cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8969201
title: Additional file 2: of Honey bee (Apis mellifera) larval pheromones may regulate gene expression related to foraging task specialization

description: Table S2. Entrez gene IDs of differentially up-regulated and down regulated genes in the context of pheromone exposure, foraging task-specialization, and their interaction. (CSV 454 kb)
DOI: 10.6084/m9.figshare.17205232
title: Additional file 3 of Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum

description: Additional file 3: Table S3. List of abbreviations for each protein used in this study.
DOI: 10.6084/m9.figshare.17205232.v1
title: Additional file 3 of Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum

description: Additional file 3: Table S3. List of abbreviations for each protein used in this study.
DOI: 10.6084/m9.figshare.25160111.v1
title: Supplementary Material for: Sex-specific behavioural deficits in adulthood following acute activation of the GABAA receptor in the neonatal mouse

description: Introduction: Sex differences exist in the prevalence of neurodevelopmental disorders (NDDs). Part of the aetiology of NDDs has been proposed to be alterations in the balance between excitatory and inhibitory neurotransmission, leading to the question of whether males and females respond differently to altered neurotransmitter balance. We investigated whether pharmacological alteration of GABAA signalling in early development results in sex-dependent changes in adult behaviours associated with NDDs. 
Methods: Male and female C57BL/6J mice received intraperitoneal injections of 0.5mg/kg muscimol or saline on postnatal days (P) 3-5 and were subjected to behavioural testing, specifically open field, light dark box, marble burying, sucralose preference, social interaction and olfactory habituation/dishabituation tests between P60-90. 
Results: Early postnatal administration of muscimol resulted in reduced anxiety in the light dark box test in both male and female adult mice. Muscimol reduced sucralose preference in males, but not females, whereas female mice showed reduced social behaviours. Regional alterations in cortical thickness were observed in the weeks following GABAA receptor activation, pointing to an evolving structural difference in the brain underlying adult behaviour.
Conclusions: We conclude that activation of the GABAA receptor in the first week of life resulted in long-lasting changes in a range of behaviours in adulthood following altered neurodevelopment. Sex of the individual affected the nature and severity of these abnormalities, explaining part of the varied pathophysiology and neurodevelopmental diagnosis that derive from excitatory/inhibitory imbalance.
DOI: 10.4121/3f5eea71-a299-48d9-a218-fdfea314fd42
title: Data underlying the research of Positive Displacement Reversible Pump-Turbine - Rotor-rotor gap and W/D ratio optimization

description: CFD simulations for optimizing efficiency in a reversible lobe pump-turbine. The goal is to verify the feasibility of such machine in low-head pumped hydro energy storage applications. It is part of the EU 2020 Horizon 2020 project : ALPHEUS. Based on a gap identified after a literature review, two design parameters were studied to check for optimized values for efficiency on such machines: 1 ) Rotor-rotor gap and 2) Channel Width - Rotor Diameter ratio. Parametric design optimization was studied through 2.5D CFD simulations with ANSYS CFX and TwinMesh software.
DOI: 10.4121/3f5eea71-a299-48d9-a218-fdfea314fd42.v1
title: Data underlying the research of Positive Displacement Reversible Pump-Turbine - Rotor-rotor gap and W/D ratio optimization

description: CFD simulations for optimizing efficiency in a reversible lobe pump-turbine. The goal is to verify the feasibility of such machine in low-head pumped hydro energy storage applications. It is part of the EU 2020 Horizon 2020 project : ALPHEUS. Based on a gap identified after a literature review, two design parameters were studied to check for optimized values for efficiency on such machines: 1 ) Rotor-rotor gap and 2) Channel Width - Rotor Diameter ratio. Parametric design optimization was studied through 2.5D CFD simulations with ANSYS CFX and TwinMesh software.
DOI: 10.6084/m9.figshare.6875006.v1
title: Additional file 1: of A case of Naegleria fowleri related primary amoebic meningoencephalitis in China diagnosed by next-generation sequencing

