cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29483831.v1
title: Elevated intracellular copper induces CTR1 monomerization and prevents copper uptake

description: The single-molecule localizations generated and analyzed for "Elevated intracellular copper induces CTR1 monomerization and prevents copper uptakes"
DOI: 10.6084/m9.figshare.28255283
title: Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity

description: AcrB_wt_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB wildtype in DDM (apo-state)

AcrB_wt_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric AcrB wildtype in SaliPro-nanodiscs (apo-state)

V612F_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612F variant in DDM (apo-state)

V612F_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612F variant in SaliPro-nanodiscs (apo-state)

V612W_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612W variant in DDM (apo-state)

OqxB_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric OqxB wildtype in SaliPro-nanodiscs (apo-state)

In total:
AcrB wt DDM - 3 maps
AcrB wt SP-ND - 16 maps
V612F DDM - 3 maps
V612F SP-ND - 4 maps
V612W DDM - 6 maps
OqxB wt SP-ND - 6 monomer maps + 1 trimer map
in sum: 39 .mrc files
DOI: 10.6084/m9.figshare.28255283.v1
title: Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity

description: AcrB_wt_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB wildtype in DDM (apo-state)

AcrB_wt_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric AcrB wildtype in SaliPro-nanodiscs (apo-state)

V612F_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612F variant in DDM (apo-state)

V612F_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612F variant in SaliPro-nanodiscs (apo-state)

V612W_apo_DDM:
Single particle cryo-EM maps (.mrc) of trimeric AcrB V612W variant in DDM (apo-state)

OqxB_apo_SP-ND:
Single particle cryo-EM maps (.mrc) of trimeric OqxB wildtype in SaliPro-nanodiscs (apo-state)

In total:
AcrB wt DDM - 3 maps
AcrB wt SP-ND - 16 maps
V612F DDM - 3 maps
V612F SP-ND - 4 maps
V612W DDM - 6 maps
OqxB wt SP-ND - 6 monomer maps + 1 trimer map
in sum: 39 .mrc files
DOI: 10.6084/m9.figshare.30417100
title: Ionomer distribution control via thiophene S-modification of carbon support for high-power proton exchange membrane fuel cells

description: This dataset contains the source data underlying all findings reported in this manuscript and its Supplementary Information.

The data are organized into several parts:

Source Data for Figures: This includes all numerical data used to generate the plots, charts, and graphs in the main text and supplementary figures. Data for each figure are compiled in a single Microsoft Excel (.xlsx) file, with individual sheets named according to the corresponding figure and panel (e.g., 'Figure_1a', 'Figure_S3b').

Computational Data: This section contains the key output files, and processed data from the Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations conducted in this study.
DOI: 10.6084/m9.figshare.30417100.v1
title: Ionomer distribution control via thiophene S-modification of carbon support for high-power proton exchange membrane fuel cells

description: This dataset contains the source data underlying all findings reported in this manuscript and its Supplementary Information.

The data are organized into several parts:

Source Data for Figures: This includes all numerical data used to generate the plots, charts, and graphs in the main text and supplementary figures. Data for each figure are compiled in a single Microsoft Excel (.xlsx) file, with individual sheets named according to the corresponding figure and panel (e.g., 'Figure_1a', 'Figure_S3b').

Computational Data: This section contains the key output files, and processed data from the Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations conducted in this study.
DOI: 10.5281/zenodo.18092984
title: Dataset Curado de ENSANUT 2022 para Análisis de Riesgo de Hipertensión
title: Curated ENSANUT 2022 Dataset for Hypertension Risk Analysis

description: This dataset is a curated and derived dataset constructed from three publicly available datasets of the National Health and Nutrition Survey (ENSANUT) Continua 2022, published by the National Institute of Public Health (INSP) of Mexico and accessible through the official government portal:

https://ensanut.insp.mx/encuestas/ensanutcontinua2022/descargas.php

The original datasets used in this work are:



ensaantro2022_entrega_w.csv (Anthropometry and Blood Pressure Questionnaire)

Determinaciones_bioquímicas_cronicas_deficiencias_9feb23.csv (Biochemical Determinations for Chronic Diseases and Deficiencies)

ensafisica2022_adultos_entrega_w.csv (Physical Activity – Adolescents and Adults)


A comprehensive data curation process was performed, including data cleaning, integration of multiple sources, variable harmonization, removal of inconsistencies, and selection of clinically relevant variables. The resulting dataset provides a unified and analysis-ready structure suitable for statistical analysis and machine learning applications in public health research.

