cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11901933.v1
title: Isotopic niche differs between seal and fish-eating killer whales (Orcinus orca) in northern Norway

description: This dataset includes the nitrogen and carbon isotopic values from killer whale skin samples (Orcinus orca, n=38), and from herring (Clupea harengus, n=4), lumpfish (Cyclopterus lumpus, n=5) and harbor seal (Phoca vitulina, n=1) muscle samples collected in 2017-2018 in northern Norway. Nitrogen values (d15N) are non-lipid extracted and (d13C) are lipid-extracted. <br>
DOI: 10.6084/m9.figshare.11901864
title: Novel and potent inhibitors for dihydropteroate synthase of <i>Helicobacter pylori</i>

description: An endless drug-resistant strains of <i>Helicobacter pylori</i> and multitudinous drug reactions are obstacles in the treatment of <i>H. pylori</i> infections, thereby ambitious novel proof-of-concept for inhibitor design was practiced in advancement of medication. Dihydropteroate synthase (DHPS) is an alluring target that plays a great role in folate synthesis pathway essential for amino acids biosynthesis was selected for designing novel drugs to prevent infections caused by pathogenic <i>H. pylori</i>. In the present study, a reliable tertiary structure of DHPS in complex with inhibitor 6MB was constructed by Modeler 9v19. DrugBank compounds of DHPS, published inhibitors, and co-crystal ligand (6MB) were docked against DHPS. The best docked compounds were screened against 28.5 million compounds resulted 1186 structural analogs. Virtual screening workflow and quantum polarized ligand dockings of these compounds against DHPS resulted three leads that showed better XP Gscores, ADME properties, and binding-free energies compared to 6MB, DrugBank compounds, and published inhibitors. The proposed leads were also validated by receiver operative characteristic (ROC) curve metrics in the presence of thousand decoys and the best docked existing compounds against DHPS. Long-range molecular dynamics (MD) simulations for 100 ns were executed after post-docking evaluations. Trajectory analysis showed the lead–DHPS docking complex’s inter-molecular interactions were stable throughout the entire runtime of MD simulations than 6MB–DHPS complex and Eliglustat–DHPS complex. The study outcomes showed good competitive binding propensity and active-tunneling of leads over the existing inhibitors, thereby these leads could be ideal inhibitors against DHPS to target <i>H. pylori</i>.
DOI: 10.6084/m9.figshare.11901864.v1
title: Novel and potent inhibitors for dihydropteroate synthase of <i>Helicobacter pylori</i>

description: An endless drug-resistant strains of <i>Helicobacter pylori</i> and multitudinous drug reactions are obstacles in the treatment of <i>H. pylori</i> infections, thereby ambitious novel proof-of-concept for inhibitor design was practiced in advancement of medication. Dihydropteroate synthase (DHPS) is an alluring target that plays a great role in folate synthesis pathway essential for amino acids biosynthesis was selected for designing novel drugs to prevent infections caused by pathogenic <i>H. pylori</i>. In the present study, a reliable tertiary structure of DHPS in complex with inhibitor 6MB was constructed by Modeler 9v19. DrugBank compounds of DHPS, published inhibitors, and co-crystal ligand (6MB) were docked against DHPS. The best docked compounds were screened against 28.5 million compounds resulted 1186 structural analogs. Virtual screening workflow and quantum polarized ligand dockings of these compounds against DHPS resulted three leads that showed better XP Gscores, ADME properties, and binding-free energies compared to 6MB, DrugBank compounds, and published inhibitors. The proposed leads were also validated by receiver operative characteristic (ROC) curve metrics in the presence of thousand decoys and the best docked existing compounds against DHPS. Long-range molecular dynamics (MD) simulations for 100 ns were executed after post-docking evaluations. Trajectory analysis showed the lead–DHPS docking complex’s inter-molecular interactions were stable throughout the entire runtime of MD simulations than 6MB–DHPS complex and Eliglustat–DHPS complex. The study outcomes showed good competitive binding propensity and active-tunneling of leads over the existing inhibitors, thereby these leads could be ideal inhibitors against DHPS to target <i>H. pylori</i>.
DOI: 10.6084/m9.figshare.11901822
title: Assessment of different carbon and salinity level on growth kinetics, lipid, and starch composition of <i>Chlorella vulgaris</i> SAG 211-12

