cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2d0xgt
title: CCDC 2205416: Experimental Crystal Structure Determination

description: Related Article: M.J. Schriver, T. George, J.D. Masuda|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1006|doi:10.1107/S205698902200888X
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: 10.6084/m9.figshare.7478324.v2
title: Systematic review on recent potential biomarkers of chronic obstructive pulmonary disease

description: <b>Introduction</b>: Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide and associated with decreased lung function and inflammation. The heterogeneity of COPD and its molecular and clinical features hinder efficient patient stratification and introduction of personalized therapeutic approaches. The available clinical tools do not efficiently predict the progression and exacerbations of the disease. <b>Areas covered</b>: An overview of the most recent studies on putative COPD protein biomarkers and the challenges for implementing their use in the clinical setting is presented. <b>Expert commentary</b>: Proteomics biomarker discovery in COPD has mostly focused on approaches evaluating specific proteins on a limited number of samples. The most promising protein candidates can be classified into five main biological categories: extracellular matrix (ECM) remodeling, inflammation/immune response, oxidative stress response, vascular tone regulation, and lipid metabolism. To efficiently stratify COPD patients and predict exacerbations, it will be necessary to implement biomarker panels to better represent the complex pathophysiology of this disease. The application of unbiased proteomics and bioinformatics followed by appropriate clinical validation studies will contribute to the achievement of this aim while increasing the number of validated biomarkers that can enter the qualification processes by the regulatory entities.
DOI: 10.6084/m9.figshare.7478324
title: Systematic review on recent potential biomarkers of chronic obstructive pulmonary disease

description: <b>Introduction</b>: Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide and associated with decreased lung function and inflammation. The heterogeneity of COPD and its molecular and clinical features hinder efficient patient stratification and introduction of personalized therapeutic approaches. The available clinical tools do not efficiently predict the progression and exacerbations of the disease. <b>Areas covered</b>: An overview of the most recent studies on putative COPD protein biomarkers and the challenges for implementing their use in the clinical setting is presented. <b>Expert commentary</b>: Proteomics biomarker discovery in COPD has mostly focused on approaches evaluating specific proteins on a limited number of samples. The most promising protein candidates can be classified into five main biological categories: extracellular matrix (ECM) remodeling, inflammation/immune response, oxidative stress response, vascular tone regulation, and lipid metabolism. To efficiently stratify COPD patients and predict exacerbations, it will be necessary to implement biomarker panels to better represent the complex pathophysiology of this disease. The application of unbiased proteomics and bioinformatics followed by appropriate clinical validation studies will contribute to the achievement of this aim while increasing the number of validated biomarkers that can enter the qualification processes by the regulatory entities.
DOI: 10.6084/m9.figshare.7478324.v1
title: Systematic review on recent potential biomarkers of chronic obstructive pulmonary disease

description: <b>Introduction</b>: Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide and associated with decreased lung function and inflammation. The heterogeneity of COPD and its molecular and clinical features hinder efficient patient stratification and introduction of personalized therapeutic approaches. The available clinical tools do not efficiently predict the progression and exacerbations of the disease. <b>Areas covered</b>: An overview of the most recent studies on putative COPD protein biomarkers and the challenges for implementing their use in the clinical setting is presented. <b>Expert commentary</b>: Proteomics biomarker discovery in COPD has mostly focused on approaches evaluating specific proteins on a limited number of samples. The most promising protein candidates can be classified into five main biological categories: extracellular matrix (ECM) remodeling, inflammation/immune response, oxidative stress response, vascular tone regulation, and lipid metabolism. To efficiently stratify COPD patients and predict exacerbations, it will be necessary to implement biomarker panels to better represent the complex pathophysiology of this disease. The application of unbiased proteomics and bioinformatics followed by appropriate clinical validation studies will contribute to the achievement of this aim while increasing the number of validated biomarkers that can enter the qualification processes by the regulatory entities.
DOI: 10.6084/m9.figshare.21066028
title: Spreadsheet data of anti-ischemic effect of TS extract in cardiomyocyte

description: The data contains replicate absorbance values for cell viability, DPPH and ABTS. It also contains replicate fluorescent intensity of ROS production, relative mRNA and protein expressions, and original immunoblots.
DOI: 10.6084/m9.figshare.21066028.v6
title: Spreadsheet data of anti-ischemic effect of TS extract in cardiomyocyte