The dataset includes demographic information, biochemical markers, anthropometric measurements, and lifestyle-related variables, such as sex, age, hemoglobin concentration, glucose and insulin levels, lipid profile (total cholesterol, HDL, LDL, triglycerides), creatinine, uric acid, C-reactive protein, ferritin, folate, vitamin B12, vitamin D, weight, height, waist circumference, physical activity indicators, and environmental temperature, among others.

The final column, risk_hypertension, is a binary variable indicating whether an individual is at risk of developing arterial hypertension (1 = at risk, 0 = not at risk). This dataset can be used for the identification of cardiovascular risk factors, epidemiological studies, and the development of predictive models related to hypertension.

This dataset constitutes a derived work. The original data remain the property of ENSANUT and the National Institute of Public Health (INSP). The author does not claim ownership of the original data, but of the processes of data integration, curation, and documentation presented in this work.
DOI: 10.5281/zenodo.18092983
title: Dataset Curado de ENSANUT 2022 para Análisis de Riesgo de Hipertensión
title: Curated ENSANUT 2022 Dataset for Hypertension Risk Analysis

description: This dataset is a curated and derived dataset constructed from three publicly available datasets of the National Health and Nutrition Survey (ENSANUT) Continua 2022, published by the National Institute of Public Health (INSP) of Mexico and accessible through the official government portal:

https://ensanut.insp.mx/encuestas/ensanutcontinua2022/descargas.php

The original datasets used in this work are:



ensaantro2022_entrega_w.csv (Anthropometry and Blood Pressure Questionnaire)

Determinaciones_bioquímicas_cronicas_deficiencias_9feb23.csv (Biochemical Determinations for Chronic Diseases and Deficiencies)

ensafisica2022_adultos_entrega_w.csv (Physical Activity – Adolescents and Adults)


A comprehensive data curation process was performed, including data cleaning, integration of multiple sources, variable harmonization, removal of inconsistencies, and selection of clinically relevant variables. The resulting dataset provides a unified and analysis-ready structure suitable for statistical analysis and machine learning applications in public health research.

The dataset includes demographic information, biochemical markers, anthropometric measurements, and lifestyle-related variables, such as sex, age, hemoglobin concentration, glucose and insulin levels, lipid profile (total cholesterol, HDL, LDL, triglycerides), creatinine, uric acid, C-reactive protein, ferritin, folate, vitamin B12, vitamin D, weight, height, waist circumference, physical activity indicators, and environmental temperature, among others.

The final column, risk_hypertension, is a binary variable indicating whether an individual is at risk of developing arterial hypertension (1 = at risk, 0 = not at risk). This dataset can be used for the identification of cardiovascular risk factors, epidemiological studies, and the development of predictive models related to hypertension.

This dataset constitutes a derived work. The original data remain the property of ENSANUT and the National Institute of Public Health (INSP). The author does not claim ownership of the original data, but of the processes of data integration, curation, and documentation presented in this work.
DOI: 10.6084/m9.figshare.28251827
title: Source Data

description: Source data about our study
DOI: 10.6084/m9.figshare.28251827.v1
title: Source Data

description: Source data about our study
DOI: 10.6084/m9.figshare.30453212
title: Strain Engineering of Single-site Cu on SWCNTs for Highly Efﬁcient Diene Cyclopropanation

description: Raman, XPS, XAFS, reaction dynamics, molecular dynamics data and structures.
DOI: 10.6084/m9.figshare.30453212.v1
title: Strain Engineering of Single-site Cu on SWCNTs for Highly Efﬁcient Diene Cyclopropanation

