cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4478354
title: Block-Diagonal Covariance Selection for High-Dimensional Gaussian Graphical Models

description: Gaussian graphical models are widely used to infer and visualize networks of dependencies between continuous variables. However, inferring the graph is difficult when the sample size is small compared to the number of variables. To reduce the number of parameters to estimate in the model, we propose a nonasymptotic model selection procedure supported by strong theoretical guarantees based on an oracle type inequality and a minimax lower bound. The covariance matrix of the model is approximated by a block-diagonal matrix. The structure of this matrix is detected by thresholding the sample covariance matrix, where the threshold is selected using the slope heuristic. Based on the block-diagonal structure of the covariance matrix, the estimation problem is divided into several independent problems: subsequently, the network of dependencies between variables is inferred using the graphical lasso algorithm in each block. The performance of the procedure is illustrated on simulated data. An application to a real gene expression dataset with a limited sample size is also presented: the dimension reduction allows attention to be objectively focused on interactions among smaller subsets of genes, leading to a more parsimonious and interpretable modular network. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4477838
title: Serotoninergic Activation during Courtship and Aggression in the Brown Anole

description: A dataset of behavioral and neural measures involving serotonin, Fos, courtship, and aggression in the brown anole lizard.
DOI: 10.6084/m9.figshare.4477667
title: SSDNA Sub-translocation Samples and Code

description: Samples and ssDNA sequences used for sub-translocation data acquisition:<br>- AAGCT92<br>- ATGTCCTCCA<br>- TGGAGGACAT<br>- CCCCCAAAAA50<br><br>Sub-translocation Analyzer V 7.1 code (C)<br>
DOI: 10.6084/m9.figshare.4477838.v1
title: Serotoninergic Activation during Courtship and Aggression in the Brown Anole

description: A dataset of behavioral and neural measures involving serotonin, Fos, courtship, and aggression in the brown anole lizard.
DOI: 10.6084/m9.figshare.4478354.v2
title: Block-Diagonal Covariance Selection for High-Dimensional Gaussian Graphical Models

description: Gaussian graphical models are widely used to infer and visualize networks of dependencies between continuous variables. However, inferring the graph is difficult when the sample size is small compared to the number of variables. To reduce the number of parameters to estimate in the model, we propose a nonasymptotic model selection procedure supported by strong theoretical guarantees based on an oracle type inequality and a minimax lower bound. The covariance matrix of the model is approximated by a block-diagonal matrix. The structure of this matrix is detected by thresholding the sample covariance matrix, where the threshold is selected using the slope heuristic. Based on the block-diagonal structure of the covariance matrix, the estimation problem is divided into several independent problems: subsequently, the network of dependencies between variables is inferred using the graphical lasso algorithm in each block. The performance of the procedure is illustrated on simulated data. An application to a real gene expression dataset with a limited sample size is also presented: the dimension reduction allows attention to be objectively focused on interactions among smaller subsets of genes, leading to a more parsimonious and interpretable modular network. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4478354.v1
title: Block-diagonal covariance selection for high-dimensional Gaussian graphical models

description: Gaussian graphical models are widely utilized to infer and visualize networks of dependencies between continuous variables. However, inferring the graph is difficult when the sample size is small compared to the number of variables. To reduce the number of parameters to estimate in the model, we propose a non-asymptotic model selection procedure supported by strong theoretical guarantees based on an oracle type inequality and a minimax lower bound. The covariance matrix of the model is approximated by a block-diagonal matrix. The structure of this matrix is detected by thresholding the sample covariance matrix, where the threshold is selected using the slope heuristic. Based on the block-diagonal structure of the covariance matrix, the estimation problem is divided into several independent problems: subsequently, the network of dependencies between variables is inferred using the graphical lasso algorithm in each block. The performance of the procedure is illustrated on simulated data. An application to a real gene expression dataset with a limited sample size is also presented: the dimension reduction allows attention to be objectively focused on interactions among smaller subsets of genes, leading to a more parsimonious and interpretable modular network.
DOI: 10.6084/m9.figshare.4476632
title: BP_datasets

description: Dataset for experimenting TDO
DOI: 10.6084/m9.figshare.4476689
title: Geochemical and Hf isotopic compositions of Late Triassic–Early Jurassic intrusions of the Erguna Block, Northeast China: petrogenesis and tectonic implications

