cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21942/uva.24745611.v1
title: WIRES - Enhanced sampling strategies for the molecular simulation of DNA

description: Molecular dynamics (MD) simulations can provide detailed insights into molecular systems, including DNA, at high resolution in space and time. With current computer architectures, time scales of tens of microseconds are feasible with the current all-atom force fields. However, these timescales are insufficiently long to accurately characterize conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale issue. One approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The novel path-metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi-dimensional collective variable space. Another strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are usually fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two-dimensional Müller-Brown potential. Applications to DNA are featured for two different processes: the Watson-Crick-Franklin to Hoogsteen transition in adenine-thymine base pairs and the binding of a DNA-binding protein domain to DNA.
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DOI: 10.14473/csda/acujml/zrw7qs
title: D_V0709.pdf

description: Dotazník
DOI: 10.14473/csda/acujml/asocnk
title: K_V0709.pdf

description: Karty
DOI: 10.14473/csda/acujml/n2cll6
title: TI_V0709.pdf

description: Technická informace
DOI: 10.14473/csda/acujml/twuori
title: OM_V0709.pdf

description: Ostatní materiály
DOI: 10.14473/csda/acujml/drgeqp
title: Nesstar_NS_DataFile_0709.tab

description: Data
DOI: 10.14473/csda/acujml/xz1afn
title: PR05_V0709.pdf

description: Výběr značky piva českými konzumenty v roce
2007. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/j3p74n
title: PR08_V0709.pdf

description: Stranické preference a volební model v září 2007. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/z6ridy
title: PR02_V0709.pdf

description: Názory Čechů na úroveň výuky na školách. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/bjcplp
title: PR04_V0709.pdf

description: Některé aspekty výběru piva českými konzumenty
v roce 2007. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/jwkyb9
title: PR03_V0709.pdf

description: Konzumace piva v České republice v roce 2007. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/oasgh7
title: PR07_V0709.pdf

description: Důvěra k vrcholným politikům. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml/socthl
title: PR06_V0709.pdf

description: Image piva v české společnosti v roce 2007. Tisková zpráva CVVM.
DOI: 10.14473/csda/acujml
title: Naše společnost 2007 - září

description: Kontinuální měsíční výzkum provedl výzkumný tým CVVM Sociologického ústavu AV ČR v rámci pravidelného měsíčního výzkumného projektu. Jsou při něm zjišťovány postoje a názory občanů. Výzkum provedl výzkumný tým CVVM Sociologického ústavu AV ČR v rámci výzkumu. "Naše společnost 2007". Sběr dat provedla tazatelská síť CVVM.
DOI: 10.14473/csda/acujml/3juot7
title: PR01_V0709.pdf

description: Okolnosti ovlivňující dosažení vzdělání. Tisková zpráva CVVM.
DOI: 10.6084/m9.figshare.20098218
title: Establishment of the prediction model and biological mechanism exploration for secondary imatinib-resistant in gastrointestinal stromal tumor

description: A gastrointestinal stromal tumor (GIST) is mostly driven by the auto-activated, mutant <i>KIT</i> receptor tyrosine kinase gene or by the platelet-derived growth factor receptor alpha. Inhibition of <i>KIT</i>-signaling is the primary molecular target therapy for GIST, which is performed by the drug imatinib clinically. However, more than half of advanced or metastatic GIST develop secondary resistance to imatinib within 2 years after initiation of treatment, and the mechanism of acquired imatinib-resistant in GIST remains unclear. Therefore, we designed the present study, and firstly analyzed the gene expression profile of imatinib-resistant and sensitive GIST from GEO DataSet and identified 44 differential expressed genes. Then, a model including nine genes with their expressed coefficients was identified as a risk score to predict imatinib-resistant GIST. Internal and external validation of the prediction model was performed through the ROC curve, and the area under the curve was 0.967 (95%CI 0.901–1.000) and 0.917 (95%CI 0.753–1.000), separately. Lastly, the effect of immune, m<sup>6</sup>A, pyroptosis, and ferroptosis-related genes on imatinib-resistant GIST was also assessed because DNA replication was the most enriched biological function of DEGs after functional annotation, pathway enrichment, and protein-protein interaction network analyses. In conclusion, the present study established a novel model to predict secondary imatinib-resistant GIST. Meanwhile, the bioinformatic mining results provided potential and promising targets for imatinib-resistant therapy.
DOI: 10.6084/m9.figshare.20098218.v1
title: Establishment of the prediction model and biological mechanism exploration for secondary imatinib-resistant in gastrointestinal stromal tumor