description: Raman, XPS, XAFS, reaction dynamics, molecular dynamics data and structures.
DOI: 10.6084/m9.figshare.30615818
title: Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

description: Supplementary Data 1. Proteins identified by XLMS of PIP5Pase-V5 immunoprecipitation. 
Total proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations with anti-V5 monoclonal antibodies. The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 2. Enrichment analysis of PIP5Pase-V5 immunoprecipitations. 
Enrichment analysis of PIP5Pase-V5 immunoprecipitations (11 biological replicates) with anti-V5 monoclonal antibodies compared to immunoprecipitations in cells that do not express V5-tagged PIP5Pase (4 biological replicates). The data shows a complete list of proteins and a subset of enriched proteins (log2 fold-change ≥ 2, p-value ≤ 0.05) selected based on their co-immunoprecipitations with PIP5Pase from previous mass spectrometry data 13, 33. All peptides identified for a protein were used for the analysis, comparing peptide spectral matches between groups. 

Supplementary Data 3. Nuclear proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations.
Nuclear proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations with anti-V5 monoclonal antibodies. The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 4. PIP5Pase-V5 direct and counterpart interactions identified by XLMS. 
The data show the complete list of cross-linked proteins, as well as multiple cross-linked proteins (i.e., proteins cross-linking with more than 6 proteins or between 3 and 6 proteins). The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 5. In vitro cross-linked proteins identified after PIP5Pase-V5 immunoprecipitation. 
Proteins identified after PIP5Pase-V5 immunoprecipitation with anti-V5 monoclonal antibodies followed by in vitro cross-linking. The immunoprecipitated proteins were cross-linked in vitro with 0.25 mM of DSS for 10 minutes, quenched with 50 mM glycine before digestion and mass spectrometry analysis. The data show results with 1% FDR. 

Supplementary Data 6. Analysis of TADs and loops from Hi-C and Pore-C data. 
The data shows TADs identified searching Hi-C or Pore-C matrices at 1Kb, 10 Kb, and 50 Kb resolutions. It also shows all merged TADs from Hi-C data, all merged TADs from Pore-C data, and all merged TADs from Hi-C and Pore-C data. TAD relatedness is also shown, i.e., TADs which are found within overlapping regions. The data also includes the list of loops identified in the Hi-C data using a 10 Kb resolution matrix.
DOI: 10.6084/m9.figshare.30615818.v1
title: Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

description: Supplementary Data 1. Proteins identified by XLMS of PIP5Pase-V5 immunoprecipitation. 
Total proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations with anti-V5 monoclonal antibodies. The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 2. Enrichment analysis of PIP5Pase-V5 immunoprecipitations. 
Enrichment analysis of PIP5Pase-V5 immunoprecipitations (11 biological replicates) with anti-V5 monoclonal antibodies compared to immunoprecipitations in cells that do not express V5-tagged PIP5Pase (4 biological replicates). The data shows a complete list of proteins and a subset of enriched proteins (log2 fold-change ≥ 2, p-value ≤ 0.05) selected based on their co-immunoprecipitations with PIP5Pase from previous mass spectrometry data 13, 33. All peptides identified for a protein were used for the analysis, comparing peptide spectral matches between groups. 

Supplementary Data 3. Nuclear proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations.
Nuclear proteins identified by XLMS of PIP5Pase-V5 immunoprecipitations with anti-V5 monoclonal antibodies. The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 4. PIP5Pase-V5 direct and counterpart interactions identified by XLMS. 
The data show the complete list of cross-linked proteins, as well as multiple cross-linked proteins (i.e., proteins cross-linking with more than 6 proteins or between 3 and 6 proteins). The data show combined results from 11 biological replicates with an FDR of 1%. 

