cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11202595
title: Lignocellulose Degradation in Bacteria and Fungi for Biomass Conversion

description: Lignocellulose biomass is one of the most abundant resources for sustainable biofuels. However, scaling up the biomass-to-biofuels conversion process for widespread usage is still pending due to the high cost of enzymes and the labor-intensive need for substrate-dependent enzyme mixtures. Current research efforts are therefore targeted at searching for or engineering lignocellulolytic enzymes of high efficiency. Some microorganisms produce multi-enzyme complexes called cellulosomes for increased degradation efficiency up to 50-fold.

Here we examined the presence of cellulosomes in all bacterial and fungal species with protein sequences available. By using cellulosome proteins of one bacteria and one fungi as search queries, a sequence similarity search was performed in two databases: 1) the non-redundant database and 2) the EnsemblFungi database.
DOI: 10.5281/zenodo.13324669
title: Lignocellulose Degradation in Bacteria and Fungi for Biomass Conversion

description: Lignocellulose biomass is one of the most abundant resources for sustainable biofuels. However, scaling up the biomass-to-biofuels conversion process for widespread usage is still pending due to the high cost of enzymes and the labor-intensive need for substrate-dependent enzyme mixtures. Current research efforts are therefore targeted at searching for or engineering lignocellulolytic enzymes of high efficiency. Some microorganisms produce multi-enzyme complexes called cellulosomes for increased degradation efficiency up to 50-fold.

Here we examined the presence of cellulosomes in all bacterial and fungal species with protein sequences available. By using cellulosome proteins of one bacteria and one fungi as search queries, a sequence similarity search was performed in two databases: 1) the non-redundant database and 2) the EnsemblFungi database.
DOI: 10.6084/m9.figshare.26704911
title: Additional file 1 of “So at least now I know how to deal with things myself, what I can do if it gets really bad again”—experiences with a long-term cross-sectoral advocacy care and case management for severe multiple sclerosis: a qualitative study

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.26704911.v1
title: Additional file 1 of “So at least now I know how to deal with things myself, what I can do if it gets really bad again”—experiences with a long-term cross-sectoral advocacy care and case management for severe multiple sclerosis: a qualitative study

description: Supplementary Material 1.
DOI: 10.15468/dl.xvt3gb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((149.014046 -32.899241, 149.014046 -32.903733, 149.016292 -32.903733, 149.016292 -32.899241, 149.014046 -32.899241))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067879-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26704935
title: Additional file 2 of Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.26704935.v1
title: Additional file 2 of Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.26615863
title: Additional file 2 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 2: Supplementary File 2. circRNA_enrich by LATS1.
DOI: 10.6084/m9.figshare.26704941
title: Additional file 1 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.26704941.v1
title: Additional file 1 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.26704944
title: Additional file 2 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26704944.v1
title: Additional file 2 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26704947
title: Additional file 3 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26704947.v1
title: Additional file 3 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26704950.v1
title: Additional file 4 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26615872.v1
title: Additional file 5 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 5: Supplementary File 5. TCCSUP circXRN2-vs-NC-RNA-seq.
DOI: 10.6084/m9.figshare.26704950
title: Additional file 4 of Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26615875
title: Additional file 6 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 6: Supplementary File 6. CUT&Tag with H3K18la in T24.peak.annotation.
DOI: 10.6084/m9.figshare.26615869.v1
title: Additional file 4 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 4: Supplementary File 4. T24 circXRN2-vs-NC-RNA-seq.
DOI: 10.6084/m9.figshare.26615863.v1
title: Additional file 2 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 2: Supplementary File 2. circRNA_enrich by LATS1.
DOI: 10.6084/m9.figshare.26615875.v1
title: Additional file 6 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 6: Supplementary File 6. CUT&Tag with H3K18la in T24.peak.annotation.
DOI: 10.15468/dl.a42nne
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trachemys scripta elegans (Wied, 1838))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Specimen)",
 "Country is one of (Singapore)",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 20000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067880-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26705001
title: Additional file 5 of Large variations in atrial fibrillation screening practice after ischemic stroke and transient ischemic attack in Sweden: a survey study