description: A gastrointestinal stromal tumor (GIST) is mostly driven by the auto-activated, mutant <i>KIT</i> receptor tyrosine kinase gene or by the platelet-derived growth factor receptor alpha. Inhibition of <i>KIT</i>-signaling is the primary molecular target therapy for GIST, which is performed by the drug imatinib clinically. However, more than half of advanced or metastatic GIST develop secondary resistance to imatinib within 2 years after initiation of treatment, and the mechanism of acquired imatinib-resistant in GIST remains unclear. Therefore, we designed the present study, and firstly analyzed the gene expression profile of imatinib-resistant and sensitive GIST from GEO DataSet and identified 44 differential expressed genes. Then, a model including nine genes with their expressed coefficients was identified as a risk score to predict imatinib-resistant GIST. Internal and external validation of the prediction model was performed through the ROC curve, and the area under the curve was 0.967 (95%CI 0.901–1.000) and 0.917 (95%CI 0.753–1.000), separately. Lastly, the effect of immune, m<sup>6</sup>A, pyroptosis, and ferroptosis-related genes on imatinib-resistant GIST was also assessed because DNA replication was the most enriched biological function of DEGs after functional annotation, pathway enrichment, and protein-protein interaction network analyses. In conclusion, the present study established a novel model to predict secondary imatinib-resistant GIST. Meanwhile, the bioinformatic mining results provided potential and promising targets for imatinib-resistant therapy.
DOI: 10.6084/m9.figshare.20069835
title: A video based benchmark data set (ENDOTEST) to evaluate computer-aided polyp detection systems

description: Computer-aided polyp detection (CADe) may become a standard for polyp detection during colonoscopy. Several systems are already commercially available. We report on a video-based benchmark technique for the first preclinical assessment of such systems before comparative randomized trials are to be undertaken. Additionally, we compare a commercially available CADe system with our newly developed one. ENDOTEST consisted in the combination of two datasets. The validation dataset contained 48 video-snippets with 22,856 manually annotated images of which 53.2% contained polyps. The performance dataset contained 10 full-length screening colonoscopies with 230,898 manually annotated images of which 15.8% contained a polyp. Assessment parameters were accuracy for polyp detection and time delay to first polyp detection after polyp appearance (FDT). Two CADe systems were assessed: a commercial CADe system (GI-Genius, Medtronic), and a self-developed new system (ENDOMIND). The latter being a convolutional neuronal network trained on 194,983 manually labeled images extracted from colonoscopy videos recorded in mainly six different gastroenterologic practices. On the ENDOTEST, both CADe systems detected all polyps in at least one image. The per-frame sensitivity and specificity in full colonoscopies was 48.1% and 93.7%, respectively for GI-Genius; and 54% and 92.7%, respectively for ENDOMIND. Median FDT of ENDOMIND with 217 ms (Inter-Quartile Range(IQR)8–1533) was significantly faster than GI-Genius with 1050 ms (IQR 358–2767, <i>p</i> = 0.003). Our benchmark ENDOTEST may be helpful for preclinical testing of new CADe devices. There seems to be a correlation between a shorter FDT with a higher sensitivity and a lower specificity for polyp detection.
DOI: 10.6084/m9.figshare.20069835.v1
title: A video based benchmark data set (ENDOTEST) to evaluate computer-aided polyp detection systems

