This file includes the equations and descriptions of the Supporting Information for the third chapter of Andrew Charbonneau's PhD thesis.
", "author_list": "Andrew Charbonneau" }, { "title": "Infrared Action Spectroscopy of Biomolecules for Planetary Science Applications: Supporting Python Files", "type": "publication", "publication_date": "2026-05-05", "publisher": "CaltechDATA", "doi": "10.22002/jwhq8-dx134", "cite_using_url": "https://data.caltech.edu/records/jwhq8-dx134", "abstract": "The search for extraterrestrial life in our solar system requires the development of novel in situ instrumentation capable of detecting biosignatures in planetary environments and biological samples. This thesis applies infrared (IR) action spectroscopy of mass-selected ions toward this goal, demonstrating the ability to unambiguously characterize planetary-relevant biomolecules in liquid samples for various test cases. Action spectra are generated by plotting a photodissociation yield for biomolecular ions of interest as a function of IR frequency. In Chapter II, I describe the setup and operating procedures of an action spectrometer that uses a quantum cascade laser (QCL) (1000-1600 cm\u207b\u00b9) and a Cr:ZnSe/S laser (3300-3800 cm\u207b\u00b9), as well as describe general data processing procedures. In Chapter III, I describe the initial demonstration of the relatively compact, QCL-based action spectrometer, highlighting its ability to record action spectra of room temperature, water-tagged amino acids and discern amino acid isomers in mixtures. In Chapter IV, I record the action spectra of planetary-relevant, water-tagged amino acid isomers using the QCL-based instrument. I distinguish between the isomers using a combination of spectrum matching and machine learning methods. In Chapter V, I use the Cr:ZnSe/S laser-based action spectrometer to record multiplexed action spectra of protonated amino acids and nucleosides from bacterial samples, with some trials at lower laser output power than contemporary methods. In Chapter VI, I show progress towards differentiating amino acid enantiomers by recording action spectra of non-covalent chiral tag-amino acid complexes using the Cr:ZnSe/S laser-based action spectrometer. In Chapter VII, I recorded action spectra of additional biomolecules, including small molecules, carbohydrates, and a pigment. Overall, this thesis will aid future development of in situ instruments for astrobiology missions and general analytical applications.
", "author_list": "Nguyen, Tyler Minh-Hung" }, { "title": "Text: Crithidia fasciculata gene of unknown function CFAC1_070014400 encodes a putative alpha/beta hydrolase with a conserved active site", "type": "publication", "publication_date": "2026-04-03", "publisher": "CaltechDATA", "doi": "10.22002/np0r4-pwt21", "cite_using_url": "https://data.caltech.edu/records/np0r4-pwt21", "abstract": "Full ConSurf results for the CFAC1_070014400 protein.", "author_list": "Davis, Justin" }, { "title": "Text: Extending Biopython to combine multiple sequence alignments with the same reference into a Multiple Sequence Alignment.", "type": "publication", "publication_date": "2026-02-13", "publisher": "CaltechDATA", "doi": "10.22002/qnbhp-4jc30", "cite_using_url": "https://data.caltech.edu/records/qnbhp-4jc30", "abstract": "Document describing the principle of the algorithm with examples.", "author_list": "Bastress, Cassia" }, { "title": "Data processing code used in \"T cell development from expanded hematopoietic progenitors reveals initiation control by Lmo2 and Flt3L priming\"", "type": "publication", "publication_date": "2026-01-11", "publisher": "CaltechDATA", "doi": "10.22002/rvaqp-nt719", "cite_using_url": "https://data.caltech.edu/records/rvaqp-nt719", "abstract": "This deposit includes the sequencing data processing/analysis code for \"T cell development from expanded hematopoietic progenitors reveals initiation control by Lmo2 and Flt3L priming\". It contains code for preprocessing and analyzing bulk and single-cell RNA-seq, bulk ATAC-seq, and bulk CUT&RUN data used in the study.
