cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1092540.v1
title: Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting

description: Supplementary Methods for PLOS ONE paper entitled Potential future impact of a partially effective HIV vaccine in a southern African setting
DOI: 10.6084/m9.figshare.1092536
title: A rapid diagnostic approach to identify poisonous plants using DNA barcoding data

description: Among plants, several groups have toxicities that are dangerous for humans. Plant exposures are indeed one of the most frequent cases reported to poison control centers. A rapid and easy screening test is required for accurate medical treatment. However, it is usually based on the morphological analysis of ingested plant portions that is expensive in terms of time and resources requiring experience in systematic botany which could also be biased by the absence of clear diagnostic traits in stomach contents. In this study, we designed specific primer pairs for the amplification of a sequence-characterized amplified region within standard barcode regions (i.e., <i>rbcL</i> and <i>trnH–psbA</i>) to detect toxic plants belonging to the genera <i>Atropa</i> and <i>Colchicum</i>. Allied edible species were also included in our data-set to exclude the cross-amplification with the toxic ones when the detection system is applied. Using real-time polymerase chain reaction, we tested the specificity of the selected primer pairs in order to develop a fast and reliable tool to be used in poison centers.
DOI: 10.6084/m9.figshare.1092537
title: Vegetation of rock crevices of the montane and colline zones in the Pamir-Alai and Tian Shan Mts in Tajikistan (Middle Asia)

description: The paper presents the results of phytosociological research conducted on the vegetation of rock habitats in the montane and colline zones of the Pamir-Alai Mountains (Tajikistan). During field surveys done in 2010–2013, 122 phytosociological relevés were sampled. Plant species were recorded according to the Braun-Blanquet cover-abundance scale. The vegetation studies were carried out generally in the western Pamir-Alai and south-western Tian Shan Mts, especially in the Zeravshan, Hissar, Hazratishoh, Darvaz, Rushan, Turkestan, Kuramin and Vanch ranges. A synopsis of the rock communities of the montane and colline zones in Tajikistan is proposed. The collected material presents most of the variability among the plant communities of rock crevices and fissures on calcareous as well as acidic substrates in the montane and colline zones in Tajikistan. As a result of field research and numerical analyses, eight associations have been distinguished: <i>Scutellarietum hissaricae</i>, <i>Scutellarietum</i><i>schugnanicae</i>, <i>Scutellarietum zaprjagaevii</i>, <i>Scutellarietum baldshuanicae</i>, <i>Tylospermetum</i><i>lignosae</i>, <i>Dionysietum involucratae</i> A. Nowak, M. Nobis, S. Nowak & A. Nobis, 2014, <i>Nanorrhinetum ramosissimi</i>, <i>Campanuletum albertii</i> and the community of <i>Scutellaria adenostegia</i> within new alliance – <i>Caricion koshevnikovii</i>. The main factors determining the species composition of classified associations seem to be the geography of the distribution range, elevation above sea level, rock type and exposition.
DOI: 10.6084/m9.figshare.1092535
title: <i>Jamesbondia</i>, a new subgenus of <i>Alternanthera</i> (Gomphrenoideae, Amaranthaceae) from Central America and the Caribbean Islands

description: <i>Jamesbondia</i> is formally proposed here as a new subgenus of <i>Alternanthera</i>, a large Neotropical genus, with four species [<i>A. costaricensis</i> Kuntze, <i>A. geniculata</i> Urb., <i>A. olivacea</i> Urb., and <i>A. serpyllifolia</i> (Poir.) Urb.], mostly found in Central America and the Caribbean Islands. In a recent phylogeny using internal transcribed spacer (ITS), <i>trnL-F</i>, and <i>rpl16</i> data and samples of three of the four species listed above, an unpublished genus <i>Jamesbondia</i> was embedded within <i>Alternanthera</i>. The other three species (not <i>A. costaricensis</i>) clustered in a clade with 97% jackknife (JK) support. Here, to determine the position of <i>A. costaricensis</i> within <i>Alternanthera</i> and taxonomically revise the species in subgenus <i>Jamesbondia</i>, we analyzed ITS, <i>trnL-F</i>, and <i>rpl16</i> data from GenBank accessions for 31 species and our new molecular data for <i>A. costaricensis</i> to reconstruct a phylogenetic tree confirming that <i>A. costaricensis</i> belongs to the <i>Jamesbondia</i> clade (88–97% JK; 0.88–1.0 posterior probability). <i>Alternanthera costaricensis</i>, <i>Telanthera olivacea</i> Urb., and <i>Achyranthes serpyllifolia</i> Poir. were lectotypified, and we document the distribution of <i>A. costaricensis</i> in Mexico for the first time. Insight from nomenclatural notes, taxonomic descriptions, morphological illustrations, distribution, and a key for species of <i>Jamesbondia</i> provided here will be used to propose a new subgeneric classification of <i>Alternanthera</i>.
DOI: 10.6084/m9.figshare.1092536.v1
title: A rapid diagnostic approach to identify poisonous plants using DNA barcoding data