description: The data contains replicate absorbance values for cell viability, DPPH and ABTS. It also contains replicate fluorescent intensity of ROS production, relative mRNA and protein expressions, and original immunoblots.
DOI: 10.6084/m9.figshare.21066028.v5
title: Spreadsheet data of anti-ischemic effect of TS extract in cardiomyocyte

description: The data contains replicate absorbance values for cell viability, DPPH and ABTS. It also contains replicate fluorescent intensity of ROS production, relative mRNA and protein expressions, and original immunoblots.
DOI: 10.5281/zenodo.7192682
title: Altered infective proficiency of the gut microbiome following COVID-19

description: <strong>The effects of SARS-CoV-2 infections comprise of many heterogeneous symptoms including several involving the human gastrointestinal tract. We assess the effects of COVID-19 on the host microbiome</strong>
DOI: 10.5281/zenodo.7192681
title: Altered infective proficiency of the gut microbiome following COVID-19

description: <strong>The effects of SARS-CoV-2 infections comprise of many heterogeneous symptoms including several involving the human gastrointestinal tract. We assess the effects of COVID-19 on the host microbiome</strong>
DOI: 10.6084/m9.figshare.21324186
title: First-principles investigation on super-hydrous kaolinite and nacrite under high temperature and high pressure

description: A dataset for "First-principles investigation on super-hydrous kaolinite and nacrite under high temperature and high pressure"
DOI: 10.6084/m9.figshare.21324186.v1
title: First-principles investigation on super-hydrous kaolinite and nacrite under high temperature and high pressure

description: A dataset for "First-principles investigation on super-hydrous kaolinite and nacrite under high temperature and high pressure"
DOI: 10.5281/zenodo.5886686
title: X-ray crystallographic data of second extracellular domain of human tetraspanin CD9

description: These X-ray diffraction data are of a crystal of the second extracellular domain of human tetraspanin CD9. The data show remarkable features that stem from twinning and concurrent diffuse scattering in streaked directions perpendicular to the twinning interface. The structure is described in [Oosterheert et al. (2020). Life Sci. Alliance, 3, e202000883] and is deposited in the PDB under accession code 6rlr. The raw data are described in details in IUCrData as a Raw Data Letter [Neviani et al., IUCrData (2022]. The .h5 files are as they were originally recorded at Diamond Light Source at beamline I04. The images were converted to separate CBF files by a local script at DLS and compressed in the tar.bz2 file.
description: The raw data are described in an exemplary Raw Data Letter, with the goal of publishing and archiving raw diffraction data. Methods and software developers are invited to upload and re-use the data. A reciprocal space reconstruction is available at 10.5281/zenodo.6961763, as a ccp4 map that can be viewed e.g. Chimera.
DOI: 10.5281/zenodo.5886687
title: X-ray crystallographic data of second extracellular domain of human tetraspanin CD9

description: These X-ray diffraction data are of a crystal of the second extracellular domain of human tetraspanin CD9. The data show remarkable features that stem from twinning and concurrent diffuse scattering in streaked directions perpendicular to the twinning interface. The structure is described in [Oosterheert et al. (2020). Life Sci. Alliance, 3, e202000883] and is deposited in the PDB under accession code 6rlr. The raw data are described in details in IUCrData as a Raw Data Letter [Neviani et al., IUCrData (2022]. The .h5 files are as they were originally recorded at Diamond Light Source at beamline I04. The images were converted to separate CBF files by a local script at DLS and compressed in the tar.bz2 file.
description: The raw data are described in an exemplary Raw Data Letter, with the goal of publishing and archiving raw diffraction data. Methods and software developers are invited to upload and re-use the data. A reciprocal space reconstruction is available at 10.5281/zenodo.6961763, as a ccp4 map that can be viewed e.g. Chimera.
DOI: 10.5281/zenodo.7193275
title: Data for "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. 132, 124401 (2022)

