cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19445830.v1
title: Additional file 9 of Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

description: Additional file 9: Supplementary Table 3. The differential expressed miRNAs and their target mRNAs.
DOI: 10.6084/m9.figshare.19445962.v1
title: Additional file 4 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 4.
DOI: 10.6084/m9.figshare.19445962
title: Additional file 4 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 4.
DOI: 10.6084/m9.figshare.19445965.v1
title: Additional file 5 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 5.
DOI: 10.6084/m9.figshare.19445965
title: Additional file 5 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 5.
DOI: 10.6084/m9.figshare.19445968
title: Additional file 6 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 6.
DOI: 10.6084/m9.figshare.19445968.v1
title: Additional file 6 of Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks

description: Additional file 6.
DOI: 10.6084/m9.figshare.19445969.v1
title: Additional file 2 of Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus

description: Additional file 2: Table S1 to Table S23.
DOI: 10.6084/m9.figshare.19445969
title: Additional file 2 of Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus

description: Additional file 2: Table S1 to Table S23.
DOI: 10.6084/m9.figshare.25125377
title: raw_data_Early_elevated_IFNa

description: Currently, HIV infection is not curable, but infected individuals can manage their condition by taking daily doses of antiretroviral therapy. Some individuals, known as elite controllers (ECs), are born with natural immunity to HIV, and studying how their immune system responds to HIV exposure could lead to a potential cure for others. Here, we compare immune cell responses between ECs and untreated non-ECs. We find that IFNa, a small protein with an important role in controlling white blood cell activity, is produced in excess in immune cells from non-ECs compared with ECs during early infection. This insight provides an important clue for the future development of a targeted cure for HIV.
DOI: 10.6084/m9.figshare.25125377.v4
title: raw_data_Early_elevated_IFNa

description: Currently, HIV infection is not curable, but infected individuals can manage their condition by taking daily doses of antiretroviral therapy. Some individuals, known as elite controllers (ECs), are born with natural immunity to HIV, and studying how their immune system responds to HIV exposure could lead to a potential cure for others. Here, we compare immune cell responses between ECs and untreated non-ECs. We find that IFNa, a small protein with an important role in controlling white blood cell activity, is produced in excess in immune cells from non-ECs compared with ECs during early infection. This insight provides an important clue for the future development of a targeted cure for HIV.
DOI: 10.6084/m9.figshare.19445806
title: Additional file 2 of Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut

description: Additional file 2: Supplementary Figure 2. The physical location of differentially expressed mRNAs in response to peanut root-knot nematode.
DOI: 10.6084/m9.figshare.25125377.v3
title: raw_data_Early_elevated_IFNa

description: Currently, HIV infection is not curable, but infected individuals can manage their condition by taking daily doses of antiretroviral therapy. Some individuals, known as elite controllers (ECs), are born with natural immunity to HIV, and studying how their immune system responds to HIV exposure could lead to a potential cure for others. Here, we compare immune cell responses between ECs and untreated non-ECs. We find that IFNa, a small protein with an important role in controlling white blood cell activity, is produced in excess in immune cells from non-ECs compared with ECs during early infection. This insight provides an important clue for the future development of a targeted cure for HIV.
DOI: 10.6084/m9.figshare.10008740.v2
title: Metadata record for: Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data

description: This dataset contains key characteristics about the data described in the Data Descriptor Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.16821524
title: Additional file 3 of Gut bacterial metabolites modulate endoplasmic reticulum stress

description: Additional file 3: Table S2. List of protease inhibitors.
DOI: 10.6084/m9.figshare.25125356
title: <b>raw_data_IFNa_</b><b>induces_CCR5</b>

description: The treatment for HIV is called antiretroviral therapy (ART), which involves taking a combination of HIV medicines every day. ART cannot cure HIV but allows individuals to live longer, healthier lives. Treatment interruption can lead to relapse, but immune processes involved in relapse are not well understood. Some people with HIV are so-called elite controllers, who have a natural immunity to the virus and cope with HIV infection without needing treatments. Here, we compared the immune responses between elite controllers and individuals whose HIV medicines were interrupted. We demonstrate that IFNα, a small protein with an important role in controlling white blood cells, is produced in excess at the beginning of HIV infection and at levels that persist, resulting in poor HIV control without therapy.
DOI: 10.6084/m9.figshare.25125356.v3
title: <b>raw_data_IFNa_</b><b>induces_CCR5</b>

