cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35097/1948
title: IMK/IAA MIPAS retrievals version 8: CH4, the data set

description: The data set comprises CH4 (methane) data of the Earth's uppere troposphere and middle atmosphere region for the years 2002-2012 as derived from MIPAS on Envisat and retrieved with the IMK/IAA level-2 processor. The MIPAS observation modes FR (2002 - 2004, CH4_61), RR-NOM (2005 - 2012, CH4_261), RR-UTLS-1 (2005 - 2007, CH4_161), RR-MA (2005 - 2012, CH4_561 & CH4_562), and RR-UA (2005-2012, CH4_662) are covered. Data versions CH4_161, CH4_261, and CH4_561 are compatible and could be used together. The same holds for data versions CH4_562 and CH4_662. The data is based on version V8 infrared spectra.
description: The data is delivered as a set of yearly archive files with each archive containing monthly netCDF files of the respective year.
DOI: 10.35097/1949
title: IMK/IAA MIPAS retrievals version 8: N2O, the data set

description: The data set comprises N2O (nitrous ocide) data of the Earth's upper troposphere and middle atmosphere region for the years 2002-2012 as derived from MIPAS on Envisat and retrieved with the IMK/IAA level-2 processor. The MIPAS observation modes FR (2002 - 2004, N2O_61), RR-NOM (2005 - 2012, N2O_261), RR-UTLS-1 (2005 - 2007, N2O_161), RR-MA (2005 - 2012, N2O_561 & N2O_562), and RR-UA (2005-2012, N2O_662) are covered. Data versions N2O_161, N2O_261, and N2O_561 are compatible and could be used together. The same holds for data versions N2O_562 and N2O_662. The data is based on version V8 infrared spectra.
description: The data is delivered as a set of yearly archive files with each archive containing monthly netCDF files of the respective year.
DOI: 10.6084/m9.figshare.25382923
title: 20240312_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.25382923.v1
title: 20240312_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.22792519
title: LncRNA DLEU2 contributes to Taxol resistance of gastric cancer cells through regulating the miR-30c-5p-LDHA axis

description: Gastric cancer (GC) is a human malignancy which is associated with high mortality rate and poor prognosis. In addition to surgery, chemo- and radio-therapies are effective strategies against GC at advanced or metastatic stage. Taxol is a traditionally anti-cancer drug which is applied to various types of cancer. However, development of drug resistance limited the anti-cancer effects of Taxol. Currently, the biological roles and mechanisms of non-coding RNA DLEU2 in Taxol resistant GC remain unclear. This study reported that DLEU2 was significantly upregulated and miR-30c-5p was remarkedly downregulated in gastric tumours and cell lines. Silencing DLEU2 or overexpression of miR-30c-5p effectively increased the Taxol sensitivity of GC cells. Through bioinformatics analysis, RNA pull-down and luciferase assay, we demonstrated that DLEU2 sponged miR-30c-5p to block its expression in GC cells. Moreover, from the established Taxol resistant GC cell line, we detected remarkedly upregulated DLEU2 and downregulated miR-30c-5p expressions and significantly elevated glucose metabolism. Under low glucose condition, Taxol resistant cells were more susceptible to Taxol. In addition, we showed overexpression of miR-30c-5p blocked glucose metabolism through inhibiting the LDHA, a glucose metabolism key enzyme by direct targeting the 3′UTR of LDHA. Finally, rescue experiments validated that restoration of miR-30c-5p in DLEU2-overexpressing Taxol resistant GC cells effectively overcame the DLEU2-promoted Taxol resistance. In summary, this study uncovered new roles and molecular mechanisms of the lncRNA DLEU2-promoted Taxol resistance of gastric cancer cells, presenting the DLEU2-miR-30c-5p-LDHA-glucose metabolism axis a potentially therapeutic target for treatment of Taxol resistant GC.
DOI: 10.6084/m9.figshare.22792519.v1
title: LncRNA DLEU2 contributes to Taxol resistance of gastric cancer cells through regulating the miR-30c-5p-LDHA axis

