Semi-pure petrobactin analyzed for metal-binding (mzML files for personal use)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Methylobacterium Aquaticum (ncbitaxon:270351)
SUBMITTER: 
Allegra Aron
PROVIDER: MSV000098913 | MassIVE | Fri Aug 22 09:02:00 BST 2025
REPOSITORIES: MassIVE
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Project description: Not available
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Project description:This dataset includes several concentrations of petrobactin infused with several concentrations of H2O, FeCl3, ZnCl2, CoCl2*H2O, MnCl2*4H2O, and NiCl2*6H2O such that potential iron binding can be approximated relative to the apo form.
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2014-12-16 | PXD001121 | Pride
Project description:mzML and mzIdentML are commonly used, powerful tools for representing mass spectrometry data and derived identification information. These formats are complex, requiring non-trivial logic to translate data into the appropriate representation. Most published implementations are tightly coupled to data structures. The most complete implementations are written in compiled languages that cannot expose the complete flexibility of the implementation to external programs or bindings. To our knowledge, there are no complete implementations for mzML or mzIdentML available to scripting languages like Python or R. We present psims, a library written in Python for writing mzML and mzIdentML. The library allows writing either XML format using built-in Python data structures. It includes a controlled vocabulary resolution system to simplify the encoding process and an identity tracking system to manage entity relationships. The source code is available at https://github.com/mobiusklein/psims, and through the Python Package Index as psims, licensed under the Apache 2 common license.
| S-EPMC6398200 | biostudies-literature
Project description:Intervention name : S-1 (tegafur + gimeracil + oteracil potassium)
INN of the intervention : S-1: tegafur, gimeracil, oteracil potassium
Dosage And administration of the intervention : 40-60 mg bid day 1 (evening) - day 15 (morning). Repeat cycles every 3 weeks
Intervention name : L-OHP (Oxaliplatin)
INN of the intervention : oxaliplatin
Dosage And administration of the intervention : 130 mg/m2 IV on day 1. Repeat cycles every 3 weeks
Intervention name : BV (Bevacizumab)
INN of the intervention : bevacizumab
Dosage And administration of the intervention : 7.5 mg/kg IV on day 1. Repeat cycles every 3 weeks
Control intervention name : 5-FU (Fluorouracil)
INN of the control intervention : fluorouracil
Dosage And administration of the control intervention : 400 mg/m2 IV bolus on day 1, followed by 2400 mg/m2 over 46 hours. Repeat cycles every 2 weeks.
Control intervention name : l-LV (Levofolinate calcium)
INN of the control intervention : folic acid
Dosage And administration of the control intervention : 200 mg IV on day 1. Repeat cycles every 2 weeks.
Control intervention name : L-OHP (Oxaliplatin)
INN of the control intervention : oxaliplatin
Dosage And administration of the control intervention : 85 mg/m2 IV on day 1. Repeat cycles every 2 weeks.
Control intervention name : BV (Bevacizumab)
INN of the control intervention : bevacizumab
Dosage And administration of the control intervention : 5 mg/kg IV on day 1. Repeat cycles every 2 weeks.
Primary outcome(s): Progression free survival(PFS)
Study Design: Randomized, open-label, comparative study
| 2610116 | ecrin-mdr-crc
Project description:The crystal symmetry of a material dictates the type of topological band structures it may host, and therefore symmetry is the guiding principle to find topological materials. Here we introduce an alternative guiding principle, which we call ‘quasi-symmetry’. This is the situation where a Hamiltonian has an exact symmetry at lower-order that is broken by higher-order perturbation terms. This enforces finite but parametrically small gaps at some low-symmetry points in momentum space. Untethered from the restraints of symmetry, quasi-symmetries eliminate the need for fine-tuning as they enforce that sources of large Berry curvature will occur at arbitrary chemical potentials. We demonstrate that a quasi-symmetry in the semi-metal CoSi stabilizes gaps below 2 meV over a large near-degenerate plane that can be measured in the quantum oscillation spectrum. The application of in-plane strain breaks the crystal symmetry and gaps the degenerate point, observable by new magnetic breakdown orbits. The quasi-symmetry, however, does not depend on spatial symmetries and hence transmission remains fully coherent. These results demonstrate a class of topological materials with increased resilience to perturbations such as strain-induced crystalline symmetry breaking, which may lead to robust topological applications as well as unexpected topology beyond the usual space group classifications.
