cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.963421
title: Differences in richness of vascular plants, mosses, and liverworts in southern Norwegian alpine vegetation

description: <b><i>Background</i>:</b> Theories regarding patterns of species richness often focus on single factors such as stress, productivity and disturbance, but these have recently been challenged. Vascular plant species richness is also frequently used as a surrogate for richness in other species groups, but species richness relationships have rarely been studied in alpine areas.<b><i>Aims</i>:</b> To establish the relationship between environmental variables and species richness of vascular plants, mosses and liverworts, and to identify common patterns across these different groups.<b><i>Methods</i>:</b> A stratified random sampling procedure was followed to select sample plots (4 m<sup>2</sup>) from ecologically different homogeneous alpine vegetation stands. The data were analysed by Pearsson correlation analysis, regression analysis, stepwise regression analysis, principal correlation analysis (PCA), and redundancy analysis (RDA).<b><i>Results</i>:</b> 210 vascular plants, 152 mosses and 89 liverworts were identified from 304 plots. Humped (quadratic) responses were found for some species groups only in relation to date of snowmelt and total vascular plant cover. Vascular plant and moss richness were strongly positively correlated with soil richness.<b><i>Conclusions</i>:</b> Richness of vascular plants and mosses, and mosses and liverworts, may be used as surrogates for one another in the alpine vegetation plots studied, but vascular plant richness cannot be used as a surrogate for liverwort richness.
DOI: 10.6084/m9.figshare.963421.v2
title: Differences in richness of vascular plants, mosses, and liverworts in southern Norwegian alpine vegetation

description: <b><i>Background</i>:</b> Theories regarding patterns of species richness often focus on single factors such as stress, productivity and disturbance, but these have recently been challenged. Vascular plant species richness is also frequently used as a surrogate for richness in other species groups, but species richness relationships have rarely been studied in alpine areas.<b><i>Aims</i>:</b> To establish the relationship between environmental variables and species richness of vascular plants, mosses and liverworts, and to identify common patterns across these different groups.<b><i>Methods</i>:</b> A stratified random sampling procedure was followed to select sample plots (4 m<sup>2</sup>) from ecologically different homogeneous alpine vegetation stands. The data were analysed by Pearsson correlation analysis, regression analysis, stepwise regression analysis, principal correlation analysis (PCA), and redundancy analysis (RDA).<b><i>Results</i>:</b> 210 vascular plants, 152 mosses and 89 liverworts were identified from 304 plots. Humped (quadratic) responses were found for some species groups only in relation to date of snowmelt and total vascular plant cover. Vascular plant and moss richness were strongly positively correlated with soil richness.<b><i>Conclusions</i>:</b> Richness of vascular plants and mosses, and mosses and liverworts, may be used as surrogates for one another in the alpine vegetation plots studied, but vascular plant richness cannot be used as a surrogate for liverwort richness.
DOI: 10.6084/m9.figshare.963421.v1
title: Differences in richness of vascular plants, mosses, and liverworts in southern Norwegian alpine vegetation

description: <b><i>Background</i>:</b> Theories regarding patterns of species richness often focus on single factors such as stress, productivity and disturbance, but these have recently been challenged. Vascular plant species richness is also frequently used as a surrogate for richness in other species groups, but species richness relationships have rarely been studied in alpine areas.<b><i>Aims</i>:</b> To establish the relationship between environmental variables and species richness of vascular plants, mosses and liverworts, and to identify common patterns across these different groups.<b><i>Methods</i>:</b> A stratified random sampling procedure was followed to select sample plots (4 m<sup>2</sup>) from ecologically different homogeneous alpine vegetation stands. The data were analysed by Pearsson correlation analysis, regression analysis, stepwise regression analysis, principal correlation analysis (PCA), and redundancy analysis (RDA).<b><i>Results</i>:</b> 210 vascular plants, 152 mosses and 89 liverworts were identified from 304 plots. Humped (quadratic) responses were found for some species groups only in relation to date of snowmelt and total vascular plant cover. Vascular plant and moss richness were strongly positively correlated with soil richness.<b><i>Conclusions</i>:</b> Richness of vascular plants and mosses, and mosses and liverworts, may be used as surrogates for one another in the alpine vegetation plots studied, but vascular plant richness cannot be used as a surrogate for liverwort richness.
DOI: 10.6084/m9.figshare.963422.v2
title: Ecological factors driving plant species diversity in the South Aegean Volcanic Arc and other central Aegean islands