description: Late Triassic–Early Jurassic intrusions of the Erguna Block, Northeast China, are located along the southern margin of the Mongol–Okhotsk orogenic belt. They comprise granodiorite, monzogranite, syenogranite, and lesser gabbro–diorite, of adakitic and calc­alkaline affinity. The adakite-like and calc­alkaline granites share similar light rare earth elements (LREE) characteristics; however, their heavy rare earth elements (HREE) trends differ from one another. The relative abundances of HREE in the calc­alkaline granites are relatively consistent and are similar to those of intrusive rocks formed from dehydration melting of garnet-free amphibolitic source rocks at relatively low pressures. In contrast, the adakite-like granites show more prominent HREE fractionation trends, indicating that they crystallized at higher pressures, where garnet in the source rocks was stable. At least two isotopically distinct sources were involved in the petrogenesis of the granites, but the extent to which they contributed varies between plutons. Most intrusions have incorporated an isotopically primitive component, possibly juvenile mafic crust. The other sources include a small proportion of old continental crustal material and isotopically evolved wall rocks. The gabbro–diorites have high MgO contents (&gt;7 wt.%), a high Mg<sup>#</sup> (&gt;0.6), and show moderate LREE and HREE fractionation, indicating they formed from the melting of subducted metasomatized lithospheric mantle. All of the intrusions in the study area are characterized by a relative enrichment in large ion lithophile elements (LILE) and depletion in high field strength elements (HFSE), indicating they were emplaced in an Andean-type active continental margin setting related to southward subduction of the Mongol–Okhotsk oceanic plate.
DOI: 10.6084/m9.figshare.4476632.v1
title: BP_datasets

description: Dataset for experimenting TDO
DOI: 10.6084/m9.figshare.4476689.v1
title: Geochemical and Hf isotopic compositions of Late Triassic–Early Jurassic intrusions of the Erguna Block, Northeast China: petrogenesis and tectonic implications

description: Late Triassic–Early Jurassic intrusions of the Erguna Block, Northeast China, are located along the southern margin of the Mongol–Okhotsk orogenic belt. They comprise granodiorite, monzogranite, syenogranite, and lesser gabbro–diorite, of adakitic and calc­alkaline affinity. The adakite-like and calc­alkaline granites share similar light rare earth elements (LREE) characteristics; however, their heavy rare earth elements (HREE) trends differ from one another. The relative abundances of HREE in the calc­alkaline granites are relatively consistent and are similar to those of intrusive rocks formed from dehydration melting of garnet-free amphibolitic source rocks at relatively low pressures. In contrast, the adakite-like granites show more prominent HREE fractionation trends, indicating that they crystallized at higher pressures, where garnet in the source rocks was stable. At least two isotopically distinct sources were involved in the petrogenesis of the granites, but the extent to which they contributed varies between plutons. Most intrusions have incorporated an isotopically primitive component, possibly juvenile mafic crust. The other sources include a small proportion of old continental crustal material and isotopically evolved wall rocks. The gabbro–diorites have high MgO contents (&gt;7 wt.%), a high Mg<sup>#</sup> (&gt;0.6), and show moderate LREE and HREE fractionation, indicating they formed from the melting of subducted metasomatized lithospheric mantle. All of the intrusions in the study area are characterized by a relative enrichment in large ion lithophile elements (LILE) and depletion in high field strength elements (HFSE), indicating they were emplaced in an Andean-type active continental margin setting related to southward subduction of the Mongol–Okhotsk oceanic plate.
DOI: 10.6084/m9.figshare.4476536
title: Disentangling the Taxonomy of the Mahseers (<i>Tor</i> spp.) of Malaysia: An Integrated Approach Using Morphology, Genetics and Historical Records