description: The quality of microalgal biofuel depends on the fatty acid (FA) distribution. A high ratio of saturated fatty acids (SFAs) favors better biofuel characteristics. Palmitic acid (C16:0) and stearic acid (C18:0) are essential FAs for required biodiesel quality. In this study, combined effects of growth medium concentrations of NaCl, glucose and glycerol on cell composition and FA profile of the <i>Chlorella vulgaris</i> SAG 211–12 were investigated. A central composite design (CCD) based design of experiments (DoE) was used for experimental setup. According to experimental results, the maximum mass fraction for palmitic acid (C16:0), 40.67% of total fatty acids, was obtained in the medium supplemented with 0.9% (w/v) NaCl, 0.3% (w/v) glucose, and 0.3% (w/v) glycerol, whereas stearic acid (C18:0) percentage reached the highest value of 22.16% of total fatty acids in the presence of 2.5% NaCl, 0.6% glucose, and 0.6% glycerol. According to the same set of designed experiments, best starch content was found as 22.08% of dry cell weight in a medium containing 2.0% NaCl, 0.3% glucose, and 0.3% glycerol. C16:0 mass fraction as a function of three medium ingredient concentrations was modeled using a Kriging model. Optimum concentrations of NaCl, glucose and glycerol to reach maximum C16:0 fraction were predicted as 0.5, 1, and 1%, respectively.
DOI: 10.6084/m9.figshare.11901822.v1
title: Assessment of different carbon and salinity level on growth kinetics, lipid, and starch composition of <i>Chlorella vulgaris</i> SAG 211-12

description: The quality of microalgal biofuel depends on the fatty acid (FA) distribution. A high ratio of saturated fatty acids (SFAs) favors better biofuel characteristics. Palmitic acid (C16:0) and stearic acid (C18:0) are essential FAs for required biodiesel quality. In this study, combined effects of growth medium concentrations of NaCl, glucose and glycerol on cell composition and FA profile of the <i>Chlorella vulgaris</i> SAG 211–12 were investigated. A central composite design (CCD) based design of experiments (DoE) was used for experimental setup. According to experimental results, the maximum mass fraction for palmitic acid (C16:0), 40.67% of total fatty acids, was obtained in the medium supplemented with 0.9% (w/v) NaCl, 0.3% (w/v) glucose, and 0.3% (w/v) glycerol, whereas stearic acid (C18:0) percentage reached the highest value of 22.16% of total fatty acids in the presence of 2.5% NaCl, 0.6% glucose, and 0.6% glycerol. According to the same set of designed experiments, best starch content was found as 22.08% of dry cell weight in a medium containing 2.0% NaCl, 0.3% glucose, and 0.3% glycerol. C16:0 mass fraction as a function of three medium ingredient concentrations was modeled using a Kriging model. Optimum concentrations of NaCl, glucose and glycerol to reach maximum C16:0 fraction were predicted as 0.5, 1, and 1%, respectively.
DOI: 10.6084/m9.figshare.11901468
title: Historical data sets and parameters of the two-area system

description: The zip file contains the generated historical data of DG output and load demand of the two-area system in numerical tests. The PDF file contains the parameters of the two-area system.
DOI: 10.6084/m9.figshare.11901468.v1
title: Historical data sets and parameters of the two-area system

description: The zip file contains the generated historical data of DG output and load demand of the two-area system in numerical tests. The PDF file contains the parameters of the two-area system.
DOI: 10.6084/m9.figshare.11901393
title: Additional file 3 of Metabolically healthy obese and metabolic syndrome of the lean: the importance of diet quality. Analysis of MAGNETIC cohort

description: Additional file 3. Dataset (imputed data): Dataset with imputed values using random forest algorithm (used for multivariable analysis).
DOI: 10.6084/m9.figshare.11901468.v2
title: Historical data sets and parameters of the two-area system

description: The zip file contains the generated historical data of DG output and load demand of the two-area system in numerical tests. The PDF file contains the parameters of the two-area system.
DOI: 10.6084/m9.figshare.11901393.v1
title: Additional file 3 of Metabolically healthy obese and metabolic syndrome of the lean: the importance of diet quality. Analysis of MAGNETIC cohort

description: Additional file 3. Dataset (imputed data): Dataset with imputed values using random forest algorithm (used for multivariable analysis).
DOI: 10.6084/m9.figshare.11901387
title: Additional file 2 of Metabolically healthy obese and metabolic syndrome of the lean: the importance of diet quality. Analysis of MAGNETIC cohort

description: Additional file 2. Dataset (raw data): Study dataset.
DOI: 10.6084/m9.figshare.11901390
title: Full-length transcriptome sequencing from multiple immune-related tissues of Paralichthys olivaceus