description: Among plants, several groups have toxicities that are dangerous for humans. Plant exposures are indeed one of the most frequent cases reported to poison control centers. A rapid and easy screening test is required for accurate medical treatment. However, it is usually based on the morphological analysis of ingested plant portions that is expensive in terms of time and resources requiring experience in systematic botany which could also be biased by the absence of clear diagnostic traits in stomach contents. In this study we designed specific primer pairs for the amplification of a Sequence-Characterized Amplified Region (SCAR) within standard barcode regions (i.e. <i>rbcL</i> and <i>trnH-psbA</i>) to detect toxic plants belonging to the genera <i>Atropa</i> and <i>Colchicum</i>. Allied edible species were also included in our dataset to exclude the cross-amplification with the toxic ones when the detection system is applied. Using real-time PCR we tested the specificity of the selected primer pairs in order to develop a fast and reliable tool to be used in poison centers.
DOI: 10.6084/m9.figshare.1092537.v1
title: Vegetation of rock crevices of the montane and colline zones in the Pamir-Alai and Tian Shan Mts in Tajikistan (Middle Asia)

description: The paper presents the results of phytosociological research conducted on the vegetation of rock habitats in the montane and colline zones of the Pamir-Alai Mountains (Tajikistan). During field surveys done in 2010?13, 122 phytosociological relevés were sampled. Plant species were recorded according to the Braun-Blanquet cover-abundance scale. The vegetation studies were done generally in the western Pamir-Alai and south-western Tian Shan Mts, especially in the Zeravshan, Hissar, Hazratishoh, Darvaz, Rushan, Turkestan, Kuramin and Vanch ranges. A synopsis of the rock communities of the montane and colline zones in Tajikistan is proposed. The collected material presents most of the variability among the plant communities of rock crevices and fissures on calcareous as well as acidic substrates in the montane and colline zones in Tajikistan. As a result of field research and numerical analyses, 8 associations have been distinguished: <i>Scutellarietum hissaricae</i>, <i>Scutellarietum</i><i>schugnanicae</i>, <i>Scutellarietum zaprjagaevii</i>, <i>Scutellarietum baldshuanicae</i>, <i>Tylospermetum</i><i>lignosae</i>, <i>Dionysietum involucratae</i> Nowak A., Nobis M., Nowak S. et Nobis A. 2014, <i>Nanorrhinetum ramosissimi</i>, <i>Campanuletum albertii</i> and the community of <i>Scutellaria adenostegia</i> within new alliance - <i>Caricion koshevnikovii</i>. The main factors determining the species composition of classified associations seem to be the geography of the distribution range, elevation above sea level, rock type and exposition.
DOI: 10.6084/m9.figshare.1092536.v2
title: A rapid diagnostic approach to identify poisonous plants using DNA barcoding data

description: Among plants, several groups have toxicities that are dangerous for humans. Plant exposures are indeed one of the most frequent cases reported to poison control centers. A rapid and easy screening test is required for accurate medical treatment. However, it is usually based on the morphological analysis of ingested plant portions that is expensive in terms of time and resources requiring experience in systematic botany which could also be biased by the absence of clear diagnostic traits in stomach contents. In this study, we designed specific primer pairs for the amplification of a sequence-characterized amplified region within standard barcode regions (i.e., <i>rbcL</i> and <i>trnH–psbA</i>) to detect toxic plants belonging to the genera <i>Atropa</i> and <i>Colchicum</i>. Allied edible species were also included in our data-set to exclude the cross-amplification with the toxic ones when the detection system is applied. Using real-time polymerase chain reaction, we tested the specificity of the selected primer pairs in order to develop a fast and reliable tool to be used in poison centers.
DOI: 10.6084/m9.figshare.1092535.v2
title: <i>Jamesbondia</i>, a new subgenus of <i>Alternanthera</i> (Gomphrenoideae, Amaranthaceae) from Central America and the Caribbean Islands

