cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14936496.v1
title: Additional file 3 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 3: Supplement Table 3. Parameter values of the common differentially expressed genes
DOI: 10.5281/zenodo.10589257
title: Data and Codes for PNAS 2024: Atmosphere teleconnections from abatement of China aerosol emissions exacerbate Northeast Pacific warm blob events

description: Processed Data and figure codes for PNAS 2024
DOI: 10.5281/zenodo.10589258
title: Data and Codes for PNAS 2024: Atmosphere teleconnections from abatement of China aerosol emissions exacerbate Northeast Pacific warm blob events

description: Processed Data and figure codes for PNAS 2024
DOI: 10.5281/zenodo.10648518
title: Data and Codes for PNAS 2024: Atmosphere teleconnections from abatement of China aerosol emissions exacerbate Northeast Pacific warm blob events

description: Processed Data and figure codes for PNAS 2024
DOI: 10.6084/m9.figshare.14331667
title: Additional file 1 of Let-7i-5p enhances cell proliferation, migration and invasion of ccRCC by targeting HABP4

description: Additional file 1: Supplementary Table S1: The let‑7i‑5p expression data and clinical information of ccRCC patients.
DOI: 10.6084/m9.figshare.14936496
title: Additional file 3 of Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer

description: Additional file 3: Supplement Table 3. Parameter values of the common differentially expressed genes
DOI: 10.6084/m9.figshare.6991994
title: Two independent grain-length mutants mapped to a single region on the long arm of chromosome 2 in rice

description: ABSTRACT Grain shape in rice is a key determinant of grain appearance, yield and market value, and thus has been widely studied. Rice mutant lines with long-grain phenotypes were previously isolated from an M2 population derived from mutagenized mature pollen grains that were treated with gamma-ray irradiation for a cultivar Ma85. To understand the genetic basis underlying the long-grain trait, two mutant lines, JF171 and JF178, were crossed with the short-grain parents JF222 and Samba, generating three F2 populations. Molecular marker-based genetic analysis was employed to detect the major QTLs that affected grain length, grain width, length-to-width ratio and grain weight. Based on the data obtained for the three populations, a joint major QTL for grain length was mapped to a 4.7 Mb region between the SSR makers RM263 and RM318 on the long arm of chromosome 2. The results suggested that the two independent mutations contained in JF171 and JF178 are likely due to alterations in the same genetic region. Furthermore, we developed a BC2F2 population using JF178 and Samba and narrowed the region to 0.6 Mb. The results of the current study will be helpful to reveal the genetic basis of the above long-grain mutant lines. In general, our results provide solid genetic data to identify the unknown gene that affects grain length by map-based cloning and practice marker-assisted breeding for long-grain rice cultivars.
DOI: 10.6084/m9.figshare.6991823
title: Improving Antioxidant Activity of Ophioglossum thermale Kom. by Fermentation with Talaromyces purpurogenus M18-11

description: Ophioglossum thermale Kom. was fermented with several fungi. The total phenolic and flavonoid contents (TPCs and TFCs) and antioxidant activities of fermented and non-fermented O. thermale (FOT and NFOT) were investigated. The results showed that Talaromyces purpurogenus M18-11 fermented O. thermale possessed significantly improved TPC and TFC and exhibited significantly stronger 1,1-diphenyl-2-picrylhydrazyl (DPPH) (half maximal inhibitory concentration (IC50) = 75.7 ± 2.1 μg mL-1) and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) (IC50 = 20.52 ± 1.68 μg mL-1) free-radical scavenging activities, ferric reducing antioxidant power (0.585 ± 0.045 mmol g-1), and reducing power (half maximal effective concentration (EC50) = 30.52 ± 1.91 μg mL-1) than original material. The determination of the contents of representative flavonoids and their glucosides revealed that the improvements are attributed to the hydrolysis of homoisoflavonoid and flavonoid glucosides, glycometabolism, as well as fungal metabolites. This paper is the first to report the fermentation of O. thermale with pure strains and T. purpurogenus is an effective strain to process O. thermale for improving the antioxidant activity.
DOI: 10.6084/m9.figshare.20098819.v1
title: Additional file 3 of Patterns of human social contact and mask wearing in high-risk groups in China