description: Gastric cancer (GC) is a human malignancy which is associated with high mortality rate and poor prognosis. In addition to surgery, chemo- and radio-therapies are effective strategies against GC at advanced or metastatic stage. Taxol is a traditionally anti-cancer drug which is applied to various types of cancer. However, development of drug resistance limited the anti-cancer effects of Taxol. Currently, the biological roles and mechanisms of non-coding RNA DLEU2 in Taxol resistant GC remain unclear. This study reported that DLEU2 was significantly upregulated and miR-30c-5p was remarkedly downregulated in gastric tumours and cell lines. Silencing DLEU2 or overexpression of miR-30c-5p effectively increased the Taxol sensitivity of GC cells. Through bioinformatics analysis, RNA pull-down and luciferase assay, we demonstrated that DLEU2 sponged miR-30c-5p to block its expression in GC cells. Moreover, from the established Taxol resistant GC cell line, we detected remarkedly upregulated DLEU2 and downregulated miR-30c-5p expressions and significantly elevated glucose metabolism. Under low glucose condition, Taxol resistant cells were more susceptible to Taxol. In addition, we showed overexpression of miR-30c-5p blocked glucose metabolism through inhibiting the LDHA, a glucose metabolism key enzyme by direct targeting the 3′UTR of LDHA. Finally, rescue experiments validated that restoration of miR-30c-5p in DLEU2-overexpressing Taxol resistant GC cells effectively overcame the DLEU2-promoted Taxol resistance. In summary, this study uncovered new roles and molecular mechanisms of the lncRNA DLEU2-promoted Taxol resistance of gastric cancer cells, presenting the DLEU2-miR-30c-5p-LDHA-glucose metabolism axis a potentially therapeutic target for treatment of Taxol resistant GC.
DOI: 10.6084/m9.figshare.24916411
title: Macrolides impact the growth ability of clinical <i>Pseudomonas aeruginosa</i> through quorum-sensing systems

description: The aim of the present study was to examine the impact of macrolides on the expression of virulence factors and QS-associated genes in clinical <i>P. aeruginosa</i> isolates. Among 60 clinical <i>P. aeruginosa</i>, pyocyanin production was detected in 27 (45%) isolates, which belonged to various STs. Erythromycin inhibited the production of pigments in 12 out of 27 isolates. Other antibiotic categories didn’t have an impact on production of pigments. Additionally, results showed that erythromycin sub-MIC inhibited the growth-rate in 17 isolates. Of note, in six isolates, the inhibition of growth-rate was greater when using both erythromycin and meropenem than using each antibiotic individually. Finally, addition of erythromycin down-regulated the expression of QS-associated genes (65.5%–81.3%) and almost all virulence-associated genes. In conclusion, our results confirmed that macrolides could be used in combination with last-line antibiotics, such as carbapenems, to treat infections caused by multidrug-resistant Gram-negative bacteria.
DOI: 10.6084/m9.figshare.24916411.v1
title: Macrolides impact the growth ability of clinical <i>Pseudomonas aeruginosa</i> through quorum-sensing systems

description: The aim of the present study was to examine the impact of macrolides on the expression of virulence factors and QS-associated genes in clinical <i>P. aeruginosa</i> isolates. Among 60 clinical <i>P. aeruginosa</i>, pyocyanin production was detected in 27 (45%) isolates, which belonged to various STs. Erythromycin inhibited the production of pigments in 12 out of 27 isolates. Other antibiotic categories didn’t have an impact on production of pigments. Additionally, results showed that erythromycin sub-MIC inhibited the growth-rate in 17 isolates. Of note, in six isolates, the inhibition of growth-rate was greater when using both erythromycin and meropenem than using each antibiotic individually. Finally, addition of erythromycin down-regulated the expression of QS-associated genes (65.5%–81.3%) and almost all virulence-associated genes. In conclusion, our results confirmed that macrolides could be used in combination with last-line antibiotics, such as carbapenems, to treat infections caused by multidrug-resistant Gram-negative bacteria.
DOI: 10.5281/zenodo.10805205
title: Neural Image Segmentation for Redacted Text Detection Dataset

