cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.776883.v1
title: Homology model file

description: Homology model information file to filter up homology models.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776884
title: Solved structures list

description: List of solved structures with the ids of the proteins being compared in the experiment.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776884.v1
title: Solved structures list

description: List of solved structures with the ids of the proteins being compared in the experiment.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776889
title: Visualization of highly connected drugs

description: gml file contanining a visualization of the highly connected drugs obtained as a result from the execution of the TB- Drugome workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776889.v1
title: Visualization of highly connected drugs

description: gml file contanining a visualization of the highly connected drugs obtained as a result from the execution of the TB- Drugome workflow.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776890
title: Solved structures file

description: The solved structures file, containing the solved structures for the proteins and homology models being compared against the drug binding sites.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776890.v1
title: Solved structures file

description: The solved structures file, containing the solved structures for the proteins and homology models being compared against the drug binding sites.
This file is part of the TB-Drugome workflow execution: http://purl.org/net/tb-drugome-run.
See more information here: http://www.wings-workflows.org/drugome/
DOI: 10.6084/m9.figshare.776891
title: TB-Drugome Workflow outputs

description: Workflow results obtained from reproducing the TB-Drugome workflow (http://purl.org/net/tb-drugome-run) experiment by Kinnings et al (http://funsite.sdsc.edu/drugome/TB/) in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000976. The highly connected drugs are the main result of the workflow. Additional information regarding the workflow and its execution can be found here: http://www.wings-workflows.org/drugome/index.php/Main_Page. A complete workflow run of the workflow (from which the current results have been derived) can be accessed here: http://purl.org/net/tb-drugome-run
DOI: 10.6084/m9.figshare.776891.v1
title: TB-Drugome Workflow outputs

description: Workflow results obtained from reproducing the TB-Drugome workflow (http://purl.org/net/tb-drugome-run) experiment by Kinnings et al (http://funsite.sdsc.edu/drugome/TB/) in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000976. The highly connected drugs are the main result of the workflow. Additional information regarding the workflow and its execution can be found here: http://www.wings-workflows.org/drugome/index.php/Main_Page. A complete workflow run of the workflow (from which the current results have been derived) can be accessed here: http://purl.org/net/tb-drugome-run
DOI: 10.6084/m9.figshare.776910
title: TB-Drugome Workflow Input Files

description: Workflow inputs used when executing the TB-Drugome workflow (http://purl.org/net/tb-drugome-run) experiment by Kinnings et al (http://funsite.sdsc.edu/drugome/TB/) in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000976. The highly connected drugs are the main result of the workflow. Additional information regarding the workflow and its execution can be found here: http://www.wings-workflows.org/drugome/index.php/Main_Page. A complete workflow run of the workflow (from which the current results have been derived) can be accessed here: http://purl.org/net/tb-drugome-run
DOI: 10.6084/m9.figshare.776910.v1
title: TB-Drugome Workflow Input Files

description: Workflow inputs used when executing the TB-Drugome workflow (http://purl.org/net/tb-drugome-run) experiment by Kinnings et al (http://funsite.sdsc.edu/drugome/TB/) in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000976. The highly connected drugs are the main result of the workflow. Additional information regarding the workflow and its execution can be found here: http://www.wings-workflows.org/drugome/index.php/Main_Page. A complete workflow run of the workflow (from which the current results have been derived) can be accessed here: http://purl.org/net/tb-drugome-run
DOI: 10.6084/m9.figshare.811811
title: Data file (subject characteristics, volume and shape)

