cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/28716458
title: Innovative Approaches and Tool Development for Proteomics Data Analysis: Applications Across Diverse Biological Systems

description: Bottum up proteomics (BUP) is a powerful analytical technique that involves digesting complex protein mixtures into peptides and analyzing them with liquid chromatography and tandem mass spectrometry to identify and quantify many proteins simultaneously. This produces massive multidimensional datasets which require informatics tools to analyze. The landscape of software tools for BUP analysis is vast and complex, and often custom programs and scripts are required to answer biological questions of interest in any given experiment. 

This dissertation introduces novel methods and tools for analyzing BUP experiments and applies those methods to new samples. First, PrIntMap-R, a custom application for intraprotein intensity mapping, is developed and validated. This application is the first open-source tool to allow for statistical comparisons of peptides within a protein sequence along with quantitative sequence coverage visualization. Next, innovative sample preparation techniques and informatics methods are applied to characterize MUC16, a key ovarian cancer biomarker. This includes the proteomic validation of a novel model of MUC16 differing from the dominant isoform reported in literature. Shifting to bacterial studies, custom differential expression workflows are employed to investigate the role of virulence lipids in mycobacterial protein secretion by analyzing mutant strains of mycobacteria. This work links lipid presence and virulence factor secretion for the first time. Building on these efforts, OnePotN??TA, a labeling technique enabling quantification of N-terminal acetylation in mycobacterial samples, introduced. This method is the first technique to simultaneously quantify protein and N-terminal acetylation abundance using bottom-up proteomics, advancing the field of post-translational modification quantification. This project resulted in the identification of 37 new putative substrates for an N-acetyltransferase, three of which have since been validated biochemically. These tools and methodologies are further applied to various biological research areas, including breast cancer drug characterization and insect saliva analysis to perform the first proteomic studies of their kind with these respective treatments and samples. Additionally, a project focused on teaching programming skills relevant to analytical chemistry is presented. Collectively, this work enhances the analytical capabilities of bottom-up proteomics, providing novel tools and methodologies that advance protein characterization, post-translational modification analysis, and biological discovery across diverse research areas.
DOI: 10.7274/28716458.v1
title: Innovative Approaches and Tool Development for Proteomics Data Analysis: Applications Across Diverse Biological Systems

description: Bottum up proteomics (BUP) is a powerful analytical technique that involves digesting complex protein mixtures into peptides and analyzing them with liquid chromatography and tandem mass spectrometry to identify and quantify many proteins simultaneously. This produces massive multidimensional datasets which require informatics tools to analyze. The landscape of software tools for BUP analysis is vast and complex, and often custom programs and scripts are required to answer biological questions of interest in any given experiment. 

This dissertation introduces novel methods and tools for analyzing BUP experiments and applies those methods to new samples. First, PrIntMap-R, a custom application for intraprotein intensity mapping, is developed and validated. This application is the first open-source tool to allow for statistical comparisons of peptides within a protein sequence along with quantitative sequence coverage visualization. Next, innovative sample preparation techniques and informatics methods are applied to characterize MUC16, a key ovarian cancer biomarker. This includes the proteomic validation of a novel model of MUC16 differing from the dominant isoform reported in literature. Shifting to bacterial studies, custom differential expression workflows are employed to investigate the role of virulence lipids in mycobacterial protein secretion by analyzing mutant strains of mycobacteria. This work links lipid presence and virulence factor secretion for the first time. Building on these efforts, OnePotN??TA, a labeling technique enabling quantification of N-terminal acetylation in mycobacterial samples, introduced. This method is the first technique to simultaneously quantify protein and N-terminal acetylation abundance using bottom-up proteomics, advancing the field of post-translational modification quantification. This project resulted in the identification of 37 new putative substrates for an N-acetyltransferase, three of which have since been validated biochemically. These tools and methodologies are further applied to various biological research areas, including breast cancer drug characterization and insect saliva analysis to perform the first proteomic studies of their kind with these respective treatments and samples. Additionally, a project focused on teaching programming skills relevant to analytical chemistry is presented. Collectively, this work enhances the analytical capabilities of bottom-up proteomics, providing novel tools and methodologies that advance protein characterization, post-translational modification analysis, and biological discovery across diverse research areas.
DOI: 10.5281/zenodo.14398053
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset and analyses for manuscript Hormonal plasticity to food restriction is heritable

Please see readme file for more information. 

