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Subject: Medicine, Health and Life Sciences Deposit Date: 2021

1 to 10 of 15 Results

Supporting Information for Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs Apr 27, 2023 - Supporting Information for Publications Fullstone, Gavin, 2023, "Supporting Information for Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs", https://doi.org/10.18419/darus-2175, DaRUS, V1 This folder contains expected inputs and outputs from the example model used in the paper "Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs". These can be used to troubleshoot unexpected problems.
Data for: Correlation of mitochondrial TOM core complex stop-and-go and open-closed channel dynamics May 18, 2022 - Biophysics Group Wang, Shuo; Findeisen, Lukas; Leptihn, Sebastian; Wallace, Mark Ian; Hörning, Marcel; Nussberger, Stephan, 2022, "Data for: Correlation of mitochondrial TOM core complex stop-and-go and open-closed channel dynamics", https://doi.org/10.18419/darus-2158, DaRUS, V1, UNF:6:9dvSdn6uEaqFUk/rRvtwoA== [fileUNF] The role of lateral diffusion of proteins in the membrane in the context of function has not been examined extensively. The data set addresses the relationship between protein lateral diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC). Opti...
Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns Dec 17, 2021 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2021, "Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns", https://doi.org/10.18419/darus-2114, DaRUS, V2 Experimental procedures for deep enzymology reactions with randomized substrates: For analysis of flanking sequence preferences of the TET enzymes, a similar approach as described for DNMTs (Emperle et al., 2019; Gao et al., 2020; Adam et al., 2020; Dukatz et al., 2020) was used....
GraphML files for sequence networks of PETases and PURases Dec 1, 2021 - PAZy Buchholz, Patrick C. F., 2021, "GraphML files for sequence networks of PETases and PURases", https://doi.org/10.18419/darus-2054, DaRUS, V1 The GraphML files contain the sequence networks and annotated metadata for protein sequences.
Profile hidden Markov model for PETase homologues Dec 1, 2021 - PAZy Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/darus-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF] Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-...
NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3 Nov 25, 2021 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2 Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem...
Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects" Nov 11, 2021 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Mack, Alexandra; Emperle, Max, 2021, "Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2231, DaRUS, V1 Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were obtained from IDT. Second strand synthesis was conducted by a primer extension reaction using one univ...
EnzymeML Metadata Block Configuration for Dataverse Aug 5, 2021 - RDM Tools Range, Jan Peter; Iglezakis, Dorothea, 2021, "EnzymeML Metadata Block Configuration for Dataverse", https://doi.org/10.18419/darus-2105, DaRUS, V1 This dataset contains a TSV-File for the configuration of a metadata block for data repositories basing on Dataverse. The block helps to describe datasets with the concepts of the metadata scheme EnzymeML, which is a data model provided to facilitate the documentation and exchang...
Dynamic CT imaging of bone cement injection through aluminium foam Jun 23, 2021 - Dynamic CT imaging Trivedi, Zubin, 2021, "Dynamic CT imaging of bone cement injection through aluminium foam", https://doi.org/10.18419/darus-2037, DaRUS, V1, UNF:6:H7VS7vaCTD5/iVSCIXdACQ== [fileUNF] The process of vertebroplasty is experimentally simulated by injecting a commercially available bone cement (rheology previously characterised) into a piece of aluminium foam (diameter 40 mm) with pore structure similar to that of cancellous bone inside a vertebra. The cement inf...
Measuring the viscoelastic properties and curing characterstics of Vertecem V+ bone cement using oscillatory rheometer Jun 23, 2021 - Rheological characterisation Trivedi, Zubin, 2021, "Measuring the viscoelastic properties and curing characterstics of Vertecem V+ bone cement using oscillatory rheometer", https://doi.org/10.18419/darus-2032, DaRUS, V1, UNF:6:/4Hsn/UYH9QPsLRp8mLktg== [fileUNF] A commercially available bone cement (Vertecem V+) is subjected to an oscillometric test using a parallel plate rheomter in order to characterise its viscoelastic properties. For this, a small amount of bone cement is placed between the plates of the rheometer and subjected to os...