description: In this data file the columns from left to right represent Diagnosis (dx=diagnosis, T = TS or chronic tic disorder, C = Control), Sex (m = male, f = female), Age at scan (in years), and handedness (L = Left, R = Right, A = Ambidextrous). Then the shape principal component (eigenvector) values are represented as demonstrated by the following example: “NaLpc01” = nucleus accumbens (Na) Left (L) principal component (pc) 01. (“Na” = nucleus accumbens, “Cd” = caudate, “Pl” = globus pallidus, “Pu” = putamen, “Th” = thalamus). Next the volumes are listed using similar notation, e.g. “volCdL” = volume in mm3 (vol) Caudate (Cd) Left (L). Finally, Freesurfer analysis values are listed using their standard notation, which can be found in the table at: http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#aseg.stats - See more at: http://62.231.116.94/black/#sthash.OO28vyHo.dpuf
DOI: 10.6084/m9.figshare.814470
title: Extrapolating weak selection in evolutionary games - source code

description: Source code for the paper "Extrapolating weak selection in evolutionary games".
DOI: 10.6084/m9.figshare.825539
title: Preparation of Fe‐Cu catalysts and treatment of a wastewater mixture by microwave‐assisted UV catalytic oxidation processes

description: Microwave‐assisted UV catalytic oxidation (MW/UV) is a potential method to treat organic pollutants that have non‐biological degradability and high toxicity. To achieve high treatment efficiency, it is crucial to prepare heterogeneous photocatalysts with a high activity. Iron–copper catalysts were prepared by four different methods. Synthetic wastewater containing aniline and nitrophenol (TOC = 1000 mg/L) was treated. The key parameters including the proportion of Fe<sub>2</sub>O<sub>3</sub> and CuO and the total content of the active components are discussed. The optimum catalyst dosage and the whole catalytic oxidation process were investigated, and different catalytic oxidation systems were also compared. The catalyst prepared by impregnation was best: the highest TOC removal efficiency reached 78%. The optimum proportion of Fe<sub>2</sub>O<sub>3</sub> and CuO and the content of the total active composition were 4:1 and 30%, respectively. The catalyst preparation method had a greater influence on the MW/UV system than on the microwave (MW) system, and the synergistic effect between MW and UV was verified. The MW/UV system was more susceptible to catalyst dosage than was the MW system, and the optimum catalyst dosage was 5 g/L. The catalyst and H<sub>2</sub>O<sub>2</sub> had a synergistic effect. The presence of a possible non‐thermal microwave effect could be expected.
DOI: 10.6084/m9.figshare.825539.v1
title: Preparation of Fe‐Cu catalysts and treatment of a wastewater mixture by microwave‐assisted UV catalytic oxidation processes

description: Microwave‐assisted UV catalytic oxidation (MW/UV) is a potential method to treat organic pollutants that have non‐biological degradability and high toxicity. To achieve high treatment efficiency, it is crucial to prepare heterogeneous photocatalysts with a high activity. Iron–copper catalysts were prepared by four different methods. Synthetic wastewater containing aniline and nitrophenol (TOC = 1000 mg/L) was treated. The key parameters including the proportion of Fe<sub>2</sub>O<sub>3</sub> and CuO and the total content of the active components are discussed. The optimum catalyst dosage and the whole catalytic oxidation process were investigated, and different catalytic oxidation systems were also compared. The catalyst prepared by impregnation was best: the highest TOC removal efficiency reached 78%. The optimum proportion of Fe<sub>2</sub>O<sub>3</sub> and CuO and the content of the total active composition were 4:1 and 30%, respectively. The catalyst preparation method had a greater influence on the MW/UV system than on the microwave (MW) system, and the synergistic effect between MW and UV was verified. The MW/UV system was more susceptible to catalyst dosage than was the MW system, and the optimum catalyst dosage was 5 g/L. The catalyst and H<sub>2</sub>O<sub>2</sub> had a synergistic effect. The presence of a possible non‐thermal microwave effect could be expected.
DOI: 10.6084/m9.figshare.825582
title: Photosynthesis-fermentation hybrid system to produce lipid feedstock for algal biofuel

