cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/25545643
title: Characteristics of <em>Mycobacterium avium </em>Biofilms and Implications of Biofilm Growth for Pathogenesis

description: Pulmonary infections with Mycobacterium avium subs. Hominissuis occur in susceptible individuals following exposure to the bacterium in the environment, where it often persists in biofilms. M. avium is able to survive and grow in many conditions, placing the opportunistic pathogen in frequent proximity to humans. Understanding of M. avium biofilms and implications of biofilm growth on subsequent pathogenesis is limited. One specific limitation is the use of different in vitro models to characterize biofilm development in different studies, leading to uncertainty about whether findings are characteristic of M. avium biofilms in general or whether they are specific to a given model. To elucidate similarities and differences between biofilms formed using different methods, we made a parallel comparison of in vitro biofilm ultrastructure, extracellular matrix (ECM) composition, and drug susceptibility of biofilm resident bacteria, using two published methods to generate biofilms. To understand transcriptional adaptations in M. avium during residence in a biofilm and following engulfment by macrophages, we undertook the first study of global differential gene expression in M. avium using RNAseq and used aerosol infections of mice with M. avium grown in planktonic culture or in a biofilm to assess the effect of biofilm growth on infectivity. Taken together, the findings presented in this dissertation indicate that the mechanism of biofilm formation in M. avium, including patterns of gene expression, varies under different environmental conditions. However, some characteristics may be common to M. avium biofilms, including the production and export of cellulose, increased antibiotic resistance, and increased expression of certain genes. While growth in a biofilm may cause patterns of expression in some genes that are similar to those observed during infection of macrophages, we did not observe a clear benefit for biofilm derived cells in establishing and persisting in lungs or tracheae in our mouse infection model.
DOI: 10.7274/25545643.v1
title: Characteristics of <em>Mycobacterium avium </em>Biofilms and Implications of Biofilm Growth for Pathogenesis

description: Pulmonary infections with Mycobacterium avium subs. Hominissuis occur in susceptible individuals following exposure to the bacterium in the environment, where it often persists in biofilms. M. avium is able to survive and grow in many conditions, placing the opportunistic pathogen in frequent proximity to humans. Understanding of M. avium biofilms and implications of biofilm growth on subsequent pathogenesis is limited. One specific limitation is the use of different in vitro models to characterize biofilm development in different studies, leading to uncertainty about whether findings are characteristic of M. avium biofilms in general or whether they are specific to a given model. To elucidate similarities and differences between biofilms formed using different methods, we made a parallel comparison of in vitro biofilm ultrastructure, extracellular matrix (ECM) composition, and drug susceptibility of biofilm resident bacteria, using two published methods to generate biofilms. To understand transcriptional adaptations in M. avium during residence in a biofilm and following engulfment by macrophages, we undertook the first study of global differential gene expression in M. avium using RNAseq and used aerosol infections of mice with M. avium grown in planktonic culture or in a biofilm to assess the effect of biofilm growth on infectivity. Taken together, the findings presented in this dissertation indicate that the mechanism of biofilm formation in M. avium, including patterns of gene expression, varies under different environmental conditions. However, some characteristics may be common to M. avium biofilms, including the production and export of cellulose, increased antibiotic resistance, and increased expression of certain genes. While growth in a biofilm may cause patterns of expression in some genes that are similar to those observed during infection of macrophages, we did not observe a clear benefit for biofilm derived cells in establishing and persisting in lungs or tracheae in our mouse infection model.
DOI: 10.7274/26211122
title: Examining the Impact of <em>Enteroccocus faecalis</em> on <em>Pseudomonas aeruginosa</em> Metabolism and Behavior

description: Pseudomonas aeruginosa is an opportunistic pathogen commonly found in a variety of infection sites, namely the lungs of those with cystic fibrosis. A flexible carbon metabolism and robust biofilm formation are fundamental to P. aeruginosa's ability to colonize and adapt to many environments. In addition to its adaptability, P. aeruginosa also harbors an arsenal of virulence factors that allow it to outcompete other bacterial species in polymicrobial infections. While competitive interactions between P. aeruginosa and staphylococcus aureus have been the most well-characterized in the cystic fibrosis lung, not as much attention has been given to interactions with other bacterial species that have also been identified in infections with P. aeruginosa. One bacterium in particular, Enterococcus faecalis, has been frequently co-isolated with P. aeruginosa in many infection sites. Little research has been done to investigate interactions between these two bacteria. Previous research identified both species as present in prosthetic joint infections. Here, I show that E. faecalis can impact P. aeruginosa's metabolism and behavior in both liquid and surface growth. This work highlights the importance of characterizing interspecies interactions in a variety of growth conditions, as nutrient availability and specificity can shift the outcomes for each bacterium. 