description: The establishment of appropriate taxonomic designations is essential for the effective management of fishery resources. Despite over a century of explorations and research, the cyprinid genus <i>Tor</i> represents a group of large-bodied freshwater fishes whose taxonomy and systematics remains poorly known. While five species of <i>Tor</i> are currently listed as “endangered” on the IUCN Red List, a further five out of 18 species currently recognized are assessed as “data deficient,” with at least one undescribed species, believed to be on the brink of extinction (i.e., the Humpback Mahseer endemic to the Cauvery River in India). <i>Tor</i> mahseers represent a suitable model for the application of an integrated approach using morphology, genetics, and historical records to resolve species identities, where one or more of these fundamental approaches may have been deficient in the past. Focusing specifically on the taxonomy and nomenclature of the <i>Tor</i> species recorded from Peninsular Malaysia, one of the aims of this review is to define the identity of two nominal species, <i>T. tambra</i> and <i>T. tambroides</i>. Original descriptions of these two nominal species contain little or practically no characters to distinguish them, and partly explains why secondary literature fails to conclusively determine species boundaries. A phylogenetic analysis of mahseer specimens from this region, based on publicly available and newly sequenced mitochondrial <i>COX1</i> genes, does not support species designation based on previously established morphological features. More importantly, multiple tree-based species delimitation approaches showed that previously sequenced <i>T. tambroides</i> from Peninsular Malaysia and the newly described <i>Tor</i> species from Vietnam could not be delimited from the topotypic <i>Tor tambra</i>. A wider investigation of mahseer taxonomy covering all of Southeast Asia, using such an integrated approach is recommended to resolve the ambiguous taxonomy and is of profound importance for the conservation and management of exploited and farmed populations of these highly valued and iconic fish.
DOI: 10.6084/m9.figshare.4476536.v1
title: Disentangling the Taxonomy of the Mahseers (<i>Tor</i> spp.) of Malaysia: An Integrated Approach Using Morphology, Genetics and Historical Records

description: The establishment of appropriate taxonomic designations is essential for the effective management of fishery resources. Despite over a century of explorations and research, the cyprinid genus <i>Tor</i> represents a group of large-bodied freshwater fishes whose taxonomy and systematics remains poorly known. While five species of <i>Tor</i> are currently listed as “endangered” on the IUCN Red List, a further five out of 18 species currently recognized are assessed as “data deficient,” with at least one undescribed species, believed to be on the brink of extinction (i.e., the Humpback Mahseer endemic to the Cauvery River in India). <i>Tor</i> mahseers represent a suitable model for the application of an integrated approach using morphology, genetics, and historical records to resolve species identities, where one or more of these fundamental approaches may have been deficient in the past. Focusing specifically on the taxonomy and nomenclature of the <i>Tor</i> species recorded from Peninsular Malaysia, one of the aims of this review is to define the identity of two nominal species, <i>T. tambra</i> and <i>T. tambroides</i>. Original descriptions of these two nominal species contain little or practically no characters to distinguish them, and partly explains why secondary literature fails to conclusively determine species boundaries. A phylogenetic analysis of mahseer specimens from this region, based on publicly available and newly sequenced mitochondrial <i>COX1</i> genes, does not support species designation based on previously established morphological features. More importantly, multiple tree-based species delimitation approaches showed that previously sequenced <i>T. tambroides</i> from Peninsular Malaysia and the newly described <i>Tor</i> species from Vietnam could not be delimited from the topotypic <i>Tor tambra</i>. A wider investigation of mahseer taxonomy covering all of Southeast Asia, using such an integrated approach is recommended to resolve the ambiguous taxonomy and is of profound importance for the conservation and management of exploited and farmed populations of these highly valued and iconic fish.
DOI: 10.6084/m9.figshare.4476440
title: DDS and Seasonality Data_Abizari et al 2016.sav

description: Data-set on the effect of seasonality on the Dietary Diversity of school children in northern Ghana. <br>We assessed the dietary diversity score (DDS) of the school-age children at two different time points using a qualitative 24-hour dietary recall (24hR). The baseline assessment (October 2010) was conducted before the intervention and corresponded with the onset of the dry season and the harvest of most crops especially cereals, legumes like cowpea and some root tubers particularly sweet potatoes. On the contrary, the follow-up assessment (May 2011) was conducted at the end of the intervention and was in the rainy season coinciding with the lean period when many households have their staple food (cereal and root tubers) stocks depleted.
DOI: 10.6084/m9.figshare.4476440.v1
title: DDS and Seasonality Data_Abizari et al 2016.sav

description: Data-set on the effect of seasonality on the Dietary Diversity of school children in northern Ghana. <br>We assessed the dietary diversity score (DDS) of the school-age children at two different time points using a qualitative 24-hour dietary recall (24hR). The baseline assessment (October 2010) was conducted before the intervention and corresponded with the onset of the dry season and the harvest of most crops especially cereals, legumes like cowpea and some root tubers particularly sweet potatoes. On the contrary, the follow-up assessment (May 2011) was conducted at the end of the intervention and was in the rainy season coinciding with the lean period when many households have their staple food (cereal and root tubers) stocks depleted.
DOI: 10.6084/m9.figshare.4476404
title: SMS for alcohol

