cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22009681.v2
title: Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales

description: Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. <i>Cladonia</i> is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the “true” reindeer lichens, <i>Cladonia</i> subgenus <i>Cladina</i>, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of <i>Cladonia, Pilophorus</i>, and <i>Stereocaulon</i> were consistently larger than those of <i>Lepraria</i> and contained more introns, suggesting a selective pressure in asexual morphology in <i>Lepraria</i> driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from <i>Cladonia ravenelii</i> and <i>Stereocaulon pileatum</i> exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in <i>Lepraria</i>, were diverse and abundant in <i>Cladonia</i>, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with <i>C. rangiferina</i> especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of <i>Cladonia</i> and related genera, allowing future study alongside a wealth of assembled genomes.
DOI: 10.6084/m9.figshare.22197149
title: Characterization of root-associated fungi and reduced plant growth in soils from a New Mexico uranium mine

description: Characterizing the diverse, root-associated fungi in mine wastes can accelerate the development of bioremediation strategies to stabilize heavy metals. Ascomycota fungi are well known for their mutualistic associations with plant roots and, separately, for roles in the accumulation of toxic compounds from the environment, such as heavy metals. We sampled soils and cultured root-associated fungi from blue grama grass (<i>Bouteloua gracilis</i>) collected from lands with a history of uranium (U) mining and contrasted against communities in nearby, off-mine sites. Plant root-associated fungal communities from mine sites were lower in taxonomic richness and diversity than root fungi from paired, off-mine sites. We assessed potential functional consequences of unique mine-associated soil microbial communities using plant bioassays, which revealed that plants grown in mine soils in the greenhouse had significantly lower germination, survival, and less total biomass than plants grown in off-mine soils but did not alter allocation patterns to roots versus shoots. We identified candidate culturable root-associated Ascomycota taxa for bioremediation and increased understanding of the biological impacts of heavy metals on microbial communities and plant growth.
DOI: 10.6084/m9.figshare.22009681.v1
title: Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales

description: Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. <i>Cladonia</i> is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the “true” reindeer lichens, <i>Cladonia</i> subgenus <i>Cladina</i>, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of <i>Cladonia, Pilophorus</i>, and <i>Stereocaulon</i> were consistently larger than those of <i>Lepraria</i> and contained more introns, suggesting a selective pressure in asexual morphology in <i>Lepraria</i> driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from <i>Cladonia ravenelii</i> and <i>Stereocaulon pileatum</i> exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in <i>Lepraria</i>, were diverse and abundant in <i>Cladonia</i>, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with <i>C. rangiferina</i> especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of <i>Cladonia</i> and related genera, allowing future study alongside a wealth of assembled genomes.
DOI: 10.6084/m9.figshare.22242790
title: Association of soil fungal community composition with incidence of Fusarium wilt of banana in Malaysia

description: Banana (<i>Musa</i> spp.), an important food crop in many parts of the world, is threatened by a deadly wilt disease caused by <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Tropical Race 4 (TR4). Increasing evidence indicates that plant actively recruits beneficial microbes in the rhizosphere to suppress soil-borne pathogens. Hence, studies on the composition and diversity of the root-associated microbial communities are important for banana health. Research on beneficial microbial communities has focused on bacteria, although fungi can also influence soil-borne disease. Here, high-throughput sequencing targeting the fungal internal transcribed spacer (ITS) was employed to systematically characterize the difference in the soil fungal community associated with Fusarium wilt (FW) of banana. The community structure of fungi in the healthy and TR4-infected rhizospheres was significantly different compared with that of bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity compared with healthy plants, with significant abundance of <i>Fusarium</i> genus at 14%. In the healthy rhizosphere soil, <i>Penicillium</i> spp. were more abundant at 7% and positively correlated with magnesium. This study produced a detailed description of fungal community structure in healthy and TR4-infected banana soils in Malaysia and identified candidate biomarker taxa that may be associated with FW disease promotion and suppression. The findings also expand the global inventory of fungal communities associated with the components of asymptomatic and symptomatic banana plants infected by TR4.
DOI: 10.6084/m9.figshare.22242790.v1
title: Association of soil fungal community composition with incidence of Fusarium wilt of banana in Malaysia