description: The treatment for HIV is called antiretroviral therapy (ART), which involves taking a combination of HIV medicines every day. ART cannot cure HIV but allows individuals to live longer, healthier lives. Treatment interruption can lead to relapse, but immune processes involved in relapse are not well understood. Some people with HIV are so-called elite controllers, who have a natural immunity to the virus and cope with HIV infection without needing treatments. Here, we compared the immune responses between elite controllers and individuals whose HIV medicines were interrupted. We demonstrate that IFNα, a small protein with an important role in controlling white blood cells, is produced in excess at the beginning of HIV infection and at levels that persist, resulting in poor HIV control without therapy.
DOI: 10.6084/m9.figshare.7387607
title: Raw data for Fig.2a

description: All images captured for Fig. 2a.
DOI: 10.6084/m9.figshare.16821721
title: Additional file 10 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 10: Table S10. GO enrichment analysis of 468 DEGs under low-temperature stress in R. xanthina f. spontanea. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.16821724.v1
title: Additional file 11 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 11: Table S11. KEGG enrichment analysis of 468 DEGs under low-temperature stress in R. xanthina f. spontanea. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.16821727
title: Additional file 12 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 12: Table S12. qRT-PCR analysis of expression levels under low-temperature stress in R. xanthina f. spontanea. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.13151775
title: Additional file 10 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 10: Table S5. Allelic variations and primer sequences for the 52 KASP assays.
DOI: 10.6084/m9.figshare.16821679
title: Additional file 2 of Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

description: Additional file 2
DOI: 10.17909/rd5r-m387
title: JWST Best-in-Class Vetted TOIs

description: This dataset corresponds to the work done by Hord, et al., 2024 in assembling a best-in-class sample of targets for atmospheric characterization with JWST. The observations contained herein represent the TESS data used in the vetting and validation of all of the unconfirmed TOIs that are members of the best-in-class sample.
DOI: 10.6084/m9.figshare.16821751.v1
title: Additional file 4 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 4: Table S4. GO classification of the assembled unigenes in R. xanthina f. spontanea. (XLSX 7387 kb)
DOI: 10.6084/m9.figshare.14727855
title: A global meta-analysis of the effects of plant diversity on biomass partitioning in grasslands

description: The partitioning
of below- to aboveground biomass is commonly described as the root-to-shoot
ratio (R/S). Although a number of studies have shown that biodiversity can influence
above- and belowground biomass in grasslands at the local and global scale, the
global-scale patterns reflecting how plant diversity affects R/S and the factors
controlling such effects remain unclear. In this study, we explored the global
patterns and associated drivers of biomass partitioning responding to plant
diversity by conducting a meta-analysis of 333 observations from 30 studies in
grasslands worldwide. Overall, plant diversity significantly increased aboveground
biomass (AGB), belowground biomass (BGB), and total biomass (TB), whereas significantly
decreased R/S. The effects of plant diversity on biomass partitioning varied
with experimental types. The effect size for AGB and BGB in the field was
larger than in greenhouse experiments, but the effect size for R/S did not significantly
differ between field and greenhouse experiments. Moreover, there was no
significant relationship between R/S and species richness and experimental
duration in greenhouse experiments. However, the effect size for AGB, BGB, and R/S
increased logarithmically with species richness and experimental duration in
the field experiments. Specifically, the effect size for R/S in the field
experiments switched from negative to neutral as the species richness and
experimental duration increased. Furthermore, the effect size for R/S was positively
correlated with complementary effects of BGB, and it increased logarithmically with
mean annual temperature and precipitation. Structural equation models showed that species
richness, experimental duration, and mean annual temperature impact R/S
indirectly by changing the BGB. Overall, our findings suggest that plant
mixtures invest less in belowground biomass than monocultures, and highlight that
low investment in belowground biomass will disappear gradually over time as
species richness increases.
DOI: 10.6084/m9.figshare.24487864
title: Macrolitter in Riverine Groyne Field

description: The dataset contains raw and processed data supplemental to the article: "Macrolitter budget and spatial distribution in a groyne field along the Waal river"
DOI: 10.6084/m9.figshare.24487864.v1
title: Macrolitter in Riverine Groyne Field

description: The dataset contains raw and processed data supplemental to the article: "Macrolitter budget and spatial distribution in a groyne field along the Waal river"
DOI: 10.17031/65c208e48311f
title: 1972 Marine Biological Association of the UK (MBA) Bay of Biscay RV Sarsia Cruise No. 18
title: 1972 MBA Bay of Biscay RV Sarsia Cruise No. 18