My research shows that E. faecalis can survive in coculture with P. aeruginosa in part by dampening the P. aeruginosa alkyl quinolone (AQ) response, an important component of P. aeruginosa's competition with other bacteria. Additionally, I show that E. faecalis can alter pyocyanin production, a significant P. aeruginosa virulence factor. I identified a metabolite from E. faecalis, L-ornithine, which is key to mediating this interaction. L-ornithine alone can also diminish P. aeruginosa AQ response and pyocyanin production. I also further studied the effect of L-ornithine on P. aeruginosa growth and behavior. Despite a limited ability to utilize L-ornithine as a carbon or nitrogen source, P. aeruginosa growth is increased when the amino acid is added to minimal medium containing hexose and pentose sugars. L-ornithine also impacted P. aeruginosa surface growth and motility by altering the AQ production and the RhlR/I quorum sensing system. 

Lastly, I determined that E. faecalis can promote the growth of P. aeruginosa when grown in media containing sugars not metabolized by P. aeruginosa, such as ribose, arabinose, and maltose. This increase in growth is observed in both planktonic and surface growth and is not contact-dependent. Despite L-ornithine from E. faecalis being important for other interactions with P. aeruginosa, it does not seem to play a significant role in these interactions centered around sugar metabolism.
DOI: 10.7274/26211122.v1
title: Examining the Impact of <em>Enteroccocus faecalis</em> on <em>Pseudomonas aeruginosa</em> Metabolism and Behavior

description: Pseudomonas aeruginosa is an opportunistic pathogen commonly found in a variety of infection sites, namely the lungs of those with cystic fibrosis. A flexible carbon metabolism and robust biofilm formation are fundamental to P. aeruginosa's ability to colonize and adapt to many environments. In addition to its adaptability, P. aeruginosa also harbors an arsenal of virulence factors that allow it to outcompete other bacterial species in polymicrobial infections. While competitive interactions between P. aeruginosa and staphylococcus aureus have been the most well-characterized in the cystic fibrosis lung, not as much attention has been given to interactions with other bacterial species that have also been identified in infections with P. aeruginosa. One bacterium in particular, Enterococcus faecalis, has been frequently co-isolated with P. aeruginosa in many infection sites. Little research has been done to investigate interactions between these two bacteria. Previous research identified both species as present in prosthetic joint infections. Here, I show that E. faecalis can impact P. aeruginosa's metabolism and behavior in both liquid and surface growth. This work highlights the importance of characterizing interspecies interactions in a variety of growth conditions, as nutrient availability and specificity can shift the outcomes for each bacterium. 

My research shows that E. faecalis can survive in coculture with P. aeruginosa in part by dampening the P. aeruginosa alkyl quinolone (AQ) response, an important component of P. aeruginosa's competition with other bacteria. Additionally, I show that E. faecalis can alter pyocyanin production, a significant P. aeruginosa virulence factor. I identified a metabolite from E. faecalis, L-ornithine, which is key to mediating this interaction. L-ornithine alone can also diminish P. aeruginosa AQ response and pyocyanin production. I also further studied the effect of L-ornithine on P. aeruginosa growth and behavior. Despite a limited ability to utilize L-ornithine as a carbon or nitrogen source, P. aeruginosa growth is increased when the amino acid is added to minimal medium containing hexose and pentose sugars. L-ornithine also impacted P. aeruginosa surface growth and motility by altering the AQ production and the RhlR/I quorum sensing system. 

Lastly, I determined that E. faecalis can promote the growth of P. aeruginosa when grown in media containing sugars not metabolized by P. aeruginosa, such as ribose, arabinose, and maltose. This increase in growth is observed in both planktonic and surface growth and is not contact-dependent. Despite L-ornithine from E. faecalis being important for other interactions with P. aeruginosa, it does not seem to play a significant role in these interactions centered around sugar metabolism.
DOI: 10.7274/25527790
title: Roles for Spatiotemporal Intracellular pH Dynamics in Single-Cell Phenotypes and Behaviors