description: Data required to reproduce the key results in: "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. <strong>132</strong>, 124401 (2022). https://doi.org/10.1063/5.0106633 The file "sec_freq.dat" contains measured secular frequencies, the rf frequency, the applied bias voltages, and the MJD of the measurement: Figures 4-5 use rows 31-33 of this data. Figure 6 uses all data corresponding to -1.1e-3 &lt; <em>a</em><sub>x</sub> &lt; -0.6e-3. Figure 7(a) uses all the data. The file "data2021-12-21_MJD.txt" contains the secular frequency data used to derive Eq. (16) and plot Figure 8. The file "RF_monitor_rectifier_1d.txt" contains the rectified monitor voltage used in Figure 8. The file "Temperature_108_1d.txt" contains the helical-resonator temperature used in Figure 8. The file "Fig9_EQS.dat" contains the measured electric quadrupole shift (EQS) used for Figure 9. The file "interleavedEQS.dat" contains the data from the interleaved EQS measurement used to determine a lower value of 1070 for the cancellation factor.
description: This work was supported by the projects 18SIB05 ROCIT and 20FUN01 TSCAC, which have received funding from the EMPIR program co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation program. This work was also supported by the Academy of Finland (REASON, decision 339821) and is part of the Academy of Finland Flagship Programme "Photonics Research and Innovation" (PREIN, decision 320168).
DOI: 10.5281/zenodo.7193276
title: Data for "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. 132, 124401 (2022)

description: Data required to reproduce the key results in: "High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction", J. Appl. Phys. <strong>132</strong>, 124401 (2022). https://doi.org/10.1063/5.0106633 The file "sec_freq.dat" contains measured secular frequencies, the rf frequency, the applied bias voltages, and the MJD of the measurement: Figures 4-5 use rows 31-33 of this data. Figure 6 uses all data corresponding to -1.1e-3 &lt; <em>a</em><sub>x</sub> &lt; -0.6e-3. Figure 7(a) uses all the data. The file "data2021-12-21_MJD.txt" contains the secular frequency data used to derive Eq. (16) and plot Figure 8. The file "RF_monitor_rectifier_1d.txt" contains the rectified monitor voltage used in Figure 8. The file "Temperature_108_1d.txt" contains the helical-resonator temperature used in Figure 8. The file "Fig9_EQS.dat" contains the measured electric quadrupole shift (EQS) used for Figure 9. The file "interleavedEQS.dat" contains the data from the interleaved EQS measurement used to determine a lower value of 1070 for the cancellation factor.
description: This work was supported by the projects 18SIB05 ROCIT and 20FUN01 TSCAC, which have received funding from the EMPIR program co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation program. This work was also supported by the Academy of Finland (REASON, decision 339821) and is part of the Academy of Finland Flagship Programme "Photonics Research and Innovation" (PREIN, decision 320168).
DOI: 10.6084/m9.figshare.21286266
title: Covid Anxiety and Uncertainty of Classes _ Devastating effect on Academic Behavior of Students (Responses) - Form Responses 1.csv

description: Survey Data
DOI: 10.5281/zenodo.7193321
title: South African Bank Risk Dataset

description: Fixing CFF author names
description: If you use this software, please cite it as below.
DOI: 10.5281/zenodo.7193340
title: South African Bank Risk Dataset

description: This repository is an initial pipeline for reading, processing, labelling and classifying unstructured annual reports of South African (SA) banks with the aim of identifying financial risk. It leveraged work by the Corporate Financial Information Environment-Final Report Structure Extractor (CFIE–FRSE) of El-Haj et al. which created a corpus of annual reports of United Kingdom (UK) companies.
description: This repository is an initial pipeline for reading, processing, labelling and classifying unstructured annual reports of South African (SA) banks with the aim of identifying financial risk. It leveraged work by the Corporate Financial Information Environment-Final Report Structure Extractor (CFIE–FRSE) of El-Haj et al. which created a corpus of annual reports of United Kingdom (UK) companies.
DOI: 10.5281/zenodo.6769918
title: South African Bank Risk Dataset

description: This repository is an initial pipeline for reading, processing, labelling and classifying unstructured annual reports of South African (SA) banks with the aim of identifying financial risk. It leveraged work by the Corporate Financial Information Environment-Final Report Structure Extractor (CFIE–FRSE) of El-Haj et al. which created a corpus of annual reports of United Kingdom (UK) companies.
description: This repository is an initial pipeline for reading, processing, labelling and classifying unstructured annual reports of South African (SA) banks with the aim of identifying financial risk. It leveraged work by the Corporate Financial Information Environment-Final Report Structure Extractor (CFIE–FRSE) of El-Haj et al. which created a corpus of annual reports of United Kingdom (UK) companies.
DOI: 10.6084/m9.figshare.21063211
title: E berryi Morsei Growth Survivorship Data.xlsx

