cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22770096
title: System-level protein interaction network analysis and molecular dynamics study reveal interaction of ferulic acid with <i>PTGS2</i> as a natural radioprotector

description: Ferulic acid is a crucial bioactive component of broccoli, wheat, and rice bran and is also an essential natural product that has undergone significant research. Ferulic acid’s precise mode of action and effect on system-level protein networks have not been thoroughly investigated. An interactome was built using the STRING database and Cytoscape tools, utilizing 788 key proteins collected from PubMed literature to identify the ferulic acid-governed regulatory action on protein interaction network (PIN). The scale-free biological network of ferulic acid-rewired PIN is highly interconnected. We discovered 15 sub-modules using the MCODE tool for sub-modulization analysis and 153 enriched signaling pathways. Further, functional enrichment of top bottleneck proteins revealed the FoxO signaling pathway involved in enhancing cellular defense against oxidative stress. The selection of the critical regulatory proteins of the ferulic acid-rewired PIN was completed by performing analyses of topological characteristics such as GO term/pathways analysis, degree, bottleneck, molecular docking, and dynamics investigations. The current research derives a precise molecular mechanism for ferulic acid’s action on the body. This in-depth <i>in silico</i> model would aid in understanding how ferulic acid origins its antioxidant and scavenging properties in the human body. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22770096.v1
title: System-level protein interaction network analysis and molecular dynamics study reveal interaction of ferulic acid with <i>PTGS2</i> as a natural radioprotector

description: Ferulic acid is a crucial bioactive component of broccoli, wheat, and rice bran and is also an essential natural product that has undergone significant research. Ferulic acid’s precise mode of action and effect on system-level protein networks have not been thoroughly investigated. An interactome was built using the STRING database and Cytoscape tools, utilizing 788 key proteins collected from PubMed literature to identify the ferulic acid-governed regulatory action on protein interaction network (PIN). The scale-free biological network of ferulic acid-rewired PIN is highly interconnected. We discovered 15 sub-modules using the MCODE tool for sub-modulization analysis and 153 enriched signaling pathways. Further, functional enrichment of top bottleneck proteins revealed the FoxO signaling pathway involved in enhancing cellular defense against oxidative stress. The selection of the critical regulatory proteins of the ferulic acid-rewired PIN was completed by performing analyses of topological characteristics such as GO term/pathways analysis, degree, bottleneck, molecular docking, and dynamics investigations. The current research derives a precise molecular mechanism for ferulic acid’s action on the body. This in-depth <i>in silico</i> model would aid in understanding how ferulic acid origins its antioxidant and scavenging properties in the human body. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22821305
title: Development of novel chromones as antioxidant COX2 inhibitors: <i>in vitro</i>, QSAR, DFT, molecular docking, and molecular dynamics studies

description: The chromone derivatives are playing a prominent role in many plant cycles, for instance, the regulation of growth, stimulation of oxygen uptake in plants, and essential food constituents with valuable pro-health properties. Determination of the antioxidant activity of these compounds is an interesting approach to drug design and development. The antioxidant activity of the novel fifteen chromone compounds was estimated by using a spectrophotometric Dichloro-5,6-dicyano 1,4-benzoquinone (DDQ) assay method and the mechanism of antioxidant activity was discussed based on the Density functional theory (DFT) calculations. The compounds showed significant antioxidant activity which was correlated to their molecular structure by considering various molecular descriptors. Further, by using regression analysis QSAR-modeled equation was proposed and it has shown a high correlation coefficient value (0.946. We perform molecular docking and molecular dynamics simulations against the cyclooxygenase (COX2) enzyme to investigate the molecule’s anti-inflammatory activity and stability of protein-ligand complexes. Molecular docking and dynamics simulations revealed the compounds B3 and B8 were interacting with essential residues TYR385, HIS386, ASN382, TRP387, and HIS388 in the binding site that were crucial for optimizing heme and the resultant peroxidase and cyclooxygenase activities. The root mean square displacement and root mean square fluctuation plots revealed the stability of the B3-COX2 and B8-COX2 complexes. Based on our results, B3 and B8 compounds are considered as best antioxidants as well as COX2 inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22821305.v1
title: Development of novel chromones as antioxidant COX2 inhibitors: <i>in vitro</i>, QSAR, DFT, molecular docking, and molecular dynamics studies