description: <i>Jamesbondia</i> is formally proposed here as a new subgenus of <i>Alternanthera</i>, a large Neotropical genus, with four species [<i>A. costaricensis</i> Kuntze, <i>A. geniculata</i> Urb., <i>A. olivacea</i> Urb., and <i>A. serpyllifolia</i> (Poir.) Urb.], mostly found in Central America and the Caribbean Islands. In a recent phylogeny using internal transcribed spacer (ITS), <i>trnL-F</i>, and <i>rpl16</i> data and samples of three of the four species listed above, an unpublished genus <i>Jamesbondia</i> was embedded within <i>Alternanthera</i>. The other three species (not <i>A. costaricensis</i>) clustered in a clade with 97% jackknife (JK) support. Here, to determine the position of <i>A. costaricensis</i> within <i>Alternanthera</i> and taxonomically revise the species in subgenus <i>Jamesbondia</i>, we analyzed ITS, <i>trnL-F</i>, and <i>rpl16</i> data from GenBank accessions for 31 species and our new molecular data for <i>A. costaricensis</i> to reconstruct a phylogenetic tree confirming that <i>A. costaricensis</i> belongs to the <i>Jamesbondia</i> clade (88–97% JK; 0.88–1.0 posterior probability). <i>Alternanthera costaricensis</i>, <i>Telanthera olivacea</i> Urb., and <i>Achyranthes serpyllifolia</i> Poir. were lectotypified, and we document the distribution of <i>A. costaricensis</i> in Mexico for the first time. Insight from nomenclatural notes, taxonomic descriptions, morphological illustrations, distribution, and a key for species of <i>Jamesbondia</i> provided here will be used to propose a new subgeneric classification of <i>Alternanthera</i>.
DOI: 10.6084/m9.figshare.1092536.v4
title: A rapid diagnostic approach to identify poisonous plants using DNA barcoding data

description: Among plants, several groups have toxicities that are dangerous for humans. Plant exposures are indeed one of the most frequent cases reported to poison control centers. A rapid and easy screening test is required for accurate medical treatment. However, it is usually based on the morphological analysis of ingested plant portions that is expensive in terms of time and resources requiring experience in systematic botany which could also be biased by the absence of clear diagnostic traits in stomach contents. In this study, we designed specific primer pairs for the amplification of a sequence-characterized amplified region within standard barcode regions (i.e., <i>rbcL</i> and <i>trnH–psbA</i>) to detect toxic plants belonging to the genera <i>Atropa</i> and <i>Colchicum</i>. Allied edible species were also included in our data-set to exclude the cross-amplification with the toxic ones when the detection system is applied. Using real-time polymerase chain reaction, we tested the specificity of the selected primer pairs in order to develop a fast and reliable tool to be used in poison centers.
DOI: 10.6084/m9.figshare.1092535.v4
title: <i>Jamesbondia</i>, a new subgenus of <i>Alternanthera</i> (Gomphrenoideae, Amaranthaceae) from Central America and the Caribbean Islands

description: <i>Jamesbondia</i> is formally proposed here as a new subgenus of <i>Alternanthera</i>, a large Neotropical genus, with four species [<i>A. costaricensis</i> Kuntze, <i>A. geniculata</i> Urb., <i>A. olivacea</i> Urb., and <i>A. serpyllifolia</i> (Poir.) Urb.], mostly found in Central America and the Caribbean Islands. In a recent phylogeny using internal transcribed spacer (ITS), <i>trnL-F</i>, and <i>rpl16</i> data and samples of three of the four species listed above, an unpublished genus <i>Jamesbondia</i> was embedded within <i>Alternanthera</i>. The other three species (not <i>A. costaricensis</i>) clustered in a clade with 97% jackknife (JK) support. Here, to determine the position of <i>A. costaricensis</i> within <i>Alternanthera</i> and taxonomically revise the species in subgenus <i>Jamesbondia</i>, we analyzed ITS, <i>trnL-F</i>, and <i>rpl16</i> data from GenBank accessions for 31 species and our new molecular data for <i>A. costaricensis</i> to reconstruct a phylogenetic tree confirming that <i>A. costaricensis</i> belongs to the <i>Jamesbondia</i> clade (88–97% JK; 0.88–1.0 posterior probability). <i>Alternanthera costaricensis</i>, <i>Telanthera olivacea</i> Urb., and <i>Achyranthes serpyllifolia</i> Poir. were lectotypified, and we document the distribution of <i>A. costaricensis</i> in Mexico for the first time. Insight from nomenclatural notes, taxonomic descriptions, morphological illustrations, distribution, and a key for species of <i>Jamesbondia</i> provided here will be used to propose a new subgeneric classification of <i>Alternanthera</i>.
DOI: 10.6084/m9.figshare.1092537.v2
title: Vegetation of rock crevices of the montane and colline zones in the Pamir-Alai and Tian Shan Mts in Tajikistan (Middle Asia)