description: Transient changes in intracellular pH (pHi) regulate normal cell behaviors such as proliferation, differentiation, migration, and apoptosis. Most studies investigating pHi-dependent cell behaviors have used population measurements, pH-sensitive dyes, and non-physiological experimental conditions. Thus, the field lacks knowledge of accurate spatiotemporal pHi measurements at the single-cell level. Many pH-dependent cell behaviors are composed of highly-ordered processes that occur on the minutes to hours timescale within an organism, so understanding spatiotemporal pHi dynamics during these processes is crucial. In addition to pHi regulating normal cell biology, dysregulated pHi is an emerging hallmark of cancer. Cancer cells have a constitutively increased pHi compared to normal cells of the same tissue, and this is an early event in cancer development. Prior work has identified that genetic, phenotypic, and extracellular heterogeneity are drivers of cancer progression, but we lack knowledge of the pHi heterogeneity present within a tumor and whether pHi heterogeneity is biologically meaningful. 
Here, we measure spatiotemporal pHi in single cells to improve our understanding of pHi-driven cell behaviors in both normal and cancer cells. We characterize spatial pHi heterogeneity in 2D cell cultures and 3D spheroid models, showing that pHi heterogeneity increases in 3D spheroids compared to 2D cultures. We measure single-cell temporal pHi dynamics on a short timescale (minutes) during growth factor stimulation and on a longer timescale (hours) during cell cycle progression. We determine that single-cell pHi dynamics are correlated with cell cycle phases and additionally find that pHi dynamics are necessary for correct timing of cell cycle phase transitions and successful cell division. Finally, we show that increasing pHi in normal cells can induce cytokinesis defects and cancer-associated phenotypes such as multinucleation, micronuclei, and entosis. We demonstrate the significance of both spatial and temporal pHi dynamics in regulating single-cell biology and lay a framework for future studies to investigate the molecular mechanisms of how single-cell pHi drives single-cell behaviors, especially in cancer.
DOI: 10.7274/25527790.v1
title: Roles for Spatiotemporal Intracellular pH Dynamics in Single-Cell Phenotypes and Behaviors

description: Transient changes in intracellular pH (pHi) regulate normal cell behaviors such as proliferation, differentiation, migration, and apoptosis. Most studies investigating pHi-dependent cell behaviors have used population measurements, pH-sensitive dyes, and non-physiological experimental conditions. Thus, the field lacks knowledge of accurate spatiotemporal pHi measurements at the single-cell level. Many pH-dependent cell behaviors are composed of highly-ordered processes that occur on the minutes to hours timescale within an organism, so understanding spatiotemporal pHi dynamics during these processes is crucial. In addition to pHi regulating normal cell biology, dysregulated pHi is an emerging hallmark of cancer. Cancer cells have a constitutively increased pHi compared to normal cells of the same tissue, and this is an early event in cancer development. Prior work has identified that genetic, phenotypic, and extracellular heterogeneity are drivers of cancer progression, but we lack knowledge of the pHi heterogeneity present within a tumor and whether pHi heterogeneity is biologically meaningful. 
Here, we measure spatiotemporal pHi in single cells to improve our understanding of pHi-driven cell behaviors in both normal and cancer cells. We characterize spatial pHi heterogeneity in 2D cell cultures and 3D spheroid models, showing that pHi heterogeneity increases in 3D spheroids compared to 2D cultures. We measure single-cell temporal pHi dynamics on a short timescale (minutes) during growth factor stimulation and on a longer timescale (hours) during cell cycle progression. We determine that single-cell pHi dynamics are correlated with cell cycle phases and additionally find that pHi dynamics are necessary for correct timing of cell cycle phase transitions and successful cell division. Finally, we show that increasing pHi in normal cells can induce cytokinesis defects and cancer-associated phenotypes such as multinucleation, micronuclei, and entosis. We demonstrate the significance of both spatial and temporal pHi dynamics in regulating single-cell biology and lay a framework for future studies to investigate the molecular mechanisms of how single-cell pHi drives single-cell behaviors, especially in cancer.
DOI: 10.15468/dl.3ew668
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lissotriton vulgaris (Linnaeus, 1758)",
 "Year is 51",
 "Country is Netherlands"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008160-241107131044228/datasets/export for details.
DOI: 10.7274/26131411
title: Oil's Film Empire: ENI, Esso, and Extractive Capitalism's Impact on Italian Commercial Cinema