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.26705001.v1
title: Additional file 5 of Large variations in atrial fibrillation screening practice after ischemic stroke and transient ischemic attack in Sweden: a survey study

description: Supplementary Material 5
DOI: 10.15468/dl.jzhs9e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.052844 -32.901487, 148.052844 -32.903733, 148.05509 -32.903733, 148.05509 -32.901487, 148.052844 -32.901487))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067881-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26705034
title: Additional file 1 of Endomucin selectively regulates vascular endothelial growth factor receptor-2 endocytosis through its interaction with AP2

description: Additional file 1: Supplemental Figure 1. Markov Clustering of EMCN-binding proteins identified by mass spectrometry. (A) EMCN-binding proteins identified through mass spectrometry were analyzed and visualized using the STRING database (https://string-db.org/). The network type was set to physical subnetwork, and the significance of network edges was based on confidence, with a minimum required interaction score of high confidence (0.700). Further functional clustering of EMCN-binding proteins was performed using Markov clustering. Proteins within the same cluster were connected by solid lines and marked with the same color, while dashed lines indicated boundaries between clusters. (B) The table lists the top five protein clusters with the highest number of proteins. Supplemental Figure 2. Confirmation of EMCN knockdown. (A) Representative image of the western blot assay showing significant reduction of EMCN at protein level in HRECs transfected with siEMCN compared to siNT control. (B) Quantification of EMCN protein by western blot analysis demonstrates a significant decrease of EMCN at 72 hr after transfection. Student-t test was used. ****P&lt;0.0001, n=3. (C) Quantification of EMCN mRNA indicates a significant decrease of EMCN (1.024 ± 0.126 vs. 0.0128 ± 0.0003) at 48 hr after transfection. Student-t test was used. ****P&lt;0.0001, n=3.
DOI: 10.6084/m9.figshare.26705034.v1
title: Additional file 1 of Endomucin selectively regulates vascular endothelial growth factor receptor-2 endocytosis through its interaction with AP2

description: Additional file 1: Supplemental Figure 1. Markov Clustering of EMCN-binding proteins identified by mass spectrometry. (A) EMCN-binding proteins identified through mass spectrometry were analyzed and visualized using the STRING database (https://string-db.org/). The network type was set to physical subnetwork, and the significance of network edges was based on confidence, with a minimum required interaction score of high confidence (0.700). Further functional clustering of EMCN-binding proteins was performed using Markov clustering. Proteins within the same cluster were connected by solid lines and marked with the same color, while dashed lines indicated boundaries between clusters. (B) The table lists the top five protein clusters with the highest number of proteins. Supplemental Figure 2. Confirmation of EMCN knockdown. (A) Representative image of the western blot assay showing significant reduction of EMCN at protein level in HRECs transfected with siEMCN compared to siNT control. (B) Quantification of EMCN protein by western blot analysis demonstrates a significant decrease of EMCN at 72 hr after transfection. Student-t test was used. ****P&lt;0.0001, n=3. (C) Quantification of EMCN mRNA indicates a significant decrease of EMCN (1.024 ± 0.126 vs. 0.0128 ± 0.0003) at 48 hr after transfection. Student-t test was used. ****P&lt;0.0001, n=3.
DOI: 10.6084/m9.figshare.26615869
title: Additional file 4 of CircXRN2 suppresses tumor progression driven by histone lactylation through activating the Hippo pathway in human bladder cancer

description: Additional file 4: Supplementary File 4. T24 circXRN2-vs-NC-RNA-seq.
DOI: 10.15468/dl.cjm9bc
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trachemys scripta elegans (Wied, 1838))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "BasisOfRecord is one of (Human Observation)",
 "Country is one of (Australia)",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 20000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 21 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067882-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26615827
title: Additional file 1 of Pyrroloquinoline quinone drives ATP synthesis in vitro and in vivo and provides retinal ganglion cell neuroprotection

description: Additional file 1: Dataset 1. Raw mass spectrometry data (area under the curve), weight normalized results, comparisons, and pathway analysis.
DOI: 10.15468/dl.tpvm42
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gastrolobium latifolium (R.Br.) G.Chandler & Crisp"
 ]
}