description: The coding regions， protein sequences and their annotation results of <i>Paralichthys olivaceus</i> were deposited in this dataset.
DOI: 10.6084/m9.figshare.11901381
title: Additional file 4 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Labels for each tumor sample. (XLSX 1443 kb)
DOI: 10.6084/m9.figshare.11901387.v1
title: Additional file 2 of Metabolically healthy obese and metabolic syndrome of the lean: the importance of diet quality. Analysis of MAGNETIC cohort

description: Additional file 2. Dataset (raw data): Study dataset.
DOI: 10.6084/m9.figshare.11901390.v1
title: Full-length transcriptome sequencing from multiple immune-related tissues of Paralichthys olivaceus

description: The coding regions， protein sequences and their annotation results of <i>Paralichthys olivaceus</i> were deposited in this dataset.
DOI: 10.6084/m9.figshare.11901378
title: Additional file 3 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Group gene membership. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.11901381.v1
title: Additional file 4 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Labels for each tumor sample. (XLSX 1443 kb)
DOI: 10.6084/m9.figshare.11901378.v1
title: Additional file 3 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Group gene membership. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.11901366
title: Additional file 2 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Expression matrix used for training. (XLSX 29 722 kb)
DOI: 10.6084/m9.figshare.11901360
title: Additional file 5 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 5: Table S4.Â Materials used for experiments. Table summarising list of antibodies used for immunostaining, kits used, as well as primers used for quantitative RT-PCR.
DOI: 10.6084/m9.figshare.11901366.v1
title: Additional file 2 of Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

description: Expression matrix used for training. (XLSX 29 722 kb)
DOI: 10.6084/m9.figshare.11901354
title: Additional file 4 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 4: Table S3.Â Transplantation of hPOs and hPC-IPMN and hPC-PDAC organoids in immunodeficient mice. Table summarising information for the healthy and cancer-derived organoid cultures transplanted into NSG mice including donor ID, passage at time of injection, injection vehicle composition (Condition), number of mice transplanted (Mice Tx), location of transplant, overall engraftment success and furthest timepoint of engraftment.
DOI: 10.6084/m9.figshare.11901354.v1
title: Additional file 4 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 4: Table S3.Â Transplantation of hPOs and hPC-IPMN and hPC-PDAC organoids in immunodeficient mice. Table summarising information for the healthy and cancer-derived organoid cultures transplanted into NSG mice including donor ID, passage at time of injection, injection vehicle composition (Condition), number of mice transplanted (Mice Tx), location of transplant, overall engraftment success and furthest timepoint of engraftment.
DOI: 10.6084/m9.figshare.11901348
title: Additional file 3 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 3: Table S2.Â Whole Genome Sequencing and Copy Number analysis of clonally derived hPO cultures. hPOs were expanded as clonal cultures from the same donor and whole genome sequencing (WGS) was performed on the three individual clonal cultures at a sequencing depth of ~35x. The Allele Specific Copy Number Analysis (ASCAT) algorithm was used to assess clonal number variation in the clonal cultures and determine existence of large structural variations.
DOI: 10.6084/m9.figshare.11901360.v1
title: Additional file 5 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 5: Table S4.Â Materials used for experiments. Table summarising list of antibodies used for immunostaining, kits used, as well as primers used for quantitative RT-PCR.
DOI: 10.6084/m9.figshare.11901339
title: Additional file 2 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 2: Table S1. Donor Demographics and organoid derivation success. Table summarising organ donor information including age range, Body Mass Index (BMI), ischaemic time of tissue, underlying pathology and success of organoid isolation. All healthy tissue was procured from deceased organ donors whose organs were retrieved for transplantation. Diseased tissue was procured from patients having undergone surgical resection. Pancreatic islets were isolated in the Scottish National Blood Transfusion Service (SNBTS) Islet Isolation Centre and were subsequently allocated for research.
DOI: 10.6084/m9.figshare.11901348.v1
title: Additional file 3 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 3: Table S2.Â Whole Genome Sequencing and Copy Number analysis of clonally derived hPO cultures. hPOs were expanded as clonal cultures from the same donor and whole genome sequencing (WGS) was performed on the three individual clonal cultures at a sequencing depth of ~35x. The Allele Specific Copy Number Analysis (ASCAT) algorithm was used to assess clonal number variation in the clonal cultures and determine existence of large structural variations.
DOI: 10.6084/m9.figshare.11901330
title: Additional file 7 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 7. Results of 5mC-RIP-Array analyses.
DOI: 10.6084/m9.figshare.11901330.v1
title: Additional file 7 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 7. Results of 5mC-RIP-Array analyses.
DOI: 10.6084/m9.figshare.11901339.v1
title: Additional file 2 of Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids

description: Additional file 2: Table S1. Donor Demographics and organoid derivation success. Table summarising organ donor information including age range, Body Mass Index (BMI), ischaemic time of tissue, underlying pathology and success of organoid isolation. All healthy tissue was procured from deceased organ donors whose organs were retrieved for transplantation. Diseased tissue was procured from patients having undergone surgical resection. Pancreatic islets were isolated in the Scottish National Blood Transfusion Service (SNBTS) Islet Isolation Centre and were subsequently allocated for research.
DOI: 10.6084/m9.figshare.11901321
title: Additional file 6 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 6. Results of selected miRNA-BS.
DOI: 10.6084/m9.figshare.11901318
title: Additional file 5 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 5. Sequence of selected miRNA-BS.
DOI: 10.6084/m9.figshare.11901318.v1
title: Additional file 5 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 5. Sequence of selected miRNA-BS.
DOI: 10.6084/m9.figshare.11901321.v1
title: Additional file 6 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 6. Results of selected miRNA-BS.
DOI: 10.6084/m9.figshare.11901312
title: Additional file 4 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 4. Results of BS experiments.
DOI: 10.6084/m9.figshare.11901312.v1
title: Additional file 4 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 4. Results of BS experiments.
DOI: 10.6084/m9.figshare.11901306
title: Additional file 3 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 3. Statistical analysis of BS experiments.
DOI: 10.6084/m9.figshare.11901306.v1
title: Additional file 3 of Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

description: Additional file 3. Statistical analysis of BS experiments.
DOI: 10.6084/m9.figshare.11900823
title: Simulated zero-crossing wave period (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp126 experiment r1i1p1f1

description: Simulated zero-crossing wave period (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp126 experiment (one of future scenarios) r1i1p1f1. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11901174
title: data Analysis-cholesterol and bodyweight of mice.docx

description: Cinnamon (cinnamommum burmanii) extract can reduce total cholesterol levels in mice (musmusculus ) that were given quail egg yolks
DOI: 10.6084/m9.figshare.11900823.v1
title: Simulated zero-crossing wave period (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp126 experiment r1i1p1f1

description: Simulated zero-crossing wave period (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp126 experiment (one of future scenarios) r1i1p1f1. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11901174.v1
title: data Analysis-cholesterol and bodyweight of mice.docx

description: Cinnamon (cinnamommum burmanii) extract can reduce total cholesterol levels in mice (musmusculus ) that were given quail egg yolks
DOI: 10.6084/m9.figshare.11901174.v2
title: data Analysis-cholesterol and bodyweight of mice.docx

description: Cinnamon (cinnamommum burmanii) extract can reduce total cholesterol levels in mice (musmusculus ) that were given quail egg yolks
DOI: 10.6084/m9.figshare.11900616
title: A new gene inventory of the ubiquitin and ubiquitin-like conjugation pathways in Giardia intestinalis

description: BACKGROUND Ubiquitin (Ub) and Ub-like proteins (Ub-L) are critical regulators of complex cellular processes such as the cell cycle, DNA repair, transcription, chromatin remodeling, signal translation, and protein degradation. Giardia intestinalis possesses an experimentally proven Ub-conjugation system; however, a limited number of enzymes involved in this process were identified using basic local alignment search tool (BLAST). This is due to the limitations of BLAST’s ability to identify homologous functional regions when similarity between the sequences dips to &lt; 30%. In addition Ub-Ls and their conjugating enzymes have not been fully elucidated in Giardia. OBJETIVE To identify the enzymes involved in the Ub and Ub-Ls conjugation processes using intelligent systems based on the hidden Markov models (HMMs). METHODS We performed an HMM search of functional Pfam domains found in the key enzymes of these pathways in Giardia’s proteome. Each open reading frame identified was analysed by sequence homology, domain architecture, and transcription levels. FINDINGS We identified 118 genes, 106 of which corresponded to the ubiquitination process (Ub, E1, E2, E3, and DUB enzymes). The E3 ligase group was the largest group with 82 members; 71 of which harbored a characteristic RING domain. Four Ub-Ls were identified and the conjugation enzymes for NEDD8 and URM1 were described for first time. The 3D model for Ub-Ls displayed the β-grasp fold typical. Furthermore, our sequence analysis for the corresponding activating enzymes detected the essential motifs required for conjugation. MAIN CONCLUSIONS Our findings highlight the complexity of Giardia’s Ub-conjugation system, which is drastically different from that previously reported, and provides evidence for the presence of NEDDylation and URMylation enzymes in the genome and transcriptome of G. intestinalis.