cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3725930
title: h/e Oscillations in Interlayer Transport of Delafossites

description: Microstructures can be carefully designed to reveal the quantum phase of the wave-like nature of electrons in a metal. Here we report phase coherent oscillations of the out-of-plane magnetoresistance in the layered delafossites PdCoO<sub>2</sub> and PtCoO<sub>2</sub>. The oscillation period is equivalent to that determined by the magnetic flux quantum, <em>h/e</em>, threading an area defined by the atomic interlayer separation and the sample width; here <em>h</em> is Planck’s constant and <em>e</em> is the charge of an electron. The phase of the electron wave function appears robust over length scales exceeding 10mm and persisting up to temperatures of T&gt;50K. We show that the experimental signal stems from a periodic field-modulation of the out-of-plane hopping. These results demonstrate extraordinary single-particle quantum coherence lengths in the delafossites.
DOI: 10.5281/zenodo.4675599
title: Sondheimer oscillations as a probe of non-ohmic flow in type-II Weyl semimetal WP2

description: As conductors in electronic applications shrink, microscopic conduction processes lead to strong deviations from Ohm’s law. Depending on the length scales of momentum conserving (<em>l<sub>MC</sub></em>) and relaxing (<em>l<sub>MR</sub></em>) electron scattering, and the device size (<em>d</em>), current flows may shift from ohmic to ballistic to hydrodynamic regimes and more exotic mixtures thereof. So far, an <em>in situ</em>, in-operando methodology to obtain these parameters self-consistently within a micro/nanodevice, and thereby identify its conduction regime, is critically lacking. In this context, we exploit Sondheimer oscillations, semi-classical magnetoresistance oscillations due to helical electronic motion, as a method to obtain <em>l<sub>MR</sub></em> in micro-devices even when <em>l<sub>MR</sub>&gt;&gt;d</em>. This gives information on the bulk <em>l<sub>MR </sub></em>complementary to quantum oscillations, which are sensitive to all scattering processes. We extract <em>l<sub>MR</sub></em> from the Sondheimer amplitude in the topological semimetal WP<sub>2</sub>, at elevated temperatures up to T~40K, in a range most relevant for hydrodynamic transport phenomena. Our data on µm-sized devices are in excellent agreement with experimental reports of the large bulk <em>l<sub>MR</sub></em> and thus confirm that WP<sub>2 </sub>can be microfabricated without degradation. Indeed, the measured scattering rates match well with those of theoretically predicted electron-phonon scattering, thus supporting the notion of strong momentum exchange between electrons and phonons in WP<sub>2</sub> at these temperatures. These results conclusively establish Sondheimer oscillations as a quantitative probe of <em>l<sub>MR</sub></em> in micro-devices in studying non-ohmic electron flow.
DOI: 10.5281/zenodo.3725929
title: h/e Oscillations in Interlayer Transport of Delafossites

description: Microstructures can be carefully designed to reveal the quantum phase of the wave-like nature of electrons in a metal. Here we report phase coherent oscillations of the out-of-plane magnetoresistance in the layered delafossites PdCoO<sub>2</sub> and PtCoO<sub>2</sub>. The oscillation period is equivalent to that determined by the magnetic flux quantum, <em>h/e</em>, threading an area defined by the atomic interlayer separation and the sample width; here <em>h</em> is Planck’s constant and <em>e</em> is the charge of an electron. The phase of the electron wave function appears robust over length scales exceeding 10mm and persisting up to temperatures of T&gt;50K. We show that the experimental signal stems from a periodic field-modulation of the out-of-plane hopping. These results demonstrate extraordinary single-particle quantum coherence lengths in the delafossites.
DOI: 10.6084/m9.figshare.14388440
title: Phylogenomic dataset, Core-genome alignment and Species tree of 155 Bradyrhizobia

