cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.34808/w3jn-h127
title: Study of the influence of the presence of Dr fimbriae on the sedimentation of recombinant Escherichia coli strains: AAEC191A and BL21(DE3)

description: Cell sedimentation in the medium is a common phenomenon in most bacterial enviroments. This study specifically investigated the impact of Dr fimbriae presence on cell deposition. To explore this, recombinant Escherichia coli strains were employed, including BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP, AAEC191A/pCC90, AAEC191A/pACYCpBAD, AAEC191A/pCC90 Dra D-mut, and AAEC191A/pCC90 D54-STOP. Spectroscopic methods were utilized for the measurements.
The dataset contains original photos of test tubes containing overnight cultures of the above-mentioned recombinant strains and a Word document with graphs showing the time dependence of cell precipitation.
DOI: 10.34808/940j-bt07
title: Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90-PBS, PBS+0.2% glucose, PBS+0.5% glucose

description: Microbial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition of the growth medium affects the movement and formation of aggregates of recombinant Escherichia coli strains.
This study focused on several recombinant strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP, AAEC191A/pCC90, AAEC191A /pACYCpBAD, AAEC191A/pCC90 Dra D-mut and AAEC191A/pCC90 D54-STOP. The experimental setup involved transferring a small portion of overnight cultures of these recombinant strains to various media compositions. These media include PBS, PBS + 0.2% glucose, PBS + 0.5% glucose, LB, LB + 0.2% glucose, LB + 0.5% glucose, M9 + 0.5% cassaminic acids, M9 + 0.5% cassaminic acids + 0.2% glucose and M9 + 0.5% cassaminic acids + 0.5% glucose.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/8rxb-8r16
title: Study of the influence of medium composition on the motility and aggregation of the recombinant Escherichia coli strain AAEC191A/pACYCpBAD-LB, LB+0.2% glucose, LB+0.5% glucose

description: Microbial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition of the growth medium affects the movement and formation of aggregates of recombinant Escherichia coli strains.
This study focused on several recombinant strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP, AAEC191A/pCC90, AAEC191A /pACYCpBAD, AAEC191A/pCC90 Dra D-mut and AAEC191A/pCC90 D54-STOP. The experimental setup involved transferring a small portion of overnight cultures of these recombinant strains to various media compositions. These media include PBS, PBS + 0.2% glucose, PBS + 0.5% glucose, LB, LB + 0.2% glucose, LB + 0.5% glucose, M9 + 0.5% cassaminic acids, M9 + 0.5% cassaminic acids + 0.2% glucose and M9 + 0.5% cassaminic acids + 0.5% glucose.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/c7mr-7b23
title: Detection of cellulose production capacity of recombinant Escherichia coli strains BL21(DE3) and AAEC191A

description: Bacteria that form biofilms generate an extracellular matrix (ECM), where cellulose stands out as a key constituent. An approach for assessing microorganisms' cellulose production involves using calcofluor white staining on colonies. In this method, a fluorescent dye (calcofluor-white) is introduced to a stable YESCA substrate composed of casamino acids, agar, and yeast extract. The fluorescent dye specifically attaches to cellulose, enabling bacterial colonies to be observed under ultraviolet light. The study employed YESCA medium supplemented with calcofluor-white, as well as YESCA + 0.2% glucose medium supplemented with calcofluor-white.
The dataset contains original photos of bacterial colonies of the following E. coli strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP AAEC191A/pCC90, AAEC191A/pACYCpBAD, AAEC191A/pCC90 Dra D-mut, AAEC191A/pCC90 D54-STOP, BL21(DE3), AAEC191A and CFT073. Bacteria were cultured in YESCA medium with the addition of calcofluor-white at a temperature of 25 degrees Celsius and 37 degrees Celsius for 5 days. Photographs of the colony were taken at one-day intervals
DOI: 10.34808/eya8-0w63
title: Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain AAEC191A/pCC90 D54-STOP-LB, LB+0.2% glucose, LB+0.5% glucose

description: Microbial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition of the growth medium affects the movement and formation of aggregates of recombinant Escherichia coli strains.
This study focused on several recombinant strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP, AAEC191A/pCC90, AAEC191A /pACYCpBAD, AAEC191A/pCC90 Dra D-mut and AAEC191A/pCC90 D54-STOP. The experimental setup involved transferring a small portion of overnight cultures of these recombinant strains to various media compositions. These media include PBS, PBS + 0.2% glucose, PBS + 0.5% glucose, LB, LB + 0.2% glucose, LB + 0.5% glucose, M9 + 0.5% cassaminic acids, M9 + 0.5% cassaminic acids + 0.2% glucose and M9 + 0.5% cassaminic acids + 0.5% glucose.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/kv57-aw49
title: Study of the influence of medium composition on motility and aggregation of recombinant Escherichia coli strain BL21(DE3)/pCC90-LB, LB+0.2% glucose, LB+0.5% glucose