description: Banana (<i>Musa</i> spp.), an important food crop in many parts of the world, is threatened by a deadly wilt disease caused by <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Tropical Race 4 (TR4). Increasing evidence indicates that plant actively recruits beneficial microbes in the rhizosphere to suppress soil-borne pathogens. Hence, studies on the composition and diversity of the root-associated microbial communities are important for banana health. Research on beneficial microbial communities has focused on bacteria, although fungi can also influence soil-borne disease. Here, high-throughput sequencing targeting the fungal internal transcribed spacer (ITS) was employed to systematically characterize the difference in the soil fungal community associated with Fusarium wilt (FW) of banana. The community structure of fungi in the healthy and TR4-infected rhizospheres was significantly different compared with that of bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity compared with healthy plants, with significant abundance of <i>Fusarium</i> genus at 14%. In the healthy rhizosphere soil, <i>Penicillium</i> spp. were more abundant at 7% and positively correlated with magnesium. This study produced a detailed description of fungal community structure in healthy and TR4-infected banana soils in Malaysia and identified candidate biomarker taxa that may be associated with FW disease promotion and suppression. The findings also expand the global inventory of fungal communities associated with the components of asymptomatic and symptomatic banana plants infected by TR4.
DOI: 10.3886/icpsr24188.v2
title: Federal Justice Statistics Program: Defendants in Federal Criminal Cases in District Court -- Pending, 2005 [United States]
title: Version 2

description: The data contain records of defendants in criminal cases filed in United States District Court before or during fiscal year 2005 and still pending as of year-end. The data were constructed from the Administrative Office of the United States District Courts' (AOUSC) criminal file. Defendants in criminal cases may be either individuals or corporations. There is one record for each defendant in each case filed. Included in the records are data from court proceedings and offense codes for up to five offenses charged at the time the case was filed. (The most serious charge at termination may differ from the most serious charge at case filing, due to plea bargaining or action of the judge or jury.) In a case with multiple charges against the defendant, a "most serious" offense charge is determined by a hierarchy of offenses based on statutory maximum penalties associated with the charges. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 4.1-4.5 and 5.1-5.6. Variables containing identifying information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Defendants in Federal Criminal Cases in District Court -- Pending, 2005 [United States]
description: Criminal cases filed in United States District Court during fiscal year 2005 and still pending as of year-end.
DOI: 10.3886/icpsr24188
title: Federal Justice Statistics Program: Defendants in Federal Criminal Cases in District Court -- Pending, 2005 [United States]
title: Archival Version

description: The data contain records of defendants in criminal cases filed in United States District Court before or during fiscal year 2005 and still pending as of year-end. The data were constructed from the Administrative Office of the United States District Courts' (AOUSC) criminal file. Defendants in criminal cases may be either individuals or corporations. There is one record for each defendant in each case filed. Included in the records are data from court proceedings and offense codes for up to five offenses charged at the time the case was filed. (The most serious charge at termination may differ from the most serious charge at case filing, due to plea bargaining or action of the judge or jury.) In a case with multiple charges against the defendant, a "most serious" offense charge is determined by a hierarchy of offenses based on statutory maximum penalties associated with the charges. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 4.1-4.5 and 5.1-5.6. Variables containing identifying information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Defendants in Federal Criminal Cases in District Court -- Pending, 2005 [United States]
description: Criminal cases filed in United States District Court during fiscal year 2005 and still pending as of year-end.
DOI: 10.3886/icpsr24189.v2
title: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2006 [United States]
title: Version 2

description: The data contain records of criminal appeals cases filed in United States Courts of Appeals during fiscal year 2006. The data were constructed from the Administrative Office of the United States Courts' (AOUSC) Court of Appeals file. These contain variables on the nature of the criminal appeal, the underlying offense, and the disposition of the appeal. An appeal can be filed by the government or the offender, and the appellant can appeal the sentence, the verdict, or both sentence and verdict. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 6.1-6.5. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2006 [United States]
description: Criminal appeals cases filed in United States Courts of Appeals during fiscal year 2006.
DOI: 10.3886/icpsr24189
title: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2006 [United States]
title: Archival Version