", "author_list": "Shin, Boyoung and Chang, Samantha, el al." }, { "title": "Text: Three isoforms of Brugia malayi daf-16 activate a reporter gene in cultured HepG2 cells", "type": "publication", "publication_date": "2025-10-03", "publisher": "CaltechDATA", "doi": "10.22002/myhrh-ftm83", "cite_using_url": "https://data.caltech.edu/records/myhrh-ftm83", "abstract": "DNA sequences of confirmed Bma-daf-16 isoforms", "author_list": "Crossgrove, Kirsten" }, { "title": "Text: A single component landing site for efficient transgenesis using recombination-mediated insertion", "type": "publication", "publication_date": "2025-09-02", "publisher": "CaltechDATA", "doi": "10.22002/cvjz8-afh27", "cite_using_url": "https://data.caltech.edu/records/cvjz8-afh27", "abstract": "DNA constructs, oligonucleotides, Transgenes, alleles, Strain and Plasmid construction methods", "author_list": "Nonet, Michael L." }, { "title": "Text: PDLIM3 expression is implicated in the invasive behavior of glioblastoma stem cells and their ability to form neurospheres", "type": "publication", "publication_date": "2025-07-08", "publisher": "CaltechDATA", "doi": "10.22002/4be9r-g4h48", "cite_using_url": "https://data.caltech.edu/records/4be9r-g4h48", "abstract": "Supplementary table S1: Genes significantly up-regulated in GSCs with a strong expression of PDLIM3 compared to GSCs expressing weakly PDLIM3 (fold change cutoff 1.7 pvalue \u2264 0.05)", "author_list": "Seva, Catherine" }, { "title": "Diethyl ether gas-phase photo-oxidation mechanism for implementation in Caltech Mechanistic Model (CMM) ver.1", "type": "publication", "publication_date": "2025-05-09", "publisher": "CaltechDATA", "doi": "10.22002/671m3-rky11", "cite_using_url": "https://data.caltech.edu/records/671m3-rky11", "abstract": "This data folder is a compilation of the gas-phase chemistry mechanisms describing the photo-oxidation of diethyl ether (DE) and its fully deuterated version diethyl ether-d10 (DE-d10), which are used for implementation in Caltech Mechanistic Model (CMM) written by Dr. John D. Crounse of California Institute of Technology (crounjd@caltech.edu). The model is applied to calculate theoretical yields of oxidation products in the DE/DE-d10 system based on the implemented mechanism in \"Atmospheric Autoxidation Chemistry of Diethyl Ether\" (Yu et al., 2025, ACS ES&T-Air).
CMM is a MATLAB-based model, using ode-15s solver to calculate time-dependent concentration of species in the system based on given initial conditions and chemical mechanism. The code for the model is not provided here.
All files in the .zip folder is in .txt format. All files are copies of their original .m files, which are run altogether by the model.
", "author_list": "Crounse, John D. and Wennberg, Paul O." }, { "title": "Text: Temporal induction of the homeodomain transcription factor Nkx2-1 is sufficient to respecify foregut and hindgut endoderm to a pulmonary fate in Xenopus laevis", "type": "publication", "publication_date": "2025-05-07", "publisher": "CaltechDATA", "doi": "10.22002/m6zye-6vx19", "cite_using_url": "https://data.caltech.edu/records/m6zye-6vx19", "abstract": "Protein alignment of Human, X.laevis NKX2-1", "author_list": "Hyatt, Brian A" }, { "title": "Text: Faster genetic mapping of complex traits in C. elegans", "type": "publication", "publication_date": "2025-04-01", "publisher": "CaltechDATA", "doi": "10.22002/g9syn-e7837", "cite_using_url": "https://data.caltech.edu/records/g9syn-e7837", "abstract": "Response to reviewer", "author_list": "Zdraljevic, Stefan" }, { "title": "Text: rab-33 is not required for cuticle integrity in Caenorhabditis elegans", "type": "publication", "publication_date": "2025-03-16", "publisher": "CaltechDATA", "doi": "10.22002/kb69a-3m263", "cite_using_url": "https://data.caltech.edu/records/kb69a-3m263", "abstract": "Sequence file for axr2 edit. Please download a plasmid editor to view the file.", "author_list": "El Bejjani, Rachid" }, { "title": "The Total Carbon Column Observing Network's GGG2020 Data Version: Data Quality, Comparison with GGG2014, and Future Outlook", "type": "publication", "publication_date": "2025-02-07", "publisher": "CaltechDATA", "doi": "10.14291/TCCON.GGG2020.DOCUMENTATION.R1", "cite_using_url": "https://data.caltech.edu/records/hb0tk-c1513", "abstract": "New atmospheric gas retrievals using the GGG2020 version of the Total Carbon Column Observing Network (TCCON) dataset are significantly improved compared with the previous GGG2014 data version. The GGG2020 retrievals have lower variability across the network, better spectral fits, and smaller biases. The exception to this is XCH4 , which is, on average across the network, 5.3 ppb lower in GGG2020 than in GGG2014, a difference we mostly attribute to the a priori profiles used to perform the scaling. We discuss the remaining biases and corrections, the TCCON approach of identifying, quantifying, and minimizing biases, and suggest future work to further minimize the biases. The GGG2020 TCCON data are available from the TCCON archive at http://tccondata.org.", "author_list": "Wunch, D. and Laughner, J., el al." }, { "title": "Text: Replication forks associated with long nuclear actin filaments in mild stress conditions display