description: Result of task 05 of the bioinformatic pipeline Pantagruel (Lassalle et al., 2019) for the reconstruction of the species tree of 155 Bradyrhizobium spp. and close relatives based on their core-genome.<br>The genomes listed in 'assemblies_list' were downloaded from the National Center for Biotechnology Information (NCBI) RefSeq or GenBank databases and used as input for the bioinformatic pipeline Pantagruel to build a phylogenomic database. <br>In short, coding sequences (CDSs) and the corresponding protein sequences were extracted from the RefSeq or GenBank annotation and then clustered into homologous gene families using MMSeqs2 (Steinegger and Söding, 2017). Homologues were aligned with clustal Omega (Sievers et al., 2011) and reverse-translated into CDS alignment with PAL2NAL (Suyama et al., 2006). 453 single-copy core gene families were selected based on their presence in at least 153 of the 155 genomes, thus allowing for rare losses or incomplete genome sequences. CDS alignments for these families were concatenated, resulting in 378 951 aligned nucleotide positions. From this core alignment, a maximum-likelihood (ML) tree was inferred using RAxML (v8.2.4) (Stamatakis et al., 2014) under the GTRCATX model, and branch lengths were then refined under the GTRGAMMAX model, while branch supports were estimated from 200 rapid bootstrap trees.<br>Parameters for the replication of the Pantagruel run are provided in the shell script file 'environ_pantagruel_Brady2019.sh'.
DOI: 10.6084/m9.figshare.14388440.v2
title: Phylogenomic dataset, Core-genome alignment and Species tree of 155 Bradyrhizobia

description: Result of task 05 of the bioinformatic pipeline Pantagruel (Lassalle et al., 2019) for the reconstruction of the species tree of 155 Bradyrhizobium spp. and close relatives based on their core-genome.<br>The genomes listed in 'assemblies_list' were downloaded from the National Center for Biotechnology Information (NCBI) RefSeq or GenBank databases and used as input for the bioinformatic pipeline Pantagruel to build a phylogenomic database. <br>In short, coding sequences (CDSs) and the corresponding protein sequences were extracted from the RefSeq or GenBank annotation and then clustered into homologous gene families using MMSeqs2 (Steinegger and Söding, 2017). Homologues were aligned with clustal Omega (Sievers et al., 2011) and reverse-translated into CDS alignment with PAL2NAL (Suyama et al., 2006). 453 single-copy core gene families were selected based on their presence in at least 153 of the 155 genomes, thus allowing for rare losses or incomplete genome sequences. CDS alignments for these families were concatenated, resulting in 378 951 aligned nucleotide positions. From this core alignment, a maximum-likelihood (ML) tree was inferred using RAxML (v8.2.4) (Stamatakis et al., 2014) under the GTRCATX model, and branch lengths were then refined under the GTRGAMMAX model, while branch supports were estimated from 200 rapid bootstrap trees.<br>Parameters for the replication of the Pantagruel run are provided in the shell script file 'environ_pantagruel_Brady2019.sh'.
DOI: 10.6084/m9.figshare.14388440.v1
title: Phylogenomic dataset, Core-genome alignment and Species tree of 155 Bradyrhizobia

description: Result of task 05 of the bioinformatic pipeline Pantagruel (Lassalle et al., 2019) for the reconstruction of the species tree of 155 Bradyrhizobium spp. and close relatives based on their core-genome.<br>The genomes listed in 'assemblies_list' were downloaded from the National Center for Biotechnology Information (NCBI) RefSeq or GenBank databases and used as input for the bioinformatic pipeline Pantagruel to build a phylogenomic database. <br>In short, coding sequences (CDSs) and the corresponding protein sequences were extracted from the RefSeq or GenBank annotation and then clustered into homologous gene families using MMSeqs2 (Steinegger and Söding, 2017). Homologues were aligned with clustal Omega (Sievers et al., 2011) and reverse-translated into CDS alignment with PAL2NAL (Suyama et al., 2006). 453 single-copy core gene families were selected based on their presence in at least 153 of the 155 genomes, thus allowing for rare losses or incomplete genome sequences. CDS alignments for these families were concatenated, resulting in 378 951 aligned nucleotide positions. From this core alignment, a maximum-likelihood (ML) tree was inferred using RAxML (v8.2.4) (Stamatakis et al., 2014) under the GTRCATX model, and branch lengths were then refined under the GTRGAMMAX model, while branch supports were estimated from 200 rapid bootstrap trees.<br>Parameters for the replication of the Pantagruel run are provided in the shell script file 'environ_pantagruel_Brady2019.sh'.
DOI: 10.5066/p95i7uk2
title: Elements in elk tissues harvested in pre-uranium mining and non-mining areas, 2019

