.6084/m9.figshare.23207838
title: Additional file 7 of Identification of two novel lipid metabolism-related long non-coding RNAs (SNHG17 and LINC00837) as potential signatures for osteosarcoma prognosis and precise treatment

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.7479209
title: Additional file 13: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S11. The seven expression patterns of transport-related DEGs in two peanut cultivars under Cd-free and Cd-treated. Items highlighted in red mean up-regulated, while in green mean down-regulated. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.16916376.v1
title: Additional file 2 of Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

description: Additional file 2. Expression data of all assembled genes of B. striata.
DOI: 10.6084/m9.figshare.7479212.v1
title: Additional file 14: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S12. The DEGs involved in cell wall metabolism and Cd chelating in two peanut cultivars. Items highlighted in red mean up-regulated, while in green mean down-regulated. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.16916373.v1
title: Additional file 1 of Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

description: Additional file 1. Annotations of all assembled genes of B. striata.
DOI: 10.6084/m9.figshare.16916376
title: Additional file 2 of Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

description: Additional file 2. Expression data of all assembled genes of B. striata.
DOI: 10.6084/m9.figshare.7479218.v1
title: Additional file 15: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S13. The primers used in RT-qPCR analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.14823138
title: Data File 1

description: Data File 1 for Organelle-specific phase contrast microscopy enables gentle monitoring and analysis of mitochondrial network dynamicshttps://doi.org/10.1364/BOE.425848<br>
DOI: 10.6084/m9.figshare.24784629
title: Additional file 1 of Germplasm characterization and SDS-PAGE analysis of caper (Capparis spinosa L.) from different provenances

description: Additional file 1: Table S1.1 is the first supplementary document to Table 1 in the main text. Table S1.2. is the second supplementary document to Table 1 in the main text. Table S2. is the supplementary document to Table 2 in the main text.
DOI: 10.6084/m9.figshare.24784629.v1
title: Additional file 1 of Germplasm characterization and SDS-PAGE analysis of caper (Capparis spinosa L.) from different provenances

description: Additional file 1: Table S1.1 is the first supplementary document to Table 1 in the main text. Table S1.2. is the second supplementary document to Table 1 in the main text. Table S2. is the supplementary document to Table 2 in the main text.
DOI: 10.6084/m9.figshare.23207839.v1
title: Additional file 1 of METTL3 and STAT3 form a positive feedback loop to promote cell metastasis in hepatocellular carcinoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.23207842.v1
title: Additional file 2 of METTL3 and STAT3 form a positive feedback loop to promote cell metastasis in hepatocellular carcinoma

description: Additional file 2.
DOI: 10.6084/m9.figshare.23207851
title: Additional file 5 of METTL3 and STAT3 form a positive feedback loop to promote cell metastasis in hepatocellular carcinoma

description: Additional file 5.
DOI: 10.6084/m9.figshare.23207839
title: Additional file 1 of METTL3 and STAT3 form a positive feedback loop to promote cell metastasis in hepatocellular carcinoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.23207848
title: Additional file 4 of METTL3 and STAT3 form a positive feedback loop to promote cell metastasis in hepatocellular carcinoma

description: Additional file 4.
DOI: 10.6084/m9.figshare.24784659
title: Additional file 4 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 4: Supplementary Table 1. Data filtering statistics.
DOI: 10.6084/m9.figshare.24784659.v1
title: Additional file 4 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 4: Supplementary Table 1. Data filtering statistics.
DOI: 10.6084/m9.figshare.24784662
title: Additional file 5 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 5: Supplementary Table 2. Statistical of base information.
DOI: 10.6084/m9.figshare.24784662.v1
title: Additional file 5 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 5: Supplementary Table 2. Statistical of base information.
DOI: 10.6084/m9.figshare.7479224.v1
title: Additional file 2: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S2. Mapping results of clean reads against the peanut reference sequence. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7479218
title: Additional file 15: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S13. The primers used in RT-qPCR analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7479227.v1
title: Additional file 3: of Comparative transcriptome analysis revealed key factors for differential cadmium transport and retention in roots of two contrasting peanut cultivars

description: Table S3. Summary of novel transcripts. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.16916373
title: Additional file 1 of Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

description: Additional file 1. Annotations of all assembled genes of B. striata.
DOI: 10.6084/m9.figshare.25204922
title: Brucite formation during the serpentinization processes

description: Data for brucite formation during the serpentinization processes
DOI: 10.6084/m9.figshare.25204922.v1
title: Brucite formation during the serpentinization processes