description: The chromone derivatives are playing a prominent role in many plant cycles, for instance, the regulation of growth, stimulation of oxygen uptake in plants, and essential food constituents with valuable pro-health properties. Determination of the antioxidant activity of these compounds is an interesting approach to drug design and development. The antioxidant activity of the novel fifteen chromone compounds was estimated by using a spectrophotometric Dichloro-5,6-dicyano 1,4-benzoquinone (DDQ) assay method and the mechanism of antioxidant activity was discussed based on the Density functional theory (DFT) calculations. The compounds showed significant antioxidant activity which was correlated to their molecular structure by considering various molecular descriptors. Further, by using regression analysis QSAR-modeled equation was proposed and it has shown a high correlation coefficient value (0.946. We perform molecular docking and molecular dynamics simulations against the cyclooxygenase (COX2) enzyme to investigate the molecule’s anti-inflammatory activity and stability of protein-ligand complexes. Molecular docking and dynamics simulations revealed the compounds B3 and B8 were interacting with essential residues TYR385, HIS386, ASN382, TRP387, and HIS388 in the binding site that were crucial for optimizing heme and the resultant peroxidase and cyclooxygenase activities. The root mean square displacement and root mean square fluctuation plots revealed the stability of the B3-COX2 and B8-COX2 complexes. Based on our results, B3 and B8 compounds are considered as best antioxidants as well as COX2 inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22770045
title: Subtractive sequence-mediated therapeutic targets from the conserved gene clusters of <i>Campylobacter hyointestinalis</i> and computational inhibition assessment

description: <i>Campylobacter hyointestinalis</i> is a causative agent of enteritis, proctitis, human gastroenteritis, and diarrhea. Reported transmission is from pigs to humans. Link with gastrointestinal carcinoma has also been established in non-<i>Helicobacter pylori</i> patients carrying this strain. The genome size of the strain LMG9260 is 1.8 MB with 1785 chromosomal and seven plasmid proteins. No therapeutic targets have been identified and reported in this bacterium. Therefore, subtractive computational screening of its genome was carried out for the purpose. In total, 31 such targets were mined and riboflavin synthase was utilized for screening natural product inhibitors against it. Among more than 30,000 screened natural compounds from the NPASS library, three (NPC472060, NPC33653, and NPC313886) were prioritized to have the potential to be developed into new antimicrobial drugs. Dynamics simulation assay along with other relevant parameters like absorption, toxicity, and distribution of the inhibiting compounds were also predicted and NPC33653 was identified as having the best drug-like properties among the prioritized compounds. Thus, it has potential to be pursued further for the inhibition of riboflavin synthesis in <i>C. hyointestinalis</i> for subsequent obstruction of its growth and survival. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22770045.v1
title: Subtractive sequence-mediated therapeutic targets from the conserved gene clusters of <i>Campylobacter hyointestinalis</i> and computational inhibition assessment

description: <i>Campylobacter hyointestinalis</i> is a causative agent of enteritis, proctitis, human gastroenteritis, and diarrhea. Reported transmission is from pigs to humans. Link with gastrointestinal carcinoma has also been established in non-<i>Helicobacter pylori</i> patients carrying this strain. The genome size of the strain LMG9260 is 1.8 MB with 1785 chromosomal and seven plasmid proteins. No therapeutic targets have been identified and reported in this bacterium. Therefore, subtractive computational screening of its genome was carried out for the purpose. In total, 31 such targets were mined and riboflavin synthase was utilized for screening natural product inhibitors against it. Among more than 30,000 screened natural compounds from the NPASS library, three (NPC472060, NPC33653, and NPC313886) were prioritized to have the potential to be developed into new antimicrobial drugs. Dynamics simulation assay along with other relevant parameters like absorption, toxicity, and distribution of the inhibiting compounds were also predicted and NPC33653 was identified as having the best drug-like properties among the prioritized compounds. Thus, it has potential to be pursued further for the inhibition of riboflavin synthesis in <i>C. hyointestinalis</i> for subsequent obstruction of its growth and survival. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23216361
title: Targeting bladder cancer with Trigonella foenum-graecum: a computational study using network pharmacology and molecular docking