description: This dataset was created for the "Redacted Text Detection Using Neural Image Segmentation Methods" project, and contains roughly 1000 pages with manually annotated redactions in Dutch documents released under the WOO, with the trained model files and the model outputs also included in the dataset. More details on the usage of the dataset and models can be found on Github: https://github.com/RubenvanHeusden/NeuralRedactedTextDetection/
DOI: 10.5281/zenodo.10805206
title: Neural Image Segmentation for Redacted Text Detection Dataset

description: This dataset was created for the "Redacted Text Detection Using Neural Image Segmentation Methods" project, and contains roughly 1000 pages with manually annotated redactions in Dutch documents released under the WOO, with the trained model files and the model outputs also included in the dataset. More details on the usage of the dataset and models can be found on Github: https://github.com/RubenvanHeusden/NeuralRedactedTextDetection/
DOI: 10.5281/zenodo.10805256
title: Investigating the Utility of Potato (Solanum tuberosum L.) Canopy Temperature and Leaf Greenness Responses to Water-Restriction for the Improvement of Irrigation Management Data

description: Traits that rapidly respond to stress in important agricultural crops have the potential to provide growers with actionable feedback. E.g., traits that respond to water-restriction could inform irrigation systems by identifying crop water status and requirements in real-time. This would be particularly useful for potato, which is extremely susceptible to drought. We conducted two pot experiments and one field experiment to evaluate the utility of two traits, canopy temperature and leaf greenness, for informing irrigation management in potatoes. We also evaluated the efficacy of Phenospex PlantEye F500 sensors for the remote sensing of leaf greenness. We found that canopy temperatures of the cvs. Maris Piper (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and Désirée (Autumn Pot Experiment, +2.5°C) increased with water-restriction and that the canopy temperatures of Maris Piper return to baseline within three days after the resumption of well-watered conditions. We also found that these responses varied between cultivars, with predictable outcomes based on reported and corroborated drought tolerance ratings. We found inconclusive evidence of leaf greenness increasing due to water-restriction (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and found no evidence that post-drought recovery periods return this trait to baseline. However, leaf greenness measurements from the Phenospex PlantEye F500 were moderately to strongly correlated with SPAD values, suggesting this tool might be useful in the screening of drought-tolerant cultivars in the future.
DOI: 10.5281/zenodo.10805257
title: Investigating the Utility of Potato (Solanum tuberosum L.) Canopy Temperature and Leaf Greenness Responses to Water-Restriction for the Improvement of Irrigation Management Data

description: Traits that rapidly respond to stress in important agricultural crops have the potential to provide growers with actionable feedback. E.g., traits that respond to water-restriction could inform irrigation systems by identifying crop water status and requirements in real-time. This would be particularly useful for potato, which is extremely susceptible to drought. We conducted two pot experiments and one field experiment to evaluate the utility of two traits, canopy temperature and leaf greenness, for informing irrigation management in potatoes. We also evaluated the efficacy of Phenospex PlantEye F500 sensors for the remote sensing of leaf greenness. We found that canopy temperatures of the cvs. Maris Piper (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and Désirée (Autumn Pot Experiment, +2.5°C) increased with water-restriction and that the canopy temperatures of Maris Piper return to baseline within three days after the resumption of well-watered conditions. We also found that these responses varied between cultivars, with predictable outcomes based on reported and corroborated drought tolerance ratings. We found inconclusive evidence of leaf greenness increasing due to water-restriction (Spring Pot Experiment, +0.8°C; Autumn Pot Experiment, +5.3°C) and found no evidence that post-drought recovery periods return this trait to baseline. However, leaf greenness measurements from the Phenospex PlantEye F500 were moderately to strongly correlated with SPAD values, suggesting this tool might be useful in the screening of drought-tolerant cultivars in the future.
DOI: 10.5519/qd.gfcy6v5v
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (11 records)
DOI: 10.6084/m9.figshare.25382860
title: Exploring the Role of Protein Motif Co-evolution in Genome Evolution: An Elusive Phenomenon