description: To avoid bacterial contamination due to medium replacement in the expanded application of a photosynthesis–fermentation model, an integrated photosynthesis-fermentation hybrid system was set up and evaluated for algal lipid production using <i>Chlorella protothecoides</i>. In this system, the CO<sub>2</sub>-rich off-gas from the fermentation process was recycled to agitate medium in the photobioreactor, which could provide initial cells for the heterotrophic fermentation. The cell concentration reached 1.03±0.07 g/L during photoautotrophic growth and then the concentrated green cells were switched to heterotrophic fermentation after removing over 99.5% of nitrogen in the medium by a nitrogen removal device. At the end of fermentation in the system, the cell concentration could reach as high as 100.51±2.03 g/L, and 60.05±1.38% lipid content was achieved simultaneously. The lipid yield (60.36±2.63 g/L) in the hybrid system was over 700 times higher than that in a photobioreactor and exceeded that by fermentation alone (47.56±7.31 g/L). The developed photosynthesis-fermentation hybrid system in this study was not only a feasible option to enhance microalgal lipid production, but also an environment-friendly approach to produce biofuel feedstock through concurrent utilization of ammonia nitrogen, CO<sub>2</sub>, and organic carbons.
DOI: 10.6084/m9.figshare.825582.v1
title: Photosynthesis-fermentation hybrid system to produce lipid feedstock for algal biofuel

description: To avoid bacterial contamination due to medium replacement in the expanded application of a photosynthesis–fermentation model, an integrated photosynthesis-fermentation hybrid system was set up and evaluated for algal lipid production using <i>Chlorella protothecoides</i>. In this system, the CO<sub>2</sub>-rich off-gas from the fermentation process was recycled to agitate medium in the photobioreactor, which could provide initial cells for the heterotrophic fermentation. The cell concentration reached 1.03±0.07 g/L during photoautotrophic growth and then the concentrated green cells were switched to heterotrophic fermentation after removing over 99.5% of nitrogen in the medium by a nitrogen removal device. At the end of fermentation in the system, the cell concentration could reach as high as 100.51±2.03 g/L, and 60.05±1.38% lipid content was achieved simultaneously. The lipid yield (60.36±2.63 g/L) in the hybrid system was over 700 times higher than that in a photobioreactor and exceeded that by fermentation alone (47.56±7.31 g/L). The developed photosynthesis-fermentation hybrid system in this study was not only a feasible option to enhance microalgal lipid production, but also an environment-friendly approach to produce biofuel feedstock through concurrent utilization of ammonia nitrogen, CO<sub>2</sub>, and organic carbons.
DOI: 10.6084/m9.figshare.825582.v2
title: Photosynthesis-fermentation hybrid system to produce lipid feedstock for algal biofuel

description: To avoid bacterial contamination due to medium replacement in the expanded application of a photosynthesis–fermentation model, an integrated photosynthesis-fermentation hybrid system was set up and evaluated for algal lipid production using <i>Chlorella protothecoides</i>. In this system, the CO<sub>2</sub>-rich off-gas from the fermentation process was recycled to agitate medium in the photobioreactor, which could provide initial cells for the heterotrophic fermentation. The cell concentration reached 1.03±0.07 g/L during photoautotrophic growth and then the concentrated green cells were switched to heterotrophic fermentation after removing over 99.5% of nitrogen in the medium by a nitrogen removal device. At the end of fermentation in the system, the cell concentration could reach as high as 100.51±2.03 g/L, and 60.05±1.38% lipid content was achieved simultaneously. The lipid yield (60.36±2.63 g/L) in the hybrid system was over 700 times higher than that in a photobioreactor and exceeded that by fermentation alone (47.56±7.31 g/L). The developed photosynthesis-fermentation hybrid system in this study was not only a feasible option to enhance microalgal lipid production, but also an environment-friendly approach to produce biofuel feedstock through concurrent utilization of ammonia nitrogen, CO<sub>2</sub>, and organic carbons.
DOI: 10.6084/m9.figshare.825582.v3
title: Photosynthesis-fermentation hybrid system to produce lipid feedstock for algal biofuel

