cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/27626406
title: Making “Scents” of the Baboon Vaginal Microbiome

description: Research on the evolutionary role microbiomes play in their animal hosts has received a great deal of attention over the past few decades. Most of this work has focused on the complex and mutually beneficial relationships between the gut microbiome and animal host. To better understand how these relationships affect animal fitness, research must expand beyond the gut, such as to the reproductive microbiome. The microbial communities in the reproductive tract of animals can play a significant role in host fitness by mediating fertility and pregnancy outcomes and may even play a role in communicating social and reproductive information about their hosts by metabolizing compounds used by the host to communicate olfactorily. This hypothesis was first posited in the 70s as the ‘fermentation hypothesis', yet to date few studies have tested its applicability. To address this gap, my PhD leveraged longitudinal and cross-sectional data on captive and wild primate vaginal odor and microbiomes. I used a solvent-less extraction thermal desorption technique and performed 16S rRNA sequencing to measure the chemical profiles and bacterial compositions of captive and wild primate vaginas, respectively. I then tested whether the chemical composition of vaginal odors and the microbiome were connected, whether they both varied over the ovarian cycle, and whether odors conveyed information about the hosts’ reproductive state by performing behavioral bioassays to measure the response of captive primates to fertile and non-fertile odors. 
I found that the vaginal odor and microbiome were correlated and co-varied over the ovarian cycle in the wild, but not in captivity. I then showed that captive primates differentiated between fertile and non-fertile odors. Additionally, I found that the vaginal odor and microbiome were individually unique in our longitudinal dataset, and that captive primates differentiated between the odors of individual females. My work tentatively confirms that the fermentation hypothesis can be applied to primate communication, while demonstrating that captivity may disrupt the ability of females to convey information relative to fitness. This work also demonstrates the importance of using longitudinal datasets, as individual chemical profiles and microbiomes were highly personalized, which must be accounted for when testing whether host-associated microbiomes affect animal fitness. Overall, my work demonstrates the need to expand beyond the gut to additional bodysites to better understand the fitness consequences of host-associated microbiomes.
DOI: 10.7274/27626406.v1
title: Making “Scents” of the Baboon Vaginal Microbiome

description: Research on the evolutionary role microbiomes play in their animal hosts has received a great deal of attention over the past few decades. Most of this work has focused on the complex and mutually beneficial relationships between the gut microbiome and animal host. To better understand how these relationships affect animal fitness, research must expand beyond the gut, such as to the reproductive microbiome. The microbial communities in the reproductive tract of animals can play a significant role in host fitness by mediating fertility and pregnancy outcomes and may even play a role in communicating social and reproductive information about their hosts by metabolizing compounds used by the host to communicate olfactorily. This hypothesis was first posited in the 70s as the ‘fermentation hypothesis', yet to date few studies have tested its applicability. To address this gap, my PhD leveraged longitudinal and cross-sectional data on captive and wild primate vaginal odor and microbiomes. I used a solvent-less extraction thermal desorption technique and performed 16S rRNA sequencing to measure the chemical profiles and bacterial compositions of captive and wild primate vaginas, respectively. I then tested whether the chemical composition of vaginal odors and the microbiome were connected, whether they both varied over the ovarian cycle, and whether odors conveyed information about the hosts’ reproductive state by performing behavioral bioassays to measure the response of captive primates to fertile and non-fertile odors. 
I found that the vaginal odor and microbiome were correlated and co-varied over the ovarian cycle in the wild, but not in captivity. I then showed that captive primates differentiated between fertile and non-fertile odors. Additionally, I found that the vaginal odor and microbiome were individually unique in our longitudinal dataset, and that captive primates differentiated between the odors of individual females. My work tentatively confirms that the fermentation hypothesis can be applied to primate communication, while demonstrating that captivity may disrupt the ability of females to convey information relative to fitness. This work also demonstrates the importance of using longitudinal datasets, as individual chemical profiles and microbiomes were highly personalized, which must be accounted for when testing whether host-associated microbiomes affect animal fitness. Overall, my work demonstrates the need to expand beyond the gut to additional bodysites to better understand the fitness consequences of host-associated microbiomes.
DOI: 10.15468/dl.hnwewm
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Arachnida Araneae do Museu Nacional (MNRJ ARAC ARAN)",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007994-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7274/26885425
title: Biomolecular Binding Mechanisms at High Temporal and Structural Resolution

description: Biomolecular binding is pervasive in biology and governs all biological process, including DNA replication and immune recognition. Determining binding mechanisms at the atomistic-level is a significant challenge due to experimental and computational limitations. All-atom molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling has shown to be capable of generating binding trajectories in which mechanisms can be curated. In this thesis, molecular dynamics simulations in coordination with WE were implemented to determine the binding mechanism of three systems: (1) Hoechst 33258 (H33258) binding to DNA, (2) daunomycin binding to DNA, and (3) a T cell receptor (TCR) binding to a peptide/major histocompatibility complex (pMHC).