description: Additional file 3: Table S2. Proportion of participants had gone to the seven places (school/workplace, public transportation, training institution, outdoor public space, non-enclosed indoor public space, enclosed indoor public space and medical place) in the last month stratified by provinces and occupations.
DOI: 10.6084/m9.figshare.6992273.v1
title: Detection and identification of huwentoxin-IV interacting proteins by biotin-avidin chemistry combined with mass spectrometry

description: Background : Numerous spider toxins are of interest as tools for neurophysiological research or as lead molecules for the development of pharmaceuticals and insecticides. Direct detection and identification of the interacting proteins of a spider toxin are helpful for its action-mechanism analysis and practical application. The present study employed a combinative strategy for the analysis of interacting proteins of huwentoxin-IV (HWTX-IV), a peptidic neurotoxin from the venom of the spiderSelenocosmia huwena.Results : HWTX-IV was first lightly labeled with biotin under the optimized mild experimental conditions and the toxin labeled with a single biotin group (monobiotinylated HWTX-IV) was demonstrated by electrophysiological experiments to retain its original bioactivity and was used in combination with far-western blotting to detect its interacting proteins. Comparative experiments indicated that some membrane proteins from rat neuromuscular junction preparations bind to monobiotinylated HWTX-IV after being transferred onto a PVDF membrane from the SDS-gel. With capillary high performance liquid chromatography-tandem mass spectrometry, several membrane proteins with which HWTX-IV potentially interacted were identified from the preparations and then bioinformatically analyzed.Conclusions : This work has provided not only a new insight into the action mechanism of HWTX-IV but also a reference technology for the relevant researches.
DOI: 10.6084/m9.figshare.14331660.v1
title: Additional file 2 of Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study

description: Additional file 2: Table S1. Grid search report for the threshold optimization in the threshold-based tumour-first aggregation method.
DOI: 10.6084/m9.figshare.14331663
title: Additional file 3 of Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study

description: Additional file 3: Table S2. TCGA image data of 422 lung samples used in this study.
DOI: 10.6084/m9.figshare.14331663.v1
title: Additional file 3 of Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study

description: Additional file 3: Table S2. TCGA image data of 422 lung samples used in this study.
DOI: 10.6084/m9.figshare.6991823.v1
title: Improving Antioxidant Activity of Ophioglossum thermale Kom. by Fermentation with Talaromyces purpurogenus M18-11

description: Ophioglossum thermale Kom. was fermented with several fungi. The total phenolic and flavonoid contents (TPCs and TFCs) and antioxidant activities of fermented and non-fermented O. thermale (FOT and NFOT) were investigated. The results showed that Talaromyces purpurogenus M18-11 fermented O. thermale possessed significantly improved TPC and TFC and exhibited significantly stronger 1,1-diphenyl-2-picrylhydrazyl (DPPH) (half maximal inhibitory concentration (IC50) = 75.7 ± 2.1 μg mL-1) and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) (IC50 = 20.52 ± 1.68 μg mL-1) free-radical scavenging activities, ferric reducing antioxidant power (0.585 ± 0.045 mmol g-1), and reducing power (half maximal effective concentration (EC50) = 30.52 ± 1.91 μg mL-1) than original material. The determination of the contents of representative flavonoids and their glucosides revealed that the improvements are attributed to the hydrolysis of homoisoflavonoid and flavonoid glucosides, glycometabolism, as well as fungal metabolites. This paper is the first to report the fermentation of O. thermale with pure strains and T. purpurogenus is an effective strain to process O. thermale for improving the antioxidant activity.
DOI: 10.6084/m9.figshare.6467636
title: Investigating oxidation state-induced toxicity of PEGylated graphene oxide in ocular tissue using gene expression profiles