description: Trigonella foenum-graecum (TF-graecum), known as Hulba or Fenugreek, is one of the oldest known medicinal plants. It has been found to have antimicrobial, antifungal, antioxidant, wound-healing, anti-diarrheal, hypoglycemic, anti-diabetic, and anti-inflammatory activities. In our current report, we have collected and screened the active compounds of TF-graecum and their potential targets <i>via</i> different pharmacology platforms. Network construction shows that eight active compounds may act on 223 potential bladder cancer targets. The pathway enrichment analysis for the seven potential targets of the eight compounds selected, based on KEGG pathway analysis, was conducted to clarify the potential pharmacological effects. Finally, molecular docking and molecular dynamics simulation showed the stability of protein-ligand interactions. This study highlights the need for increased research into the potential medical benefits of this plant. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23216361.v1
title: Targeting bladder cancer with Trigonella foenum-graecum: a computational study using network pharmacology and molecular docking

description: Trigonella foenum-graecum (TF-graecum), known as Hulba or Fenugreek, is one of the oldest known medicinal plants. It has been found to have antimicrobial, antifungal, antioxidant, wound-healing, anti-diarrheal, hypoglycemic, anti-diabetic, and anti-inflammatory activities. In our current report, we have collected and screened the active compounds of TF-graecum and their potential targets <i>via</i> different pharmacology platforms. Network construction shows that eight active compounds may act on 223 potential bladder cancer targets. The pathway enrichment analysis for the seven potential targets of the eight compounds selected, based on KEGG pathway analysis, was conducted to clarify the potential pharmacological effects. Finally, molecular docking and molecular dynamics simulation showed the stability of protein-ligand interactions. This study highlights the need for increased research into the potential medical benefits of this plant. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.25449739
title: New Verbatim

description: digital literacy
DOI: 10.6084/m9.figshare.25449739.v1
title: New Verbatim

description: digital literacy
DOI: 10.6084/m9.figshare.24925356
title: 数据整理111.savexperimental data

description: This study aims to explore the mechanism of the impact of physical exercise on social anxiety among college students, and analyze the chain mediating effect of body imagery and self-esteem.
DOI: 10.6084/m9.figshare.24925356.v1
title: 数据整理111.savexperimental data

description: This study aims to explore the mechanism of the impact of physical exercise on social anxiety among college students, and analyze the chain mediating effect of body imagery and self-esteem.
DOI: 10.5281/zenodo.10844273
title: Epidemiological changes of acute respiratory infections in children: A single-center experience after COVID-19 lockdown

description: Data of the study "Epidemiological changes of acute respiratory infections in children: A single-center experience after COVID-19 lockdown".
DOI: 10.5281/zenodo.10844274
title: Epidemiological changes of acute respiratory infections in children: A single-center experience after COVID-19 lockdown

description: Data of the study "Epidemiological changes of acute respiratory infections in children: A single-center experience after COVID-19 lockdown".
DOI: 10.5281/zenodo.10783500
title: JTCT - Annex 3 - Results of the Interdisciplinary Policy Analysis
DOI: 10.5281/zenodo.10783501
title: JTCT - Annex 3 - Results of the Interdisciplinary Policy Analysis
DOI: 10.5281/zenodo.10839063
title: JTCT - Annex 3 - Results of the Interdisciplinary Policy Analysis
DOI: 10.5281/zenodo.10818754
title: JTCT - Annex 2 - Interdisciplinary analytical framework on the  socio-ecological justice and sustainability implications of a circularity transition
DOI: 10.5281/zenodo.10818755
title: JTCT - Annex 2 - Interdisciplinary analytical framework on the  socio-ecological justice and sustainability implications of a circularity transition
DOI: 10.5281/zenodo.10847421
title: JTCT - Annex 2 - Interdisciplinary analytical framework on the  socio-ecological justice and sustainability implications of a circularity transition
DOI: 10.5281/zenodo.8020004
title: Replication data for the working paper "The Illusive Slump of Disruptive Patents", published as "Is there a secular decline in disruptive patents? Correcting for measurement bias" in the journal Research Policy