description: Results from a trial comparing different types of text messaging on problem drinking outcomes. To be published in PLoS One for review of methods.
DOI: 10.6084/m9.figshare.4476392
title: Synthesis and biological screening of some chromonyl-substituted heterocycles derived from 2(3<i>H</i>)-furanone derivative

description: A 2(3<i>H</i>)-furanone bearing chromonyl moiety at position-3 was synthesized and utilized for the construction of <i>N</i>-heterocycles such as pyrrolone, <i>N</i>-aminoquinolone, and pyridazinone derivatives. The reactivity of the chromonylfuranone toward some nitrogen nucleophiles such as ammonia, benzylamine, hydrazine, and phenylhydrazine was studied. On the other hand, thiation of the starting chromonylfuranone interestingly provides mono- and di-thiated products. The chemoselectivity of these reactions is discussed. The structures of all products obtained were elucidated from their analytical and spectral data. The antimicrobial activities of selected examples of the synthesized compounds were examined against two strains of bacteria and two fungus strains. Some of them showed promising antimicrobial activities.
DOI: 10.6084/m9.figshare.4476404.v1
title: PrimaryoutcomePLOSONEMUENCH.sav

description: Results from a trial comparing different types of text messaging on problem drinking outcomes. To be published in PLoS One for review of methods.
DOI: 10.6084/m9.figshare.4476392.v2
title: Synthesis and biological screening of some chromonyl-substituted heterocycles derived from 2(3<i>H</i>)-furanone derivative

description: A 2(3<i>H</i>)-furanone bearing chromonyl moiety at position-3 was synthesized and utilized for the construction of <i>N</i>-heterocycles such as pyrrolone, <i>N</i>-aminoquinolone, and pyridazinone derivatives. The reactivity of the chromonylfuranone toward some nitrogen nucleophiles such as ammonia, benzylamine, hydrazine, and phenylhydrazine was studied. On the other hand, thiation of the starting chromonylfuranone interestingly provides mono- and di-thiated products. The chemoselectivity of these reactions is discussed. The structures of all products obtained were elucidated from their analytical and spectral data. The antimicrobial activities of selected examples of the synthesized compounds were examined against two strains of bacteria and two fungus strains. Some of them showed promising antimicrobial activities.
DOI: 10.6084/m9.figshare.4476404.v2
title: SMS for alcohol

description: Results from a trial comparing different types of text messaging on problem drinking outcomes. To be published in PLoS One for review of methods.
DOI: 10.6084/m9.figshare.4476392.v1
title: Synthesis and Biological Screening of Some Chromonyl-Substituted Heterocycles Derived From 2(3 <i>H</i> )-Furanone Derivative

description: A 2(3H)-furanone bearing chromonyl moiety at position-3 was synthesized and utilized for the construction of <i>N</i>-heterocycles such as pyrrolone, <i>N</i>-aminoquinolone and pyridazinone derivatives. The reactivity of the chromonylfuranone towards some nitrogen nucleophiles such as ammonia, benzylamine, hydrazine and phenylhydrazine was studied. On the other hand, thiation of the starting chromonylfuranone interestingly provides mono- and di-thiated products. The chemoselectivity of these reactions is discussed. The structures of all products obtained were elucidated from their analytical and spectral data. The antimicrobial activities of selected examples of the synthesized compounds were examined against two strains of bacteria and two fungus strains. Some of them showed promising antimicrobial activities.
DOI: 10.6084/m9.figshare.4476374
title: Systematic characterization of artificial small RNA-mediated inhibition of <i>Escherichia coli</i> growth

description: A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of <i>Escherichia coli</i> was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing <i>E. coli</i> and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An <i>in vitro</i> translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting <i>E. coli</i> growth. These data also suggest that S-20 acts like an endogenous sRNA and that <i>E. coli</i> can utilize artificial sRNAs.
DOI: 10.6084/m9.figshare.4476374.v1
title: Systematic characterization of artificial small RNA-mediated inhibition of <i>Escherichia coli</i> growth

description: A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of <i>Escherichia coli</i> was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing <i>E. coli</i> and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An <i>in vitro</i> translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting <i>E. coli</i> growth. These data also suggest that S-20 acts like an endogenous sRNA and that <i>E. coli</i> can utilize artificial sRNAs.
DOI: 10.6073/pasta/3854b65179da448a21097e59ba73ecfb
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 11 meteorological station: 1-hour summary data: 2017 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-11 met station. Air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.