cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10361039
title: EPFL EPFL_2009 33 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 33 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/33.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10390205
title: DETERMINATION OF VITAMINS IN CARROTS AND THEIR BENEFICIAL EFFECTS ON HUMAN HEALTH
DOI: 10.5281/zenodo.10390204
title: DETERMINATION OF VITAMINS IN CARROTS AND THEIR BENEFICIAL EFFECTS ON HUMAN HEALTH
DOI: 10.5281/zenodo.10065723
title: Plexcitonic Nanorattles as Highly Efficient SERS-Encoded Tags

description: Recent publication: 

Plexcitonic Nanorattles as Highly Efficient SERS-Encoded Tags

 







Carla Estévez-Varela, Sara Núñez-Sánchez, Paula Piñeiro-Varela, Dorleta Jiménez de Aberasturi, Luis M. Liz-Marzán, Jorge Pérez-Juste, Isabel Pastoriza-Santos






First published: 27 November 2023


https://doi.org/10.1002/smll.202306045


 

Abstract: Plexcitonic nanoparticles exhibit strong light-matter interactions, mediated by localized surface plasmon resonances, and thereby promise potential applications in fields such as photonics, solar cells, and sensing, among others. Herein, these light-matter interactions are investigated by UV-visible and surface-enhanced Raman scattering (SERS) spectroscopies, supported by finite-difference time-domain (FDTD) calculations. Our results reveal the importance of combining plasmonic nanomaterials and J-aggregates with near-zero-refractive index. As plexcitonic nanostructures nanorattles are employed, based on J-aggregates of the cyanine dye 5,5,6,6-tetrachloro-1,1-diethyl-3,3-bis(4-sulfobutyl)benzimidazolocarbocyanine (TDBC) and plasmonic silver-coated gold nanorods, confined within mesoporous silica shells, which facilitate the adsorption of the J-aggregates onto the metallic nanorod surface, while providing high colloidal stability. Electromagnetic simulations show that the electromagnetic field is strongly confined inside the J-aggregate layer, at wavelengths near the upper plexcitonic mode, but it is damped toward the J-aggregate/water interface at the lower plexcitonic mode. This behavior is ascribed to the sharp variation of dielectric properties of the J-aggregate shell close to the plasmon resonance, which leads to a high opposite refractive index contrast between water and the TDBC shell, at the upper and the lower plexcitonic modes. This behavior is responsible for the high SERS efficiency of the plexcitonic nanorattles under both 633 nm and 532 nm laser illumination. SERS analysis showed a detection sensitivity down to the single-nanoparticle level and, therefore, an exceptionally high average SERS intensity per particle. These findings may open new opportunities for ultrasensitive biosensing and bioimaging, as superbright and highly stable optical labels based on the strong coupling effect.
DOI: 10.5281/zenodo.10065722
title: Plexcitonic Nanorattles as Highly Efficient SERS-Encoded Tags

description: Recent publication: 

Plexcitonic Nanorattles as Highly Efficient SERS-Encoded Tags

 







Carla Estévez-Varela, Sara Núñez-Sánchez, Paula Piñeiro-Varela, Dorleta Jiménez de Aberasturi, Luis M. Liz-Marzán, Jorge Pérez-Juste, Isabel Pastoriza-Santos






First published: 27 November 2023


https://doi.org/10.1002/smll.202306045


 

Abstract: Plexcitonic nanoparticles exhibit strong light-matter interactions, mediated by localized surface plasmon resonances, and thereby promise potential applications in fields such as photonics, solar cells, and sensing, among others. Herein, these light-matter interactions are investigated by UV-visible and surface-enhanced Raman scattering (SERS) spectroscopies, supported by finite-difference time-domain (FDTD) calculations. Our results reveal the importance of combining plasmonic nanomaterials and J-aggregates with near-zero-refractive index. As plexcitonic nanostructures nanorattles are employed, based on J-aggregates of the cyanine dye 5,5,6,6-tetrachloro-1,1-diethyl-3,3-bis(4-sulfobutyl)benzimidazolocarbocyanine (TDBC) and plasmonic silver-coated gold nanorods, confined within mesoporous silica shells, which facilitate the adsorption of the J-aggregates onto the metallic nanorod surface, while providing high colloidal stability. Electromagnetic simulations show that the electromagnetic field is strongly confined inside the J-aggregate layer, at wavelengths near the upper plexcitonic mode, but it is damped toward the J-aggregate/water interface at the lower plexcitonic mode. This behavior is ascribed to the sharp variation of dielectric properties of the J-aggregate shell close to the plasmon resonance, which leads to a high opposite refractive index contrast between water and the TDBC shell, at the upper and the lower plexcitonic modes. This behavior is responsible for the high SERS efficiency of the plexcitonic nanorattles under both 633 nm and 532 nm laser illumination. SERS analysis showed a detection sensitivity down to the single-nanoparticle level and, therefore, an exceptionally high average SERS intensity per particle. These findings may open new opportunities for ultrasensitive biosensing and bioimaging, as superbright and highly stable optical labels based on the strong coupling effect.
DOI: 10.6084/m9.figshare.24826527
title: code used for C4_mtscATAC.