description: Graphene and its derivatives are widely used for a variety of industrial, biomedical, and environmental applications. However, the potential harm caused by exposure of the eyes to graphene-based nanomaterials is scarce. Given the potential for these materials to be used in multiple applications, there is a pressing need to evaluate their ocular toxicity, and understand the relationships between their physico-chemical properties and the resulting toxicity. In this study, the toxicity of PEGylated graphene oxide (PEG-GO) with differing oxidation levels and/or surface charges (positive, negative and neutral charge) was evaluated using two <i>in-vitro</i> models of the eye: primary human corneal epithelial cells and human retinal capillary endothelial cells. The results showed that oxidation level, but not surface charge, had a pivotal effect on the toxicity of graphene-based nanomaterials. Typically, PEG-GO sample with a higher oxidation level caused more serious cytotoxicity than those with a lower oxidation level. Furthermore, by analysis of global gene expression profiles, we found that the foremost cellular response to PEG-GO sample with a high oxidation level was the oxidative stress response. Next, via exploring the underlying molecular mechanism of oxidative stress-induced cytotoxicity, we showed that PEG-GO sample with a high degree of oxidation induced reactive oxygen species (ROS) via NDUFB9-mediated biological pathway. This work has significant implications for design of safe graphene-based nanomaterials for biomedical applications.
DOI: 10.6084/m9.figshare.6467636.v1
title: Investigating oxidation state-induced toxicity of PEGylated graphene oxide in ocular tissue using gene expression profiles

description: Graphene and its derivatives are widely used for a variety of industrial, biomedical, and environmental applications. However, the potential harm caused by exposure of the eyes to graphene-based nanomaterials is scarce. Given the potential for these materials to be used in multiple applications, there is a pressing need to evaluate their ocular toxicity, and understand the relationships between their physico-chemical properties and the resulting toxicity. In this study, the toxicity of PEGylated graphene oxide (PEG-GO) with differing oxidation levels and/or surface charges (positive, negative and neutral charge) was evaluated using two <i>in-vitro</i> models of the eye: primary human corneal epithelial cells and human retinal capillary endothelial cells. The results showed that oxidation level, but not surface charge, had a pivotal effect on the toxicity of graphene-based nanomaterials. Typically, PEG-GO sample with a higher oxidation level caused more serious cytotoxicity than those with a lower oxidation level. Furthermore, by analysis of global gene expression profiles, we found that the foremost cellular response to PEG-GO sample with a high oxidation level was the oxidative stress response. Next, via exploring the underlying molecular mechanism of oxidative stress-induced cytotoxicity, we showed that PEG-GO sample with a high degree of oxidation induced reactive oxygen species (ROS) via NDUFB9-mediated biological pathway. This work has significant implications for design of safe graphene-based nanomaterials for biomedical applications.
DOI: 10.6084/m9.figshare.6992273
title: Detection and identification of huwentoxin-IV interacting proteins by biotin-avidin chemistry combined with mass spectrometry

description: Background : Numerous spider toxins are of interest as tools for neurophysiological research or as lead molecules for the development of pharmaceuticals and insecticides. Direct detection and identification of the interacting proteins of a spider toxin are helpful for its action-mechanism analysis and practical application. The present study employed a combinative strategy for the analysis of interacting proteins of huwentoxin-IV (HWTX-IV), a peptidic neurotoxin from the venom of the spiderSelenocosmia huwena.Results : HWTX-IV was first lightly labeled with biotin under the optimized mild experimental conditions and the toxin labeled with a single biotin group (monobiotinylated HWTX-IV) was demonstrated by electrophysiological experiments to retain its original bioactivity and was used in combination with far-western blotting to detect its interacting proteins. Comparative experiments indicated that some membrane proteins from rat neuromuscular junction preparations bind to monobiotinylated HWTX-IV after being transferred onto a PVDF membrane from the SDS-gel. With capillary high performance liquid chromatography-tandem mass spectrometry, several membrane proteins with which HWTX-IV potentially interacted were identified from the preparations and then bioinformatically analyzed.Conclusions : This work has provided not only a new insight into the action mechanism of HWTX-IV but also a reference technology for the relevant researches.
DOI: 10.6084/m9.figshare.6992084
title: Knockdown of long non-coding RNA ANRIL inhibits tumorigenesis in human gastric cancer cells via microRNA-99a-mediated down-regulation of BMI1