description: These data are comprised of measurements of elements (e.g., uranium, cobalt, nickel, copper, zinc, cadmium, lead, etc.) in elk tissue samples (livers and muscle) collected from tribal hunting grounds (pre-uranium mining site) and an elk farm in Wisconsin (non-mining site) in calendar year 2019.
DOI: 10.3886/e126442
title: Data and code for: Cross-Region Transfer Multipliers in a Monetary Union: Evidence from Social Security and Stimulus Payments

description: US federal transfers to individuals are large, countercyclical, vary geographically, and are often credited with helping to stabilize regional economies. This paper estimates the short-run effects of these transfers using plausibly exogenous regional variation in temporary stimulus payments and permanent Social Security benefit increases. States that received larger transfers tended to grow faster contemporaneously, with a multiplier of around 1.5 for permanent transfers and 1/3 for temporary transfers. Results are broadly consistent with an open-economy New Keynesian model. At business cycle frequencies, cross-region transfer multipliers are not large, suggesting only modest gains in regional stabilization from US federal automatic stabilizers.
description: US State-level Data. Smallest Geographic Unit: US State
DOI: 10.3886/e126442v1
title: Data and code for: Cross-Region Transfer Multipliers in a Monetary Union: Evidence from Social Security and Stimulus Payments

description: US federal transfers to individuals are large, countercyclical, vary geographically, and are often credited with helping to stabilize regional economies. This paper estimates the short-run effects of these transfers using plausibly exogenous regional variation in temporary stimulus payments and permanent Social Security benefit increases. States that received larger transfers tended to grow faster contemporaneously, with a multiplier of around 1.5 for permanent transfers and 1/3 for temporary transfers. Results are broadly consistent with an open-economy New Keynesian model. At business cycle frequencies, cross-region transfer multipliers are not large, suggesting only modest gains in regional stabilization from US federal automatic stabilizers.
description: US State-level Data. Smallest Geographic Unit: US State
DOI: 10.5281/zenodo.4675615
title: Morphological traits and bioindicators: a case study on dung beetles in the Maputaland Centre of Endemism

description: Dung beetles have been identified as important indicators of habitat change in the Maputaland centre of Endemism, an area of southern Mozambique and northern Kwazulu-Natal in South Africa. Maptutaland harbours one of the rarest vegetation types, sand forest, of which only small portions are currently protected in four conservation parks of South. Sand forest habitats are rapidly undergoing transformation due to increasing elephant browsing activities that create a sand forest-mixed woodland matrix. It has been observed that dung beetle assemblages are significantly different in sand forest and mixed woodland habitats, and if elephant activity continues in sand forest patches, it is predicted that dung beetle assemblages will become more homogenous across habitats. Two habitats, namely undisturbed sand forest and mixed woodland, were sampled and I investigated the morphological differences (wing loading and aspect ratio) of wings across habitats using generalists and indicator species. Low wing loading combined with a high aspect ratio enhances lift production and take-off ability with a mechanical power output improving dispersal abilities in mixed woodland indicator species compared to sand forest indicators. Conversely, predictions regarding generalist species were rejected because they had overall similar wing morphology across habitats. Furthermore, if fragmentation of sand forest patches is not managed, dung beetles are expected to become constrained by their wing morphology and a homogeneous arthropod assemblage will occur across habitats. This could jeopardize long-term studies which use dung beetles to monitor the biodiversity and ecosystem functioning in the MC.
description: Dataset used to obtain results of wing morphology in different habitats between species (inter and intra results)
DOI: 10.5281/zenodo.4675614
title: Morphological traits and bioindicators: a case study on dung beetles in the Maputaland Centre of Endemism