description: This dataset presents the results of a comprehensive investigation into protein motif co-evolution in eukaryotic genomes utilizing the MEME (Multiple Em for Motif Elicitation) and MAST (Motif Alignment and Search Tool) algorithms. The data, hosted on Figshare, offers valuable insights into the evolutionary dynamics of protein motifs within orthologous groups across diverse eukaryotic species.The dataset includes:MEME Results: Detailed findings from the MEME analysis, including identified protein motifs, position-specific scoring matrix (PSSM) data, statistical significance scores, and sequence logos representing the motifs.MAST Results: Comprehensive outcomes of the MAST searches, indicating the occurrences of identified motifs within protein sequences derived from orthologous groups. Statistical significance scores accompanying motif occurrences provide insights into motif conservation and prevalence across different species.
DOI: 10.6084/m9.figshare.25382860.v2
title: Exploring the Role of Protein Motif Co-evolution in Genome Evolution: An Elusive Phenomenon

description: This dataset presents the results of a comprehensive investigation into protein motif co-evolution in eukaryotic genomes utilizing the MEME (Multiple Em for Motif Elicitation) and MAST (Motif Alignment and Search Tool) algorithms. The data, hosted on Figshare, offers valuable insights into the evolutionary dynamics of protein motifs within orthologous groups across diverse eukaryotic species.The dataset includes:MEME Results: Detailed findings from the MEME analysis, including identified protein motifs, position-specific scoring matrix (PSSM) data, statistical significance scores, and sequence logos representing the motifs.MAST Results: Comprehensive outcomes of the MAST searches, indicating the occurrences of identified motifs within protein sequences derived from orthologous groups. Statistical significance scores accompanying motif occurrences provide insights into motif conservation and prevalence across different species.
DOI: 10.6084/m9.figshare.25382860.v1
title: EggNOg_corrected

description: This dataset presents the results of a comprehensive investigation into protein motif co-evolution in eukaryotic genomes utilizing the MEME (Multiple Em for Motif Elicitation) and MAST (Motif Alignment and Search Tool) algorithms. The data, hosted on Figshare, offers valuable insights into the evolutionary dynamics of protein motifs within orthologous groups across diverse eukaryotic species.The dataset includes:MEME Results: Detailed findings from the MEME analysis, including identified protein motifs, position-specific scoring matrix (PSSM) data, statistical significance scores, and sequence logos representing the motifs.MAST Results: Comprehensive outcomes of the MAST searches, indicating the occurrences of identified motifs within protein sequences derived from orthologous groups. Statistical significance scores accompanying motif occurrences provide insights into motif conservation and prevalence across different species.
DOI: 10.5519/qd.53l7o24t
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (31 records)
DOI: 10.6069/332v-vt13
title: Effect of burn wound treatment with fish skin on mouse skin proteome

description: This study explored the feasibility of using fish skin bandages as a therapeutic option for third-degree skin burns. Following the California wildfires, clinical observations of animals with third-degree skin burns demonstrated increased comfort levels and reduced pain when treated with tilapia fish skin. Proteomic analysis of the fish skin revealed the presence of antimicrobial peptides. In combination with histological and other data, these results suggest that fish skin can serve as an innovative and cost-effective therapeutic alternative for burn victims to facilitate vascularization and reduce bacterial infection.
DOI: 10.5519/qd.7i70jl1i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (67 records)
DOI: 10.5281/zenodo.10801167
title: The 3'-RACE data (InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data)
DOI: 10.5281/zenodo.10801168
title: The 3'-RACE data (InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data)
DOI: 10.5519/qd.avzgi8od
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (67 records)
DOI: 10.5281/zenodo.10805178
title: Supplementary Figure 6 spontaneous brain activity data

description: This data set contains a single ten-minute run of spontaneous brain activity. This data was collected using a CMOS camera that costs approximately $750. Wide field images of the mouse brain at four different wavelengths are provided as .tif files. Processed data are included in a .h5 file that contains relative changes in neuronal calcium activity, extracellular acetylcholine, oxyhemoglobin, and deoxyhemoglobin. A video of the mouse face and a recording from an accelerometer placed under the mouse are also included. A trigger file recorded by the data acquisition system shows the timing of measurements. This data was used to produce the spontaneous activity part of supplementary figure 6 in the following article.

