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opencc-by-4.0Sep 2019View details →

Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages.

Cells of the monocyte/macrophage lineage play essential roles in tissue homeostasis and immune responses, but mechanisms underlying the coordinated expression of cytoskeletal genes required for specialized functions of these cells, such as directed migration and phagocytosis, remain unknown. Here, using genetic and genomic approaches, we provide evidence that serum response factor (SRF) regulates both general and cell type-restricted components of the cytoskeletal gene expression program in macrophages. Genome-wide location analysis of SRF in macrophages demonstrates enrichment of SRF binding at ubiquitously expressed target gene promoters, as expected, but also reveals that the majority of SRF binding sites associated with cell type-restricted target genes are at distal inter- and intragenic locations. Most of these distal SRF binding sites are established by the prior binding of the macrophage- and the B cell-specific transcription factor PU.1 and exhibit histone modifications characteristic of enhancers. Consistent with this, representative cytoskeletal target genes associated with these elements require both SRF and PU.1 for full expression. These findings suggest that SRF uses two distinct molecular strategies to regulate programs of cytoskeletal gene expression: a promoter-based strategy for ubiquitously expressed target genes and an enhancer-based strategy at target genes that exhibit cell type-restricted patterns of expression.

opencc-by-4.0Sep 2019View details →

data set related to article Independent adaptation mechanisms for numerosity and size perception provide evidence against a common sense of magnitude

This record contains raw data related to article Independent adaptation mechanisms for numerosity and size perception provide evidence against a common sense of magnitude

opencc-by-4.0Sep 2019View details →

The theory of technological machines mechanisms

<pre>The basis of this textbook is the general methods of analysis and synthesis of mechanisms by which students should study the rational construction of the structure of a modern technological machine during its design. For students of mechanical specialties of higher education institutions and specialists of mechanical profile of operation and design of technological machines for advanced training.</pre>

Fig. 5. E in First host record of Epipompilus (Hymenoptera: Pompilidae) from Brazil and discussion of prey carriage mechanism

Fig. 5. E. tucumanus ♀ metasoma in dorsolateral view.

Fig. 7. E in First host record of Epipompilus (Hymenoptera: Pompilidae) from Brazil and discussion of prey carriage mechanism

Fig. 7. E. tucumanus ♀ frontal view of head.

Fig. 3. E in First host record of Epipompilus (Hymenoptera: Pompilidae) from Brazil and discussion of prey carriage mechanism

Fig. 3. E. tucumanus ♀ dorsal view of head and thorax.

Fig. 2. E in First host record of Epipompilus (Hymenoptera: Pompilidae) from Brazil and discussion of prey carriage mechanism

Fig. 2. E. tucumanus ♀ lateral habitus.

Fig. 6. E in First host record of Epipompilus (Hymenoptera: Pompilidae) from Brazil and discussion of prey carriage mechanism

Fig. 6. E. tucumanus ♀ hind tibia.

opencc-by-4.0Mar 2024View details →

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

This Zenodo repository contains data used for running <a href="https://github.com/sheynkman-lab/biosurfer_analysis" target="_blank" rel="noopener">Biosurfer_analysis</a>, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology. Repository content: <ol> <li>biosurfer_gencode_toy_data.zip: is a small subset of the GENCODE version 38 files (GTF, transcript FASTA, and protein FASTA) for the purpose of trial run and testing Biosurfer scripts. </li> <li>biosurfer_gencode_toy_output.zip: Biosurfer generated output files for the toy data.  </li> <li>biosurfer_gencode_v42_data.zip: contains GENCODE version 42 (basic) files (GTF, transcript FASTA, and protein FASTA). </li> <li>biosurfer_gencode_v42_output.zip: Biosurfer generated output files for GENCODE 42 input files. </li> <li>biosurfer_wtc11_data.zip: contains karyotypically normal human stem cell line data (WTC11) file (GTF, transcript FASTA, and protein FASTA). </li> <li>biosurfer_wtc11_output.zip: Biosurfer generated output files for WTC11 files. </li> <li>APPRIS analysis.zip: Intermediate files (CSV) detailing the APPRIS isoforms information utilized in the associated manuscript.</li> <li>biosurfer_mouse.zip: contains GENCODE Mouse version M35 (basic) files (GTF, transcript FASTA, and protein FASTA).</li> <li>biosurfer_mouse_output.zip: Biosurfer generated output files for GENCODE M35 input files.</li> </ol>

Molecular Simulation Elaborating the Structural Mechanism of Spiri forming nitrilase from Bacillus safensis