Updated analysis file (.rmd) in version 3. Please refer to ver2 for readme and datasets.
DOI: 10.5281/zenodo.8377792
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset for manuscript Hormonal plasticity to food restriction is heritable Please see readme file for more information.
DOI: 10.5281/zenodo.12697746
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset for manuscript Hormonal plasticity to food restriction is heritable


Please see readme file for more information.
DOI: 10.5281/zenodo.14502781
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset and analyses for manuscript Hormonal plasticity to food restriction is heritable

Please see readme file for more information. 

Updated analysis file (.rmd) in version 3. Please refer to ver2 for readme and datasets.
DOI: 10.5281/zenodo.15132797
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset and analyses for manuscript Hormonal plasticity to food restriction is heritable

Please see readme file for more information. 

Updated analysis file (.rmd) in version 5. Please refer to ver2 and ver1 for readme and datasets.
DOI: 10.5281/zenodo.8377791
title: Dataset for Hormonal plasticity to food restriction is heritable

description: Dataset and analyses for manuscript Hormonal plasticity to food restriction is heritable

Please see readme file for more information. 

Updated analysis file (.rmd) in version 5. Please refer to ver2 and ver1 for readme and datasets.
DOI: 10.15468/dl.dfvy82
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Picea mexicana Martínez"
 ]
}

 The dataset includes 23 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002504-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/5072
title: taxallnomy
DOI: 10.25318/4210007501-fra
title: Fournisseurs de services de garde d’enfants en centre ayant des employés rémunérés, selon le rôle, mars 2024, Canada

description: Proportion, moyenne et nombre d’employés rémunérés dans les services de garde d’enfants en centre, y compris le nombre total et le nombre moyen d’employés de supervision rémunérés, d’employés sans fonctions de supervision et de membres du personnel de soutien selon le statut d’employé à temps plein, à temps partiel, occasionnel, sur appel ou en tant que personnel d’approvisionnement, Canada.
DOI: 10.7274/28665866
title: An Evaluation of the Presence and Persistence of Viruses in Varying Water Matrices

description: A majority of sewage worldwide enters the environment untreated, creating a global health problem. Understanding and characterizing the presence and persistence of enteric viruses is critical to preserve public health, inform mitigation techniques, and feed risk assessment analyses. The main motivation of the work described in this dissertation is to characterize the inactivation kinetics under different conditions, specifically for human norovirus and Lassa virus. This dissertation investigates the presence and persistence of pathogenic viruses in water to inform best practices for water quality management. The four main objectives addressed in this dissertation were to (1) determine the persistence of viable human norovirus and associated RNA in different water sources, (2) understand the heat inactivation kinetics of human norovirus compared to surrogate MS2 bacteriophage, (3) evaluate the stability of infectious Lassa virus in wastewater and surfaces and chlorine inactivation, and (4) characterize the concentration efficacy of novel Nanotrap Microbiome Particles. Ultimately, the results from this research will improve risk assessments to protect public health and better wastewater-based epidemiology methods to track viral pathogens of interest.

The research presented in this dissertation addresses critical gaps in viral persistence, inactivation, and detection in various water environments and treatment scenarios, offering significant implications for public health. The work with viable human norovirus provides the first robust assessment of the persistence in different water matrices, filling a historical gap that was due to a lack of cell culture systems. This study, along with the results from the heat inactivation study, emphasizes the limitations of molecular methods in representing viable virus decay, and therefore, the associated infectious risk, which will guide future efforts in developing more accurate risk assessment models. Furthermore, the environmental persistence of Lassa virus results are the first of their kind, which will inform future strategies to mitigate environmental transmission in real-world scenarios.
The heat inactivation work for viable human norovirus and MS2 bacteriophage and the chemical disinfectant treatment with Lassa virus highlight effective treatment strategies for both viruses. These results can inform treatment protocols for heat inactivation and disinfection to safeguard public health. Using Nanotrap Microbiome Particles in wastewater as a viral concentration method underscores the potential of advanced concentration technologies in future wastewater surveillance workflows. The results provides a pathway for optimizing surveillance pipelines, ultimately improving our ability to monitor and respond to viral pathogen spread throughout our communities. Together, the findings of this dissertation offers a comprehensive framework to improve environmental monitoring, public health interventions, and viral risk assessments and management strategies.
DOI: 10.7274/28665866.v1
title: An Evaluation of the Presence and Persistence of Viruses in Varying Water Matrices

