cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/957fb0bd-6d51-46fc-b4fa-731d21731eda
title: Borehole optical televiewer logs from the southern sector of Larsen C Ice Shelf, Antarctic Peninsula, November-December 2022

description: These are digital optical televiewer logs of two boreholes drilled by hot water to 120 m (Site 1) and 160 m (Site 2) on Larsen C Ice Shelf, Antarctic Peninsula. Boreholes were drilled in December 2022 to investigate the internal properties of a suture zone (Site 1) and a meteoric ice band (Site 2) of an ice shelf, as part of the NERC-funded RiPIce (Rift Propagation for Ice sheet models) research project.

NERC standard grant NE/T008016/1.
description: The datasets are optical televiewer logs from two boreholes drilled to 120 m (Site 1) and 160 m (Site 2) on Larsen C Ice Shelf, Antarctica, in December 2022. They were acquired using a slim-hole optical televiewer borehole probe manufactured by Robertson Geologging Ltd, comprising a 360 degree camera. Boreholes were logged whilst the optical televiewer was travelling up the borehole.

The optical televiewer has internal LEDs to illuminate the borehole wall, indicated by a % lighting level controlled by the user. Lighting changes were made whilst logging, as follows:

RiPIce OPTV Site1

Depth (m),Lighting (%)
25.74 - 45.58,60
45.58 - 45.61,55
45.61 - 48.80,80
48.80 - 54.08,85
54.08 - 57.97,90
57.97 - 82.40,95
82.40 - 82.94,90
82.94 - 88.25,100
88.25 - 88.34,95
88.34 - 88.76,90
88.76 - 119.94,100

RiPICE OPTV Site2

Depth (m),Lighting (%)
1.97 - 50.30,50
50.30 - 69.90,70
69.90 - 159.97,90
description: Logs were acquired using Robertson Geologging OPTV probe, mini winch and Micrologger II.
description: Images are unaltered from those logged in the field. The OPTV technique is described by Hubbard et al. (2008).
DOI: 10.6084/m9.figshare.c.3609596_d4.v1
title: Additional file 4: of 
                     De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia

description: Expression levels (FPKM) of the transcripts of the sainfoin assembly. Excel file with expression levels (FPKM) of transcripts from each of the five sainfoin accessions. (XLSX 4336Â kb)
DOI: 10.6084/m9.figshare.c.3609608_d2.v1
title: Additional file 2: Table S1. of Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.

description: Genus-unique genes for Fructobacillus and Leuconostoc. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3609596_d5.v1
title: Additional file 5: of 
                     De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia

description: SSRs identified in the sainfoin combined assembly. Excel file with list of SSR motifs identified in transcripts from Sainfoin Transcriptome 1.0. (XLSX 498Â kb)
DOI: 10.6084/m9.figshare.c.3609596_d6.v1
title: Additional file 6: of 
                     De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia

description: SNP polymorphisms in the five sainfoin transcript assemblies. A csv file listing putative SNP variants identified in one or more of the five sainfoin transcriptome assemblies. (CSV 6315Â kb)
DOI: 10.6084/m9.figshare.c.3609638_d1.v1
title: Additional file 1: Table S1. of Mosquito-borne heartworm Dirofilaria immitis in dogs from Australia

description: Summary of the Dirofilaria immitis diagnostics. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3609680_d3.v1
title: Additional file 3: Table S3. of Sex differences in protein expression in the mouse brain and their perturbations in a model of Down syndrome

description: Results of all pairwise comparisons: all proteins in each brain region. (XLS 168Â kb)
DOI: 10.6084/m9.figshare.c.3609692_d1.v1
title: Additional file 3: Table S2. of Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health

description: Raw abundance estimates for each locus and sample in the antioxidant differential expression comparison. (XLSX 6056 kb)
DOI: 10.6084/m9.figshare.c.3609695_d1.v1
title: Additional file 3: Figure S2. of Bacterial calpains and the evolution of the calpain (C2) family of peptidases