description: The paper presents the results of phytosociological research conducted on the vegetation of rock habitats in the montane and colline zones of the Pamir-Alai Mountains (Tajikistan). During field surveys done in 2010–2013, 122 phytosociological relevés were sampled. Plant species were recorded according to the Braun-Blanquet cover-abundance scale. The vegetation studies were carried out generally in the western Pamir-Alai and south-western Tian Shan Mts, especially in the Zeravshan, Hissar, Hazratishoh, Darvaz, Rushan, Turkestan, Kuramin and Vanch ranges. A synopsis of the rock communities of the montane and colline zones in Tajikistan is proposed. The collected material presents most of the variability among the plant communities of rock crevices and fissures on calcareous as well as acidic substrates in the montane and colline zones in Tajikistan. As a result of field research and numerical analyses, eight associations have been distinguished: <i>Scutellarietum hissaricae</i>, <i>Scutellarietum</i><i>schugnanicae</i>, <i>Scutellarietum zaprjagaevii</i>, <i>Scutellarietum baldshuanicae</i>, <i>Tylospermetum</i><i>lignosae</i>, <i>Dionysietum involucratae</i> A. Nowak, M. Nobis, S. Nowak & A. Nobis, 2014, <i>Nanorrhinetum ramosissimi</i>, <i>Campanuletum albertii</i> and the community of <i>Scutellaria adenostegia</i> within new alliance – <i>Caricion koshevnikovii</i>. The main factors determining the species composition of classified associations seem to be the geography of the distribution range, elevation above sea level, rock type and exposition.
DOI: 10.6084/m9.figshare.1092532
title: Reconstruction and Analysis of a Genome-wide Metabolic Model of Sulfurospirillum multivorans

description: <strong>Supplementary information</strong> <strong><br></strong> <strong>rec_progress.csv - </strong>Manual curation documentation <strong>cyc_access.py - </strong>lib for cyc2sbml <strong>cyc2sbml.py - </strong>python script to export data from pathwaytools to sbml <strong>sm.xml - </strong>sbml model of S. multivorans (bounds are set to a growth with 20mM pyruvate and 5% oxygen) <strong>smul-26_extended.xml - </strong>raw sbml model of S. multivorans (has to be complemented and run by test.py) <strong>test.py - </strong>python script to read, complement and simulate the sbml model of S. multivorans The recently sequenced and annotated genome of Sulfurospirillum multivorans provides insight into a versatile metabolism. For instance, S. multivorans can mediate organohalide respiration which is a useful bioremediation process to degrade carcinogens like tetra chloroethene. Furthermore, a wide range of of electron donor oxidizing and electron acceptor reducing enzymes was identi?ed in S. multivorans and even oxygen can be used as terminal electron acceptor which is unusual for organohalide respiring organisms. Herein, I want to present a metabolic reconstruction of S. multivorans based on the genome annotation and experimental as well as expert knowledge. In total, it accounts for 761 metabolic genes, 1266 reactions and 995 metabolites. The reconstruction was used to derive a computational model of the metabolism of S. multivorans: Given a certain growth condition, a method called Flux Balance Analysis was applied to predict reaction flows in mmol g^−1 h−1 (gram dry weight) for each reconstructed reaction. Thus, a set of active reactions can be inferred that enables a specific phenotype. Simulations were compared to experimental findings and suggestions for open research topics (carbon unbalance) were made.
DOI: 10.6084/m9.figshare.1092536.v3
title: A rapid diagnostic approach to identify poisonous plants using DNA barcoding data