 The dataset includes 195 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022216-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.948511
title: Stable water isotopes of snow during MOSAiC expedition

description: Snow samples were collected from several locations on the main MOSAiC ice floe on weekly basis. Snow samples for measurement of stable water isotopes (δ18O, δD,) were collected in three different layers (top, middle, bottom) using a metal density cutter. At first, samples were stored in sealed plastic bags and the air was squeezed out before closing the bags. At later stages of the expedition, samples were stored in plastic cups with lids. Later the samples were thawed completely at room temperature and poured into 20 ml glass vials and sealed with parafilm tape and stored at 4°C. Oxygen and hydrogen isotope analyses were carried out at the ISOLAB Facility at AWI Potsdam (https://hdl.handle.net/10013/sensor.ddc92f54-4c63-492d-81c7-696260694001) with mass spectrometers (DELTA-S Finnigan MAT, USA): https://hdl.handle.net/10013/sensor.af148dea-fe65-4c87-9744-50dc4c81f7c9 https://hdl.handle.net/10013/sensor.62e86761-9fae-4f12-9c10-9b245028ea4c. employing the equilibration method (details in Meyer et al., 2000). δ18O and δD values were given in per mil (‰) vs. Vienna standard mean ocean water (V-SMOW) as the standard. The second order parameter d excess was computed according to: d excess = δD-8 δ18O (Dansgaard, 1964).
DOI: 10.1594/pangaea.958466
title: Stable water isotopes of sea ice at Main Coring Site (MCS) during MOSAiC expedition

description: Sea ice cores were collected from the Biogeochemistry (BGC) team at different stations located on the main ice floe of MOSAiC expedition. Flat sea ice on the floe was categorized into three types based on the age: sea ice which grew during the same winter referred to as First-Year-Ice (FYI); sea ice which had survived one or more summer melting periods referred to as Second-Year-Ice (SYI). Sea ice cores were collected using a Kovacs Mark II 9 cm diameter corer. The core was extracted and placed in an aluminum holder equipped with a metric ruler. Using a standard Kovacs ice thickness gauge, the freeboard was taken and the length of the core was measured. The snow on top of the sea ice was brushed off the top of the cores to minimize the snow affecting the ice surface. Onboard RV Polarstern, the cores were cut in 10 cm sections using a handsaw at 4° C (leg 1) or an electric saw at -20° C (legs 2 and 3). Each section was transferred into a gas-tight TedlarTM bag. The closed bags were carefully degassed with a vacuum pump (NKF Neuberger, type N035). Melting occurred within 12 to 15 hours in a water bath in the dark. After shaking the melted ice within the TedlarTM bags, discrete sampling started by first rising the melt water carefully through a Tygon tube connected with the opened valves of the gas tide bags and then into prepared sample vials. Here we present the data from samples collected at Main Core Site (MCS) at the Dark Sector (DS).Oxygen and hydrogen isotope analyses were carried out at the ISOLAB Facility at AWI Potsdam (https://hdl.handle.net/10013/sensor.ddc92f54-4c63-492d-81c7-696260694001) with mass spectrometers (DELTA-S Finnigan MAT, USA): https://hdl.handle.net/10013/sensor.af148dea-fe65-4c87-9744-50dc4c81f7c9 https://hdl.handle.net/10013/sensor.62e86761-9fae-4f12-9c10-9b245028ea4c employing the equilibration method (details in Meyer et al., 2000). δ18O and δD values were given in per mil (‰) vs. Vienna standard mean ocean water (V-SMOW) as the standard. The second order parameter d excess was computed according to: d excess = δD-8 δ18O (Dansgaard, 1964).
DOI: 10.21227/xh2f-kh37
title: Multimodal Object Detection dataset

description: VEDAI: The VEDAI dataset comprises 1246 high-resolution RGB and infrared images, containing 3640 objects categorized into 8 common vehicle classes. Each image, with a resolution of 1024 × 1024 pixels, spans diverse terrains and environments. Notably, vehicles occupy only a small portion of the image pixels, making small object detection particularly challenging.DroneVehicle: The DroneVehicle dataset is a large-scale RGB-IR (visible-light and infrared) multimodal dataset designed for vehicle detection in drone imagery. It encompasses a variety of shooting conditions and scenarios, covering different perspectives, altitudes, and lighting conditions. The dataset includes five vehicle categories: car, truck, bus, van, and freight-car.
DOI: 10.15468/dl.vw83j6
title: Occurrence Download

description: A dataset containing 5689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "TaxonKey is Phoca vitulina Linnaeus, 1758"
 ]
}