description: Computer-aided polyp detection (CADe) may become a standard for polyp detection during colonoscopy. Several systems are already commercially available. We report on a video-based benchmark technique for the first preclinical assessment of such systems before comparative randomized trials are to be undertaken. Additionally, we compare a commercially available CADe system with our newly developed one. ENDOTEST consisted in the combination of two datasets. The validation dataset contained 48 video-snippets with 22,856 manually annotated images of which 53.2% contained polyps. The performance dataset contained 10 full-length screening colonoscopies with 230,898 manually annotated images of which 15.8% contained a polyp. Assessment parameters were accuracy for polyp detection and time delay to first polyp detection after polyp appearance (FDT). Two CADe systems were assessed: a commercial CADe system (GI-Genius, Medtronic), and a self-developed new system (ENDOMIND). The latter being a convolutional neuronal network trained on 194,983 manually labeled images extracted from colonoscopy videos recorded in mainly six different gastroenterologic practices. On the ENDOTEST, both CADe systems detected all polyps in at least one image. The per-frame sensitivity and specificity in full colonoscopies was 48.1% and 93.7%, respectively for GI-Genius; and 54% and 92.7%, respectively for ENDOMIND. Median FDT of ENDOMIND with 217 ms (Inter-Quartile Range(IQR)8–1533) was significantly faster than GI-Genius with 1050 ms (IQR 358–2767, <i>p</i> = 0.003). Our benchmark ENDOTEST may be helpful for preclinical testing of new CADe devices. There seems to be a correlation between a shorter FDT with a higher sensitivity and a lower specificity for polyp detection.
DOI: 10.6084/m9.figshare.25451323
title: Data including soil physicochemical properties, soil biota diversity, ecosystem functions and multifunctionality indices.

description: Data including soil physicochemical properties, soil biota diversity, ecosystem functions and multifunctionality indices.
DOI: 10.6084/m9.figshare.25451323.v1
title: Data including soil physicochemical properties, soil biota diversity, ecosystem functions and multifunctionality indices.

description: Data including soil physicochemical properties, soil biota diversity, ecosystem functions and multifunctionality indices.
DOI: 10.5281/zenodo.10213571
title: A Terrylene Bisimide based Universal Host for Aromatic Guests to Derive Contact Surface-Dependent Dispersion Energies

description: Additional data to report https://doi.org/10.1002/anie.202318451:π–π interactions are among the most important intermolecular interactions in supramolecular systems. Here we determine experimentally a universal parameter for their strength that is simply based on the size of the interacting contact surfaces. Toward this goal we designed a new cyclophane based on terrylene bisimide (TBI) π-walls connected by para-xylylene spacer units. With its extended π-surface this cyclophane proved to be an excellent and universal host for the complexation of π-conjugated guests, including small and large polycyclic aromatic hydrocarbons (PAHs) as well as dye molecules. The observed binding constants range up to 108 M−1 and show a linear dependence on the 2D area size of the guest molecules. This correlation can be used for the prediction of binding constants and for the design of new host–guest systems based on the herewith derived universal Gibbs interaction energy parameter of 0.31 kJ/molÅ2 in chloroform.
description: Original spectroscopic data to report: https://doi.org/10.1002/anie.202318451
DOI: 10.5281/zenodo.10213572
title: A Terrylene Bisimide based Universal Host for Aromatic Guests to Derive Contact Surface-Dependent Dispersion Energies

description: Additional data to report https://doi.org/10.1002/anie.202318451:π–π interactions are among the most important intermolecular interactions in supramolecular systems. Here we determine experimentally a universal parameter for their strength that is simply based on the size of the interacting contact surfaces. Toward this goal we designed a new cyclophane based on terrylene bisimide (TBI) π-walls connected by para-xylylene spacer units. With its extended π-surface this cyclophane proved to be an excellent and universal host for the complexation of π-conjugated guests, including small and large polycyclic aromatic hydrocarbons (PAHs) as well as dye molecules. The observed binding constants range up to 108 M−1 and show a linear dependence on the 2D area size of the guest molecules. This correlation can be used for the prediction of binding constants and for the design of new host–guest systems based on the herewith derived universal Gibbs interaction energy parameter of 0.31 kJ/molÅ2 in chloroform.
description: Original spectroscopic data to report: https://doi.org/10.1002/anie.202318451
DOI: 10.34740/kaggle/dsv/7905508
title: COVID Vaccination in World (updated daily)
DOI: 10.21954/ou.rd.24981669.v2
title: OpenMARS MY34-35 database

description: The Open access to Mars Assimilated Remote Soundings (OpenMARS) database is a reanalysis product combining past spacecraft observations with a state-of-the-art Mars Global Circulation Model (GCM). The OpenMARS product is a global surface/atmosphere reference database of key variables for multiple Mars years.Spacecraft observations of column dust optical depth and temperature profiles from the Mars Climate Sounder (MCS) instrument on the Mars Reconnaissance Orbiter spacecraft, water vapour profiles and water vapour column from the Nadir and Occultation for MArs Discovery (NOMAD) instrument and water vapour and temperature profiles from the Atmospheric Chemistry Suite (ACS) on the ExoMars Trace Gas Orbiter (TGO) spacrcraft are combined with a Mars GCM used at the Open University. The database includes hourly output of key atmospheric and surface variables such as water vapour volume mixing ratio, zonal/meridional wind, temperature as a function of altitude and column dust optical depth.Extended details on this dataset can be found in the OpenMARS-MY34-35-reference-manual.pdf document included in this repository.
DOI: 10.21954/ou.rd.24981669.v1
title: OpenMARS MY34-35 database