description: Data for brucite formation during the serpentinization processes
DOI: 10.6084/m9.figshare.24784665
title: Additional file 6 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 6: Supplementary Table 3. The statistical of mapping reference genome.
DOI: 10.6084/m9.figshare.24784665.v1
title: Additional file 6 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 6: Supplementary Table 3. The statistical of mapping reference genome.
DOI: 10.6084/m9.figshare.24784668
title: Additional file 7 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 7: Supplementary Table 4. The mapping region statistics.
DOI: 10.6084/m9.figshare.24784668.v1
title: Additional file 7 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 7: Supplementary Table 4. The mapping region statistics.
DOI: 10.6084/m9.figshare.24784671
title: Additional file 8 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 8: Supplementary Table 5. Identification of metabolites.
DOI: 10.6084/m9.figshare.24784671.v1
title: Additional file 8 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 8: Supplementary Table 5. Identification of metabolites.
DOI: 10.6084/m9.figshare.24784677
title: Additional file 9 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 9: Supplementary Table 6. The correlation analysis list of DEGs and DAMs.
DOI: 10.6084/m9.figshare.24784677.v1
title: Additional file 9 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 9: Supplementary Table 6. The correlation analysis list of DEGs and DAMs.
DOI: 10.6084/m9.figshare.24784680
title: Additional file 10 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 10: Supplementary Table 7. The correlation matrix of 23 DAMs and 118 DEGs.
DOI: 10.6084/m9.figshare.24784680.v1
title: Additional file 10 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 10: Supplementary Table 7. The correlation matrix of 23 DAMs and 118 DEGs.
DOI: 10.6084/m9.figshare.24784683
title: Additional file 11 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 11: Supplementary Table 8. The WRKY40 transcription factor targets predicted.
DOI: 10.6084/m9.figshare.24784683.v1
title: Additional file 11 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 11: Supplementary Table 8. The WRKY40 transcription factor targets predicted.
DOI: 10.6084/m9.figshare.24784686
title: Additional file 12 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 12: Supplementary Table 9. The gene expression patten in phenylpropanoid biosynthesis pathways.
DOI: 10.6084/m9.figshare.24784686.v1
title: Additional file 12 of Transcriptomic and metabolomic analyses reveals keys genes and metabolic pathways in tea (Camellia sinensis) against six-spotted spider mite (Eotetranychus Sexmaculatus)

description: Additional file 12: Supplementary Table 9. The gene expression patten in phenylpropanoid biosynthesis pathways.
DOI: 10.6084/m9.figshare.24260475
title: Development of a CFD model indicating the quantitative relationship among reactor dimension, bed flow unevenness, and performance for VOCs biofilters

description: This study presents a Computational Fluid Dynamics (CFD) based biofiltration model to investigate the airflow distribution and the impact of bed flow unevenness (BFU) on the removal of Volatile Organic Compounds (VOCs) in biofilters. The biofiltration model consists of a gas flow sub-model and a VOCs removal sub-model, which were validated by pilot-scale experiments. The model was used to examine the quantitative relationship among reactor dimensions, including the width to height ratio of the filter bed and empty bed residence time (EBRT), BFU, and performance for VOCs biofilters. Simulation results demonstrate that the flow unevenness index (FUI) of the packing layer changes from 0.06 to 0.48 m<sup>2</sup>‧s<sup>−1</sup> with reactor dimension changes. With an increase in the width to height ratio at a constant EBRT, FUI increases, BFU changes, and flow velocity fluctuation on the cross-section becomes larger, leading to a reduction of about 10% in VOCs removal efficiency. Concentration distribution of VOCs becomes uneven in the horizontal direction. At a constant width to height ratio of the filter bed, an increase in EBRT causes an increase in FUI, leading to a decrease in VOCs removal efficiency. When the width to height ratio is 0.5, velocity fluctuation of filter bed cross-section is small, the concentration of VOCs decreases evenly across the filter bed layer, and FUI is at a low level (0.06–0.11 m<sup>2</sup>‧s<sup>−1</sup>). <i>Implication</i>: In this manuscript, a biofiltration model of VOCs biofilter based on CFD has constructed and validated. And the manuscript gave the quantitative relationship among reactor dimension, bed flow unevenness and performance for VOCs biofilters for the first time. This study can lead to enhanced VOCs removal efficiency and improved overall performance of biofilters in practical engineering applications.