 The dataset includes 5689 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022217-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hv7w88
title: Occurrence Download

description: A dataset containing 21657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "TaxonKey is Lagopus muta (Montin, 1781)"
 ]
}

 The dataset includes 21657 records from 167 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022218-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.msad4z
title: Occurrence Download

description: A dataset containing 113472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Martes martes (Linnaeus, 1758)"
 ]
}

 The dataset includes 113472 records from 1142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022204-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13895748
title: Depletion-dependent Activity-Based Protein Profiling coupled to SWATH/DIA Mass Spectrometry detects serine hydrolase lipid remodeling in lung adenocarcinoma progression
title: Relative comparison of FA levels obtained through a full scan untargeted LC-HRMS profiling and in-house library matching based on accurate mass and retention time (AMRT) . Raw.data. Agilent 6550 IonFunnel QTOF
title: Absolute quantification of FA of interest  raw.data.validation_with_standards_Orbitrap™ IQ-X™ Tribrid™ MS

description: These raw data correspond to a lipidomic analysis of free fatty acids in tumour biopsies to validate the results of the chemical proteomic method. 

Main point of the study

The results of proteomic profiling of (clinical) sample cohorts are generally assumed to more closely represent the functional state of the samples tested than transcript profiles. Yet, standard proteomic methods display the abundance and not the state of activity of the detected proteins. Systematic profiling of enzyme activities in the context of whole proteome measurements would provide a further significant step towards the description of the functional state of a cell. 

We describe a novel concept in chemoproteomics that concurrently quantifies the active and inactive fraction and the total amount of tested enzymes in the context of the total tissue proteome. The method relies on well tested  activity-based probes  but used advanced mass spectrometric and bespoke software tools to generate mechanistic insights into the regulations of enzyme activity.  

The method was benchmarked against state of the art techniques and applied to classify a cohort of lung adenocarcinoma tissues into aggressive and less aggressive samples based the activity profiles of serine hydrolases and to propose a mechanistic explanation of the disease phenotypes based on environmental and genetic vulnerabilities of patients.
DOI: 10.5281/zenodo.13895747
title: Depletion-dependent Activity-Based Protein Profiling coupled to SWATH/DIA Mass Spectrometry detects serine hydrolase lipid remodeling in lung adenocarcinoma progression
title: Experiment 1 - Relative comparison of Fatty acids. Raw.data recorded on Agilent 6550 IonFunnel QTOF
title: Experiment 2 - Absolute quantification of Fatty acids of interest. Raw.data recorded on  Orbitrap™ IQ-X™ Tribrid™ MS

description: These raw data correspond to a lipidomic analysis of free fatty acids in tumour biopsies to validate the results of the chemical proteomic method. 

Main point of the study

The results of proteomic profiling of (clinical) sample cohorts are generally assumed to more closely represent the functional state of the samples tested than transcript profiles. Yet, standard proteomic methods display the abundance and not the state of activity of the detected proteins. Systematic profiling of enzyme activities in the context of whole proteome measurements would provide a further significant step towards the description of the functional state of a cell. 

We describe a novel concept in chemoproteomics that concurrently quantifies the active and inactive fraction and the total amount of tested enzymes in the context of the total tissue proteome. The method relies on well tested  activity-based probes  but used advanced mass spectrometric and bespoke software tools to generate mechanistic insights into the regulations of enzyme activity.  

The method was benchmarked against state of the art techniques and applied to classify a cohort of lung adenocarcinoma tissues into aggressive and less aggressive samples based the activity profiles of serine hydrolases and to propose a mechanistic explanation of the disease phenotypes based on environmental and genetic vulnerabilities of patients.
DOI: 10.5281/zenodo.14688887
title: Pilea database

description: GTDB R220 representative bacterial genomes.