description: This dissertation is a study of oil company branding as it occurs in the cinema of the Italian Economic Boom (circa 1958-1963). It considers the historical and cultural impact of the oil industry and extractive capitalism on Italian society and its cinematic output, with specific reference to two oil conglomerates that each have a major presence and influence in Italy. The first, ENI (l’Ente Nazionale Idrocarburi), is the majority state-owned Italian energy company that was developed from the fascist era entity AGIP (Azienda Generale Italiana Petroli), and the second, Esso, is the trading name for ExxonMobil in Italy, a branch of the Standard Oil Company of Jersey, established in 1870 by the American tycoon John D. Rockefeller, the richest man in modern history.
Italy’s Economic Miracle, particularly within the parameters of oil company marketing, proposed financial prosperity and access to consumer goods as the keys to happiness. With my examination of oil branding, I interrogate the ways in which the cinema of the Economic Boom depicted life for the Italian people, and I determine how these depictions challenge the conception of economic, industrial, and technological advancement in Italy as beneficial to the individual’s quality of life. Rather than sustaining the Boom’s promises of consumer contentment, this analysis establishes that the films undermine them, with depictions of characters who frequently do not realize their ambitions, and are instead endlessly discontent, oftentimes miserable, even when they experience economic prosperity. 
Consequently, this dissertation deals with two myths: that economic stability and consumption will ensure the individual’s happiness, and that middle class prosperity was accessible to everyone during the Economic Boom. I contend that the films I analyze from the period document the false promise being sold and, in the same text, critique that promise.
DOI: 10.7274/26131411.v1
title: Oil's Film Empire: ENI, Esso, and Extractive Capitalism's Impact on Italian Commercial Cinema

description: This dissertation is a study of oil company branding as it occurs in the cinema of the Italian Economic Boom (circa 1958-1963). It considers the historical and cultural impact of the oil industry and extractive capitalism on Italian society and its cinematic output, with specific reference to two oil conglomerates that each have a major presence and influence in Italy. The first, ENI (l’Ente Nazionale Idrocarburi), is the majority state-owned Italian energy company that was developed from the fascist era entity AGIP (Azienda Generale Italiana Petroli), and the second, Esso, is the trading name for ExxonMobil in Italy, a branch of the Standard Oil Company of Jersey, established in 1870 by the American tycoon John D. Rockefeller, the richest man in modern history.
Italy’s Economic Miracle, particularly within the parameters of oil company marketing, proposed financial prosperity and access to consumer goods as the keys to happiness. With my examination of oil branding, I interrogate the ways in which the cinema of the Economic Boom depicted life for the Italian people, and I determine how these depictions challenge the conception of economic, industrial, and technological advancement in Italy as beneficial to the individual’s quality of life. Rather than sustaining the Boom’s promises of consumer contentment, this analysis establishes that the films undermine them, with depictions of characters who frequently do not realize their ambitions, and are instead endlessly discontent, oftentimes miserable, even when they experience economic prosperity. 
Consequently, this dissertation deals with two myths: that economic stability and consumption will ensure the individual’s happiness, and that middle class prosperity was accessible to everyone during the Economic Boom. I contend that the films I analyze from the period document the false promise being sold and, in the same text, critique that promise.
DOI: 10.15468/dl.gjdgfm
title: Occurrence Download

description: A dataset containing 1629 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myiothlypis leucophrys (Pelzeln, 1868)"
 ]
}

 The dataset includes 1629 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008161-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sec7va
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Troglodytes troglodytes (Linnaeus, 1758)",
 "Year is 52",
 "Country is Netherlands"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008162-241107131044228/datasets/export for details.
DOI: 10.15468/dl.xgd7tu
title: Occurrence Download

description: A dataset containing 817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.515 7.347,-74.781 7.347,-74.781 9.448,-76.515 9.448,-76.515 7.347))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cordia alliodora (Ruiz & Pav.) Oken"
 ]
}

 The dataset includes 817 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008163-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c6k8ng
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriotheca ruizii (K.Schum.) A.Robyns"
 ]
}

 The dataset includes 220 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008164-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7zebr
title: Occurrence Download

description: A dataset containing 1056 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "CoordinateUncertaintyInMeters 1060.0-1000000.0",
 "Country is United States of America",
 "Geometry POLYGON((-126.18939 10.63062,-61.53545 10.63062,-61.53545 49.35665,-126.18939 49.35665,-126.18939 10.63062))",
 "TaxonKey is Reynoutria japonica Houtt."
 ]
}

 The dataset includes 1056 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008165-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxgvst
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dendrocopos major (Linnaeus, 1758)",
 "Year is 52",
 "Country is Netherlands"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008166-241107131044228/datasets/export for details.
DOI: 10.15468/dl.d5wtj6
title: Occurrence Download

description: A dataset containing 2545940 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Denmark",
 "OccurrenceStatus is Present",
 "CoordinateUncertaintyInMeters is less than 50000",
 "Year is 2023",
 "DecimalLongitude is greater than or equal to 7.0",
 "DecimalLongitude is less than or equal to 15.5",
 "DecimalLatitude is greater than or equal to 54.5",
 "DecimalLatitude is less than or equal to 58.0"
 ]
}

 The dataset includes 2545940 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008145-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ww88d8
title: Occurrence Download

description: A dataset containing 15842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Cassia fistula L."
 ]
}

 The dataset includes 15842 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008167-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.