description: We primarily follow the analysis workflow described in Signac(https://stuartlab.org/signac/articles/mito and https://github.com/caleblareau/mtscATACpaper_reproducibility). The specific steps are as follows:Step 1: Merge the RDS files containing the nuclear-derived epigenetic gene activity from each sample. We provide the main script "signac_merge_tsne.R" and reference commands in "work.sh".Step 2: Perform cell type annotation using three methods. The cell type annotation scripts for each tissue are provided in separate files.Step 3: Identify SNPs. First, use mgatk for SNP identification. Then, utilize "SignaC_mgatk.r" for SNP filtering and obtaining SNP distribution information in each cell.<br>
DOI: 10.6084/m9.figshare.24826527.v1
title: code used for C4_mtscATAC.

description: We primarily follow the analysis workflow described in Signac(https://stuartlab.org/signac/articles/mito and https://github.com/caleblareau/mtscATACpaper_reproducibility). The specific steps are as follows:Step 1: Merge the RDS files containing the nuclear-derived epigenetic gene activity from each sample. We provide the main script "signac_merge_tsne.R" and reference commands in "work.sh".Step 2: Perform cell type annotation using three methods. The cell type annotation scripts for each tissue are provided in separate files.Step 3: Identify SNPs. First, use mgatk for SNP identification. Then, utilize "SignaC_mgatk.r" for SNP filtering and obtaining SNP distribution information in each cell.<br>
DOI: 10.34740/kaggle/dsv/7207805
title: Egypt Gold Prices | Daily Updated
DOI: 10.5281/zenodo.10361035
title: EPFL EPFL_2009 11 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 11 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/11.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361022
title: EPFL EPFL_2009 13 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 13 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/13.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361023
title: EPFL EPFL_2009 13 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 13 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/13.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.6718813
title: Matrix N, TEs vs promoters, weighted with L = 1e5kb

description: Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 1e5kb
DOI: 10.5281/zenodo.6718812
title: Matrix N, TEs vs promoters, weighted with L = 2.5e5kb, hg19

description: Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 2.5e5kb
DOI: 10.5281/zenodo.8117257
title: Matrix N, TEs vs promoters, weighted with L = 2.5e5kb, hg19

description: Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 2.5e5kb
DOI: 10.5281/zenodo.6818282
title: Matrices N, TEs vs promoters, weighted with L in [1e3kB, 1e10kB], hg19

description: Related to "Statistical learning quantifies transposable element-mediated cis-regulation", Pulver et al. 2023


Regulatory susceptibility matrices N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with varying bandwiths spanning the range L = 1e3kB to 1e10kB.


The "TAD_restricted" N matrices were built by bounding the distances until which TEs were considered as putative cis-regulatory elements for protein-coding genes to TAD boundaries. Pairs of genes - TEs that do not overlap TADs are weighted irrespective of TAD boundaries.


The "weighted_mappability" N matrices only contain selected subfamilies and should be incorporated into N_weighted computed with L = 2.5e5kb before usage. Low vs high mappability fractions of subfamilies were separated using a median split on per-integrant average mappability scores.
DOI: 10.5281/zenodo.6818283
title: Matrices N, TEs vs promoters, weighted with L in [1e3kB, 1e10kB]

description: Regulatory susceptibility matrices N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with varying bandwiths spanning the range L = 1e3kB to 1e10kB.
DOI: 10.5281/zenodo.7863295
title: Matrices N, TEs vs promoters, weighted with L in [1e3kB, 1e10kB]

description: Regulatory susceptibility matrices N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with varying bandwiths spanning the range L = 1e3kB to 1e10kB.
DOI: 10.5281/zenodo.8117286
title: Matrices N, TEs vs promoters, weighted with L in [1e3kB, 1e10kB], hg19

description: Related to "Statistical learning quantifies transposable element-mediated cis-regulation", Pulver et al. 2023


Regulatory susceptibility matrices N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with varying bandwiths spanning the range L = 1e3kB to 1e10kB.


The "TAD_restricted" N matrices were built by bounding the distances until which TEs were considered as putative cis-regulatory elements for protein-coding genes to TAD boundaries. Pairs of genes - TEs that do not overlap TADs are weighted irrespective of TAD boundaries.


The "weighted_mappability" N matrices only contain selected subfamilies and should be incorporated into N_weighted computed with L = 2.5e5kb before usage. Low vs high mappability fractions of subfamilies were separated using a median split on per-integrant average mappability scores.
DOI: 10.5281/zenodo.6769793
title: Functional matrices N, TEs vs promoters, weighted with L = 2.5e5kb, hg19

description: Refers to the manuscript: "Statistical learning quantifies transposable element-mediated cis-regulation", by Pulver et al., 2023.