description: To avoid bacterial contamination due to medium replacement in the expanded application of a photosynthesis–fermentation model, an integrated photosynthesis-fermentation hybrid system was set up and evaluated for algal lipid production using <i>Chlorella protothecoides</i>. In this system, the CO<sub>2</sub>-rich off-gas from the fermentation process was recycled to agitate medium in the photobioreactor, which could provide initial cells for the heterotrophic fermentation. The cell concentration reached 1.03±0.07 g/L during photoautotrophic growth and then the concentrated green cells were switched to heterotrophic fermentation after removing over 99.5% of nitrogen in the medium by a nitrogen removal device. At the end of fermentation in the system, the cell concentration could reach as high as 100.51±2.03 g/L, and 60.05±1.38% lipid content was achieved simultaneously. The lipid yield (60.36±2.63 g/L) in the hybrid system was over 700 times higher than that in a photobioreactor and exceeded that by fermentation alone (47.56±7.31 g/L). The developed photosynthesis-fermentation hybrid system in this study was not only a feasible option to enhance microalgal lipid production, but also an environment-friendly approach to produce biofuel feedstock through concurrent utilization of ammonia nitrogen, CO<sub>2</sub>, and organic carbons.
DOI: 10.6084/m9.figshare.825603
title: Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins

description: <sup>1</sup>Cysteine (Cys) has unique chemical properties of catalysis, metal chelation, and protein stabilization. While Cys biosynthesis is assumed to be very ancient, the actual time of origin of these metabolic pathways remains unknown. Here, we use the molecular clocks of protein folds and fold superfamilies to time the origin of Cys biosynthesis. We find that the tRNA-dependent biosynthetic pathway appeared ∼3.5 billion years ago while the tRNA-independent counterpart emerged ∼500 million years later. A deep analysis of the origins of Cys biosynthesis in the context of emerging biochemistry uncovers some intriguing features of the planetary environment of early Earth. Results suggest that iron-sulfur (Fe-S) proteins that use cysteinyl sulfur to bind iron atoms were not the first to arise in evolution. Instead, their origin coincides with the appearance of the first Cys biosynthetic pathway. It is therefore likely that Cys did not play an important role in the make up of primordial protein molecules and that Fe-S clusters were not part of active sites at the beginning of biological history.
<sup>1</sup>Current address: Biochemical Engineering Institute, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
DOI: 10.6084/m9.figshare.825603.v1
title: Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins

description: <sup>1</sup>Cysteine (Cys) has unique chemical properties of catalysis, metal chelation, and protein stabilization. While Cys biosynthesis is assumed to be very ancient, the actual time of origin of these metabolic pathways remains unknown. Here, we use the molecular clocks of protein folds and fold superfamilies to time the origin of Cys biosynthesis. We find that the tRNA-dependent biosynthetic pathway appeared ∼3.5 billion years ago while the tRNA-independent counterpart emerged ∼500 million years later. A deep analysis of the origins of Cys biosynthesis in the context of emerging biochemistry uncovers some intriguing features of the planetary environment of early Earth. Results suggest that iron-sulfur (Fe-S) proteins that use cysteinyl sulfur to bind iron atoms were not the first to arise in evolution. Instead, their origin coincides with the appearance of the first Cys biosynthetic pathway. It is therefore likely that Cys did not play an important role in the make up of primordial protein molecules and that Fe-S clusters were not part of active sites at the beginning of biological history.
<sup>1</sup>Current address: Biochemical Engineering Institute, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
DOI: 10.6084/m9.figshare.825611
title: Predicting protein oxidation sites with feature selection and analysis approach