description: Microbe reads counts. Other microbe reads including that of bacterium, fungi and virus were listed in the excel table. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.22600546.v1
title: Additional file 1 of Decreased CD44v3 expression impairs endometrial stromal cell proliferation and decidualization in women with recurrent implantation failure

description: Additional file1: Supplemental figure 1. CD44v6 showed three different expression patterns in endometrial tissues Immunohistochemical staining for assessing the expression of CD44v6 in the control and RIF groups (n = 15 per group). Bar = 50 µm. Supplemental figure 2. Staining of CD44v3 and CD45 in mid-secretory phase endometrial specimens from RIF and control (Ctrl) women. Immunofluorescence staining for assessing the colocalization of CD44v3 and CD45 in the control and RIF groups (n = 4 per group). Bar = 20 µm. Supplemental figure 3. Effects of CD44v3 knockdown/overexpression on the cell migration, proliferation, and adhesiveness capabilities of Ishikawa cells. (A) Wound healing analysis and (B) semiquantitative analysis of wound closure in Ishikawa cells. (C) Cell proliferation after the knockdown and overexpression of CD44v3 in Ishikawa cells. (D and E) In the cell adhesion assay, the number of attached JAR cells was calculated and expressed as a fold change in the negative group. *p &lt; 0.05.
DOI: 10.6084/m9.figshare.22600546
title: Additional file 1 of Decreased CD44v3 expression impairs endometrial stromal cell proliferation and decidualization in women with recurrent implantation failure

description: Additional file1: Supplemental figure 1. CD44v6 showed three different expression patterns in endometrial tissues Immunohistochemical staining for assessing the expression of CD44v6 in the control and RIF groups (n = 15 per group). Bar = 50 µm. Supplemental figure 2. Staining of CD44v3 and CD45 in mid-secretory phase endometrial specimens from RIF and control (Ctrl) women. Immunofluorescence staining for assessing the colocalization of CD44v3 and CD45 in the control and RIF groups (n = 4 per group). Bar = 20 µm. Supplemental figure 3. Effects of CD44v3 knockdown/overexpression on the cell migration, proliferation, and adhesiveness capabilities of Ishikawa cells. (A) Wound healing analysis and (B) semiquantitative analysis of wound closure in Ishikawa cells. (C) Cell proliferation after the knockdown and overexpression of CD44v3 in Ishikawa cells. (D and E) In the cell adhesion assay, the number of attached JAR cells was calculated and expressed as a fold change in the negative group. *p &lt; 0.05.
DOI: 10.20394/7z4ta8k3
title: Public transport availability indicators (PTAI)

description: PTAI provides public transport data. These data offer public transport availability indicators at both the stop/station and small area levels across Great Britain (England, Wales and Scotland). Specifically, we offer stop-level public transport availability data “GB_STOP_PTAI_2016.csv”, LSOA-level public transport availability data “GB_LSOA_PTAI_2016.csv”, and MSOA-level public transport availability data “GB_MSOA_PTAI_2016.csv”. Additionally, these data also include the LSOA and MSOA boundaries across Great Britain (“GB_LSOA_2011” and “GB_MSOA_2011”).
DOI: 10.25430/researchdata.cab.unipd.it.00001195
title: Two-Dimensional Electronic Spectroscopy Characterization of Fucoxanthin – Chlorophyll Protein

description: The collection includes the results of the two-dimensional electronic spectroscopy measurements performed on a solution of Fucoxanthin – Chlorophyll Protein from Cyclotella meneghiniana.
Sample: FCPa @ room temperature 
Rephasing (R), non-rephasing (N) and total (T) signal datasets are provided

data published in Marcolin et al. JPCLett 2024
DOI: 10.6084/m9.figshare.17205229.v1
title: Additional file 2 of Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum

description: Additional file 2: Table S2. Predicted subcellular localization of partial proteins from pathways of interest in P. tricornutum. Data are shown for enzymes putatively involved in biochemical C4 pathways, central carbon metabolism, photorespiration, the ornithine–urea cycle, and fatty acid synthesis. Protein expression at LC and HC conditions here are noted as Up or Down, and those not quantified in either replicate proteome are indicated by ND. Predictions of signal peptides, chloroplast transit peptides, mitochondrial targeting, and targeting based on a heterokont-trained HMM utilized the following programs: http://www.cbs.dtu.dk/services/SignalP/ , http://www.cbs.dtu.dk/services/ChloroP/ , http://www.cbs.dtu.dk/services/TargetP/ , http://ihg.gsf.de/ihg/mitoprot.html , https://webtools.sb-roscoff.fr/root?tool_id=abims_hectar . Hypothesized locations are given based on data derived from the five programs and those with majority consensus were chosen as the predicted localization for a particular protein.
DOI: 10.6084/m9.figshare.22600798
title: Additional file 11 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 11: Table S3. Univariate cox regression for senescence-related genes.
DOI: 10.6084/m9.figshare.22600798.v1
title: Additional file 11 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 11: Table S3. Univariate cox regression for senescence-related genes.
DOI: 10.6084/m9.figshare.8969225
title: Additional file 7: of Honey bee (Apis mellifera) larval pheromones may regulate gene expression related to foraging task specialization

description: Table S4. Top 5 hub genes for each WGCNA module. (CSV 1 kb)
DOI: 10.6084/m9.figshare.22600801.v1
title: Additional file 12 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 12: Table S4. The difference of 22 kinds of immune cells between high and low risk groups.
DOI: 10.6084/m9.figshare.22600792.v1
title: Additional file 9 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 9: Table S1. Senescence-Related Genes in three gene sets.
DOI: 10.6084/m9.figshare.22600795.v1
title: Additional file 10 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 10: Table S2. Difference analysis between normal and tumor groups of LIHC.
DOI: 10.6084/m9.figshare.22600801
title: Additional file 12 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 12: Table S4. The difference of 22 kinds of immune cells between high and low risk groups.
DOI: 10.6084/m9.figshare.22600795
title: Additional file 10 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 10: Table S2. Difference analysis between normal and tumor groups of LIHC.
DOI: 10.6084/m9.figshare.22599290.v1
title: Additional file 4 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 4. F-vs-M DESs and predicted targets.
DOI: 10.6084/m9.figshare.22599296
title: Additional file 6 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 6. GO terms enriched for target genes.
DOI: 10.6084/m9.figshare.14736573.v1
title: Polystyrene nanoplastics exposure caused defective neural tube morphogenesis through caveolae-mediated endocytosis and faulty apoptosis

description: Growing evidence demonstrated that bioaccumulation of polystyrene nanoplastics (PS-NPs) in various organisms including human beings caused destructive effects on health. Nanoplastics may adversely affect fetal development potentially since they can pass through the placental barrier. However, very little has been known about the embryonic toxicity of polystyrene nanoplastics, especially in embryonic neurulation, the early developmental stage of the fetus, as well as the corresponding mechanisms. In this study, we first observed that 60- or 900-nm PS-NPs (especially 60-nm PS-NPs) could cross mouse placentas and affect developing mice fetuses. To avoid the indirect adverse effects derived from the restricted placenta, we employed early chick embryos as a developmental model to evaluate direct adverse effects of PS-NPs on embryo/fetal development, revealing suppressive effects on embryo development and an increased frequency of congenital abnormalities (especially in the nervous system), including neural tube defects. Thus, we focused on the potential negative effects of PS-NPs on neurulation, the earliest stage of nervous system development. Using caveolin-1 immunofluorescent staining of SH-SY5Y cells exposed to PS-NPs-GFP, we demonstrated that PS-NPs were internalized by SH-SY5Y cells via caveolae-mediated endocytosis. Transmission electron microscopy; LC3B immunofluorescent staining; and Atg7, Atg5, p62 and LC3B western blot results revealed that autophagy was activated in SH-SY5Y cells exposed to PS-NPs. However, PS-NPs were not degraded by the autophagic-lysosomal system given the lack of LAMP1 changes and minimal PS-NPs-GFP and LAMP1 colocalization. Furthermore, the cytoplasmic accumulation of PS-NPs caused faulty apoptotic cell death in SH-SY5Y cells and the developing neural tube as revealed by c-caspase3 immunofluorescent staining. Thus, defective neural tube morphogenesis, as demonstrated by neural tube defects, occurred during embryogenesis in the context of PS-NP exposure.
DOI: 10.6084/m9.figshare.14736573.v2
title: Polystyrene nanoplastics exposure caused defective neural tube morphogenesis through caveolae-mediated endocytosis and faulty apoptosis