description: A majority of sewage worldwide enters the environment untreated, creating a global health problem. Understanding and characterizing the presence and persistence of enteric viruses is critical to preserve public health, inform mitigation techniques, and feed risk assessment analyses. The main motivation of the work described in this dissertation is to characterize the inactivation kinetics under different conditions, specifically for human norovirus and Lassa virus. This dissertation investigates the presence and persistence of pathogenic viruses in water to inform best practices for water quality management. The four main objectives addressed in this dissertation were to (1) determine the persistence of viable human norovirus and associated RNA in different water sources, (2) understand the heat inactivation kinetics of human norovirus compared to surrogate MS2 bacteriophage, (3) evaluate the stability of infectious Lassa virus in wastewater and surfaces and chlorine inactivation, and (4) characterize the concentration efficacy of novel Nanotrap Microbiome Particles. Ultimately, the results from this research will improve risk assessments to protect public health and better wastewater-based epidemiology methods to track viral pathogens of interest.

The research presented in this dissertation addresses critical gaps in viral persistence, inactivation, and detection in various water environments and treatment scenarios, offering significant implications for public health. The work with viable human norovirus provides the first robust assessment of the persistence in different water matrices, filling a historical gap that was due to a lack of cell culture systems. This study, along with the results from the heat inactivation study, emphasizes the limitations of molecular methods in representing viable virus decay, and therefore, the associated infectious risk, which will guide future efforts in developing more accurate risk assessment models. Furthermore, the environmental persistence of Lassa virus results are the first of their kind, which will inform future strategies to mitigate environmental transmission in real-world scenarios.
The heat inactivation work for viable human norovirus and MS2 bacteriophage and the chemical disinfectant treatment with Lassa virus highlight effective treatment strategies for both viruses. These results can inform treatment protocols for heat inactivation and disinfection to safeguard public health. Using Nanotrap Microbiome Particles in wastewater as a viral concentration method underscores the potential of advanced concentration technologies in future wastewater surveillance workflows. The results provides a pathway for optimizing surveillance pipelines, ultimately improving our ability to monitor and respond to viral pathogen spread throughout our communities. Together, the findings of this dissertation offers a comprehensive framework to improve environmental monitoring, public health interventions, and viral risk assessments and management strategies.
DOI: 10.15468/dl.xv7nhj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lachnus tatakaensis Takahashi, 1937",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002508-250402121839773/datasets/export for details.
DOI: 10.15468/dl.2wcmr3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizaphis minuta (van der Goot, 1917)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002507-250402121839773/datasets/export for details.
DOI: 10.15468/dl.hqkyqd
title: Occurrence Download

description: A dataset containing 185985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-73.8827 11.30104,-73.96754 11.34731,-74.07123 11.35446,-74.22349 11.32618,-74.19121 11.27504,-74.13179 11.25933,-74.03838 11.26733,-73.98896 11.2939,-73.9244 11.26476,-73.8847 11.27504,-73.8827 11.30104))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 185985 records from 241 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002487-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7274/28681343
title: Capillary Electrophoretic Methods for Protein and Microorganism Separations

description: Capillary electrophoresis (CE) is an analytical technique for the separation of molecules in a capillary under an applied electric field. CE generates high resolution separations in relatively short analysis times, with low reagent, and sample volume requirements. Two of the most common modes of CE are capillary zone electrophoresis (CZE) and capillary isoelectric focusing (cIEF). CZE separates analytes based on their size-to-charge ratios. It is the most common mode of CE due to its ability to separate molecules with high resolution and relative simplicity. cIEF is an orthogonal technique that separates analytes based on their isoelectric point (pI), which is the pH at which the average net charge of the molecule is zero. CZE and cIEF offer distinct advantages for high resolution separations of molecules in numerous fields including pharmaceutical, proteomic, genomic, and microbial analysis. CE instrumentation typically employs optical detection methods. However, optical detectors limit the information that you can obtain about the analytes. In this work, I improve instrumentation and methods for CE separations with two alternative detection schemes. (1) I developed an in-line cIEF interface to remove the concentration of ampholytes required for cIEF prior to MS detection. With the interface, an over 90% increase in area under the curve protein signal was observed. (2) I developed methods that enabled separation and collection of intact microorganisms for subsequent offline detection and analyses of cultured and uncultured species. These data represent significant improvement vs. existing methods. These efforts highlight the utility of CE for a diverse range of analytes with enhanced sensitivity and characterization.
DOI: 10.7274/28681343.v1
title: Capillary Electrophoretic Methods for Protein and Microorganism Separations