description: Protein oxidation is a ubiquitous post-translational modification that plays important roles in various physiological and pathological processes. Owing to the fact that protein oxidation can also take place as an experimental artifact or caused by oxygen in the air during the process of sample collection and analysis, and that it is both time-consuming and expensive to determine the protein oxidation sites purely by biochemical experiments, it would be of great benefit to develop <i>in silico</i> methods for rapidly and effectively identifying protein oxidation sites. In this study, we developed a computational method to address this problem. Our method was based on the nearest neighbor algorithm in which, however, the maximum relevance minimum redundancy and incremental feature selection approaches were incorporated. From the initial 735 features, 16 features were selected as the optimal feature set. Of such 16 optimized features, 10 features were associated with the position-specific scoring matrix conservation scores, three with the amino acid factors, one with the propensity of conservation of residues on protein surface, one with the side chain count of carbon atom deviation from mean, and one with the solvent accessibility. It was observed that our prediction model achieved an overall success rate of 75.82%, indicating that it is quite encouraging and promising for practical applications. Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation.
DOI: 10.6084/m9.figshare.825611.v1
title: Predicting protein oxidation sites with feature selection and analysis approach

description: Protein oxidation is a ubiquitous post-translational modification that plays important roles in various physiological and pathological processes. Owing to the fact that protein oxidation can also take place as an experimental artifact or caused by oxygen in the air during the process of sample collection and analysis, and that it is both time-consuming and expensive to determine the protein oxidation sites purely by biochemical experiments, it would be of great benefit to develop <i>in silico</i> methods for rapidly and effectively identifying protein oxidation sites. In this study, we developed a computational method to address this problem. Our method was based on the nearest neighbor algorithm in which, however, the maximum relevance minimum redundancy and incremental feature selection approaches were incorporated. From the initial 735 features, 16 features were selected as the optimal feature set. Of such 16 optimized features, 10 features were associated with the position-specific scoring matrix conservation scores, three with the amino acid factors, one with the propensity of conservation of residues on protein surface, one with the side chain count of carbon atom deviation from mean, and one with the solvent accessibility. It was observed that our prediction model achieved an overall success rate of 75.82%, indicating that it is quite encouraging and promising for practical applications. Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation.
DOI: 10.6084/m9.figshare.825654
title: Molecular cloning and sequence analysis of the gene encoding interleukin‐6 of the giant panda (<i>Ailuropoda melanoleuca</i>)

description: In the present study, the cloning and sequence analysis of interleukin‐6 (IL‐6) from the giant panda (<i>Ailuropoda melanoleuca</i>) were described. Sequencing revealed that IL‐6 complementary DNA contains a 636 base‐pair open reading frame encoding 211 amino acids. Homology analyses indicated that the identity levels of nucleotide and deduced amino acid sequences of IL‐6 between the giant panda and other species in Carnivora ranged from 90.5% to 85.6% and from 82.9% to 76.5%, respectively. Phylogenetic analyses based on nucleotide and amino acid sequences showed that the harbour seal shared a closer relationship with the giant panda than other carnivores (ursids not included). The functionally important domains and sites that have previously been recognized in other carnivores were all observed in the IL‐6 sequence of the giant panda. These findings suggest that the complementary DNA fragment cloned is indeed the IL‐6 molecule with biological activity and can be used in immunological studies of the giant panda.
DOI: 10.6084/m9.figshare.825654.v1
title: Molecular cloning and sequence analysis of the gene encoding interleukin‐6 of the giant panda (<i>Ailuropoda melanoleuca</i>)

description: In the present study, the cloning and sequence analysis of interleukin‐6 (IL‐6) from the giant panda (<i>Ailuropoda melanoleuca</i>) were described. Sequencing revealed that IL‐6 complementary DNA contains a 636 base‐pair open reading frame encoding 211 amino acids. Homology analyses indicated that the identity levels of nucleotide and deduced amino acid sequences of IL‐6 between the giant panda and other species in Carnivora ranged from 90.5% to 85.6% and from 82.9% to 76.5%, respectively. Phylogenetic analyses based on nucleotide and amino acid sequences showed that the harbour seal shared a closer relationship with the giant panda than other carnivores (ursids not included). The functionally important domains and sites that have previously been recognized in other carnivores were all observed in the IL‐6 sequence of the giant panda. These findings suggest that the complementary DNA fragment cloned is indeed the IL‐6 molecule with biological activity and can be used in immunological studies of the giant panda.