description: Growing evidence demonstrated that bioaccumulation of polystyrene nanoplastics (PS-NPs) in various organisms including human beings caused destructive effects on health. Nanoplastics may adversely affect fetal development potentially since they can pass through the placental barrier. However, very little has been known about the embryonic toxicity of polystyrene nanoplastics, especially in embryonic neurulation, the early developmental stage of the fetus, as well as the corresponding mechanisms. In this study, we first observed that 60- or 900-nm PS-NPs (especially 60-nm PS-NPs) could cross mouse placentas and affect developing mice fetuses. To avoid the indirect adverse effects derived from the restricted placenta, we employed early chick embryos as a developmental model to evaluate direct adverse effects of PS-NPs on embryo/fetal development, revealing suppressive effects on embryo development and an increased frequency of congenital abnormalities (especially in the nervous system), including neural tube defects. Thus, we focused on the potential negative effects of PS-NPs on neurulation, the earliest stage of nervous system development. Using caveolin-1 immunofluorescent staining of SH-SY5Y cells exposed to PS-NPs-GFP, we demonstrated that PS-NPs were internalized by SH-SY5Y cells via caveolae-mediated endocytosis. Transmission electron microscopy; LC3B immunofluorescent staining; and Atg7, Atg5, p62 and LC3B western blot results revealed that autophagy was activated in SH-SY5Y cells exposed to PS-NPs. However, PS-NPs were not degraded by the autophagic-lysosomal system given the lack of LAMP1 changes and minimal PS-NPs-GFP and LAMP1 colocalization. Furthermore, the cytoplasmic accumulation of PS-NPs caused faulty apoptotic cell death in SH-SY5Y cells and the developing neural tube as revealed by c-caspase3 immunofluorescent staining. Thus, defective neural tube morphogenesis, as demonstrated by neural tube defects, occurred during embryogenesis in the context of PS-NP exposure.
DOI: 10.6084/m9.figshare.22600792
title: Additional file 9 of Comprehensive Analysis of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma

description: Additional file 9: Table S1. Senescence-Related Genes in three gene sets.
DOI: 10.6084/m9.figshare.22599281.v1
title: Additional file 1 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 1. The primers for 5'RACE and RT-qPCR.
DOI: 10.6084/m9.figshare.22599296.v1
title: Additional file 6 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 6. GO terms enriched for target genes.
DOI: 10.6084/m9.figshare.22599287
title: Additional file 3 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 3. The mature and precursor sequences for identified miRNAs.
DOI: 10.6084/m9.figshare.22599287.v1
title: Additional file 3 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 3. The mature and precursor sequences for identified miRNAs.
DOI: 10.6084/m9.figshare.22599281
title: Additional file 1 of Identification and analysis of miRNAs differentially expressed in male and female Trichosanthes kirilowii maxim

description: Additional file 1. The primers for 5'RACE and RT-qPCR.
DOI: 10.5442/nd000003
title: Focused Ion Beam tomography on fossilized osteocytes