Nitrilases are indispensable in the biocatalytic hydrolysis of nitrile compounds, which presents promising applications in industrial biocatalysis and environmental remediation. In this study, we conduct an extensive investigation into the structural and functional properties of Bacillus safensis nitrilase (BsNIT), highlighting its assembly, substrate binding mechanisms, stability, evolutionary relationships, and active site conservation. Using a combination of molecular modeling and extensive molecular dynamics simulations, we unveil the intricate architecture of BsNIT, which exhibits a left-handed spiri-forming structure stabilized by interchain interactions and salt-bridge formations. The substrate-binding pocket, surrounded by aromatic residues, displays multifaceted accessibility through distinct channels. Our simulations reveal substrate-specific catalytic orientations, with glutaronitrile and 4-cyanobutanoic acid displaying stable binding, while benzonitrile exhibits a propensity for rapid product diffusion. Analysis of active site conservation emphasizes the functional significance of preserved catalytic residues, providing insights into BsNIT's catalytic efficiency. This comprehensive study offers a thorough understanding of BsNIT's structure-function relationships, paving the way for future advancements in enzyme engineering and bioremediation strategies targeting nitrile pollutants.

opencc-by-4.0Feb 2024View details →

Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD

Set of data and scripts for the analysis of RAMD dissociation trajectories generated for BN-NS and BT/BCT-BPTI mutants, reported in the manuscript: "Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD" by Giulia D'Arrigo, Daria B. Kokh, Ariane Nunes-Alves and Rebecca C. Wade   <ol> <li>RAMD movies of WT Bn-Bs and D35Abn mutant dissociation pathway (WT-diss.mp4 and D35Abn-diss.mp4)</li> <li>Protein-Protein.zip contains:</li> </ol> <ul> <li>README - set of instructions to go through files and for the use of the scripts</li> <li>Jupyter notebooks: tauRAMD_PP_Residence_time.ipynb and tauRAMD_PP_Unbinding_pathways.ipynb</li> <li>Scripts used for analysis and postprocessing RAMD simulations - for the correct usage of the scripts check the corresponding file header</li> <li>System input files in BN-BS/ and BT_BCT-BPTI/</li> <li>Experimental data used</li> <li>2 RAMD movies (.mp4) showing dissociation of WT Bn-Bs and D35Abn mutant</li> </ul>

Database of the RILEM TC 304-ADC interlaboratory study on mechanical properties of 3D printed concrete (ILS-mech)

The RILEM TC 304-ADC has set up a large interlaboratory study on the mechanical properties of 3D printed concrete (ILS-mech).  The study was prepared in 2022 by a preparation group leading to a Study Plan which the TC approved on 29 November 2022 (<a href="https://doi.org/10.14459/2023mp1705940">https://doi.org/10.14459/2023mp1705940</a>). The ILS-mech was performed in 2023. The data was collected using a pre-prepared spreadsheet template. For data management, a database was derived and set-up in openBIS. The underlying Postgres database of openBIS was exported to the here-published SQLite database for sharing without maintaining a server. The structure of the database is described in (<a href="https://doi.org/10.1617/s11527-025-02650-9">https://doi.org/10.1617/s11527-025-02650-9</a>). The results are discussed in three associated papers focusing on the overall outcomes and evaluation of the procedures (<a href="https://doi.org/10.1617/s11527-025-02686-x">https://doi.org/10.1617/s11527-025-02686-x</a>), the compressive test results (<a href="https://doi.org/10.1617/s11527-025-02688-9">https://doi.org/10.1617/s11527-025-02688-9</a>), and the tensile test results (<a href="https://doi.org/10.1617/s11527-025-02687-w">https://doi.org/10.1617/s11527-025-02687-w</a>). contact via freek.bos@tum.de

opencc-by-4.0Jan 2024View details →

Additional information for Acidification from microbial oxidation of N, S, Fe and Mn as potential key mechanism for sprayed concrete deterioration in a subsea road tunnel

Here we include additional files for Karacic et al. Acidification from microbial oxidation of N, S, Fe and Mn as potential key mechanism for sprayed concrete deterioration in a subsea road tunnel Metagenome reads and MAGs are avaliable in the NCBI BioProject PRJNA755678 The following files are included here <ul> <li>MAGs_summary_Oslofjord.tsv: Information about the Oslofjord MAGs (GTDB R207 taxonomy, relative abundance, Completness, Contamination, NCBI accessions)</li> <li>gtdbtk.ar53.summary. Output from GTDB-Tk v2.1.0 with GTDB R207_v2. Archaeal MAGs</li> <li>gtdbtk.bac120.summary.tsv. Output from GTDB-Tk v2.1.0 with GTDB R207_v2. Bacterial MAGs</li> <li>FeGenie-geneSummary.csv: Output from FeGenie</li> <li>Annotations_1.tsv : Output from DRAM (215 MAGs)</li> <li>Annotations_2.tsv: Output from DRAM (186 MAGs)</li> <li>OFTMs_DRAM_genes.DiSCo.filtered.txt. Output from DiSCo</li> <li>code_R.zip: R-code and additional files used for making MAGs figures</li> </ul> This is version 2 of the dataset and it replaces version 1 (https://doi.org/10.5281/zenodo.5292093)

Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist – Tsix locus

Data and codes for Figure reprodicbility, image processing and demo.

