cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7879686
title: A High-Level Quantum Chemical Study of the Thermodynamics Associated with Chlorine Transfer between N-Chlorinated Nucleobases

description: Geometries of the isomers of the N-Chlorinated nucleobases (adenine, guanine and thymine) as well as the lowest energy structures of the DNA bases (adenine, cytosine, guanine and thymine) obtained at the B3LYP/6-31G(2df,p) level of theory (in Cartesian Coordinates). <strong>ABSTRACT: </strong>The relative free energies of the isomers formed upon <em>N</em>-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the <em>N</em>-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy <em>N</em>-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from <em>N</em>-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from an <em>N</em>-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from <em>N</em>-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with D<em>G</em><sup>o</sup> values of ­–50.3 (cytosine), –28.0 (guanine), and –6.7 (adenine) kJ mol<sup>–1</sup>. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In an aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from <em>N</em>-chlorothymine to the three other nucleobases: –58.4 (cytosine), –26.4 (adenine), and –18.7 (guanine) kJ mol<sup>–1</sup>. Therefore, our calculations, whether in the gas phase or in an aqueous solution, clearly indicate that chlorine transfer from any of the <em>N</em>-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in <em>N</em>-chlorinated cytidine than in other <em>N</em>-chlorinated nucleosides.
DOI: 10.22002/jcawz-nn069
title: Protein sequences and IQ-TREE files for select gene families highlighted in "The genomic and cellular basis of biosynthetic innovation in rove beetles"

description: This dataset contains the curated protein sequences and raw tree files constructed with IQ-TREE. Gene families include fatty acid synthase (MFASN), very long chain fatty acid coa bubblegum ligase (VLFABGM), copper-transporting ATPase (CU_ATPase), esterases (est), fatty acyl-CoA reductase (FAR), steryol-CoA, cytochrome P450 4g (CYP), laccases (dmd), farnesyl pyrophosphate synthase (FFPS), geranylgeranyl diphosphate synthase (GGPS), isopentenyl diphosphate isomerase (IDI), and ubiquinone biosynthesis O-methyltransferase, mitochondrial (meos).
DOI: 10.22002/cgsw0-9kk67
title: Protein sequences and IQ-TREE files for select gene families highlighted in "The genomic and cellular basis of biosynthetic innovation in rove beetles"

description: This dataset contains the curated protein sequences and raw tree files constructed with IQ-TREE. Gene families include fatty acid synthase (MFASN), very long chain fatty acid coa bubblegum ligase (VLFABGM), copper-transporting ATPase (CU_ATPase), esterases (est), fatty acyl-CoA reductase (FAR), steryol-CoA, cytochrome P450 4g (CYP), laccases (dmd), farnesyl pyrophosphate synthase (FFPS), geranylgeranyl diphosphate synthase (GGPS), isopentenyl diphosphate isomerase (IDI), and ubiquinone biosynthesis O-methyltransferase, mitochondrial (meos).
DOI: 10.25582/data.2022-05.2506462/1932199
title: Data for EMSL Project 51743 from May 2022
DOI: 10.5517/ccdc.csd.cc2fsbj3
title: CCDC 2257715: Experimental Crystal Structure Determination

description: Related Article: Haina Zhang|2023|CSD Communication|||
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: 10.3886/e183663v1-137580
title: Replication data and code for Monetary Policy and Inequality

description: These replication files use data from the Survey of Consumer Finances to compute household-level exposures to changes in monetary policy. The replication file also estimates the causal effect of monetary policy on a list of macroeconomic variables.<br>
DOI: 10.6084/m9.figshare.22722943
title: Dataset on type of buffer for suspending cells in biotransformation

description: Different buffers are frequently used in biological and biotechnological research with few or poor explanation for use. This small dataset catalogues a list of buffers used for suspending cells in biotransformation mediated by biocatalytic routes. It is hoped that the list will offer some guidance as researchers choose an appropriate buffer for their biotransformation experiments.
DOI: 10.6084/m9.figshare.22722943.v1
title: Dataset on type of buffer for suspending cells in biotransformation

description: Different buffers are frequently used in biological and biotechnological research with few or poor explanation for use. This small dataset catalogues a list of buffers used for suspending cells in biotransformation mediated by biocatalytic routes. It is hoped that the list will offer some guidance as researchers choose an appropriate buffer for their biotransformation experiments.
DOI: 10.5281/zenodo.7879530
title: Geospatial analysis of mining areas reclamation potential through Technosols in Brazil