description: Protein sequence alignment for selected members of the calpain family. The alignment generated by ClustalW is shown. Residues conserved in 80Â % of sequences are highlighted in light yellow. Residues that are similar in 80Â % of sequences are highlighted in dark yellow. Active site residues are indicated by an asterisk. Calcium-binding residues are indicated by a plus sign. Residue numbers are shown on the right hand side. For the key to sequences, see Additional file 4: Table S2. (TXT 12 kb)
DOI: 10.6084/m9.figshare.c.3609692_d3.v1
title: Additional file 1: Table S1. of Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health

description: Complete annotation and differential expression data for watercress transcripts assembled and analysed in this study. (XLSX 12441 kb)
DOI: 10.6084/m9.figshare.c.3609692_d4.v1
title: Additional file 4: Table S3. of Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health

description: Raw abundance estimates for each locus and sample in the glucosinolate differential expression comparison. (XLSX 3990 kb)
DOI: 10.5281/zenodo.14501107
title: Database of Quaternary volcanic vents in the Turkana Depression

description: This dataset contains the coordinates of all the Quaternary volcanic vents charactserising the Turkana Depression, East Africa. Vent mapping relied on 3 sources: (1) analyzing SRTM digital elevation models with a cell size of 30 m (http://www2.jpl.nasa.gov/srtm/), (2) interpreting panchromatic satellite images with pixel resolution of 2.5-20 m by using Google Earth (http://earth.google.com/), and (3) integrating previous work by Mazzarini and Isola (2022). Vents with a diameter smaller than a few pixels (i.e., <60 m), disrupted vents (vents without a well-preserved morphology), and vents covered by younger volcanic products have been filtered out.

The coordinates are georeferenced in the ESPSG 4326 WGS84 system.

The dataset is a supplementary material for the manuscript 'Control of gravitational potential energy on the distribution of off-rift volcanic activity in the Turkana Depression, East African Rift' by Corti et al.
DOI: 10.5281/zenodo.14501106
title: Database of Quaternary volcanic vents in the Turkana Depression

description: This dataset contains the coordinates of all the Quaternary volcanic vents charactserising the Turkana Depression, East Africa. Vent mapping relied on 3 sources: (1) analyzing SRTM digital elevation models with a cell size of 30 m (http://www2.jpl.nasa.gov/srtm/), (2) interpreting panchromatic satellite images with pixel resolution of 2.5-20 m by using Google Earth (http://earth.google.com/), and (3) integrating previous work by Mazzarini and Isola (2022). Vents with a diameter smaller than a few pixels (i.e., <60 m), disrupted vents (vents without a well-preserved morphology), and vents covered by younger volcanic products have been filtered out.

The coordinates are georeferenced in the ESPSG 4326 WGS84 system.

The dataset is a supplementary material for the manuscript 'Control of gravitational potential energy on the distribution of off-rift volcanic activity in the Turkana Depression, East African Rift' by Corti et al.

 

The figure shows the volcanic vents in the different volcanic fields. Green dots illustrate in-axis volcanoes (Em: Emuruangogolak, Ba: Barrier, CI: Central Island, Ko: Korath range, Na: Namarunu, Si: Silali, SI: South Island); black dots illustrate off-rift volcanoes (As: Asie volcanic field; DD: Dilo-Dukana volcanic field; HH: Hurri Hills volcanic field; Ma: Marsabit volcanic field; Me: Mega volcanic field). LT: Lake Turkana; RR: Ririba Rift.
DOI: 10.5281/zenodo.14505741
title: Database of Quaternary volcanic vents in the Turkana Depression

description: This dataset contains the coordinates of all the Quaternary volcanic vents charactserising the Turkana Depression, East Africa. Vent mapping relied on 3 sources: (1) analyzing SRTM digital elevation models with a cell size of 30 m (http://www2.jpl.nasa.gov/srtm/), (2) interpreting panchromatic satellite images with pixel resolution of 2.5-20 m by using Google Earth (http://earth.google.com/), and (3) integrating previous work by Mazzarini and Isola (2022). Vents with a diameter smaller than a few pixels (i.e., <60 m), disrupted vents (vents without a well-preserved morphology), and vents covered by younger volcanic products have been filtered out.