description: Long non-coding RNA antisense non-coding RNA in the INK4 locus (ANRIL) has been reported to promote tumorigenesis via regulating microRNA (miR)-99a in gastric cancer cells. However, the role of each component involved in it is still not well understood. This study aimed to verify the role of ANRIL in gastric cancer as well as the underlying mechanisms. ANRIL levels in clinical gastric cancer tissues and cell lines were tested by qPCR. Effects of ANRIL silence on cell viability, migration and invasion, apoptosis, and miR-99a expression in MKN-45 and SGC-7901 cells were measured using CCK-8, Transwell assay, flow cytometry, and qPCR assays, respectively. Then, effects of miR-99a inhibition on ANRIL-silenced cells were evaluated. B-lymphoma Mo-MLV insertion region 1 (BMI1) expression, after abnormal expression of ANRIL and miR-99a, was determined. Finally, expression of key proteins in the apoptotic, Notch, and mTOR pathways was assessed. ANRIL level was elevated in gastric cancer tissues and cell lines. Knockdown of ANRIL suppressed cell viability, migration, and invasion, and increased apoptosis through up-regulating miR-99a. Furthermore, ANRIL silence down-regulated BMI1 via up-regulating miR-99a. BMI1 silence down-regulated Bcl-2 and key kinases in the Notch and mTOR pathways and up-regulated p16 and cleaved caspases. We verified the tumor suppressive effects of ANRIL knockdown in gastric cancer cells via crosstalk with miR-99a. Together, we provided a novel regulatory mechanism for ANRIL in gastric cancer, in which ANRIL silence down-regulated BMI1 via miR-99a, along with activation of the apoptotic pathway and inhibition of the Notch and mTOR pathways.
DOI: 10.6084/m9.figshare.7516355
title: Causes, effects and connectivity changes in MS-related cognitive decline

description: Cognitive decline is a frequent but undervalued aspect of multiple sclerosis (MS). Currently, it remains unclear what the strongest determinants of cognitive dysfunction are, with grey matter damage most directly related to cognitive impairment. Multi-parametric studies seem to indicate that individual factors of MS-pathology are highly interdependent causes of grey matter atrophy and permanent brain damage. They are associated with intermediate functional effects (e.g. in functional MRI) representing a balance between disconnection and (mal) adaptive connectivity changes. Therefore, a more comprehensive MRI approach is warranted, aiming to link structural changes with functional brain organization. To better understand the disconnection syndromes and cognitive decline in MS, this paper reviews the associations between MRI metrics and cognitive performance, by discussing the interactions between multiple facets of MS pathology as determinants of brain damage and how they affect network efficiency.
DOI: 10.6084/m9.figshare.7516355.v1
title: Causes, effects and connectivity changes in MS-related cognitive decline

description: Cognitive decline is a frequent but undervalued aspect of multiple sclerosis (MS). Currently, it remains unclear what the strongest determinants of cognitive dysfunction are, with grey matter damage most directly related to cognitive impairment. Multi-parametric studies seem to indicate that individual factors of MS-pathology are highly interdependent causes of grey matter atrophy and permanent brain damage. They are associated with intermediate functional effects (e.g. in functional MRI) representing a balance between disconnection and (mal) adaptive connectivity changes. Therefore, a more comprehensive MRI approach is warranted, aiming to link structural changes with functional brain organization. To better understand the disconnection syndromes and cognitive decline in MS, this paper reviews the associations between MRI metrics and cognitive performance, by discussing the interactions between multiple facets of MS pathology as determinants of brain damage and how they affect network efficiency.
DOI: 10.6084/m9.figshare.6992084.v1
title: Knockdown of long non-coding RNA ANRIL inhibits tumorigenesis in human gastric cancer cells via microRNA-99a-mediated down-regulation of BMI1