description: Among plants, several groups have toxicities that are dangerous for humans. Plant exposures are indeed one of the most frequent cases reported to poison control centers. A rapid and easy screening test is required for accurate medical treatment. However, it is usually based on the morphological analysis of ingested plant portions that is expensive in terms of time and resources requiring experience in systematic botany which could also be biased by the absence of clear diagnostic traits in stomach contents. In this study, we designed specific primer pairs for the amplification of a sequence-characterized amplified region within standard barcode regions (i.e., <i>rbcL</i> and <i>trnH–psbA</i>) to detect toxic plants belonging to the genera <i>Atropa</i> and <i>Colchicum</i>. Allied edible species were also included in our data-set to exclude the cross-amplification with the toxic ones when the detection system is applied. Using real-time polymerase chain reaction, we tested the specificity of the selected primer pairs in order to develop a fast and reliable tool to be used in poison centers.
DOI: 10.6084/m9.figshare.1092532.v1
title: Reconstruction and Analysis of a Genome-wide Metabolic Model of Sulfurospirillum multivorans

description: <strong>Supplementary information</strong> <strong><br></strong> <strong>rec_progress.csv - </strong>Manual curation documentation <strong>cyc_access.py - </strong>lib for cyc2sbml <strong>cyc2sbml.py - </strong>python script to export data from pathwaytools to sbml <strong>sm.xml - </strong>sbml model of S. multivorans (bounds are set to a growth with 20mM pyruvate and 5% oxygen) <strong>smul-26_extended.xml - </strong>raw sbml model of S. multivorans (has to be complemented and run by test.py) <strong>test.py - </strong>python script to read, complement and simulate the sbml model of S. multivorans The recently sequenced and annotated genome of Sulfurospirillum multivorans provides insight into a versatile metabolism. For instance, S. multivorans can mediate organohalide respiration which is a useful bioremediation process to degrade carcinogens like tetra chloroethene. Furthermore, a wide range of of electron donor oxidizing and electron acceptor reducing enzymes was identi?ed in S. multivorans and even oxygen can be used as terminal electron acceptor which is unusual for organohalide respiring organisms. Herein, I want to present a metabolic reconstruction of S. multivorans based on the genome annotation and experimental as well as expert knowledge. In total, it accounts for 761 metabolic genes, 1266 reactions and 995 metabolites. The reconstruction was used to derive a computational model of the metabolism of S. multivorans: Given a certain growth condition, a method called Flux Balance Analysis was applied to predict reaction flows in mmol g^−1 h−1 (gram dry weight) for each reconstructed reaction. Thus, a set of active reactions can be inferred that enables a specific phenotype. Simulations were compared to experimental findings and suggestions for open research topics (carbon unbalance) were made.
DOI: 10.6084/m9.figshare.1092535.v3
title: <i>Jamesbondia</i>, a new subgenus of <i>Alternanthera</i> (Gomphrenoideae, Amaranthaceae) from Central America and the Caribbean Islands

description: <i>Jamesbondia</i> is formally proposed here as a new subgenus of <i>Alternanthera</i>, a large Neotropical genus, with four species [<i>A. costaricensis</i> Kuntze, <i>A. geniculata</i> Urb., <i>A. olivacea</i> Urb., and <i>A. serpyllifolia</i> (Poir.) Urb.], mostly found in Central America and the Caribbean Islands. In a recent phylogeny using internal transcribed spacer (ITS), <i>trnL-F</i>, and <i>rpl16</i> data and samples of three of the four species listed above, an unpublished genus <i>Jamesbondia</i> was embedded within <i>Alternanthera</i>. The other three species (not <i>A. costaricensis</i>) clustered in a clade with 97% jackknife (JK) support. Here, to determine the position of <i>A. costaricensis</i> within <i>Alternanthera</i> and taxonomically revise the species in subgenus <i>Jamesbondia</i>, we analyzed ITS, <i>trnL-F</i>, and <i>rpl16</i> data from GenBank accessions for 31 species and our new molecular data for <i>A. costaricensis</i> to reconstruct a phylogenetic tree confirming that <i>A. costaricensis</i> belongs to the <i>Jamesbondia</i> clade (88–97% JK; 0.88–1.0 posterior probability). <i>Alternanthera costaricensis</i>, <i>Telanthera olivacea</i> Urb., and <i>Achyranthes serpyllifolia</i> Poir. were lectotypified, and we document the distribution of <i>A. costaricensis</i> in Mexico for the first time. Insight from nomenclatural notes, taxonomic descriptions, morphological illustrations, distribution, and a key for species of <i>Jamesbondia</i> provided here will be used to propose a new subgeneric classification of <i>Alternanthera</i>.