 


TE subfamilies are split between so-called "functional" and complementary "non-functional" fractions. Functional integrants were defined as such based on overlapping epigenomics data (e.g. transcription factor binding by ChIP-seq, open chromatin by ATAC-seq).


 


The "functional_weighted_mappability" only contain cis-regulatory weights for selected subfamilies, split between low and high mappability (median split over averages per integrants). They should be incorporated into N_functional_weighted matrices for the appropriate experiments, and not be used on their own.
DOI: 10.5281/zenodo.6769794
title: Functional matrices N, TEs vs promoters, weighted with L = 1e5kb

description: TE subfamilies are split between so-called "functional" and complementary "non-functional" fractions. Functional integrants were defined as such based on overlapping epigenomics data (e.g. transcription factor binding by ChIP-seq, open chromatin by ATAC-seq).
DOI: 10.5281/zenodo.8117285
title: Functional matrices N, TEs vs promoters, weighted with L = 2.5e5kb, hg19

description: Refers to the manuscript: "Statistical learning quantifies transposable element-mediated cis-regulation", by Pulver et al., 2023.


 


TE subfamilies are split between so-called "functional" and complementary "non-functional" fractions. Functional integrants were defined as such based on overlapping epigenomics data (e.g. transcription factor binding by ChIP-seq, open chromatin by ATAC-seq).


 


The "functional_weighted_mappability" only contain cis-regulatory weights for selected subfamilies, split between low and high mappability (median split over averages per integrants). They should be incorporated into N_functional_weighted matrices for the appropriate experiments, and not be used on their own.
DOI: 10.5281/zenodo.6707954
title: Matrix N, TEs vs promoters, 100kb-wide windows, hg19

description: Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene.
DOI: 10.5281/zenodo.6707955
title: Matrix N, TEs vs promoters, 100kb-wide windows, hg19

description: Regulatory susceptibility matrix N, with rows as hg19 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene.
DOI: 10.5281/zenodo.10361040
title: EPFL EPFL_2009 23 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 23 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/23.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361041
title: EPFL EPFL_2009 23 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 23 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/23.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10390240
title: ХИМИЧЕСКИЙ СОСТАВ ЭФИРНОГО МАСЛА ROEMERIA HYBRIDA, ПРОИЗРАСТАЮЩЕГО В УЗБЕКИСТАНЕ
DOI: 10.5281/zenodo.10390241
title: ХИМИЧЕСКИЙ СОСТАВ ЭФИРНОГО МАСЛА ROEMERIA HYBRIDA, ПРОИЗРАСТАЮЩЕГО В УЗБЕКИСТАНЕ
DOI: 10.5281/zenodo.10361049
title: EPFL EPFL_2009 41 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 41 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/41.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361048
title: EPFL EPFL_2009 41 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 41 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/41.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361053
title: EPFL EPFL_2009 21 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 21 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/21.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10361052
title: EPFL EPFL_2009 21 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_2009 21 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_2009/metadata/21.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10390213
title: JWST ERS Ice Age working version internal repository

description: Test version of the eventual repository for the full set of "working" version of the Ice Age data, as of December 2023.
DOI: 10.5281/zenodo.10390212
title: JWST ERS Ice Age working version internal repository

description: Test version of the eventual repository for the full set of "working" version of the Ice Age data, as of December 2023.
DOI: 10.5281/zenodo.10390247
title: Matrix N, TEs vs promoters, 100kb-wide windows, hg38

description: Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.
DOI: 10.5281/zenodo.10390246
title: Matrix N, TEs vs promoters, 100kb-wide windows, hg38

description: Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.
DOI: 10.5281/zenodo.10360990
title: EPFL EPFL_ROOF_2008 40 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2008 40 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2008/metadata/40.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360989
title: EPFL EPFL_ROOF_2008 40 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2008 40 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2008/metadata/40.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10390261
title: Matrix N, TEs vs promoters, weighted with L = 2.5e5kb, hg38

description: Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 2.5e5kb. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.
DOI: 10.5281/zenodo.10390262
title: Matrix N, TEs vs promoters, weighted with L = 2.5e5kb, hg38

description: Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with a bandwidth L = 2.5e5kb. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.
DOI: 10.5281/zenodo.10360991
title: EPFL EPFL_ROOF_2008 03 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2008 03 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2008/metadata/03.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360992
title: EPFL EPFL_ROOF_2008 03 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2008 03 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2008/metadata/03.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .
DOI: 10.5281/zenodo.10360993
title: EPFL EPFL_ROOF_2008 01 disdrometer station data

description: Disdrometer measurements of the EPFL EPFL_ROOF_2008 01 station. This dataset is part of the DISDRODB project. Station metadata are available at https://github.com/ltelab/disdrodb-data/blob/main/DISDRODB/Raw/EPFL/EPFL_ROOF_2008/metadata/01.yml . The software to easily process and standardize the raw data into netCDF files is available at https://github.com/ltelab/disdrodb .