description: This repository contains two datasets: 1. An update of metadata analysis with data published before 2021 resulting from the search equation "TS = (Technosol* AND (Organic carbon OR Organic matter)" in the Web of Science (WOS) database. Update from Allory 2022: https://doi.org/10.24396/ORDAR-60. 2. A database containing geospatial datasets (inputs and outputs), R scripts, and other FOSS software files used for the geospatial analysis of land reclamation potential through Technosols in Brazil.
DOI: 10.5281/zenodo.7879529
title: Geospatial analysis of mining areas reclamation potential through Technosols in Brazil

description: This repository contains two datasets: 1. An update of metadata analysis with data published before 2021 resulting from the search equation "TS = (Technosol* AND (Organic carbon OR Organic matter)" in the Web of Science (WOS) database. Update from Allory 2022: https://doi.org/10.24396/ORDAR-60. 2. A database containing geospatial datasets (inputs and outputs), R scripts, and other FOSS software files used for the geospatial analysis of land reclamation potential through Technosols in Brazil.
DOI: 10.6084/m9.figshare.22722946
title: Dataset of promoters of genes on the human mitochondrial chromosome

description: Promoters are gene expression control elements critical to controlling the on or off state of the gene as well as the amount of gene expression from a particular gene. This work attempts to output the promoter of genes on the human mitochondrial chromosome for reference use by other researchers in different fields. Specifically, an in-house MATLAB software outputs a segment of the DNA sequence upstream of the particular gene in the mitochondria chromosome as the segment that contains the promoter of the gene. This is a coarse approximation of the promoter region. In particular, the gene segment named “Promoter” in the accompanying Excel file contains the promoter as well as other sequence segment of unknown function. It is hoped that this dataset would be useful for researchers interested in the broad topic of mitochondrial gene expression.
DOI: 10.6084/m9.figshare.22722946.v1
title: Dataset of promoters of genes on the human mitochondrial chromosome

description: Promoters are gene expression control elements critical to controlling the on or off state of the gene as well as the amount of gene expression from a particular gene. This work attempts to output the promoter of genes on the human mitochondrial chromosome for reference use by other researchers in different fields. Specifically, an in-house MATLAB software outputs a segment of the DNA sequence upstream of the particular gene in the mitochondria chromosome as the segment that contains the promoter of the gene. This is a coarse approximation of the promoter region. In particular, the gene segment named “Promoter” in the accompanying Excel file contains the promoter as well as other sequence segment of unknown function. It is hoped that this dataset would be useful for researchers interested in the broad topic of mitochondrial gene expression.
DOI: 10.6084/m9.figshare.22722967
title: Additional file 1 of The effect of dentin surface pretreatment using dimethyl sulfoxide on the bond strength of a universal bonding agent to dentin

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22722967.v1
title: Additional file 1 of The effect of dentin surface pretreatment using dimethyl sulfoxide on the bond strength of a universal bonding agent to dentin

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22722985
title: Additional file 5 of Risk factors for postpartum maternal mortality and hospital readmission in low- and middle-income countries: a systematic review

description: Additional file 5.
DOI: 10.6084/m9.figshare.22722985.v1
title: Additional file 5 of Risk factors for postpartum maternal mortality and hospital readmission in low- and middle-income countries: a systematic review

description: Additional file 5.
DOI: 10.6084/m9.figshare.22722986.v1
title: Additional file 1 of Time to postpartum family planning initiation and its predictors among mothers coming for first measles vaccination at Family Guidance Association of Ethiopia, Dessie Model Clinic, Northeast Ethiopia: cox-regression model

description: Additional file 1. S2: Data set used for this study.
DOI: 10.6084/m9.figshare.22722986
title: Additional file 1 of Time to postpartum family planning initiation and its predictors among mothers coming for first measles vaccination at Family Guidance Association of Ethiopia, Dessie Model Clinic, Northeast Ethiopia: cox-regression model

description: Additional file 1. S2: Data set used for this study.
DOI: 10.6084/m9.figshare.22722958
title: RNA sequences (Sequence Read Archive submission template)

description: Our dataset gathers data collected from a time-course experiment, with four treatments: 1) control trees; 2) trees infected with <em>P. cinnamomi</em>; 3) trees inoculated with the BCA; 4) trees infected with <em>P. cinnamomi </em>and inoculated with the BCA. During the infection process, we measured plant morphological and physiological variables and collected rhizosphere soil samples for bacterial and fungal amplicon sequencing, bacterial RNA-seq and metabolomic analyses.
DOI: 10.6084/m9.figshare.22723058
title: Additional file 1 of Expanding the role of PSMA PET in active surveillance