description: Long non-coding RNA antisense non-coding RNA in the INK4 locus (ANRIL) has been reported to promote tumorigenesis via regulating microRNA (miR)-99a in gastric cancer cells. However, the role of each component involved in it is still not well understood. This study aimed to verify the role of ANRIL in gastric cancer as well as the underlying mechanisms. ANRIL levels in clinical gastric cancer tissues and cell lines were tested by qPCR. Effects of ANRIL silence on cell viability, migration and invasion, apoptosis, and miR-99a expression in MKN-45 and SGC-7901 cells were measured using CCK-8, Transwell assay, flow cytometry, and qPCR assays, respectively. Then, effects of miR-99a inhibition on ANRIL-silenced cells were evaluated. B-lymphoma Mo-MLV insertion region 1 (BMI1) expression, after abnormal expression of ANRIL and miR-99a, was determined. Finally, expression of key proteins in the apoptotic, Notch, and mTOR pathways was assessed. ANRIL level was elevated in gastric cancer tissues and cell lines. Knockdown of ANRIL suppressed cell viability, migration, and invasion, and increased apoptosis through up-regulating miR-99a. Furthermore, ANRIL silence down-regulated BMI1 via up-regulating miR-99a. BMI1 silence down-regulated Bcl-2 and key kinases in the Notch and mTOR pathways and up-regulated p16 and cleaved caspases. We verified the tumor suppressive effects of ANRIL knockdown in gastric cancer cells via crosstalk with miR-99a. Together, we provided a novel regulatory mechanism for ANRIL in gastric cancer, in which ANRIL silence down-regulated BMI1 via miR-99a, along with activation of the apoptotic pathway and inhibition of the Notch and mTOR pathways.
DOI: 10.6084/m9.figshare.14329688.v1
title: Additional file 3 of Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

description: Additional file 3. The GO annotations of the genes harboring KASP SNP markers.
DOI: 10.6084/m9.figshare.14329439
title: Additional file 6 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 6: Table S3. Transcriptional level of genes involved in (hemi)cellulase production in T. reesei RUT-C30.
DOI: 10.6084/m9.figshare.8045813.v1
title: Additional file 4: of The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis)

description: Table S3. Promoter analysis of TTF proteins in Moso bamboo. (XLS 50 kb)
DOI: 10.6084/m9.figshare.19572594
title: Additional file 3 of Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer

description: Additional file 3: Supplementary Table S2. Matrix of identified phophoproteins in EESCC and EDAC.
DOI: 10.6084/m9.figshare.8045843.v1
title: Additional file 1: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S1. Chromosomal locations and segmental duplication of ItfbZIP genes. (EMF 15058 kb)
DOI: 10.5281/zenodo.10265625
title: Dataset for first resonant PXCT experiments at the SWING beamline at Synchrotron Soleil

description: This dataset was acquired at the SWING beamline at the French synchrotron SOLEIL. The ptychographic scans consisted of 205 diffraction patterns from a field of view of 14x12 µm² with an exposure time of 100 ms per point. The ptychographic reconstruction was carried out using the PtychoShelves Matlab software package [1], involving 200 iterations of the difference map (DM) algorithm, followed by 100 iterations of the maximum likelihood (ML) algorithm.

The dataset consists of the ptychographic reconstructions of two ptychographic tomography scans at energies 8383 eV and 8337 eV, the angle files, and the corresponding tomograms as slices.

Niwire_3D_8383 - ptychographic reconstructions of the 200 projections at 3838 eV

Niwire_3D_8337 - ptychographic reconstructions of the 210 projections at 8337 eV (10 duplicate angles)

Niwire8383_TIFF_delta_FBP_ram-lak_freqscl_1.00 - tomographic reconstruction (with PtychoShelves [2]) of the Niwire measured at 8383 eV

Niwire8337_TIFF_delta_FBP_ram-lak_freqscl_1.00 - tomographic reconstruction (with PtychoShelves [2]) of the Niwire measured at 8337 eV

angles_Niwire8383 - the angles of the tomographic scan at 8383 eV

angles_Niwire8383 - the angles of the tomographic scan at 8337 eV

 

[1] Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E. H. R., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A. & Guizar-Sicairos, M. (2020). PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data. J. Appl. Cryst. 53, 574-586.

[2] Michal Odstrčil, Mirko Holler, Jörg Raabe, and Manuel Guizar-Sicairos, "Alignment methods for nanotomography with deep subpixel accuracy," Opt. Express 27, 36637-36652 (2019)