The coordinates are georeferenced in the ESPSG 4326 WGS84 system.

The dataset is a supplementary material for the manuscript 'Control of gravitational potential energy on the distribution of off-rift volcanic activity in the Turkana Depression, East African Rift' by Corti et al.

 

The figure shows the volcanic vents in the different volcanic fields. Green dots illustrate in-axis volcanoes (Em: Emuruangogolak, Ba: Barrier, CI: Central Island, Ko: Korath range, Na: Namarunu, Si: Silali, SI: South Island); black dots illustrate off-rift volcanoes (As: Asie volcanic field; DD: Dilo-Dukana volcanic field; HH: Hurri Hills volcanic field; Ma: Marsabit volcanic field; Me: Mega volcanic field). LT: Lake Turkana; RR: Ririba Rift.
DOI: 10.18419/darus-4448/2
title: Interview_results.tab
DOI: 10.18419/darus-4448
title: Supplemental Material for: Testing the Test: Observations When Assessing Visualization Literacy of Domain Experts

description: These documents contain supplemental material for the paper "Testing the Test: Observations When Assessing Visualization Literacy of Domain Experts" which was conditionally accepted at the BELIV 2024 Workshop in conjunction with the IEEE VIS 2024 Conference.
&lt;ul&gt;
&lt;li&gt;The CSV file contains the summaries of the important parts of the interview, each assigned to a category. &lt;/li&gt;
&lt;li&gt;The PDF document contains the interview questions, the defined categories, and the questionnaire.&lt;/li&gt;
&lt;/ul&gt;
DOI: 10.18419/darus-4448/1
title: Supplemental_Material_for__2024_BELIV__Assessing_Visualization_Literacy_.pdf
DOI: 10.6084/m9.figshare.c.3609734_d2.v1
title: Additional file 2 of Large scale analysis of amino acid substitutions in bacterial proteomics

description: Table with identifications of MS/MS spectra of H. pylori E48 and H-13 in classical Mascot search against sequence database and speptide search. (XLSX 89.6 kb)
DOI: 10.6084/m9.figshare.c.3609710_d8.v1
title: Additional file 15: Table S7. of ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins

description: MGSDA classification accuracy. This table contains tables of accuracy as determined by 5-fold cross validation for MGSDA. MGSDA was run using the covariate-corrected, transformed abundances of all common OTUs and taxa (table “common_taxa”). Additionally, MGSDA was run on the abundances of OTUs present in at least 10% of individuals in the dataset (table “OTUs_in_10_percent”). The groups considered in MGSDA with each data set were ABO status, secretor status, and ABO status in secreting individuals only, which are indicated as columns in each tab. A description of what is represented in each row is included in the document. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3609710_d9.v1
title: Additional file 13: Table S6. of ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins

description: P- and q-values for linear mixed models for Bifidobacteria, including LCT allele status in the model. This table contains the p-values and Benjamini-Hochberg adjusted p-values for the linear mixed models relating the abundances of the common Bifidobacterium OTUs and collapsed taxa to ABO and secretor status, while including LCT variation in the model (rs1446585 genotype). Models 1-9 are described fully in the methods section, but a brief description of each is included below. P-values were calculated by comparing a full model to a reduced model, which consisted of only the random effects for family and twin status and a fixed effect for LCT allele status. P-values were adjusted within each model separately. Descriptions of each column are included in the document. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.c.3609773_d7.v1
title: Additional file 6: of Effect of 90Sr internal emitter on gene expression in mouse blood

description: IPA upstream regulators: miRNA, with z-scores, details of Fig.Â  6. (XLS 26 kb)
DOI: 10.6084/m9.figshare.c.3609710_d19.v1
title: Additional file 1: Table S1. of ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins

description: Cohort characteristics in the full and ‘healthy’ datasets. The total nubmer (n) or percent of total (%) for each category is listed for either the full or ‘healthy’ datasets, along with the standard deviation for each measure. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3609803_d3.v1
title: Additional file 3: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: Relative abundance of each microbiota at genus level. (XLSX 873Â kb)
DOI: 10.5281/zenodo.11396387
title: Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset

description: This repository contains some point spread functions (PSFs) distilled from imaging fluorescent beads, 200nm, F8811 in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope. The bead images from which the PSF were distilled are contained in this repo.

Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).

These three parameters were varied:

FS: focus sheet (-100, -75, -25, 0)

FW: focus waist (40, 45, 50, 55, 60, 65, 70, 75, 80, 85)

AC: aberration control (150, 155, 160, 165, 170, 175, 180, 185, 190)

The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.

The all-psfs.tif contains the deskewed psf ordered similarly as the poster uploaded in this version of the repository (ELMI-2024-poster.pdf).

A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.

Note that none of these data is deskewed.

--------------------

Here's a protocol to prepare a gel containing beads at a good enough density:





Material:



Agarose 2%

Fluorescent beads, 200nm, F8811. Stock is 1000x





Protocol:



Put the agarose to warm up at 90C.

Vortex the beads stock.

Dilute a 100 times the bead dilution in PBS (10 uL in 1mL), vortex.

Prepare a clean slide, and a clean coverglass (22x22mm).

Take 90uL of agarose, put in a 1.5mL tube, add 10uL of the diluted beads, vortex.

Take 50uL of this agarose solution, put it on the slide, add the coverglass on top.

Put this slide in the fridge and wait a few minutes.

Use nailpolish to seal the coverglass. Wait long enoughfor the nailpolish to dry.




You should a gel of about 100um thickness.

It should be possible to add a bit of free dye in the gel in order to help focusing the light sheet. Ideally a bit of far-red free dye, like Alexa 647.
DOI: 10.5281/zenodo.11396388
title: Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset

description: This repository contains some point spread functions distilled from imaging fluorescent beads, 200nm, F8811 in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope.

Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).

These three parameters were varied:

FS: focus sheet 

FW: focus waist

AC: aberration control

 

The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.

 

A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.

 

Note that none of these data is deskewed.
DOI: 10.5281/zenodo.14203207
title: Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset

description: This repository contains some point spread functions (PSFs) distilled from imaging fluorescent beads, 200nm, F8811 in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope. The bead images from which the PSF were distilled are contained in this repo.

Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).

These three parameters were varied:

FS: focus sheet (-100, -75, -25, 0)

FW: focus waist (40, 45, 50, 55, 60, 65, 70, 75, 80, 85)

AC: aberration control (150, 155, 160, 165, 170, 175, 180, 185, 190)

The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.

A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.

Note that none of these data is deskewed.

--------------------

Here's a protocol to prepare a gel containing beads at a good enough density:





Material:



Agarose 2%

Fluorescent beads, 200nm, F8811. Stock is 1000x





Protocol:



Put the agarose to warm up at 90C.

Vortex the beads stock.

Dilute a 100 times the bead dilution in PBS (10 uL in 1mL), vortex.

Prepare a clean slide, and a clean coverglass (22x22mm).

Take 90uL of agarose, put in a 1.5mL tube, add 10uL of the diluted beads, vortex.

Take 50uL of this agarose solution, put it on the slide, add the coverglass on top.

Put this slide in the fridge and wait a few minutes.

Use nailpolish to seal the coverglass. Wait long enoughfor the nailpolish to dry.




You should a gel of about 100um thickness.

It should be possible to add a bit of free dye in the gel in order to help focusing the light sheet. Ideally a bit of far-red free dye, like Alexa 647.
DOI: 10.5281/zenodo.14505724
title: Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset

description: This repository contains some point spread functions (PSFs) distilled from imaging fluorescent beads, 200nm, F8811 in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope. The bead images from which the PSF were distilled are contained in this repo.

Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).

These three parameters were varied:

FS: focus sheet (-100, -75, -25, 0)

FW: focus waist (40, 45, 50, 55, 60, 65, 70, 75, 80, 85)

AC: aberration control (150, 155, 160, 165, 170, 175, 180, 185, 190)

The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.