description: Growth and Survivorship data for Euprymna morsei and Euprymna berryi.
DOI: 10.6084/m9.figshare.21063211.v1
title: E berryi Morsei Growth Survivorship Data.xlsx

description: Growth and Survivorship data for Euprymna morsei and Euprymna berryi.
DOI: 10.6084/m9.figshare.19615074
title: Co-expression patterns explain how a basic transcriptional role for MYC modulates <i>Wnt</i> and MAPK pathways in colon and lung adenocarcinomas

description: A subset of proliferation genes that are associated with origin licensing, firing, and DNA synthesis has been compared to known drivers of colon (COAD) and lung (LUAD) adenocarcinomas using Spearman’s rank correlation coefficients. The frequency with which APC, CTNNB1, KRAS, MYC, Braf, TP53, Rb1, EGFR, and cell cycle components have direct or indirect co-expression with the proliferation factors permits identification of their expression relative to the G1-S phase of the cell cycle. Here, adenomatous polyposis coli (APC), a negative regulator of <i>Wnt</i> signaling known to function through MYC, indirectly co-expresses at the same frequency as proliferation genes in both COAD and LUAD, consistent with M phase expression. However, APC is indirectly co-expressed with MYC and is found mutated only in COAD. MYC is thought to function at the interface of transcription and replication, acting through the SWI/SNF chromatin remodeling complex, and increased or decreased expression of MYC can induce or repress tumorigenesis, respectively. These data suggest that transcription of APC during the M phase with low MYC co-expression contributes by an unknown mechanism to APC mutations and <i>Wnt</i> pathway deregulation in COAD and that upper and lower limits of MYC expression, enforced by the cell cycle, may influence cancer differentially. Other <i>Wnt</i> signaling components co-expressed in the low MYC context in COAD also have significantly higher mutation frequencies, supporting the hypothesis. Additionally, Braf is found here to have direct co-expression with multiple proliferation factors in non-EGFR activated LUAD, and EGFR-activated LUAD are completely deregulated with respect to E2F(s) 4/5/6 expression, potentially explaining the low proliferation rates seen in LUAD. <b>Abbreviations:</b> TCGA: The cancer genome atlas; PANCAN: Pan cancer; CDK: Cyclin-dependent kinase; COAD: Colon adenocarcinoma; LUAD: Lung adenocarcinoma; <i>Wnt</i>: Wingless/integrated signaling; MAPK: Mitogen-activated protein kinase; APC: Adenomatous polyposis coli gene; CIN: Chromosomal instability; GS: Genome stabile; MMR: Mismatch repair; mRNA: Messenger RNA; RPKM: Reads per kilobase of transcription per million mapped reads; RSEM: RNA Seq by expectation maximization; FDR: False discovery rate; GTEx: Genotype-Tissue Expression portal; MPF: Maturation-promoting factor; SCF: Skp1-Cul1-F-box; HH: Hedgehog; EMT: Epithelial mesenchymal transition; RB: Retinoblastoma; EGFR: Epidermal growth factor receptor; r<sub>s</sub> or ρ: Spearman’s correlation
DOI: 10.6084/m9.figshare.19615074.v1
title: Co-expression patterns explain how a basic transcriptional role for MYC modulates <i>Wnt</i> and MAPK pathways in colon and lung adenocarcinomas