description: The Open access to Mars Assimilated Remote Soundings (OpenMARS) database is a reanalysis product combining past spacecraft observations with a state-of-the-art Mars Global Circulation Model (GCM). The OpenMARS product is a global surface/atmosphere reference database of key variables for multiple Mars years.Spacecraft observations of column dust optical depth and temperature profiles from the Mars Climate Sounder (MCS) instrument on the Mars Reconnaissance Orbiter spacecraft, water vapour profiles and water vapour column from the Nadir and Occultation for MArs Discovery (NOMAD) instrument and water vapour and temperature profiles from the Atmospheric Chemistry Suite (ACS) on the ExoMars Trace Gas Orbiter (TGO) spacrcraft are combined with a Mars GCM used at the Open University. The database includes hourly output of key atmospheric and surface variables such as water vapour volume mixing ratio, zonal/meridional wind, temperature as a function of altitude and column dust optical depth.Extended details on this dataset can be found in the OpenMARS-MY34-35-reference-manual.pdf document included in this repository.
DOI: 10.6084/m9.figshare.14345759
title: Down-regulation of HLA-DRs and HLA-DPs reflects the deficiency of antigen-presenting cells in endometrium from infertile women with and without ovarian endometriosis

description: This study aimed to explore common molecular changes in the infertile endometrium from women with and without endometriosis (EM). By analyzing the dataset GSE120103 from Gene Expression Omnibus, a total of 3252 shared differentially expressed genes were identified between ovarian EM in infertile vs. fertile endometrium and EM-free infertile vs. fertile endometrium. In addition, the gene annotation and pathway analysis of the shared differentially expressed genes with the same expression trend indicated that the pathway ‘MHC class II antigen presentation’ and five candidate genes: HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DPA1, HLA-DPB1 were both down-regulated in infertile endometrium with or without EM. Logistic regression showed that HLA-DRA might be an independent predictor of the infertile status of the endometrium. Single sample gene set enrichment analysis (ssGSEA) showed that some classic antigen-presenting cells: macrophages type 1, macrophages type 2, and mature dendritic cells were significantly down-regulated in infertile endometrium with or without EM, whose enrichment correlated positively with the expression of candidate HLA molecules. Hence, the down-regulation of HLA-DRs and HLA-DPs reflecting the deficiency of antigen-presenting cells in endometrium might serve as a common biomarker for diagnosing endometrium-associated infertility in women with and without endometriosis.
DOI: 10.6084/m9.figshare.14345759.v1
title: Down-regulation of HLA-DRs and HLA-DPs reflects the deficiency of antigen-presenting cells in endometrium from infertile women with and without ovarian endometriosis

description: This study aimed to explore common molecular changes in the infertile endometrium from women with and without endometriosis (EM). By analyzing the dataset GSE120103 from Gene Expression Omnibus, a total of 3252 shared differentially expressed genes were identified between ovarian EM in infertile vs. fertile endometrium and EM-free infertile vs. fertile endometrium. In addition, the gene annotation and pathway analysis of the shared differentially expressed genes with the same expression trend indicated that the pathway ‘MHC class II antigen presentation’ and five candidate genes: HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DPA1, HLA-DPB1 were both down-regulated in infertile endometrium with or without EM. Logistic regression showed that HLA-DRA might be an independent predictor of the infertile status of the endometrium. Single sample gene set enrichment analysis (ssGSEA) showed that some classic antigen-presenting cells: macrophages type 1, macrophages type 2, and mature dendritic cells were significantly down-regulated in infertile endometrium with or without EM, whose enrichment correlated positively with the expression of candidate HLA molecules. Hence, the down-regulation of HLA-DRs and HLA-DPs reflecting the deficiency of antigen-presenting cells in endometrium might serve as a common biomarker for diagnosing endometrium-associated infertility in women with and without endometriosis.
DOI: 10.6084/m9.figshare.14672262
title: Genetic and <i>in silico</i> analysis show a role of <i>SMAD3</i> on recurrent pregnancy loss