description: Additional File 1: Raw data of all patients included in the study
DOI: 10.6084/m9.figshare.22723108
title: Additional file 12 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 12: Data S1. Related to Fig. 1. Assigned 'integrated cluster' (iClust) groups for TCGA liver cancer samples where available (from the original TCGA-LIHC manuscript), together with inferred iClusters for unspecified samples, as determined by clustering of gene set scores (as shown in Figure S1; further details given in “Methods”).
DOI: 10.6084/m9.figshare.22723108.v1
title: Additional file 12 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 12: Data S1. Related to Fig. 1. Assigned 'integrated cluster' (iClust) groups for TCGA liver cancer samples where available (from the original TCGA-LIHC manuscript), together with inferred iClusters for unspecified samples, as determined by clustering of gene set scores (as shown in Figure S1; further details given in “Methods”).
DOI: 10.6084/m9.figshare.22723111
title: Additional file 13 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 13: Data S2. Related to Fig. 1. mRNA transcript abundance, probe methylation (beta) values, and copy number variation data for all TCGA liver samples (including matched adjacent normal liver tissue). Corresponds to pre-transformed data shown in Fig. 1.
DOI: 10.6084/m9.figshare.22723111.v1
title: Additional file 13 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 13: Data S2. Related to Fig. 1. mRNA transcript abundance, probe methylation (beta) values, and copy number variation data for all TCGA liver samples (including matched adjacent normal liver tissue). Corresponds to pre-transformed data shown in Fig. 1.
DOI: 10.6084/m9.figshare.22723114
title: Additional file 14 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 14: Data S3. Related to Fig. 1. z-score normalized mRNA transcript abundance, probe methylation (beta) values, and copy number variation for all TCGA liver samples (including matched adjacent normal liver tissue). Corresponds to data shown in Fig. 1.
DOI: 10.6084/m9.figshare.22723114.v1
title: Additional file 14 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 14: Data S3. Related to Fig. 1. z-score normalized mRNA transcript abundance, probe methylation (beta) values, and copy number variation for all TCGA liver samples (including matched adjacent normal liver tissue). Corresponds to data shown in Fig. 1.
DOI: 10.6084/m9.figshare.22723117.v1
title: Additional file 15 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 15: Data S4. Related to Fig. 2, Fig. 3, Fig. 4, and Fig. 6. Comparison of the fold change in mRNA expression for the tumor suppressor genes targeted individually or multiplexed by CRISPRa system (SpdCas9-VPR and MS2-MCP-p65-HSF1) versus treatments with the epi-drugs (5-aza and SAHA) in Hep3B and HuH-7 cells.
DOI: 10.6084/m9.figshare.22723117
title: Additional file 15 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 15: Data S4. Related to Fig. 2, Fig. 3, Fig. 4, and Fig. 6. Comparison of the fold change in mRNA expression for the tumor suppressor genes targeted individually or multiplexed by CRISPRa system (SpdCas9-VPR and MS2-MCP-p65-HSF1) versus treatments with the epi-drugs (5-aza and SAHA) in Hep3B and HuH-7 cells.
DOI: 10.6084/m9.figshare.22723120
title: Additional file 16 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 16: Data S5. Related to Figs. 3, 4, and 7. Comprehensive bioinformatic analysis of predicted potential off-targets for the ten TSGs targeted by CRISPRa technology utilizing the most active gRNAs.
DOI: 10.6084/m9.figshare.22723120.v1
title: Additional file 16 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 16: Data S5. Related to Figs. 3, 4, and 7. Comprehensive bioinformatic analysis of predicted potential off-targets for the ten TSGs targeted by CRISPRa technology utilizing the most active gRNAs.
DOI: 10.6084/m9.figshare.22723123
title: Additional file 17 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 17: Data S6. Related to Figure S6. Probe methylation (beta) values for HHIP in transiently transfected Hep3B cells with SpdCas9-VPR and MS2-MCP-p65-HSF1, or SpdCas9-TET1-CD and MS2-MCP-p65-HSF1 targeting HHIP promoter.
DOI: 10.6084/m9.figshare.22723123.v1
title: Additional file 17 of Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

description: Additional file 17: Data S6. Related to Figure S6. Probe methylation (beta) values for HHIP in transiently transfected Hep3B cells with SpdCas9-VPR and MS2-MCP-p65-HSF1, or SpdCas9-TET1-CD and MS2-MCP-p65-HSF1 targeting HHIP promoter.
DOI: 10.6084/m9.figshare.22722949
title: <strong>Combinative effects of β-elemene and propranolol on the proliferation, migration,</strong> <strong>and angiogenesis of hemangioma</strong>