description: Microbial motility is a fundamental aspect of many microbial life cycles and is a key survival mechanism that enables microorganisms to navigate diverse and dynamic environmental conditions. This phenomenon becomes particularly important in response to changes in stimuli in time and space. The following experiment aimed to investigate how the composition of the growth medium affects the movement and formation of aggregates of recombinant Escherichia coli strains.
This study focused on several recombinant strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP, AAEC191A/pCC90, AAEC191A /pACYCpBAD, AAEC191A/pCC90 Dra D-mut and AAEC191A/pCC90 D54-STOP. The experimental setup involved transferring a small portion of overnight cultures of these recombinant strains to various media compositions. These media include PBS, PBS + 0.2% glucose, PBS + 0.5% glucose, LB, LB + 0.2% glucose, LB + 0.5% glucose, M9 + 0.5% cassaminic acids, M9 + 0.5% cassaminic acids + 0.2% glucose and M9 + 0.5% cassaminic acids + 0.5% glucose.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/9m9b-mw81
title: Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pCC90 to polystyrene in a dynamic system

description: The attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this study, the adherence ability of four genetically modified Escherichia coli strains—BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra, AAEC191A/pCC90, and AAEC191A/pACYCpBAD—was examined on both glass and polystyrene surfaces. The aim was to investigate the effect of the presence of Dr fimbriae on the adherence of bacteria to various carriers. The experiments were performed under various flow conditions.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/4atn-xm47
title: Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to glass in a dynamic system

description: The attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this study, the adherence ability of four genetically modified Escherichia coli strains—BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra, AAEC191A/pCC90, and AAEC191A/pACYCpBAD—was examined on both glass and polystyrene surfaces. The aim was to investigate the effect of the presence of Dr fimbriae on the adherence of bacteria to various carriers. The experiments were performed under various flow conditions.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.6084/m9.figshare.24935934
title: Fission Track and (U-Th)/He Data - Chiloe / North Patagonian Andes

description: Fission Tracks in apatite and (U-Th)/He samples from rocks of Chiloe Island in the North Patagonian Andes.
DOI: 10.6084/m9.figshare.24935934.v1
title: Fission Track and (U-Th)/He Data - Chiloe / North Patagonian Andes

description: Fission Tracks in apatite and (U-Th)/He samples from rocks of Chiloe Island in the North Patagonian Andes.
DOI: 10.6084/m9.figshare.24936054
title: Degradation and protection of cut slopes in weathered gneiss; a 40-year case study

description: A figure showing slope retreat over time and two tables giving details of calculated cross-sectional area losses and approximate inter-sectional volumetric losses of slope material.
DOI: 10.6084/m9.figshare.24936054.v1
title: Degradation and protection of cut slopes in weathered gneiss; a 40-year case study

description: A figure showing slope retreat over time and two tables giving details of calculated cross-sectional area losses and approximate inter-sectional volumetric losses of slope material.
DOI: 10.6084/m9.figshare.24936057
title: Degradation and protection of cut slopes in weathered gneiss; a 40-year case study

description: A figure showing slope retreat over time and two tables giving details of calculated cross-sectional area losses and approximate inter-sectional volumetric losses of slope material.
DOI: 10.6084/m9.figshare.24936057.v1
title: Degradation and protection of cut slopes in weathered gneiss; a 40-year case study

description: A figure showing slope retreat over time and two tables giving details of calculated cross-sectional area losses and approximate inter-sectional volumetric losses of slope material.
DOI: 10.17031/65952aacd76e1
title: 1977 Natural Environment Research Council (NERC) European Continental Slope Ireland RV Shackleton Cruise 2A
title: 1977 NERC European Continental Slope Ireland RV Shackleton Cruise 2A

description: Records from the RV Shackleton Cruise 2A to the European continental slope off the north west coast of Ireland. Samples collected using either an Agassiz trawl, Scottish Marine Biological Association (SMBA) box dredge or rock dredge. Records supplied by Dr. Eve Southward and collated by DASSH as part of the 'Dredging the Depths' project.
DOI: 10.5281/zenodo.10453442
title: Datasets of positive and negative miRNA-target interactions

description: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Computational approaches that predict miRNA target interactions (MTIs) facilitate the process of narrowing down potential targets for experimental validation. The availability of new datasets of high-throughput, direct MTIs has led to the development of machine learning (ML) based methods for MTI prediction. To train an ML algorithm, there is a need to supply entries from all class labels (i.e., positive and negative). Currently, no high-throughput assays exist for capturing negative examples, hindering effective classifier construction. Therefore, current ML approaches must rely on artificially generated negative examples for training. Moreover, the lack of uniform standards for generating such data leads to biased results and hampers comparisons between studies.  We investigated the impact of different methods to generate negative data on the classification of true MTIs. The study relies on training ML models on a fixed positive dataset in combination with different negative datasets and evaluating their intra- and cross-dataset performance. As a result, we were able to examine each method independently and evaluate ML models’ sensitivity to the methodologies utilized in negative data generation.