The all-psfs.tif contains the deskewed psf ordered similarly as the poster uploaded in this version of the repository (ELMI-2024-poster.pdf).

A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.

Note that none of these data is deskewed.

--------------------

Here's a protocol to prepare a gel containing beads at a good enough density:





Material:



Agarose 2%

Fluorescent beads, 200nm, F8811. Stock is 1000x





Protocol:



Put the agarose to warm up at 90C.

Vortex the beads stock.

Dilute a 100 times the bead dilution in PBS (10 uL in 1mL), vortex.

Prepare a clean slide, and a clean coverglass (22x22mm).

Take 90uL of agarose, put in a 1.5mL tube, add 10uL of the diluted beads, vortex.

Take 50uL of this agarose solution, put it on the slide, add the coverglass on top.

Put this slide in the fridge and wait a few minutes.

Use nailpolish to seal the coverglass. Wait long enoughfor the nailpolish to dry.




You should a gel of about 100um thickness.

It should be possible to add a bit of free dye in the gel in order to help focusing the light sheet. Ideally a bit of far-red free dye, like Alexa 647.
DOI: 10.6084/m9.figshare.c.3609824_d1.v1
title: Additional file 4: of De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.)

description: Calling 12,518 SNPs based on raw VCF files from the transcription sequence of jute with the GATK standard filter method. (XLS 2092 kb)
DOI: 10.6084/m9.figshare.c.3609803_d4.v1
title: Additional file 6: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: Bacterial groups at genus-like level in each CAG. (XLSX 863Â kb)
DOI: 10.6084/m9.figshare.c.3609803_d10.v1
title: Additional file 11: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: Taxa that are found in more than 50Â % of the subjects in any cluster (shown in Additional file 8) with significantly difference between elderly 1 and elderly 2 clusters. (XLSX 859Â kb)
DOI: 10.6084/m9.figshare.c.3609824_d7.v1
title: Additional file 5: of De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.)

description: Major genes involved in cellulose biosynthesis based on the transcriptome sequence of jute. (XLS 32 kb)
DOI: 10.6084/m9.figshare.28043600
title: <b>Intra-bladder and Insufflation Pressure Readings During Laparoscopic Surgery (dataset)</b>

description: The raw data supporting the findings of the original article.
DOI: 10.6084/m9.figshare.c.3609803_d12.v1
title: Additional file 16: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: Bacterial strains used in this study. (XLSX 855Â kb)
DOI: 10.6084/m9.figshare.c.3609866_d2.v1
title: Additional file 7: Table S5. of Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs

description: Putative G-quadruplex-forming sequences in the P. reichenowi CDC genome. Genome searched using ‘QGRS Mapper’ [35] with the parameters G3 N(0–11) G3 N(0–11) G3 N(0–11) G3 [17]. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3609803_d13.v1
title: Additional file 12: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: Individual data. (XLSX 875Â kb)
DOI: 10.6084/m9.figshare.c.3609872_d2.v1
title: Additional file 2: Table S1. of Transposable element polymorphisms recapitulate human evolution

description: List of human polyTE loci with allele frequencies and FST and Î´ values. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3609875_d1.v1
title: Additional file 1: of Rubus crataegifolius Bunge regulates adipogenesis through Akt and inhibits high-fat diet-induced obesity in rats

description: Effects of supplementing RCB on body weight gain, and serum profiles in rats fed a high fat diet for two weeks. (A) Weight gain, (B) serum triglyceride level, and (C) total cholesterol level. The values are expressed as the mean ± SD. The bars showing different letters indicate significant differences among each group of bars, according to Duncan’s test; *p
DOI: 10.6084/m9.figshare.c.3609803_d14.v1
title: Additional file 17: of Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

description: PCR primers for detection of each species. (XLSX 857Â kb)
DOI: 10.6084/m9.figshare.c.3609878_d1.v1
title: Additional file 2: of TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

description: Contains tables of the data matrices used for training and testing the two methods described, as well as the data matrices from two validation data sets. (XLSX 12273 kb)