Supplementary Data 5. In vitro cross-linked proteins identified after PIP5Pase-V5 immunoprecipitation. 
Proteins identified after PIP5Pase-V5 immunoprecipitation with anti-V5 monoclonal antibodies followed by in vitro cross-linking. The immunoprecipitated proteins were cross-linked in vitro with 0.25 mM of DSS for 10 minutes, quenched with 50 mM glycine before digestion and mass spectrometry analysis. The data show results with 1% FDR. 

Supplementary Data 6. Analysis of TADs and loops from Hi-C and Pore-C data. 
The data shows TADs identified searching Hi-C or Pore-C matrices at 1Kb, 10 Kb, and 50 Kb resolutions. It also shows all merged TADs from Hi-C data, all merged TADs from Pore-C data, and all merged TADs from Hi-C and Pore-C data. TAD relatedness is also shown, i.e., TADs which are found within overlapping regions. The data also includes the list of loops identified in the Hi-C data using a 10 Kb resolution matrix.
DOI: 10.57903/uj/7gc2br
title: The influence of caffeine on siesta and nighttime sleep in Drosophila melanogaster - research data

description: Excel file of the raw data.
DOI: 10.6084/m9.figshare.30198562
title: State-correlated reaction dynamics unveiled in full from a single product-image measurement

description: The datasets contain both experimental and theoretical results.
DOI: 10.6084/m9.figshare.30198562.v1
title: State-correlated reaction dynamics unveiled in full from a single product-image measurement

description: The datasets contain both experimental and theoretical results.
DOI: 10.6084/m9.figshare.30126502
title: Tumbleweed-inspired robots with hybrid mobility for terrestrial exploration

description: Nature's tumbleweeds harbour an aerodynamic secret: strategic holes that amplify drag and improve wind dispersal. Scientists decoded this and engineered bio-inspired drones that harness wind for rolling and switch to flight when needed.
DOI: 10.6084/m9.figshare.30126502.v1
title: Tumbleweed-inspired robots with hybrid mobility for terrestrial exploration

description: Nature's tumbleweeds harbour an aerodynamic secret: strategic holes that amplify drag and improve wind dispersal. Scientists decoded this and engineered bio-inspired drones that harness wind for rolling and switch to flight when needed.
DOI: 10.6084/m9.figshare.28620101
title: Wnt signaling restores evolutionary loss of regenerative potential in Hydra

description: The regenerative potential of animals varies widely, even among closely-related species. In a comparative study of regeneration across the Hydra genus, we found that while most species exhibit robust whole-body regeneration, Hydra oligactis and other members of the Oligactis clade consistently fail to regenerate their feet. To investigate the mechanisms underlying this deficiency, we analyzed transcriptional responses during head and foot regeneration in H. oligactis. Our analysis revealed that the general injury response in H. oligactis lacks activation of Wnt signaling, a pathway essential for Hydra vulgaris foot regeneration. Notably, transient treatment with a Wnt agonist in H. oligactis triggered a foot-specific transcriptional program, successfully rescuing foot regeneration. Our transcriptional profiling also revealed dlx2 as a likely high-level regulator of foot regeneration, dependent on Wnt signaling activation. Our study establishes a comparative framework for understanding the molecular basis of regeneration and its evolutionary loss in closely-related species. The experimental design of this study included transcriptional profiling of H. oligactis head and foot regeneration, all timepoints, tissues and treatment included at least 3 biological samples each composed of tissue extracted from ~30 animals. A first batch of Illumina sequencing was comprised of 4 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue at 0, 3, 12 and 48 hours after a transverse bisection at the midpoint of the body column. Regenerating tissue was collected by cutting 1/3 of the body column adjacent to the wound site. Homeostatic heads and feet and 0 hpa head and foot regenerating tissue were treated for 30 seconds with 0.05% DMSO, while 3, 12 and 48 hpa samples were left in 0.5% DMSO for 3 hours before washing. In addition, this first sequencing batch included at least 3 biological replicates of foot regenerating tissue treated with Alsterpaullone 5 uM for 3 hours after amputation and collected at 3, 12 and 48 hours hpa. A second RNA-sequencing batch was comprised of 2 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue collected at 0 and 24 hpa after 0.05% DMSO treatment and foot regenerating tissue collected at 24 hpa after treatment a 3 hours treatment with 5uM Alsterpaullone. In total this dataset is comprised of 60 RNA-seq samples.
DOI: 10.6084/m9.figshare.28620101.v1
title: Wnt signaling restores evolutionary loss of regenerative potential in Hydra