description: To access the updated repository for the Research Policy article "Is there a secular decline in disruptive patents? Correcting for measurementbias", please click here.

 

Authors: Jeffrey T. Macher, Christian Rutzer, and Rolf Weder

The repository contains replication data and scripts for the paper titled "The Illusive Slump of Disruptive Patents" (https://arxiv.org/abs/2306.10774). The core component of the repository is the file `replication_file.R` which is an R script to replicate all figures and tables in the paper.

The script relies on multiple data files, all of which are stored in the `final_data` directory. The datasets contain values for granted USPTO utility patents for the years 1976-2016. 

 

Dataset Descriptions

Main Datasets:

1. `dat_no_trunc`: This dataset contains the CD index of patents based on a method without truncation. Available in two formats, `.fst` and `.csv`.

2. `dat_cd_trunc_1975`: This dataset contains the CD index of patents based on a truncation method as in Park et al. (Nature, 2023). Available in two formats, `.fst` and `.csv`.

3. `dat_no_trunc_app_adj`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021. Available in two formats, `.fst` and `.csv`.

4. `dat_no_trunc_app`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021, as well as those not yet granted. Available in two formats, `.fst` and `.csv`.

 

Additional Datasets:

5. `share_untrunc_cit`: This dataset is loaded by the script when illustrating the No Truncation method.

6. share_trunc_cit: This dataset is used when using the truncation method as in Park et al. (Nature, 2023).

7. `age_bwc_untrunc`: This dataset contains the age of backward citations using untruncated data.

8. age_bwc_trunc: This dataset contains the age of backward citations using the tuncation methods as in Park et al. (Nature, 2023).

9. `age_bwc_untrunc_app_adj`: This dataset contains the age of backward citations using untruncated data and considering citations of patent applications granted until 2021.

To successfully run the script `replication_file.R`, make sure all data files are in the directory and the `mainDir1` variable at the beginning of the script is set to the correct path.

For questions, please contact christian.rutzer@unibas.ch
DOI: 10.5281/zenodo.8152081
title: Replication Data for The Illusive Slump of Disruptive Patents

description: <strong>Replication Data for "The Illusive Slump of Disruptive Patents"</strong> <em>Authors: Christian Rutzer, Jeffrey T. Macher, and Rolf Weder</em> The repository contains replication data and scripts for the paper titled "The Illusive Slump of Disruptive Patents" (https://arxiv.org/abs/2306.10774). The core component of the repository is the file `replication_file.R` which is an R script to replicate all figures and tables in the paper. The script relies on multiple data files. The datasets contain values for granted USPTO utility patents for the years 1976-2016. <strong>Dataset Descriptions</strong> <strong>Main Datasets:</strong> 1. `dat_no_trunc`: This dataset contains the CD index of patents based on a method without truncation. Available in two formats, `.fst` and `.csv`. 2. `dat_cd_trunc_1975`: This dataset contains the CD index of patents based on a truncation method as in Park et al. (Nature, 2023). Available in two formats, `.fst` and `.csv`. 3. `dat_no_trunc_app_adj`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021. Available in two formats, `.fst` and `.csv`. 4. `dat_no_trunc_app`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021, as well as those not yet granted. Available in two formats, `.fst` and `.csv`. <strong>Additional Datasets:</strong> 5. `share_untrunc_cit`: This dataset is loaded by the script when illustrating the No Truncation method. 6. share_trunc_cit: This dataset is used when using the truncation method as in Park et al. (Nature, 2023). 7. `age_bwc_untrunc`: This dataset contains the age of backward citations using untruncated data. 8. age_bwc_trunc: This dataset contains the age of backward citations using the tuncation methods as in Park et al. (Nature, 2023). 9. `age_bwc_untrunc_app_adj`: This dataset contains the age of backward citations using untruncated data and considering citations of patent applications granted until 2021. To successfully run the script `replication_file.R`, make sure all data files are in the directory and the `mainDir1` variable at the beginning of the script is set to the correct path. For questions, please contact christian.rutzer@unibas.ch
DOI: 10.5281/zenodo.8152177
title: Replication Data for The Illusive Slump of Disruptive Patents