description: Hemangioma (HA) is one of the most common benign vascular tumors among children. Propranolol is used as the first-line treatment for hemangioma and is a non-selective blocker of the β-adrenergic receptor. β-elemene is a compound extracted from Rhizoma zedoariae and has been approved for the treatment of tumors in clinical practice. However, the combinatorial effects of β-elemene and propranolol in the treatment of HA remains unclear. This study explored, the combinative effects and mechanisms of β-elemene and propranolol using hemangioma-derived endothelial cells (HemEC). Cytotoxic assays showed that the combinatorial treatment of β-elemene and propranolol did not increase the cytotoxic effects of HemEC cells. Furthermore, functional analysis showed that the combinatorial treatment with β-elemene and propranolol significantly inhibited proliferation, migration, and tube formation of the HemEC cells compared to the single treatment regimens. Mechanistic analysis showed that combinative treatment with β-elemene and propranolol synergistically down-regulated the hypoxia-inducible factor-1 alpha/vascular endothelial growth factor-A (HIF-1-α/VEGFA) signaling pathway. Additionally, in a xenograft tumor model, angiogenesis in the combinatorial treatment group was significantly lower than in the control, propranolol, and β-elemene treatment alone groups. Our results suggest that β-elemene combined with propranolol can significantly inhibit the proliferation, migration, and tube formation of HemEC cells via synergistically down-regulating the HIF-1-α/VEGFA signaling pathway without increasing any cytotoxic side effects.
DOI: 10.6084/m9.figshare.22722949.v1
title: <strong>Combinative effects of β-elemene and propranolol on the proliferation, migration,</strong> <strong>and angiogenesis of hemangioma</strong>

description: Hemangioma (HA) is one of the most common benign vascular tumors among children. Propranolol is used as the first-line treatment for hemangioma and is a non-selective blocker of the β-adrenergic receptor. β-elemene is a compound extracted from Rhizoma zedoariae and has been approved for the treatment of tumors in clinical practice. However, the combinatorial effects of β-elemene and propranolol in the treatment of HA remains unclear. This study explored, the combinative effects and mechanisms of β-elemene and propranolol using hemangioma-derived endothelial cells (HemEC). Cytotoxic assays showed that the combinatorial treatment of β-elemene and propranolol did not increase the cytotoxic effects of HemEC cells. Furthermore, functional analysis showed that the combinatorial treatment with β-elemene and propranolol significantly inhibited proliferation, migration, and tube formation of the HemEC cells compared to the single treatment regimens. Mechanistic analysis showed that combinative treatment with β-elemene and propranolol synergistically down-regulated the hypoxia-inducible factor-1 alpha/vascular endothelial growth factor-A (HIF-1-α/VEGFA) signaling pathway. Additionally, in a xenograft tumor model, angiogenesis in the combinatorial treatment group was significantly lower than in the control, propranolol, and β-elemene treatment alone groups. Our results suggest that β-elemene combined with propranolol can significantly inhibit the proliferation, migration, and tube formation of HemEC cells via synergistically down-regulating the HIF-1-α/VEGFA signaling pathway without increasing any cytotoxic side effects.
DOI: 10.5517/ccdc.csd.cc2fvcrf
title: CCDC 2259675: Experimental Crystal Structure Determination

description: Related Article: Hao Qi|2023|CSD Communication|||
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: 10.5281/zenodo.7747847
title: Slip distribution of the February 6, 2023 Mw 7.8 and Mw 7.6, Kahramanmaras, Turkey earthquake sequence in the East Anatolian Fault Zone

description: On February 6, 2023, two large earthquakes occurred near the Turkish town of Kahramanmaras. The moment magnitude (Mw) 7.8 mainshock ruptured a 310 km-long segment of the left-lateral East Anatolian Fault, propagating through multiple releasing step-overs. The Mw 7.6 aftershock involved nearby left-lateral strike-slip faults of the East Anatolian Fault Zone, causing a 150 km-long rupture. We use remote-sensing observations to constrain the spatial distribution of coseismic slip for these two events and the February 20 Mw 6.4 aftershock near Antakya. Pixel tracking of optical and synthetic aperture radar data of the Sentinel-2 and Sentinel-1 satellites, respectively, provide near-field surface displacements. High-rate Global Navigation Satellite System data constrain each event separately. Coseismic slip extends from the surface to about 15 km depth with a shallow slip deficit. For the mainshock, rupture propagation stopped southward at the diffuse termination of the East Anatolian fault and tapered off northward into the Pütürrge segment, some 20 km south of the 2020 Mw 6.8 Elazığ earthquake, highlighting a potential seismic gap. This repository contains the finite slip distribution of the February 6, 2023 Mw 7.8 Kahramanmaras mainshock and Mw 7.6 Elbinstan aftershock, as well as the slip distribution of the second largest aftershock, the February 20, 2023 Mw 6.4 Antakya earthquake. The repository also provides the slip distribution of the 2020 Mw 6.8 Elazığ earthquake.