description: Dung beetles have been identified as important indicators of habitat change in the Maputaland centre of Endemism, an area of southern Mozambique and northern Kwazulu-Natal in South Africa. Maptutaland harbours one of the rarest vegetation types, sand forest, of which only small portions are currently protected in four conservation parks of South. Sand forest habitats are rapidly undergoing transformation due to increasing elephant browsing activities that create a sand forest-mixed woodland matrix. It has been observed that dung beetle assemblages are significantly different in sand forest and mixed woodland habitats, and if elephant activity continues in sand forest patches, it is predicted that dung beetle assemblages will become more homogenous across habitats. Two habitats, namely undisturbed sand forest and mixed woodland, were sampled and I investigated the morphological differences (wing loading and aspect ratio) of wings across habitats using generalists and indicator species. Low wing loading combined with a high aspect ratio enhances lift production and take-off ability with a mechanical power output improving dispersal abilities in mixed woodland indicator species compared to sand forest indicators. Conversely, predictions regarding generalist species were rejected because they had overall similar wing morphology across habitats. Furthermore, if fragmentation of sand forest patches is not managed, dung beetles are expected to become constrained by their wing morphology and a homogeneous arthropod assemblage will occur across habitats. This could jeopardize long-term studies which use dung beetles to monitor the biodiversity and ecosystem functioning in the MC.
description: Dataset used to obtain results of wing morphology in different habitats between species (inter and intra results)
DOI: 10.5281/zenodo.4675664
title: The response of native ant communities to an alien invasive species (Chromolaena odorata) - the effect of temporal variation in invasion and clearing

description: Alien invasive species can potentially alter each and every trophic level of the ecosystem through its action of habitat change. Chromolaena odorata is an aggressive invader that has the widest distribution of all alien invasive plant species within the Hluhluwe- iMfolozi Park. It is known to invade to an impenetrable extent, shading out and competitively excluding large areas of native vegetation. Ant assemblages of intact native vegetation were compared with ant assemblages of vegetation invaded by C. odorata for different time periods and also to ant assemblages in vegetation cleared of C. odorata for different time periods. Results showed species compositional changes and ant faunal abundance declines for habitats with long invasion periods compared with recently invaded and intact habitats. Clearing of C. odorata seemed effective as no difference in ant faunal abundance was found between cleared and intact habitats. The effect and changes associated with C. odorata invasion thus seems to be reversible and native ant faunal assemblages may be restored and likely reflects similar responses of other fauna. Temporal assessment also indicated important differences in long and short term effects of invasion and clearing.
description: To determine the response of ant communities to Chromolaena odorata and its clearing.
DOI: 10.5281/zenodo.4675663
title: The response of native ant communities to an alien invasive species (Chromolaena odorata) - the effect of temporal variation in invasion and clearing

description: Alien invasive species can potentially alter each and every trophic level of the ecosystem through its action of habitat change. Chromolaena odorata is an aggressive invader that has the widest distribution of all alien invasive plant species within the Hluhluwe- iMfolozi Park. It is known to invade to an impenetrable extent, shading out and competitively excluding large areas of native vegetation. Ant assemblages of intact native vegetation were compared with ant assemblages of vegetation invaded by C. odorata for different time periods and also to ant assemblages in vegetation cleared of C. odorata for different time periods. Results showed species compositional changes and ant faunal abundance declines for habitats with long invasion periods compared with recently invaded and intact habitats. Clearing of C. odorata seemed effective as no difference in ant faunal abundance was found between cleared and intact habitats. The effect and changes associated with C. odorata invasion thus seems to be reversible and native ant faunal assemblages may be restored and likely reflects similar responses of other fauna. Temporal assessment also indicated important differences in long and short term effects of invasion and clearing.
description: To determine the response of ant communities to Chromolaena odorata and its clearing.
DOI: 10.6084/m9.figshare.14394392
title: Relational database of phylo-pangenomic dataset of 155 Bradyrhizobium spp.

description: Relational database in SQLite 3 format as well as input table files, corresponding to the output of task 03 of the bioinfomatic pipeline Pantagruel (Lassalle et al., 2019) on a dataset of 155 genomes of <i>Bradyrhizobium</i> spp. and close relatives.<br>the database schema is defined by scripts 'pantagruel_sqlitedb_genome_initiate.sql' and 'pantagruel_sqlitedb_phylogeny_initiate.sql' available at: https://github.com/flass/pantagruel/tree/usingGeneRax/scripts
DOI: 10.6084/m9.figshare.14394392.v1
title: Relational database of phylo-pangenomic dataset of 155 Bradyrhizobium spp.