description: The regenerative potential of animals varies widely, even among closely-related species. In a comparative study of regeneration across the Hydra genus, we found that while most species exhibit robust whole-body regeneration, Hydra oligactis and other members of the Oligactis clade consistently fail to regenerate their feet. To investigate the mechanisms underlying this deficiency, we analyzed transcriptional responses during head and foot regeneration in H. oligactis. Our analysis revealed that the general injury response in H. oligactis lacks activation of Wnt signaling, a pathway essential for Hydra vulgaris foot regeneration. Notably, transient treatment with a Wnt agonist in H. oligactis triggered a foot-specific transcriptional program, successfully rescuing foot regeneration. Our transcriptional profiling also revealed dlx2 as a likely high-level regulator of foot regeneration, dependent on Wnt signaling activation. Our study establishes a comparative framework for understanding the molecular basis of regeneration and its evolutionary loss in closely-related species. The experimental design of this study included transcriptional profiling of H. oligactis head and foot regeneration, all timepoints, tissues and treatment included at least 3 biological samples each composed of tissue extracted from ~30 animals. A first batch of Illumina sequencing was comprised of 4 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue at 0, 3, 12 and 48 hours after a transverse bisection at the midpoint of the body column. Regenerating tissue was collected by cutting 1/3 of the body column adjacent to the wound site. Homeostatic heads and feet and 0 hpa head and foot regenerating tissue were treated for 30 seconds with 0.05% DMSO, while 3, 12 and 48 hpa samples were left in 0.5% DMSO for 3 hours before washing. In addition, this first sequencing batch included at least 3 biological replicates of foot regenerating tissue treated with Alsterpaullone 5 uM for 3 hours after amputation and collected at 3, 12 and 48 hours hpa. A second RNA-sequencing batch was comprised of 2 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue collected at 0 and 24 hpa after 0.05% DMSO treatment and foot regenerating tissue collected at 24 hpa after treatment a 3 hours treatment with 5uM Alsterpaullone. In total this dataset is comprised of 60 RNA-seq samples.
DOI: 10.6084/m9.figshare.30118162
title: Rescuing the bacterial replisome at a nick: essential functions for recombinational repair and helicase reloading

description: DNA damage occurs in all cells and must be repaired to maintain genome integrity. Many DNA lesions are targeted for removal by repair systems that excise the damage, thereby generating a temporary single-strand discontinuity in the chromosome. If DNA repair has not been completed prior to a round of genome duplication, the single-strand discontinuity (nick or gap) can be converted to a double-strand break (DSB) by an oncoming replication fork. Because the genomic location of nucleobase damage is stochastic, investigating the fate of replication machinery (replisome) at DNA repair sites with single-strand discontinuities has been limited. Here we have addressed this issue by expressing Cas9 nickases in Bacillus subtilis to create site specific single-strand discontinuities in a bacterial chromosome. We find that a nick in either leading or lagging strand arrests DNA replication, while the fate of the replicative helicase is distinct and depends upon the strand nicked. Genetic, biochemical, and single cell analyses indicate that replisome/nick encounters generate a single-end DSB which requires recombinational repair to enable PriA-dependent replication restart. Together this work defines the physiologically relevant pathway used by B. subtilis to reinitiate DNA synthesis following replication fork inactivation at a single-strand discontinuity.
DOI: 10.6084/m9.figshare.30768716
title: Alfalfa Genome

description: ZM-4 near T2T genome
DOI: 10.6084/m9.figshare.30768716.v1
title: Alfalfa Genome

description: ZM-4 near T2T genome