description: Osteocytes play a central role in bone metabolism in extant vertebrates, but their evolutionary history is poorly understood. Therefore osteocyte lacunae microstructure of fossil bone was studied on the nanometer scale by means of focused ion beam tomography (FIB). A osteostracan and a “placoderm” were imaged, the earliest groups with cellular bone, and secondary osteons respectively. To visualize and characterize the early bone composition via the morphology and distribution of osteocyte lacunae, thereby imaging the predecessor to all modern bone cells.
The data provided represents two fossil samples (with 2 files each):
Bothriolepis trautscholdi. (Antiarchi, 'Placodermi'), MB.f.9188 (Late Devonian, ~372-382 million years ago). The sample was measured using a ZEISS Crossbeam 340 with an original voxel size of 30 nm. The "9188_Bothriolepis_normlized_bin2_60nm.zip" file represents the two times binned and normalized image stack. "MB.f.9188.mesh_files.zip" represents the derived surface information.
Tremataspis mammillata. (Osteostraci), MB.f.9025 (Late Silurian; ~423-428 million years ago). The sample was measured using a ZEISS Crossbeam 340 with an original voxel size of 20 nm. The "9025_Tremataspis_normalized_nocrack_bin2_40nm.zip" file represents the two times binned and normalized image stack. Additionally a crack in the measured volume has been removed. "MB.f.9025.mesh_files.zip" represents the derived surface information. The surface information data contains the .blend, .obj, .x3d and the .stl file format. The volume data consists of .tif images.
DOI: 10.6084/m9.figshare.12637857
title: Additional file 2 of Understanding Horizontal Gene Transfer network in human gut microbiota

description: Additional file 2. Jaccard similarity of nodes in HGT networks in IBD dataset.
DOI: 10.6084/m9.figshare.12637857.v1
title: Additional file 2 of Understanding Horizontal Gene Transfer network in human gut microbiota

description: Additional file 2. Jaccard similarity of nodes in HGT networks in IBD dataset.
DOI: 10.25375/uct.24850782
title: Grid panel display of line graphs illustrating Sentinel-2 single-date composite image surface reflectance spectra of all 11-land cover classes arranged as alien vegetation, native vegetation, and the rest of the land cover classes for 2019.

description: This dataset forms part of Figure 2.2 in the master's thesis titled- Repeatable method of classification of alien and native vegetation in the Montane grasslands (2024).This dataset includes four Excel spreadsheets and an r script. The Excel spreadsheets each contain spectral analysis of different land cover classes namely: alien vegetation; (gmf) grassland, mixed woody grassland, and forest; (nbbr) non-vegetated features, bracken and bare rock; (pwbrcp) permanent water bodies and recently cleared plantations. Then the r script combines and runs the code to produce a panel of line graphs depicting the surface reflectance of the 11 land cover classes.The dataset was collected in February 2020 in the Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.
DOI: 10.25375/uct.24850782.v1
title: Grid panel display of line graphs illustrating Sentinel-2 single-date composite image surface reflectance spectra of all 11-land cover classes arranged as alien vegetation, native vegetation, and the rest of the land cover classes for 2019.

description: This dataset forms part of Figure 2.2 in the master's thesis titled- Repeatable method of classification of alien and native vegetation in the Montane grasslands (2024).This dataset includes four Excel spreadsheets and an r script. The Excel spreadsheets each contain spectral analysis of different land cover classes namely: alien vegetation; (gmf) grassland, mixed woody grassland, and forest; (nbbr) non-vegetated features, bracken and bare rock; (pwbrcp) permanent water bodies and recently cleared plantations. Then the r script combines and runs the code to produce a panel of line graphs depicting the surface reflectance of the 11 land cover classes.The dataset was collected in February 2020 in the Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.
DOI: 10.25375/uct.24850965
title: Grid display of line graphs representing Sentinel-2 multi-temporal imagery for mean surface reflectance spectra of land cover classes for 2019, with 95% confidence interval

description: The dataset is used to produce Figure 2.3 in the master's thesis titled: Repeatable methods for classification of alien and native vegetation in the Montane grasslands (2024).This dataset includes an Excel spreadsheet and a r script. The Excel spreadsheet named Figure 2.3 contains spectral mean reflectance values vs time of land cover classes for 2020. This is followed by an r script which runs the code to display the reflectance behaviour of land cover classes for each Sentinel-2 band captured in 2019.Period of data collection: February 2020.Location of data collection: Blyde River Canyon Conservancy and its surrounds, in Mpumalanga/Limpopo Provinces, South Africa.