description: <strong>Replication Data for "The Illusive Slump of Disruptive Patents"</strong> <em>Authors: Christian Rutzer, Jeffrey T. Macher, and Rolf Weder</em> The repository contains replication data and scripts for the paper titled "The Illusive Slump of Disruptive Patents" (https://arxiv.org/abs/2306.10774). The core component of the repository is the file `replication_file.R` which is an R script to replicate all figures and tables in the paper. The script relies on multiple data files. The datasets contain values for granted USPTO utility patents for the years 1976-2016. <strong>Dataset Descriptions</strong> <strong>Main Datasets:</strong> 1. `dat_no_trunc`: This dataset contains the CD index of patents based on a method without truncation. Available in two formats, `.fst` and `.csv`. 2. `dat_cd_trunc_1975`: This dataset contains the CD index of patents based on a truncation method as in Park et al. (Nature, 2023). Available in two formats, `.fst` and `.csv`. 3. `dat_no_trunc_app_adj`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021. Available in two formats, `.fst` and `.csv`. 4. `dat_no_trunc_app`: This dataset contains the CD index of patents based on a method without truncation and including citations to patent applications granted by 2021, as well as those not yet granted. Available in two formats, `.fst` and `.csv`. <strong>Additional Datasets:</strong> 5. `share_untrunc_cit`: This dataset is loaded by the script when illustrating the No Truncation method. 6. share_trunc_cit: This dataset is used when using the truncation method as in Park et al. (Nature, 2023). 7. `age_bwc_untrunc`: This dataset contains the age of backward citations using untruncated data. 8. age_bwc_trunc: This dataset contains the age of backward citations using the tuncation methods as in Park et al. (Nature, 2023). 9. `age_bwc_untrunc_app_adj`: This dataset contains the age of backward citations using untruncated data and considering citations of patent applications granted until 2021. To successfully run the script `replication_file.R`, make sure all data files are in the directory and the `mainDir1` variable at the beginning of the script is set to the correct path. For questions, please contact christian.rutzer@unibas.ch
DOI: 10.5281/zenodo.7895565
title: Dataset A of article "A machine learning approach for classifying Mediterranean obsidian of archaeometric interest by SEM investigation"

description: Dataset A used for the manuscript titled "A machine learning approach for classifying Mediterranean obsidian of archaeometric interest by SEM investigation".
This dataset is a txt file, tab separated, encoded in UTF-8, with newline line terminator.
A compressed zip file is also provided, which, expanded, will create a directory containing 890 files. The files come in couples with the same name and two different extensions: spc (with SEM-EDS spectroscopy data) and tif (with SEM-BSE images). The SEM-EDS data refers to the same sample area shown in the SEM-BSE image going under the same name.
DOI: 10.5281/zenodo.8421922
title: Dataset A of article "A machine learning approach for classifying Mediterranean obsidian of archaeometric interest by SEM investigation"

description: Dataset A used for the manuscript titled "A machine learning approach for classifying Mediterranean obsidian of archaeometric interest by SEM investigation".
This dataset is a txt file, tab separated, encoded in UTF-8, with newline line terminator.
A compressed zip file is also provided, which, expanded, will create a directory containing 890 files. The files come in couples with the same name and two different extensions: spc (with SEM-EDS spectroscopy data) and tif (with SEM-BSE images). The SEM-EDS data refers to the same sample area shown in the SEM-BSE image going under the same name.