description: Records from the RV Sarsia Cruise No. 18 to the underwater canyons off the north coast of Spain in the Bay of Biscay. Most samples were collected using an Agassiz dredge with one (12th July) being collected using an anchor dredge. Records supplied by Dr. Eve Southward and collated by DASSH as part of the 'Dredging the Depths' project.
DOI: 10.5281/zenodo.10625343
title: Data from the validation of experimental large scale tilting table results with the in-house ALMA limit analysis code for the case of walls with different texture and aspect ratio

description: The dataset is produced by running a series of 816 simulations (204 each for ENG, RUN, SRU and STK) using the in-house code ALMA (Analisi Limite Murature Attritive) that implements the upper bound approach of limit analysis to detect the collapse multiplier and mechanism for masonry structures. This set of data contains the results of 816 simulations achieved for the limit analysis of masonry walls with different aspect ratios of the wall and various internal textures. Wall aspect ratios differ from squat walls (denoted with 05), square walls (denoted with 10) and slender walls (denoted with 15), for ratios 2:1, 1:1 and 1:2, respectively.  Regarding levels of texure, four have been used, namely STK, ENG, RUN and SRU. STK is the stacked bond, ENG is for an English bond, RUN is for the running bond with larger bricks compared to the SRU ruinning bond with smaller bricks.

Various imperfections have been implemented in the geometry for the simulations which are introduced based on some parameters. WallsPiers have horizontal reductions denoted with the greek letter xi (in files denoted with KS) and vertical reductions denoted with the greek letter eta (in files denoted with ET). Finally, four different levels of friction angle are considered (30o, 33o, 36o and 39o) that in the files are denoted with F. Another imperfection was introduced with the inclusion of a horizontal gap for the vertical joints denoted with VD, where VD-00 means no gap and VD-99 means there is a gap. The aspect ratio of walls are differentiated with RAT. Therefore, the files are separated in folders differing from the type of wall texture (ENG, RUN, SRU and STK) and each file is based on an acronym system formed for example:

"ENG_RAT-05_VD-99_KS-15_ET-05_F36" --> ENG - the nomination of texture; RAT-05 - the aspect ratio of the wall as 05; VD-99 - the switch between gap and no gap, in this case 99 means gap; KS-15 - is the horizontal reduction for a value of 15 mm; ET-05 - is the vertical reduction for a value of 50 mm; F36 - is the friction angle with a value of 36o. For KS and ET with values of 0, a perfect geometry is intended.

Each folder of this database contains  *.dxf, *.txt, .vtk, *.xml and *.png files. In the .dxf files are stored the geometries of the structures under study. In the .txt file the elapsed time and the collapse multiplier of each simulation can be found. The .vtk file contains all the geometry and displacement values of every masonry panel. The .xml files have the input files required for the ALMA code. Finally, the .png file presents the collapse mechanism obtained.
DOI: 10.5281/zenodo.10625344
title: Data from the validation of experimental large scale tilting table results with the in-house ALMA limit analysis code for the case of walls with different texture and aspect ratio

description: The dataset is produced by running a series of 816 simulations (204 each for ENG, RUN, SRU and STK) using the in-house code ALMA (Analisi Limite Murature Attritive) that implements the upper bound approach of limit analysis to detect the collapse multiplier and mechanism for masonry structures. This set of data contains the results of 816 simulations achieved for the limit analysis of masonry walls with different aspect ratios of the wall and various internal textures. Wall aspect ratios differ from squat walls (denoted with 05), square walls (denoted with 10) and slender walls (denoted with 15), for ratios 2:1, 1:1 and 1:2, respectively.  Regarding levels of texure, four have been used, namely STK, ENG, RUN and SRU. STK is the stacked bond, ENG is for an English bond, RUN is for the running bond with larger bricks compared to the SRU ruinning bond with smaller bricks.

Various imperfections have been implemented in the geometry for the simulations which are introduced based on some parameters. WallsPiers have horizontal reductions denoted with the greek letter xi (in files denoted with KS) and vertical reductions denoted with the greek letter eta (in files denoted with ET). Finally, four different levels of friction angle are considered (30o, 33o, 36o and 39o) that in the files are denoted with F. Another imperfection was introduced with the inclusion of a horizontal gap for the vertical joints denoted with VD, where VD-00 means no gap and VD-99 means there is a gap. The aspect ratio of walls are differentiated with RAT. Therefore, the files are separated in folders differing from the type of wall texture (ENG, RUN, SRU and STK) and each file is based on an acronym system formed for example:

"ENG_RAT-05_VD-99_KS-15_ET-05_F36" --> ENG - the nomination of texture; RAT-05 - the aspect ratio of the wall as 05; VD-99 - the switch between gap and no gap, in this case 99 means gap; KS-15 - is the horizontal reduction for a value of 15 mm; ET-05 - is the vertical reduction for a value of 50 mm; F36 - is the friction angle with a value of 36o. For KS and ET with values of 0, a perfect geometry is intended.