Dataset: Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates

The derived data is part of a manuscript submitted to the journal Green Chemistry, entitled "Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates". [DOI https://doi.org/10.1039/d4gc03143a. This work is supported by the Swiss National Science Foundation (project number 200021_178952) Raw data can be found: https://doi.org/10.16907/1ac46f03-6e1b-4230-b5c0-3df2cec87b5e The raw Photoelectron Photoion Coincidence (PEPICO) data were obtained during catalytic fast pyrolysis of eugenol, vanillin, syringol over H-ZSM-5 and HFAU. The analysis software can be obtained from: https://www.psi.ch/en/sls/vuv/pepico. The folders contain mass spectra and threshold photoelectron raw data at different reactor temperatures.

A mechanical qubit

This is a repository of all files related to the publication "A mechanical qubit" by Yu Yang, Igor Kladarić, Maxwell Drimmer, Uwe von Lüpke, Daan Lenterman, Joost Bus, Stefano Marti, Matteo Fadel and Yiwen Chu. The repository contains a folder data_analysis which contains all python scripts used for data analysis and plotting the figures presented in the publication. The final data analysis is executed and figures ploted in Mecha_qubit_plotting.ipynb The repository also contains a file phonon_qubit.ipynb which contains the code for all simulations presented in the publication. phonon_qubit.ipynb requires dependencies of a repository located on a ETH version control system. Read access can be obtained as follows:  Link to repository: https://gitlab.ethz.ch/yangyuethz/hyqu_simulato     The repository can be accessed in the following manner:     "Use a project access token to authenticate:     -With the GitLab API.     -With Git, when using HTTP Basic Authentication, use:         Any non-blank value as a username.         The project access token as the password.     The project access token for this repository is:         67UpFZHSicoBsyRiHQRY

opencc-by-4.0Apr 2024View details →

Data for: Synergistic mechanisms of plant phosphorus (P) resorption and microbial P-limitation affecting soil P during grassland vegetation succession

Data for: Synergistic mechanisms of plant phosphorus (P) resorption and microbial P-limitation affecting soil P during grassland vegetation succession

opencc-by-4.0Sep 2024View details →

Datasets and geometries for "MORE-Q, Dataset for molecular olfactorial receptor engineering by quantum mechanics"

We introduce the MORE-Q dataset, a quantum-mechanical (QM) dataset encompassing the structural and electronic data of non-covalent molecular sensors formed by combining 18 mucin-derived olfactorial receptors with 102 body odor volatilome (BOV) molecules. To have a better understanding of their intra- and inter-molecular interactions, we have performed accurate QM calculations in different stages of the sensor design and, accordingly, MORE-Q splits into three subsets: i) MORE-Q-G1: QM data of 18 receptors and 102 BOV molecules, ii) MORE-Q-G2: QM data of 23, 838 BOV-receptor configurations, and iii) MORE-Q-G3: QM data of 1, 836 BOV-receptor-graphene systems. Each subset involves geometries optimized using GFN2-xTB with D4 dispersion correction and up to 39 physicochemical properties, including global and local properties as well as binding features, all computed at the tightly converged PBE+D3 level of theory. By addressing BOV-receptor-graphene systems from a QM perspective, MORE-Q can serve as a benchmark dataset for state-of-the-art machine learning methods developed to predict binding features. This, in turn, can provide valuable insights for developing the next-generation mucin-derived olfactory receptor sensing devices. The dataset is provided in 3 HDF5 based files. One can also find here a README file with technical usage details and examples of how to access the information stored in the dataset (see createDF.py). We also offer a Github repository for user guide, see https://github.com/LiC1117/MORE-Q. For more details, one can refer to the manuscript doi: <a href="https://doi.org/10.1038/s41597-025-04616-6" rel="nofollow">https://doi.org/10.1038/s41597-025-04616-6</a>

opencc-by-4.0Sep 2024View details →

New insights into the driving mechanism of the mid-Eocene (43 Ma) tectonic transition in the western Pacific margin—A case study of stress field modeling in Pingbei

This is the dataset for " New insights into the driving mechanism of the mid-Eocene (43 Ma) tectonic transition in the western Pacific margin—A case study of stress field modeling in Pingbei" including modeling parameters and raw results.