We curated a binding mechanism using 2562 WE-simulated trajectories of H33258 binding to a DNA duplex. Specifically, the initial contacts between H33258 and DNA are driven electrostatically by H33258's positively charged group and the DNA's negatively charged backbone. Following the initial contacts, H33258 forms a hinge-like intermediate with one end in the minor groove of DNA. After hinge state formation, the other end of H33258 swings into the minor groove in a concerted motion and the spine of hydration along the minor groove is dehydrated. 
 
We simulated 469 trajectories of daunomycin binding to a DNA duplex. Throughout the binding process, the DNA strand underwent structural changes, including DNA base pair rise, bending, and minor groove width changes. Post-intercalation, most binding trajectories needed an additional one to five nanoseconds of rearrangement to achieve the bound configuration.

75 binding trajectories of a TCR binding to a pMHC were compiled into a binding mechanism. The initial phase of the binding process consists of contacts being formed, some forming hydrogen bonds. Hydrogen bond lifetimes vary; some persist throughout binding and others are transient. The final phase of the binding process involves water exiting the interface as final contacts form.
DOI: 10.7274/26885425.v1
title: Biomolecular Binding Mechanisms at High Temporal and Structural Resolution

description: Biomolecular binding is pervasive in biology and governs all biological process, including DNA replication and immune recognition. Determining binding mechanisms at the atomistic-level is a significant challenge due to experimental and computational limitations. All-atom molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling has shown to be capable of generating binding trajectories in which mechanisms can be curated. In this thesis, molecular dynamics simulations in coordination with WE were implemented to determine the binding mechanism of three systems: (1) Hoechst 33258 (H33258) binding to DNA, (2) daunomycin binding to DNA, and (3) a T cell receptor (TCR) binding to a peptide/major histocompatibility complex (pMHC).

We curated a binding mechanism using 2562 WE-simulated trajectories of H33258 binding to a DNA duplex. Specifically, the initial contacts between H33258 and DNA are driven electrostatically by H33258's positively charged group and the DNA's negatively charged backbone. Following the initial contacts, H33258 forms a hinge-like intermediate with one end in the minor groove of DNA. After hinge state formation, the other end of H33258 swings into the minor groove in a concerted motion and the spine of hydration along the minor groove is dehydrated. 
 
We simulated 469 trajectories of daunomycin binding to a DNA duplex. Throughout the binding process, the DNA strand underwent structural changes, including DNA base pair rise, bending, and minor groove width changes. Post-intercalation, most binding trajectories needed an additional one to five nanoseconds of rearrangement to achieve the bound configuration.

75 binding trajectories of a TCR binding to a pMHC were compiled into a binding mechanism. The initial phase of the binding process consists of contacts being formed, some forming hydrogen bonds. Hydrogen bond lifetimes vary; some persist throughout binding and others are transient. The final phase of the binding process involves water exiting the interface as final contacts form.
DOI: 10.15468/dl.cbwwue
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is BCCM/IHEM - Fungi Collection: Human & Animal Health",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007995-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zv5jjm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Haematopus ostralegus Linnaeus, 1758",
 "Year is 44",
 "Country is Netherlands"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007996-241107131044228/datasets/export for details.
DOI: 10.5281/zenodo.14074472
title: Web Scraping Universidad de Sevilla