description: Relational database in SQLite 3 format as well as input table files, corresponding to the output of task 03 of the bioinfomatic pipeline Pantagruel (Lassalle et al., 2019) on a dataset of 155 genomes of <i>Bradyrhizobium</i> spp. and close relatives.<br>the database schema is defined by scripts 'pantagruel_sqlitedb_genome_initiate.sql' and 'pantagruel_sqlitedb_phylogeny_initiate.sql' available at: https://github.com/flass/pantagruel/tree/usingGeneRax/scripts
DOI: 10.5281/zenodo.4072016
title: Downscaling of an unstructured model from the coastal-ocean to the Goro lagoon and the Po river delta branches (Italy): results of the GOLFEM finite element model

description: The GOLFEM model (Goro Lagoon Finite Element Model, based on the SHYFEM code) focuses on the high-resolution modelling of the Goro Lagoon, along with five Po river branches and the coastal area of the Po delta in the northern Adriatic Sea (Italy). An unstructured 3D triangular mesh was designed with a variable resolution from 2 km at the open sea boundary (12 km offshore), up to 10 m in the lagoon channel and river branches. The GOLFEM model (Goro Lagoon Finite Element Model, based on the SHYFEM code) focuses on the high-resolution modelling of the Goro Lagoon, along with five Po river branches and the coastal area of the Po delta in the northern Adriatic Sea (Italy). An unstructured 3D triangular mesh was designed with a variable resolution from 2 km at the open sea boundary (12 km offshore), up to 10 m in the lagoon channel and river branches. GOLFEM is based on SHYFEM (Umgiesser et al. 2004, 2014), a shallow water, finite elements model, running on a staggered triangular grid. The model configuration is 3D baroclinic, forced at the open sea boundary by AdriaROMS model (Russo et al. 2013) and the analysis of the atmospheric model COSMO-I2. The model results of the 2018 simulation have been converted in a regular grid format (NetCDF) at 100m resolution for each variable. The additional postprocessed results that are discussed in the paper "Downscaling with an unstructured coastal-ocean model to the Po river delta branches and the Goro lagoon" (<strong>DOI:</strong> 10.3389/fmars.2021.647781), have been also converted at 50m resolution. Several lateral boundary condition of freshwater input and climatological water temperature from pumping stations and Po di Volano were uploaded, as like for the Po river.
description: Please refer to the README file for the complete list of the files available and their content.
DOI: 10.5281/zenodo.4072015
title: Downscaling of an unstructured model from the coastal-ocean to the Goro lagoon and the Po river delta branches (Italy): results of the GOLFEM finite element model

description: The GOLFEM model (Goro Lagoon Finite Element Model, based on the SHYFEM code) focuses on the high-resolution modelling of the Goro Lagoon, along with five Po river branches and the coastal area of the Po delta in the northern Adriatic Sea (Italy). An unstructured 3D triangular mesh was designed with a variable resolution from 2 km at the open sea boundary (12 km offshore), up to 10 m in the lagoon channel and river branches. The GOLFEM model (Goro Lagoon Finite Element Model, based on the SHYFEM code) focuses on the high-resolution modelling of the Goro Lagoon, along with five Po river branches and the coastal area of the Po delta in the northern Adriatic Sea (Italy). An unstructured 3D triangular mesh was designed with a variable resolution from 2 km at the open sea boundary (12 km offshore), up to 10 m in the lagoon channel and river branches. GOLFEM is based on SHYFEM (Umgiesser et al. 2004, 2014), a shallow water, finite elements model, running on a staggered triangular grid. The model configuration is 3D baroclinic, forced at the open sea boundary by AdriaROMS model (Russo et al. 2013) and the analysis of the atmospheric model COSMO-I2. The model results of the 2018 simulation have been converted in a regular grid format (NetCDF) at 100m resolution for each variable. The additional postprocessed results that are discussed in the paper "Downscaling with an unstructured coastal-ocean model to the Po river delta branches and the Goro lagoon" (<strong>DOI:</strong> 10.3389/fmars.2021.647781), have been also converted at 50m resolution. Several lateral boundary condition of freshwater input and climatological water temperature from pumping stations and Po di Volano were uploaded, as like for the Po river.
description: Please refer to the README file for the complete list of the files available and their content.