cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12828000
title: Supplementary Table 4 from New ancient Eastern European <i>Yersinia pestis</i> genomes illuminate the dispersal of plague in Europe

description: <i>Yersinia pestis</i>, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of <i>Y. pestis</i> have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled <i>Y. pestis</i> genomes from Eastern Europe (Poland and Southern Russia), dating to the fifteenth and eighteenth centuries AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern <i>Y. pestis</i> strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial <i>Y. pestis</i> genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning <i>Y. pestis</i> transmission and its evolutionary history in Eastern Europe.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12828000.v1
title: Supplementary Table 4 from New ancient Eastern European <i>Yersinia pestis</i> genomes illuminate the dispersal of plague in Europe

description: <i>Yersinia pestis</i>, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of <i>Y. pestis</i> have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled <i>Y. pestis</i> genomes from Eastern Europe (Poland and Southern Russia), dating to the fifteenth and eighteenth centuries AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern <i>Y. pestis</i> strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial <i>Y. pestis</i> genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning <i>Y. pestis</i> transmission and its evolutionary history in Eastern Europe.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827982
title: Distribution_Confined_Velocities from Microfluidic monitoring of the growth of individual hyphae in confined environments

description: Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered as promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of <i>Talaromyces helicus</i>, a soil isolate, and of the model fungus <i>Neurospora crassa</i> through parallel microchannels. The distributions of growth velocity obtained for each strain were compared with measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, <i>N. crassa</i> was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for <i>T. helicus</i>. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behaviour of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to address its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
DOI: 10.6084/m9.figshare.12827982.v1
title: Distribution_Confined_Velocities from Microfluidic monitoring of the growth of individual hyphae in confined environments

description: Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered as promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of <i>Talaromyces helicus</i>, a soil isolate, and of the model fungus <i>Neurospora crassa</i> through parallel microchannels. The distributions of growth velocity obtained for each strain were compared with measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, <i>N. crassa</i> was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for <i>T. helicus</i>. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behaviour of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to address its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
DOI: 10.6084/m9.figshare.12827962
title: BED file containing phage, 16S rRNA and rRNA gene regions masked in the Anaerolineaceae sp. oral taxon 439 alignments. from Investigating the demographic history of Japan using ancient oral microbiota

description: While microbial communities in the human body (microbiota) are now commonly associated with health and disease in Industrialised populations, we know very little about how these communities co-evolved with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 BP (years before present) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a key oral species—<i>Anaerolineaceae</i> oral taxa 439. This research represents the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827959
title: Supplementary tables S1-S7 from Investigating the demographic history of Japan using ancient oral microbiota

description: While microbial communities in the human body (microbiota) are now commonly associated with health and disease in Industrialised populations, we know very little about how these communities co-evolved with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 BP (years before present) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a key oral species—<i>Anaerolineaceae</i> oral taxa 439. This research represents the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827945
title: R0186_20170813a_videos

description: Rat 0186, skilled reaching data collected on 8/13/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12827962.v1
title: BED file containing phage, 16S rRNA and rRNA gene regions masked in the Anaerolineaceae sp. oral taxon 439 alignments. from Investigating the demographic history of Japan using ancient oral microbiota

description: While microbial communities in the human body (microbiota) are now commonly associated with health and disease in Industrialised populations, we know very little about how these communities co-evolved with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 BP (years before present) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a key oral species—<i>Anaerolineaceae</i> oral taxa 439. This research represents the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827959.v1
title: Supplementary tables S1-S7 from Investigating the demographic history of Japan using ancient oral microbiota

description: While microbial communities in the human body (microbiota) are now commonly associated with health and disease in Industrialised populations, we know very little about how these communities co-evolved with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 BP (years before present) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a key oral species—<i>Anaerolineaceae</i> oral taxa 439. This research represents the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827942
title: AEM Images

description: AEM Images of Xenopus laevis cortical vesicles in the animal pole egg<br>
DOI: 10.6084/m9.figshare.12827945.v1
title: R0186_20170813a_videos

description: Rat 0186, skilled reaching data collected on 8/13/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12827894
title: TEM Cortical Images

description: TEM images of the entire circumference of the animal poles of a Xenopus laevis egg and embryo<br>
DOI: 10.6084/m9.figshare.12827855
title: XFM Data

description: XFM data of Xenopus laevis egg and embryo cortices. Data acquired at Beamline 2-ID-D at Argonne National Laboratory<br>
DOI: 10.6084/m9.figshare.12827795
title: Astrocyte Phagocytosis Under Shear Flow

description: Phagocytic response of astrocytes in response to shear flow
DOI: 10.6084/m9.figshare.12827786
title: Wellcome clinical trials May 2020

description: Database of clinical trials funded/supported by Wellcome included in grants that were either ongoing at/or awarded after 1<sup>st</sup> May 2018. Data was collected in May 2020.
DOI: 10.6084/m9.figshare.12827855.v1
title: XFM Data

description: XFM data of Xenopus laevis egg and embryo cortices. Data acquired at Beamline 2-ID-D at Argonne National Laboratory<br>
DOI: 10.6084/m9.figshare.12827786.v1
title: Wellcome clinical trials May 2020

description: Database of clinical trials funded/supported by Wellcome included in grants that were either ongoing at/or awarded after 1<sup>st</sup> May 2018. Data was collected in May 2020.
DOI: 10.6084/m9.figshare.12827726
title: Using Machine Learning to Unveil Demographic and Clinical Features of COVID-19 Symptomatic and Asymptomatic Patients