This data include all the negative datasets that generated by the different methods and the positive data that was used.
DOI: 10.5281/zenodo.8199848
title: Datasets of positive and negative miRNA-target interactions

description: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Computational approaches that predict miRNA target interactions (MTIs) facilitate the process of narrowing down potential targets for experimental validation. The availability of new datasets of high-throughput, direct MTIs has led to the development of machine learning (ML) based methods for MTI prediction. To train an ML algorithm, there is a need to supply entries from all class labels (i.e., positive and negative). Currently, no high-throughput assays exist for capturing negative examples, hindering effective classifier construction. Therefore, current ML approaches must rely on artificially generated negative examples for training. Moreover, the lack of uniform standards for generating such data leads to biased results and hampers comparisons between studies. We investigated the impact of different methods to generate negative data on the classification of true MTIs. The study relies on training ML models on a fixed positive dataset in combination with different negative datasets and evaluating their intra- and cross-dataset performance. As a result, we were able to examine each method independently and evaluate ML models’ sensitivity to the methodologies utilized in negative data generation. This data include all the negative datasets that generated by the different methods and the positive data that was used.
DOI: 10.6084/m9.figshare.24936051
title: Procrastination, Employability, and Delayed Adulthood of University Students in Poland

description: This empirical research examines links between temperament, procrastination tendencies, and perceived employability among Polish university students. Contextual factors impacting Polish higher education are first discussed, including fluctuating enrollment rates and graduate underemployment.
DOI: 10.34740/kaggle/dsv/7330124
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.4121/21583710
title: Dataset "Methodology for in-situ microsensor profiling of hydrogen, pH, ORP and electric potential throughout 3D porous cathodes of (bio)electrochemical systems"

description: Raw data for Method development of application for microsensors in (bio)electrochemical systems to measure pH, H2 and ORP in 3D graphite cathodes
DOI: 10.4121/21583710.v1
title: Dataset "Methodology for in-situ microsensor profiling of hydrogen, pH, ORP and electric potential throughout 3D porous cathodes of (bio)electrochemical systems"

description: Raw data for Method development of application for microsensors in (bio)electrochemical systems to measure pH, H2 and ORP in 3D graphite cathodes
DOI: 10.5281/zenodo.10450588
title: SETDB1 modulates the TGFβ response in Duchenne muscular dystrophy myotubes

description: The R source code to reproduce all the analyses for the study "SETDB1 modulates the TGFβ response in Duchenne muscular dystrophy myotubes" as well as the raw BAM files ffrom the WT experiment.

Data files have been generated under the colaboration of the late Armando Felsani from CNR (Italy) and all this work is dedicated to his memory!

All code is produced by Costas Bouyioukos with small contributions of Alice Granados.

Code is released under a GNU GPL v3.0 or later license and data under a CC Attribution 4.0 International license.

(this repository contains the WT experiment files, the DMD BAM files are on: 

10.5281/zenodo.10453818 )
DOI: 10.5281/zenodo.10450589
title: SETDB1 modulates the TGFβ response in Duchenne muscular dystrophy myotubes

description: The R source code to reproduce all the analyses for the study "SETDB1 modulates the TGFβ response in Duchenne muscular dystrophy myotubes" as well as the raw BAM files ffrom the WT experiment.

Data files have been generated under the colaboration of the late Armando Felsani from CNR (Italy) and all this work is dedicated to his memory!

All code is produced by Costas Bouyioukos with small contributions of Alice Granados.

Code is released under a GNU GPL v3.0 or later license and data under a CC Attribution 4.0 International license.