Doran, P., Fomin-Thunemann, N., Tang, R., Zimmerman, B., Kilic, K., Kura, S., Fisher, H., Chabbot, G., Herbert, J., Jiang, J., Sakadzic, S., Boas, D., Devor, A., Chen, I., & Thunemann, M. (2023). Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination. bioRxiv. https://doi.org/https://doi.org/10.1101/2023.11.07.566086do
DOI: 10.5281/zenodo.10805179
title: Supplementary Figure 6 spontaneous brain activity data

description: This data set contains a single ten-minute run of spontaneous brain activity. This data was collected using a CMOS camera that costs approximately $750. Wide field images of the mouse brain at four different wavelengths are provided as .tif files. Processed data are included in a .h5 file that contains relative changes in neuronal calcium activity, extracellular acetylcholine, oxyhemoglobin, and deoxyhemoglobin. A video of the mouse face and a recording from an accelerometer placed under the mouse are also included. A trigger file recorded by the data acquisition system shows the timing of measurements. This data was used to produce the spontaneous activity part of supplementary figure 6 in the following article.

Doran, P., Fomin-Thunemann, N., Tang, R., Zimmerman, B., Kilic, K., Kura, S., Fisher, H., Chabbot, G., Herbert, J., Jiang, J., Sakadzic, S., Boas, D., Devor, A., Chen, I., & Thunemann, M. (2023). Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination. bioRxiv. https://doi.org/https://doi.org/10.1101/2023.11.07.566086do
DOI: 10.5281/zenodo.10805337
title: KOnPoTe resources for boats and restaurants
DOI: 10.5281/zenodo.10805338
title: KOnPoTe resources for boats and restaurants
DOI: 10.5517/ccdc.csd.cc2f44wm
title: CCDC 2238320: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Zaguzin, Pavel A. Abramov, Marianna I. Rakhmanova, Andrey N. Usoltsev, Maxim N. Sokolov, Vladimir P. Fedin, Sergey A. Adonin|2024|Polyhedron|253|116908|doi:10.1016/j.poly.2024.116908
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.
DOI: 10.5517/ccdc.csd.cc2f44xn
title: CCDC 2238321: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Zaguzin, Pavel A. Abramov, Marianna I. Rakhmanova, Andrey N. Usoltsev, Maxim N. Sokolov, Vladimir P. Fedin, Sergey A. Adonin|2024|Polyhedron|253|116908|doi:10.1016/j.poly.2024.116908
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.
DOI: 10.5517/ccdc.csd.cc2f44yp
title: CCDC 2238322: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Zaguzin, Pavel A. Abramov, Marianna I. Rakhmanova, Andrey N. Usoltsev, Maxim N. Sokolov, Vladimir P. Fedin, Sergey A. Adonin|2024|Polyhedron|253|116908|doi:10.1016/j.poly.2024.116908
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.
DOI: 10.5517/ccdc.csd.cc2f44zq
title: CCDC 2238323: Experimental Crystal Structure Determination

description: Related Article: Alexander S. Zaguzin, Pavel A. Abramov, Marianna I. Rakhmanova, Andrey N. Usoltsev, Maxim N. Sokolov, Vladimir P. Fedin, Sergey A. Adonin|2024|Polyhedron|253|116908|doi:10.1016/j.poly.2024.116908
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.
DOI: 10.5517/ccdc.csd.cc24q9ls
title: CCDC 1987645: Experimental Crystal Structure Determination

description: Related Article: Tuğba AYCAN, Filiz ÖZTÜRK, Tuğrul DORUK|2024|J.Mol.Struct.|1306|137865|doi:10.1016/j.molstruc.2024.137865
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.