Supporting Information for Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs

Apr 27, 2023 - Supporting Information for Publications

Fullstone, Gavin, 2023, "Supporting Information for Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs", https://doi.org/10.18419/darus-2175, DaRUS, V1

This folder contains expected inputs and outputs from the example model used in the paper "Rapid Particle-based Simulations of Cellular Signalling with the FLAME-accelerated Signalling Tool (FaST) and GPUs". These can be used to troubleshoot unexpected problems.

Data for: Correlation of mitochondrial TOM core complex stop-and-go and open-closed channel dynamics

May 18, 2022 - Biophysics Group

Wang, Shuo; Findeisen, Lukas; Leptihn, Sebastian; Wallace, Mark Ian; Hörning, Marcel; Nussberger, Stephan, 2022, "Data for: Correlation of mitochondrial TOM core complex stop-and-go and open-closed channel dynamics", https://doi.org/10.18419/darus-2158, DaRUS, V1, UNF:6:9dvSdn6uEaqFUk/rRvtwoA== [fileUNF]

The role of lateral diffusion of proteins in the membrane in the context of function has not been examined extensively. The data set addresses the relationship between protein lateral diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC). Opti...

Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns

Dec 17, 2021 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2021, "Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns", https://doi.org/10.18419/darus-2114, DaRUS, V2

Experimental procedures for deep enzymology reactions with randomized substrates: For analysis of flanking sequence preferences of the TET enzymes, a similar approach as described for DNMTs (Emperle et al., 2019; Gao et al., 2020; Adam et al., 2020; Dukatz et al., 2020) was used....

GraphML files for sequence networks of PETases and PURases

Dec 1, 2021 - PAZy

Buchholz, Patrick C. F., 2021, "GraphML files for sequence networks of PETases and PURases", https://doi.org/10.18419/darus-2054, DaRUS, V1

The GraphML files contain the sequence networks and annotated metadata for protein sequences.

Profile hidden Markov model for PETase homologues

Dec 1, 2021 - PAZy

Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/darus-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF]

Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-...

NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3

Nov 25, 2021 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2

Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem...

Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

Nov 11, 2021 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Mack, Alexandra; Emperle, Max, 2021, "Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2231, DaRUS, V1

Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were obtained from IDT. Second strand synthesis was conducted by a primer extension reaction using one univ...

EnzymeML Metadata Block Configuration for Dataverse

Aug 5, 2021 - RDM Tools

Range, Jan Peter; Iglezakis, Dorothea, 2021, "EnzymeML Metadata Block Configuration for Dataverse", https://doi.org/10.18419/darus-2105, DaRUS, V1

This dataset contains a TSV-File for the configuration of a metadata block for data repositories basing on Dataverse. The block helps to describe datasets with the concepts of the metadata scheme EnzymeML, which is a data model provided to facilitate the documentation and exchang...

Dynamic CT imaging of bone cement injection through aluminium foam

Jun 23, 2021 - Dynamic CT imaging

Trivedi, Zubin, 2021, "Dynamic CT imaging of bone cement injection through aluminium foam", https://doi.org/10.18419/darus-2037, DaRUS, V1, UNF:6:H7VS7vaCTD5/iVSCIXdACQ== [fileUNF]

The process of vertebroplasty is experimentally simulated by injecting a commercially available bone cement (rheology previously characterised) into a piece of aluminium foam (diameter 40 mm) with pore structure similar to that of cancellous bone inside a vertebra. The cement inf...

Measuring the viscoelastic properties and curing characterstics of Vertecem V+ bone cement using oscillatory rheometer

Jun 23, 2021 - Rheological characterisation

Trivedi, Zubin, 2021, "Measuring the viscoelastic properties and curing characterstics of Vertecem V+ bone cement using oscillatory rheometer", https://doi.org/10.18419/darus-2032, DaRUS, V1, UNF:6:/4Hsn/UYH9QPsLRp8mLktg== [fileUNF]

A commercially available bone cement (Vertecem V+) is subjected to an oscillometric test using a parallel plate rheomter in order to characterise its viscoelastic properties. For this, a small amount of bone cement is placed between the plates of the rheometer and subjected to os...

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