description: A subset of proliferation genes that are associated with origin licensing, firing, and DNA synthesis has been compared to known drivers of colon (COAD) and lung (LUAD) adenocarcinomas using Spearman’s rank correlation coefficients. The frequency with which APC, CTNNB1, KRAS, MYC, Braf, TP53, Rb1, EGFR, and cell cycle components have direct or indirect co-expression with the proliferation factors permits identification of their expression relative to the G1-S phase of the cell cycle. Here, adenomatous polyposis coli (APC), a negative regulator of <i>Wnt</i> signaling known to function through MYC, indirectly co-expresses at the same frequency as proliferation genes in both COAD and LUAD, consistent with M phase expression. However, APC is indirectly co-expressed with MYC and is found mutated only in COAD. MYC is thought to function at the interface of transcription and replication, acting through the SWI/SNF chromatin remodeling complex, and increased or decreased expression of MYC can induce or repress tumorigenesis, respectively. These data suggest that transcription of APC during the M phase with low MYC co-expression contributes by an unknown mechanism to APC mutations and <i>Wnt</i> pathway deregulation in COAD and that upper and lower limits of MYC expression, enforced by the cell cycle, may influence cancer differentially. Other <i>Wnt</i> signaling components co-expressed in the low MYC context in COAD also have significantly higher mutation frequencies, supporting the hypothesis. Additionally, Braf is found here to have direct co-expression with multiple proliferation factors in non-EGFR activated LUAD, and EGFR-activated LUAD are completely deregulated with respect to E2F(s) 4/5/6 expression, potentially explaining the low proliferation rates seen in LUAD. <b>Abbreviations:</b> TCGA: The cancer genome atlas; PANCAN: Pan cancer; CDK: Cyclin-dependent kinase; COAD: Colon adenocarcinoma; LUAD: Lung adenocarcinoma; <i>Wnt</i>: Wingless/integrated signaling; MAPK: Mitogen-activated protein kinase; APC: Adenomatous polyposis coli gene; CIN: Chromosomal instability; GS: Genome stabile; MMR: Mismatch repair; mRNA: Messenger RNA; RPKM: Reads per kilobase of transcription per million mapped reads; RSEM: RNA Seq by expectation maximization; FDR: False discovery rate; GTEx: Genotype-Tissue Expression portal; MPF: Maturation-promoting factor; SCF: Skp1-Cul1-F-box; HH: Hedgehog; EMT: Epithelial mesenchymal transition; RB: Retinoblastoma; EGFR: Epidermal growth factor receptor; r<sub>s</sub> or ρ: Spearman’s correlation
DOI: 10.6084/m9.figshare.19576502
title: Long noncoding RNA BMPR1B-AS1 facilitates endometrial cancer cell proliferation and metastasis by sponging miR-7-2-3p to modulate the DCLK1/Akt/NF-κB pathway

description: Endometrial carcinoma (EC) originates from the endometrium and is one of the most common tumors in female patients, and its incidence has continued to increase in recent decades. LncRNAs are involved in the pathogenesis and metastasis of a variety of malignant tumors, which indicates that lncRNAs can be used as tumor diagnostic markers and potential therapeutic targets. In this study, we analyzed the RNA transcripts of EC cells from The Cancer Genome Atlas (TCGA) and first reported a novel lncRNA, BMPR1B-AS1, that was more highly expressed in endometrial cancer tissues than in adjacent tissues, and BMPR1B-AS1 could promote endometrial cancer cell proliferation and metastasis. Bioinformatics prediction and experimental results both suggested that BMPR1B-AS1 could modulate the malignant behaviors of endometrial cancer cell lines by sponging miR-7-2-3p to modulate DCLK1, and a DCLK1 inhibitor blocked the activation of the PI3K/Akt/NF-κB signaling pathway. Collectively, this study suggests that the BMPR1B-AS1/miR-7-2-3p/DCLK1 axis contributes to the proliferation and metastasis of endometrial cancer cells via the PI3K/Akt/NF-κB pathway.
DOI: 10.6084/m9.figshare.19576502.v1
title: Long noncoding RNA BMPR1B-AS1 facilitates endometrial cancer cell proliferation and metastasis by sponging miR-7-2-3p to modulate the DCLK1/Akt/NF-κB pathway

description: Endometrial carcinoma (EC) originates from the endometrium and is one of the most common tumors in female patients, and its incidence has continued to increase in recent decades. LncRNAs are involved in the pathogenesis and metastasis of a variety of malignant tumors, which indicates that lncRNAs can be used as tumor diagnostic markers and potential therapeutic targets. In this study, we analyzed the RNA transcripts of EC cells from The Cancer Genome Atlas (TCGA) and first reported a novel lncRNA, BMPR1B-AS1, that was more highly expressed in endometrial cancer tissues than in adjacent tissues, and BMPR1B-AS1 could promote endometrial cancer cell proliferation and metastasis. Bioinformatics prediction and experimental results both suggested that BMPR1B-AS1 could modulate the malignant behaviors of endometrial cancer cell lines by sponging miR-7-2-3p to modulate DCLK1, and a DCLK1 inhibitor blocked the activation of the PI3K/Akt/NF-κB signaling pathway. Collectively, this study suggests that the BMPR1B-AS1/miR-7-2-3p/DCLK1 axis contributes to the proliferation and metastasis of endometrial cancer cells via the PI3K/Akt/NF-κB pathway.