description: Original Dataset
DOI: 10.6084/m9.figshare.12827579
title: Modern and LGM water mass distributions

description: All files are needed to reproduce results and plots using the analysis code (https://github.com/cspencerjones/tracers_LGM)
DOI: 10.6084/m9.figshare.12827726.v1
title: Using Machine Learning to Unveil Demographic and Clinical Features of COVID-19 Symptomatic and Asymptomatic Patients

description: Original Dataset
DOI: 10.6084/m9.figshare.12827579.v1
title: Modern and LGM water mass distributions

description: All files are needed to reproduce results and plots using the analysis code (https://github.com/cspencerjones/tracers_LGM)
DOI: 10.6084/m9.figshare.12827423
title: Table S1. Description of VIPs from Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

description: Over the course of the last several million years of evolution, humans likely have been plagued by hundreds or perhaps thousands of epidemics. Little is known about such ancient epidemics and a deep evolutionary perspective on current pathogenic threats is lacking. The study of past epidemics has typically been limited in temporal scope to recorded history, and in physical scope to pathogens that left sufficient DNA behind, such as <i>Yersinia pestis</i> during the Great Plague. Host genomes, however, offer an indirect way to detect ancient epidemics beyond the current temporal and physical limits. Arms races with pathogens have shaped the genomes of the hosts by driving a large number of adaptations at many genes, and these signals can be used to detect and further characterize ancient epidemics. Here, we detect the genomic footprints left by ancient viral epidemics that took place in the past approximately 50 000 years in the 26 human populations represented in the 1000 Genomes Project. By using the enrichment in signals of adaptation at approximately 4500 host loci that interact with specific types of viruses, we provide evidence that RNA viruses have driven a particularly large number of adaptive events across diverse human populations. These results suggest that different types of viruses may have exerted different selective pressures during human evolution. Knowledge of these past selective pressures will provide a deeper evolutionary perspective on current pathogenic threats.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827399
title: Climatology file for online simulation

description: This file is input as climatology in a simulation of the north Gulf of Mexico.
DOI: 10.6084/m9.figshare.12827423.v1
title: Table S1. Description of VIPs from Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

description: Over the course of the last several million years of evolution, humans likely have been plagued by hundreds or perhaps thousands of epidemics. Little is known about such ancient epidemics and a deep evolutionary perspective on current pathogenic threats is lacking. The study of past epidemics has typically been limited in temporal scope to recorded history, and in physical scope to pathogens that left sufficient DNA behind, such as <i>Yersinia pestis</i> during the Great Plague. Host genomes, however, offer an indirect way to detect ancient epidemics beyond the current temporal and physical limits. Arms races with pathogens have shaped the genomes of the hosts by driving a large number of adaptations at many genes, and these signals can be used to detect and further characterize ancient epidemics. Here, we detect the genomic footprints left by ancient viral epidemics that took place in the past approximately 50 000 years in the 26 human populations represented in the 1000 Genomes Project. By using the enrichment in signals of adaptation at approximately 4500 host loci that interact with specific types of viruses, we provide evidence that RNA viruses have driven a particularly large number of adaptive events across diverse human populations. These results suggest that different types of viruses may have exerted different selective pressures during human evolution. Knowledge of these past selective pressures will provide a deeper evolutionary perspective on current pathogenic threats.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12827336
title: Test_AtacSeq

description: Testing ATAcseq data
DOI: 10.6084/m9.figshare.12827381
title: Boundary file for online simulation

description: This file is input as boundary info in a simulation of the north Gulf of Mexico.
DOI: 10.6084/m9.figshare.12827390
title: New Evidence of State Variation in Medicaid Payment Policies for Dual Medicare-Medicaid Enrollees: Policy Database and Index

description: These data track state Medicaid programs' policies for paying Medicare's cost sharing for low-income individuals who have Medicare and Medicaid ("dual eligibles"). Our database focuses on Medicaid policies for paying the cost sharing for outpatient and physician services covered by the Medicare Part B program. We track state policies longitudinally from 2004-2018 based on information abstracted from online Medicaid policy documents, legal databases, and policy data reported to us by 22 state Medicaid programs. We also developed a Medicaid payment index, which reflects the proportion of the Medicare Part B allowed amount (i.e., price) for physician office visits that providers would expect to be paid per service provided to a dual eligible patient, in aggregate from Medicare and Medicaid, given these state policies. One version of this index reflects payments to physicians who qualified for higher Medicaid fees under the Affordable Care Act's Medicaid Fee Bump (implemented nationally from 2013-14) and one version reflects payments to physicians who were ineligible for the fee bump.<br>Download the attached Excel files to retrieve the database and additional documentation. The compressed folder 'final document library' contains the original source policy documents (in PDF format) that are catalogued in the database.<br><br>More detail about this database and our findings can be found in the article:<br>Roberts ET, Nimgaonkar A, Aarons J, Tomko H, Shartzer A, Zuckerman SB, and James AE. "New Evidence of State Variation in Medicaid Payment Policies for Low-Income Medicare Beneficiaries," <i>Health Services Research</i> 2020 (doi: 10.1111/1475-6773.13545).
DOI: 10.6084/m9.figshare.12827336.v1
title: Test_AtacSeq

description: Testing ATAcseq data
DOI: 10.6084/m9.figshare.12827300
title: R0187_20170919a_videos

description: Rat 0187, skilled reaching data collected on 9/19/2017 in Leventhal laboratory by Alexandra Bova