| S-EPMC7613062 | biostudies-literature
Project description:This repository contains all the FASTQ files for the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) used in the article \\"An Atlas of Cells in The Human Tonsil,\\" published in Immunity in 2024. Inspired by the TCGA barcodes, we have named each fastq file with the following convention: [TECHNOLOGY].[DONOR_ID].[SUBPROJECT].[GEM_ID].[LIBRARY_ID].[LIBRARY_TYPE].[LANE].[READ].fastq.gz which allows to retrieve all metadata from the name itself. Here is a full description of each field: - TECHNOLOGY: scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics (Visium). We also include the fastq files associated with the multiome experiments performed on two mantle cell lymphoma patients (MCL). - DONOR_ID: identifier for each of the 17 patients included in the cohort. We provide the donor-level metadata in the file \\"tonsil_atlas_donor_metadata.csv\\", including the hospital, sex, age, age group, cause for tonsillectomy and cohort type for every donor. - SUBPROJECT: each subproject corresponds to one run of the 10x Genomics Chromium™ Chip. - GEM_ID: each run of the 10x Genomics Chromium™ Chip consists of up to 8 \\"GEM wells\\" (see https://www.10xgenomics.com/support/software/cell-ranger/getting-started/cr-glossary): a set of partitioned cells (Gel Beads-in-emulsion) from a single 10x Genomics Chromium™ Chip channel. We give a unique identifier to each of these channels. - LIBRARY_ID: one or more sequencing libraries can be derived from a GEM well. For instance, multiome yields two libraries (ATAC and RNA) and CITE-seq+scVDJ yields 4 libraries (RNA, ADT, BCR, TCR). - LIBRARY_TYPE: the type of library for each library_id. Note that we used cell hashing () for a subset of the scRNA-seq libraries, and thus the library_type can be \\"not_hashed\\", \\"hashed_cdna\\" (RNA expression) or \\"hashed_hto\\" (the hashtag oligonucleotides). - LANE: to increase sequencing depth, each library was sequenced in more than one lane. Important: all lanes corresponding to the same sequencing library need to be inputed together to cellranger, because they come from the same set of cells. - READ: for scATAC-seq we have three reads (R1, R2 or R3), see cellranger-atac's documentation. While we find these names to be the most useful, they need to be changed to follow cellranger's conventions. We provide a code snippet in the README file of the GitHub repository associated with the tonsil atlas to convert between both formats (https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas/). Besides the fastq files, cellranger (and other mappers) require additional files, which we also provide in this repository: - cell_hashing_metadata.csv: as mentioned above, we ran cell hashing (10.1186/s13059-018-1603-1) to detect doublets and reduce cost per cell. This file provides the sequence of the hashtag oligonucleotides in cellranger convention to allow demultiplexing. - cite_seq_feature_reference.csv: similar to the previous file, this one links each protein surface marker to the hashtag oligonucleotide that identified it in the CITE-seq experiment. - V10M16-059.gpr and V19S23-039.gpr: these correspond to the two slides of the two Visium experiments performed in the tonsil atlas. They are needed to run spaceranger. - [GEM_ID]_[SLIDE]_[CAPTURE_AREA].jpg: 8 images associated with the Visium experiments. Here, GEM_ID refers to each of the 4 capture areas in each slide. - [TECHNOLOGY]_sequencing_metadata.csv: the GEM-level metadata for each technology. It includes the relationship between subproject, gem_id, library_id, library_type and donor_id. These are the other repositories associated with the tonsil atlas: - Expression and accessibility matrices: https://zenodo.org/records/10373041 - Seurat objects: https://zenodo.org/records/8373756 - HCATonsilData package: https://bioconductor.org/packages/release/data/experiment/html/HCATonsilData.html - Azimuth: https://azimuth.hubmapconsortium.org/ - Github: https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas
2024-05-02 | E-MTAB-13687 | biostudies-arrayexpress
Project description:Metal ions are critical for the proper folding of RNA, and the GAAA tetraloop-receptor is necessary for the optimal folding and function of many RNAs. We have used NMR to investigate the role of metal ions in the structure of the tetraloop-receptor in solution. The NMR data indicate native tertiary structure is formed under a wide range of ionic conditions. The lack of conformational adaptation in response to very different ionic conditions argues against a structural role for divalent ions. Nuclear Overhauser effects to cobalt hexammine and paramagnetic relaxation enhancement induced by manganese ions were used to determine the NMR structures of the tetraloop receptor in association with metal ions, providing the first atomic-level view of these interactions in the solution state. Five manganese and two cobalt hexammine ions could be localized to the RNA surface. The locations of the associated metal ions are similar, but not identical to, those of previously determined crystal structures. The sites of association are in general agreement with nonlinear Poisson-Boltzmann calculations of the electrostatic surface, emphasizing the general importance of diffusely associated ions in RNA tertiary structure.
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