description: Recurrent pregnancy loss (RPL) is one of the most common reproductive failures affecting 1–5% of couples. Smad3 is an effector of signalling of the Transforming Growth Factors-β superfamily (TGF-β), regulating the transcription of several target genes of these cytokines. The objective of this study was to evaluate the influence of a variant on <i>SMAD3</i> (rs17293443) in RPL. A case-control study was carried out with 149 women who experienced RPL and 159 controls, as well as bioinformatics tools to determine the role of this variant in this condition. Our study showed an allelic (<i>p</i> = 0.023) and genotypic (<i>p</i> &lt; 0.01) association of this variant with the RPL. Our functional <i>in silico</i> predictions suggest that this variant causes a change in <i>SMAD3</i> expression levels. Alterations in the expression of this gene can directly compromise the Smad3-dependent signalling pathway that is fundamental for key processes for gestation such as steroid hormone regulation and implantation, as demonstrated by ontologies analyses performed and the literature. Our findings regarding the involvement of Smad3 on RPL are a novelty in this field, and they seem to be promising to the clinical management of this condition.
DOI: 10.6084/m9.figshare.14672262.v1
title: Genetic and <i>in silico</i> analysis show a role of <i>SMAD3</i> on recurrent pregnancy loss

description: Recurrent pregnancy loss (RPL) is one of the most common reproductive failures affecting 1–5% of couples. Smad3 is an effector of signalling of the Transforming Growth Factors-β superfamily (TGF-β), regulating the transcription of several target genes of these cytokines. The objective of this study was to evaluate the influence of a variant on <i>SMAD3</i> (rs17293443) in RPL. A case-control study was carried out with 149 women who experienced RPL and 159 controls, as well as bioinformatics tools to determine the role of this variant in this condition. Our study showed an allelic (<i>p</i> = 0.023) and genotypic (<i>p</i> &lt; 0.01) association of this variant with the RPL. Our functional <i>in silico</i> predictions suggest that this variant causes a change in <i>SMAD3</i> expression levels. Alterations in the expression of this gene can directly compromise the Smad3-dependent signalling pathway that is fundamental for key processes for gestation such as steroid hormone regulation and implantation, as demonstrated by ontologies analyses performed and the literature. Our findings regarding the involvement of Smad3 on RPL are a novelty in this field, and they seem to be promising to the clinical management of this condition.
DOI: 10.6084/m9.figshare.25451335
title: Epiblast.WT-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

description: definitive endoderm
DOI: 10.6084/m9.figshare.25451335.v1
title: Epiblast.WT-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

description: definitive endoderm
DOI: 10.48597/u3ag-5nr7
title: Measurement of Heavy metals at Råö

description: Measurement of Heavy metals at Råö
DOI: 10.48597/dnuc-dc9j
title: Measurement of Chromium at Råö

description: Measurement of Chromium at Råö
DOI: 10.48597/e9t6-rfpv
title: Measurement of Chromium at Råö

description: Measurement of Chromium at Råö
DOI: 10.48597/mjxj-dpyu
title: Measurement of Chromium at Råö

description: Measurement of Chromium at Råö
DOI: 10.48597/rp3a-3d3m
title: Measurement of Chromium at Råö

description: Measurement of Chromium at Råö
DOI: 10.48597/sr2h-64se
title: Measurement of Chromium at Råö

description: Measurement of Chromium at Råö
DOI: 10.48597/hsv4-vnwb
title: Measurement of Manganese at Råö

description: Measurement of Manganese at Råö
DOI: 10.48597/t5gs-8ry2
title: Measurement of Manganese at Råö

description: Measurement of Manganese at Råö
DOI: 10.48597/vbk5-7pax
title: Measurement of Manganese at Råö

description: Measurement of Manganese at Råö
DOI: 10.48597/4chc-8sb8
title: Measurement of Manganese at Råö

description: Measurement of Manganese at Råö
DOI: 10.48597/4ke8-s8gg
title: Measurement of Zinc at Råö

description: Measurement of Zinc at Råö
DOI: 10.48597/7vwv-j3g6
title: Measurement of Zinc at Råö

description: Measurement of Zinc at Råö
DOI: 10.48597/e95h-c9j6
title: Measurement of Zinc at Råö

description: Measurement of Zinc at Råö