description: Proyecto de Web Scraping con Beautiful Soup (Python) realizado para la asignatura Tipología y ciclo de vida de los datos, del Master en Ciencia de Datos de la UOC.Se aplican las técnicas necesarias para extraer información de la web de la Universidad de Sevilla y generar un dataset con información sobre los grados que ofrece la misma.El dataset generado contiene las siguientes variables:    * grado: nombre del título en cuestión    * rama: rama del conocimiento al que pertenece (Ciencias Sociales, Ciencias de la Salud, Ingeniería..., etc.)    * facultad: centro de la Universidad de Sevilla responsable del título    * duracion: número en años en los que se plantea el título    * creditos: número de créditos necesarios para obtener el título    * oferta: número total de plazas ofertadas por la Universidad de Sevilla el curso anterior    * demanda: número total de veces que se ha solicitado una plaza durante las fases de inscripción
DOI: 10.5281/zenodo.14074473
title: Web Scraping Universidad de Sevilla

description: Proyecto de Web Scraping con Beautiful Soup (Python) realizado para la asignatura Tipología y ciclo de vida de los datos, del Master en Ciencia de Datos de la UOC.Se aplican las técnicas necesarias para extraer información de la web de la Universidad de Sevilla y generar un dataset con información sobre los grados que ofrece la misma.El dataset generado contiene las siguientes variables:    * grado: nombre del título en cuestión    * rama: rama del conocimiento al que pertenece (Ciencias Sociales, Ciencias de la Salud, Ingeniería..., etc.)    * facultad: centro de la Universidad de Sevilla responsable del título    * duracion: número en años en los que se plantea el título    * creditos: número de créditos necesarios para obtener el título    * oferta: número total de plazas ofertadas por la Universidad de Sevilla el curso anterior    * demanda: número total de veces que se ha solicitado una plaza durante las fases de inscripción
DOI: 10.15468/dl.j8we63
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bell Museum algae",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007997-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hwdkps
title: Occurrence Download

description: A dataset containing 3391598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is one of (North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cardinalis cardinalis (Linnaeus, 1758)",
 "Year 2023-2023"
 ]
}

 The dataset includes 3391598 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007952-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6k66wy
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Birds (coll. Bonnetain)",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007998-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69x69v
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bryophyte herbarium, Göttingen (GOET)",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007999-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.su4zdq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vanessa atalanta (Linnaeus, 1758)",
 "Year is 44",
 "Country is Netherlands"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008000-241107131044228/datasets/export for details.
DOI: 10.15468/dl.xkazs5
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyathostegia matthewsii (Benth.) Schery"
 ]
}

 The dataset includes 335 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008001-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8jg94j
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bryophyte herbarium, UiB",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008002-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.823s79
title: Occurrence Download

description: A dataset containing 166551 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Populus nigra L."
 ]
}

 The dataset includes 166551 records from 1738 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007906-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b3rux8
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Silene kigesiensis (R.D.Good) F.Jafari, Oxelman & Rabeler"
 ]
}

 The dataset includes 69 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045936-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2f6j6r
title: Occurrence Download

description: A dataset containing 1130 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acacia stipuligera F.Muell."
 ]
}

 The dataset includes 1130 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038277-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aexbfg
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrence of mammalia relicts at site Icoana"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007717-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bagp7f
title: Occurrence Download

description: A dataset containing 2622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "TaxonKey is Cedrela P.Browne"
 ]
}

 The dataset includes 2622 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045945-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dd2vjk
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lapeirousia kamiesmontana Goldblatt & J.C.Manning"
 ]
}

 The dataset includes 11 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038295-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q75kyx
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Swertia forrestii Harry Sm."
 ]
}

 The dataset includes 47 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045952-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qniehp
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Obovaria olivaria (Rafinesque, 1820)",
 "Country is Canada"
 ]
}

 The dataset includes 50 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007718-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqcyny
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Korshinskia assyriaca (Freyn & Bornm.) Pimenov & Kljuykov"
 ]
}

 The dataset includes 29 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038323-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qmzwd
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nicotiana pauciflora J.Rémy"
 ]
}

 The dataset includes 31 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007718-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4krrb9
title: Occurrence Download

description: A dataset containing 5543 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Syrichtus Boisduval, 1834"
 ]
}

 The dataset includes 5543 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045951-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m33qkq
title: Occurrence Download

description: A dataset containing 523 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lapeirousia anceps (L.f.) Ker Gawl."
 ]
}

 The dataset includes 523 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038228-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r4cpz2
title: Occurrence Download

description: A dataset containing 690 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Mergus squamatus Gould, 1864"
 ]
}

 The dataset includes 690 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045956-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wlezkg
title: Occurrence Download

description: A dataset containing 264 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solanum accrescens Standl. & C.V.Morton"
 ]
}

 The dataset includes 264 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007718-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.