increased dynamics", "type": "publication", "publication_date": "2024-07-31", "publisher": "CaltechDATA", "doi": "10.22002/x5gxk-2xk32", "cite_using_url": "https://data.caltech.edu/records/x5gxk-2xk32", "abstract": "Extended data script 1. This script enables automated pre-processing of focus positional data for MSD analyses. The input is an Excel file extracted from Imaris ('Detailed'.csv), and re-ordered by track ID. In this file, the positional data for each focus are shown for subsequent time points, and followed by the next focus. The script creates separate files, one for each focus, already formatted for MSD analyses, i.e. with time points starting from 001 in the first column and XYZ coordinates in the 3 subsequent columns. The resulting set of files is entered as is a previously published script for MSD calculation (Caridi et al. 2018b).", "author_list": "Merigliano, Chiara" }, { "title": "Text: Physical presence of chemical synapses is necessary for turning behavior of anterograde synaptic vesicles at the branch point of PLM neurons in C. elegans", "type": "publication", "publication_date": "2024-06-25", "publisher": "CaltechDATA", "doi": "10.22002/x9mw9-bds71", "cite_using_url": "https://data.caltech.edu/records/x9mw9-bds71", "abstract": "Legend and caption for Extended Figure1", "author_list": "Vasudevan, Amruta" }, { "title": "Text: Identifying Ciliary Proteins in Mammalian Retinas using a Gentle Extraction Method", "type": "publication", "publication_date": "2024-06-13", "publisher": "CaltechDATA", "doi": "10.22002/qjwch-e0t24", "cite_using_url": "https://data.caltech.edu/records/qjwch-e0t24", "abstract": "Identifying Ciliary Proteins", "author_list": "Fredrick, Adeline S." }, { "title": "Text: A DTC morphometrics package for quantification of complex and variable cellular morphology using ImageJ", "type": "publication", "publication_date": "2024-05-20", "publisher": "CaltechDATA", "doi": "10.22002/g04bh-7br78", "cite_using_url": "https://data.caltech.edu/records/g04bh-7br78", "abstract": "User Manual", "author_list": "Hubbard, E. Jane Albert" }, { "title": "Text: A DTC morphometrics package for quantification of complex and variable cellular morphology using ImageJ", "type": "publication", "publication_date": "2024-05-20", "publisher": "CaltechDATA", "doi": "10.22002/ya1gg-j4484", "cite_using_url": "https://data.caltech.edu/records/ya1gg-j4484", "abstract": "Macro file", "author_list": "Hubbard, E. Jane Albert" }, { "title": "Text: The Alpha-Ketoacid Dehydrogenase Complexes of Drosophila melanogaster.", "type": "publication", "publication_date": "2024-04-27", "publisher": "CaltechDATA", "doi": "10.22002/vpate-7c171", "cite_using_url": "https://data.caltech.edu/records/vpate-7c171", "abstract": "OMIM phenotype-gene relationships for genes encoding subunits of the human AKDHCs.", "author_list": "Marygold, Steven J" }, { "title": "Text: The Alpha-Ketoacid Dehydrogenase Complexes of Drosophila melanogaster.", "type": "publication", "publication_date": "2024-04-27", "publisher": "CaltechDATA", "doi": "10.22002/9ampc-7df66", "cite_using_url": "https://data.caltech.edu/records/9ampc-7df66", "abstract": "Current GO terms relevant to the complexes and catalytic activities shown in Table 1, following their revision. Entries are taken from the go-basic.obo file (data-version: releases/2024-03-28) obtained from http://current.geneontology.org/ontology/go-basic.obo.", "author_list": "Marygold, Steven J" }, { "title": "Text: Secondary analysis of Staphylococcus aureus whole genomes reveals diverse antimicrobial resistance profiles", "type": "publication", "publication_date": "2024-04-25", "publisher": "CaltechDATA", "doi": "10.22002/f3csp-ahq16", "cite_using_url": "https://data.caltech.edu/records/f3csp-ahq16", "abstract": "FAIR-compliant Metadata for Assemblies of Six S. aureus genomes.", "author_list": "Pickett, Brett E" }, { "title": "Report: TCCON GGG2020 switch to GEOS IT met products", "type": "publication", "publication_date": "2024-04-22", "publisher": "CaltechDATA", "doi": "10.14291/tccon.ggg2020.report.geosit-change", "cite_using_url": "https://data.caltech.edu/records/hhxye-tav30", "abstract": "The GGG2020 TCCON data product relies on the Goddard GEOS product for a priori meteorological information. In particular, it was developed with the GEOS FP-IT (Forward Processing for Instrument Teams) product, as we required the longer record of FP-IT (circa 2000 on) compared to the more recent FP product (circa 2013 on). In 2023, we were informed that the FP-IT product would be succeeded by the GEOS IT product. Due to the effort required to perform a full reprocessing of the TCCON data set (\u223c 30 sites with records up to 10 years long), it is not practical at this time to redo the GGG2020 retrievals with the GEOS IT input data. Therefore, we have made arrangements to switch our retrievals over to the GEOS IT product starting at midnight UTC, 1 Apr 2024. This date was chosen to coincide with the switch of OCO-2 and -3 processing to also use GEOS IT, rather than GEOS FP-IT. This document describes the testing done to quantify the impact this change will have on the GGG2020 data product.
", "author_list": "Laughner, Joshua L. and Roehl, Coleen M., el al." } ]