description: Capillary electrophoresis (CE) is an analytical technique for the separation of molecules in a capillary under an applied electric field. CE generates high resolution separations in relatively short analysis times, with low reagent, and sample volume requirements. Two of the most common modes of CE are capillary zone electrophoresis (CZE) and capillary isoelectric focusing (cIEF). CZE separates analytes based on their size-to-charge ratios. It is the most common mode of CE due to its ability to separate molecules with high resolution and relative simplicity. cIEF is an orthogonal technique that separates analytes based on their isoelectric point (pI), which is the pH at which the average net charge of the molecule is zero. CZE and cIEF offer distinct advantages for high resolution separations of molecules in numerous fields including pharmaceutical, proteomic, genomic, and microbial analysis. CE instrumentation typically employs optical detection methods. However, optical detectors limit the information that you can obtain about the analytes. In this work, I improve instrumentation and methods for CE separations with two alternative detection schemes. (1) I developed an in-line cIEF interface to remove the concentration of ampholytes required for cIEF prior to MS detection. With the interface, an over 90% increase in area under the curve protein signal was observed. (2) I developed methods that enabled separation and collection of intact microorganisms for subsequent offline detection and analyses of cultured and uncultured species. These data represent significant improvement vs. existing methods. These efforts highlight the utility of CE for a diverse range of analytes with enhanced sensitivity and characterization.
DOI: 10.6084/m9.figshare.28724600
title: Fichas técnicas. Indicadores Vía de Atención Integrada para la salud materna, neonatal e infantil.

description: Fichas técnicas de indicadores que se evaluaron en el proyecto "Innovación para la mejora de la calidad: Diseño e implementación de Vías Clínicas para una atención materna, neonatal e infantil integral y coordinada”, financiado por el entonces Consejo Nacional de Ciencia y Tecnología (CONACYT) FORDECYT-PRONACES/1564484/2020.
DOI: 10.5281/zenodo.15126995
title: Data Set Accompanying: Comparison of Gap-Enhanced Raman Tags and Nanoparticle Aggregates with Polarization Dependent Super-Resolution Spectral SERS Imaging

description: Raw data files and extracted data used in the published manuscript.  

Coordinates of particles analyzed in tiff stacks:

BPA1, coordinates: y = 335:343, x = 280

BPA2, coordinates: y = 49:59, x = 250

BPA3, coordinates: y = 121:131, x = 170

BPG1, coordinates: y = 325:336, x = 270

BPG2 coordinates: y = 152:162, x = 220

BPG3 coordinates: y = 365:374, x = 200
DOI: 10.5281/zenodo.15126996
title: Data Set Accompanying: Comparison of Gap-Enhanced Raman Tags and Nanoparticle Aggregates with Polarization Dependent Super-Resolution Spectral SERS Imaging

description: Raw data files and extracted data used in the published manuscript.  

Coordinates of particles analyzed in tiff stacks:

BPA1, coordinates: y = 335:343, x = 280

BPA2, coordinates: y = 49:59, x = 250

BPA3, coordinates: y = 121:131, x = 170

BPG1, coordinates: y = 325:336, x = 270

BPG2 coordinates: y = 152:162, x = 220

BPG3 coordinates: y = 365:374, x = 200
DOI: 10.5517/ccdc.csd.cc2kwg1z
title: CCDC 2379871: Experimental Crystal Structure Determination

description: Related Article: Qurat Ul Ain, Iqubal Singh, Kamaldeep Paul, Ray J. Butcher, Rekha Sharma|2025|J.Mol.Struct.|1335|141846|doi:10.1016/j.molstruc.2025.141846
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2kwg20
title: CCDC 2379872: Experimental Crystal Structure Determination

description: Related Article: Qurat Ul Ain, Iqubal Singh, Kamaldeep Paul, Ray J. Butcher, Rekha Sharma|2025|J.Mol.Struct.|1335|141846|doi:10.1016/j.molstruc.2025.141846
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lms12
title: CCDC 2402284: Experimental Crystal Structure Determination

description: Related Article: Luan-Ting Wu, Honglin Diao, Yi Wu, Jun-Sheng Shu, Zeng-Yang He, Peng Xu, Si-Qi Chen, Pinhua Li, Ze Zhang, Hui Xu|2025|J.Org.Chem.|90|4046|doi:10.1021/acs.joc.5c00026
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.