description: The data contain records of criminal appeals cases filed in United States Courts of Appeals during fiscal year 2006. The data were constructed from the Administrative Office of the United States Courts' (AOUSC) Court of Appeals file. These contain variables on the nature of the criminal appeal, the underlying offense, and the disposition of the appeal. An appeal can be filed by the government or the offender, and the appellant can appeal the sentence, the verdict, or both sentence and verdict. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 6.1-6.5. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2006 [United States]
description: Criminal appeals cases filed in United States Courts of Appeals during fiscal year 2006.
DOI: 10.3886/icpsr24186.v2
title: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 2005 [United States]
title: Version 2

description: The data contain records of defendants in criminal cases filed in United States District Court during fiscal year 2005. The data were constructed from the Administrative Office of the United States District Courts' (AOUSC) criminal file. Defendants in criminal cases may be either individuals or corporations. There is one record for each defendant in each case filed. Included in the records are data from court proceedings and offense codes for up to five offenses charged at the time the case was filed. (The most serious charge at termination may differ from the most serious charge at case filing, due to plea bargaining or action of the judge or jury.) In a case with multiple charges against the defendant, a "most serious" offense charge is determined by a hierarchy of offenses based on statutory maximum penalties associated with the charges. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF variables," that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 4.1-4.5 and 5.1-5.6. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Defendants in Federal Criminal Cases Filed in District Court, 2005 [United States]
description: Criminal cases filed in United States District Court during fiscal year 2005.
DOI: 10.3886/icpsr24172.v2
title: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2005 [United States]
title: Version 2

description: The data contain records of criminal appeals cases filed in United States Courts of Appeals during fiscal year 2005. The data were constructed from the Administrative Office of the United States Courts' (AOUSC) Court of Appeals file. These contain variables on the nature of the criminal appeal, the underlying offense, and the disposition of the appeal. An appeal can be filed by the government or the offender, and the appellant can appeal the sentence, the verdict, or both sentence and verdict. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 6.1-6.5. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2005 [United States]
description: Criminal appeals cases filed in United States Courts of Appeals during fiscal year 2005.
DOI: 10.3886/icpsr24172
title: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2005 [United States]
title: Archival Version

description: The data contain records of criminal appeals cases filed in United States Courts of Appeals during fiscal year 2005. The data were constructed from the Administrative Office of the United States Courts' (AOUSC) Court of Appeals file. These contain variables on the nature of the criminal appeal, the underlying offense, and the disposition of the appeal. An appeal can be filed by the government or the offender, and the appellant can appeal the sentence, the verdict, or both sentence and verdict. The data file contains variables from the original AOUSC files as well as additional analysis variables, or "SAF" variables, that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 6.1-6.5. Variables containing information (e.g., name, Social Security number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Criminal Appeals Cases Filed in Courts of Appeals, 2005 [United States]
description: Criminal appeals cases filed in United States Courts of Appeals during fiscal year 2005.
DOI: 10.3886/icpsr24036.v2
title: Federal Justice Statistics Program: Offenders Released From Prison, 1996
title: Version 2

description: The data contain records of sentenced offenders released from the custody of the Bureau of Prisons (BOP) during fiscal year 1996. The data include commitments of United States District Court, violators of conditions of release (e.g., parole, probation, or supervised release violators), offenders convicted in other courts (e.g., military or District of Columbia courts), and persons admitted to prison as material witnesses or for purposes of treatment, examination, or transfer to another authority. Records of offenders who exit federal prison temporarily, such as for transit to another location, to serve a weekend sentence, or for health care, are not included in the exiting cohort. These data include variables that describe the offender, such as age, race, citizenship, as well as variables that describe the sentences and expected prison terms. The data file contains original variables from the Bureau of Prisons' SENTRY database, as well as "SAF" variables that denote subsets of the data. These SAF variables are related to statistics reported in the Compendium of Federal Justice Statistics, Tables 7.9-7.16. Variables containing identifying information (e.g., name, Social Security Number) were replaced with blanks, and the day portions of date fields were also sanitized in order to protect the identities of individuals. These data are part of a series designed by the Urban Institute (Washington, DC) and the Bureau of Justice Statistics. Data and documentation were prepared by the Urban Institute.
description: Datasets: DS1: Federal Justice Statistics Program: Offenders Released From Prison, 1996
description: Offenders released from the custody of the United States Bureau of Prisons during fiscal year 1996.