Each folder of this database contains  *.dxf, *.txt, .vtk, *.xml and *.png files. In the .dxf files are stored the geometries of the structures under study. In the .txt file the elapsed time and the collapse multiplier of each simulation can be found. The .vtk file contains all the geometry and displacement values of every masonry panel. The .xml files have the input files required for the ALMA code. Finally, the .png file presents the collapse mechanism obtained.
DOI: 10.6084/m9.figshare.13152004.v1
title: Additional file 2 of Genetic polymorphisms of PGF and TNFAIP2 genes related to cervical cancer risk among Uygur females from China

description: Additional file 2.
DOI: 10.5281/zenodo.8349425
title: Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (ChR2(C34A/C36A)-mEos3.2)

description: This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)

Zip file contains PALM measurements of HEK293 cells expressing ChR2C34A/C36A fused with mEos3.2.Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.

Detailed protocols for sample preparation and data acquisition are described in the article.Some details are listed below.

SAMPLE PREPARATION

cell line: Flp-In™ T-REx™ 293transfection method: modified calcium-phosphate transient transfection [1]fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperatureimaging buffer: PBS

PALM ACQUISITION

A custom-built setup for single-molecule localization microscopy is described in [2].mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:exposure time = 100 msframe size = 512x512 pixelspixel size = 80 nm

 

[1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.[2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073
DOI: 10.5281/zenodo.8349426
title: Dataset from "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (ChR2(C34A/C36A)-mEos3.2)

description: This dataset contains raw microscopy data from the article "Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy" (doi.org/10.1002/anie.202307555)

Zip file contains PALM measurements of HEK293 cells expressing ChR2C34A/C36A fused with mEos3.2.Each folder in .zip file contains one PALM measurement (TIFF format) and recording settings (.xml) automatically created by acquiring software. For technical reasons, single measurements are divided into TIFF files of =<4088 frames.

Detailed protocols for sample preparation and data acquisition are described in the article.Some details are listed below.

SAMPLE PREPARATION

cell line: Flp-In™ T-REx™ 293transfection method: modified calcium-phosphate transient transfection [1]fixation method: 4% paraformaldehyde solution in PBS for 30 min at room temperatureimaging buffer: PBS

PALM ACQUISITION

A custom-built setup for single-molecule localization microscopy is described in [2].mEos3.2 was simultaneously photoconverted, imaged and photobleached by gradually increasing UV illumination (405 nm; up to 1 mW at the sample) and continuous excitation at 561 nm (approximately 50 mW at the sample).PALM movies of cell plasma membrane were recorded in total internal reflection fluorescence (TIRF) mode using an EMCCD camera:exposure time = 100 msframe size = 512x512 pixelspixel size = 80 nm

 

[1] Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Molecular and cellular biology. 1987 Aug 1;7(8):2745-52.[2] Tang Y, Dai L, Zhang X, Li J, Hendriks J, Fan X, Gruteser N, Meisenberg A, Baumann A, Katranidis A, Gensch T. SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy. Scientific reports. 2015 Jun 22;5(1):11073
DOI: 10.5281/zenodo.10625443
title: Four tables in the manuscript
DOI: 10.5281/zenodo.10625444
title: Four tables in the manuscript
DOI: 10.6084/m9.figshare.16821698
title: Additional file 1 of Genetic and treatment profiles of patients with concurrent Epidermal Growth Factor Receptor (EGFR) and Anaplastic Lymphoma Kinase (ALK) mutations

description: Additional file 1: Table S1. The list of 59 gene targeted by NGS. Table S2. The list of all mutations detected by NGS.
DOI: 10.6084/m9.figshare.16821698.v1
title: Additional file 1 of Genetic and treatment profiles of patients with concurrent Epidermal Growth Factor Receptor (EGFR) and Anaplastic Lymphoma Kinase (ALK) mutations

description: Additional file 1: Table S1. The list of 59 gene targeted by NGS. Table S2. The list of all mutations detected by NGS.