(this repository contains the WT experiment files, the DMD BAM files are on: 

10.5281/zenodo.10453818 )
DOI: 10.25345/c5610w338
title: MassIVE MSV000093753 - GNPS_WE of ficus carica L 20240103
title: Figs (Ficus carica L.) represents one of the main species of this genus, whose sweet and succulent fruits are widely cultivated and consumed worldwide
DOI: 10.25345/c52805900
title: MassIVE MSV000093754 - Activity-Based Protein Profiling for the identification of HSP90 client proteins in gastric cancer cells
title: Activity-Based Protein Profiling for the identification of HSP90 client proteins in gastric cancer cells
DOI: 10.25345/c5xg9fn5f
title: MassIVE MSV000093755 - GNPS_WP of ficus carica L 20240103
title: Figs (Ficus carica L.) represents one of the main species of this genus, whose sweet and succulent fruits are widely cultivated and consumed worldwide.
DOI: 10.5281/zenodo.10429746
title: Dataset from: Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network

description: Original data and code for the study:

Wei, J., Xu, F., Cole, E. F., Sheldon, B. C., de Boer, W. F., Wielstra, B., Fu, H., Gong, P., & Si, Y. (2024, Accepted). Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network. Global Change Biology.

The dataset mainly contains data showing the climate change-induced heterogeneous shifts in vegetation phenology and the migration integrity change from 2000 to 2020 for 16 Asian herbivorous waterfowl species. These data were derived from the following resources available in the public domain.

The Global Lakes and Wetlands Database is available from “https://www.worldwildlife.org/pages/global-lakes-and-wetlands-database”. The global land cover datasets are available from European Space Agency (ESA) Climate Change Initiative (CCI) products, “https://maps.elie.ucl.ac.be/CCI/viewer/download.php”. The Global Multi-resolution Terrain Elevation Data are available from “https://www.usgs.gov/centers/eros/science/terrain-monitoring-and-modeling”. The Moderate Resolution Imaging Spectroradiometer (MODIS) Terra surface reflectance product is available from “https://modis.gsfc.nasa.gov/data/dataprod/mod09.php”. The bird distribution maps are available from Birdlife International, “https://www.birdlife.org/”. The bird foraging attribute data are available from EltonTraits 1.0, “https://figshare.com”. The bird occurrence data are available from eBird Basic Dataset (EBD), “https://science.ebird.org/en/use-ebird-data/download-ebird-data-products”. The Hackett backbone phylogenetic trees are available from “https://birdtree.org/”.

The code contains the R scripts and MATLAB scripts that we used for this study.

For details please see the file “Readme.txt”, and the research paper.
DOI: 10.5281/zenodo.10429747
title: Dataset from: Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network

description: Original data and code for the study:

Wei, J., Xu, F., Cole, E. F., Sheldon, B. C., de Boer, W. F., Wielstra, B., Fu, H., Gong, P., & Si, Y. (2024, Accepted). Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network. Global Change Biology.

The dataset mainly contains data showing the climate change-induced heterogeneous shifts in vegetation phenology and the migration integrity change from 2000 to 2020 for 16 Asian herbivorous waterfowl species. These data were derived from the following resources available in the public domain.

The Global Lakes and Wetlands Database is available from “https://www.worldwildlife.org/pages/global-lakes-and-wetlands-database”. The global land cover datasets are available from European Space Agency (ESA) Climate Change Initiative (CCI) products, “https://maps.elie.ucl.ac.be/CCI/viewer/download.php”. The Global Multi-resolution Terrain Elevation Data are available from “https://www.usgs.gov/centers/eros/science/terrain-monitoring-and-modeling”. The Moderate Resolution Imaging Spectroradiometer (MODIS) Terra surface reflectance product is available from “https://modis.gsfc.nasa.gov/data/dataprod/mod09.php”. The bird distribution maps are available from Birdlife International, “https://www.birdlife.org/”. The bird foraging attribute data are available from EltonTraits 1.0, “https://figshare.com”. The bird occurrence data are available from eBird Basic Dataset (EBD), “https://science.ebird.org/en/use-ebird-data/download-ebird-data-products”. The Hackett backbone phylogenetic trees are available from “https://birdtree.org/”.

The code contains the R scripts and MATLAB scripts that we used for this study.

For details please see the file “Readme.txt”, and the research paper.
DOI: 10.34740/kaggle/dsv/7330204
title: Stay Gold: BTS’s Impact with YT videos ✨✨
DOI: 10.5281/zenodo.10454189
title: Elaborating the atmospheric transformation...
DOI: 10.5281/zenodo.10454190
title: Elaborating the atmospheric transformation...
DOI: 10.34740/kaggle/ds/4254915
title: 🎵Taylor Swift's YouTube Stats Symphony 🌟
DOI: 10.5517/ccdc.csd.cc2dk033
title: CCDC 2220874: Experimental Crystal Structure Determination

description: Related Article: Zhe-Yang Wang, Yong-Yao Liu, Shuang Dong, Xiao-Xian Deng, Rui-Ning Li, Xiang He|2023|J.Coord.Chem.|76|1543|doi:10.1080/00958972.2023.2260538
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.