description: <b><i>Background:</i></b> The South Aegean Volcanic Arc (SAVA), one of the most notable geological structures of the Mediterranean Sea, is floristically well known. Nevertheless, the factors that contribute to shaping the plant species richness of the SAVA remain unclear.<b><i>Aims:</i></b> To investigate the factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean islands.<b><i>Methods:</i></b> We used stepwise multiple regression to test the relationship between a number of environmental factors and plant species richness in the SAVA, as well as the residuals from the species–area linear regressions of native, Greek and Cycladian endemic taxa as indicators of relative species richness.<b><i>Results:</i></b> The area was confirmed to be the most powerful single explanatory variable of island species richness, while geodiversity, maximum elevation and mean annual precipitation explained a large proportion of variance for almost all the species richness measures. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots.<b><i>Conclusions:</i></b> We have demonstrated that geodiversity is an important factor in shaping plant species diversity in the Cyclades, while mean annual precipitation, human population density and maximum elevation were significant predictors of the Greek endemics present in the Cyclades. Finally, Anafi was found to be a plant diversity hotspot in the South Aegean Sea.
DOI: 10.6084/m9.figshare.963422.v1
title: Ecological factors driving plant species diversity in the South Aegean Volcanic Arc and other central Aegean islands

description: <b><i>Background:</i></b> The South Aegean Volcanic Arc (SAVA), one of the most notable geological structures of the Mediterranean Sea, is floristically well known. Nevertheless, the factors that contribute to shaping the plant species richness of the SAVA remain unclear.<b><i>Aims:</i></b> To investigate the factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean islands.<b><i>Methods:</i></b> We used stepwise multiple regression to test the relationship between a number of environmental factors and plant species richness in the SAVA, as well as the residuals from the species–area linear regressions of native, Greek and Cycladian endemic taxa as indicators of relative species richness.<b><i>Results:</i></b> The area was confirmed to be the most powerful single explanatory variable of island species richness, while geodiversity, maximum elevation and mean annual precipitation explained a large proportion of variance for almost all the species richness measures. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots.<b><i>Conclusions:</i></b> We have demonstrated that geodiversity is an important factor in shaping plant species diversity in the Cyclades, while mean annual precipitation, human population density and maximum elevation were significant predictors of the Greek endemics present in the Cyclades. Finally, Anafi was found to be a plant diversity hotspot in the South Aegean Sea.
DOI: 10.6084/m9.figshare.963411
title: Basin-wide variations in Amazon forest nitrogen-cycling characteristics as inferred from plant and soil <sup>15</sup>N:<sup>14</sup>N measurements

description: <b><i>Background:</i></b> Patterns in tropical forest nitrogen cycling are poorly understood. In particular, the extent to which leguminous trees in these forests fix nitrogen is unclear. <b><i>Aims:</i></b> We aimed to determine factors that explain variation in foliar δ<sup>15</sup>N (δ<sup>15</sup>N<sub>F</sub>) for Amazon forest trees, and to evaluate the extent to which putatively N<sub>2</sub>-fixing Fabaceae acquire nitrogen from the atmosphere. <b><i>Methods:</i></b> Upper-canopy δ<sup>15</sup>N<sub>F</sub> values were determined for 1255 trees sampled across 65 Amazon forest plots. Along with plot inventory data, differences in δ<sup>15</sup>N<sub>F</sub> between nodule-forming Fabaceae and other trees were used to estimate the extent of N<sub>2</sub> fixation. <b><i>Results:</i></b> δ<sup>15</sup>N<sub>F</sub> ranged from −12.1‰ to +9.3‰. Most of this variation was attributable to site-specific conditions, with extractable soil phosphorus and dry-season precipitation having strong influences, suggesting a restricted availability of nitrogen on both young and old soils and/or at low precipitation. Fabaceae constituted fewer than 10% of the sampled trees, and only 36% were expressed fixers. We estimated an average Amazon forest symbiotic fixation rate of 3 kg N ha<sup>−1</sup> year<sup>−1</sup>. <b><i>Conclusion:</i></b> Plant δ<sup>15</sup>N indicate that low levels of nitrogen availability are only likely to influence Amazon forest function on immature or old weathered soils and/or where dry-season precipitation is low. Most Fabaceae species that are capable of nodulating do not fix nitrogen in Amazonia.
DOI: 10.6084/m9.figshare.963409
title: Changes in forest structure and composition after fire in tropical montane cloud forests near the Andean treeline

description: <b><i>Background:</i></b> In tropical montane cloud forests (TMCFs) fires can be a frequent source of disturbance near the treeline. <b><i>Aims:</i></b> To identify how forest structure and tree species composition change in response to fire and to identify fire-tolerant species, and determine which traits or characteristics are associated with fire tolerance. <b><i>Methods:</i></b> Shifts in forest structure and diversity were assessed on 15 paired plots in burnt and unburnt (control) forests, along a fire chronosequence. Species were classified as fire-sensitive, fire survivors or fire thrivers, using a fire tolerance index. Regression and tree analyses were used to determine which traits contributed to the fire tolerance of species. <b><i>Results:</i></b> There were more small- and medium-sized trees in the burnt plots independent of time since the last fire. There were shifts in family importance value and in species diversity among the plots. Of the 73 species analysed there were 39 fire-sensitive species, 19 fire survivors and 14 fire thrivers. Sprouting ability and biomass showed a positive relationship with the fire tolerance of species. <b><i>Conclusions:</i></b> There were immediate as well as long-term (up to 15 years) effects of fire on forest structure and species composition, suggesting that TMCFs take more than 15 years to regenerate from a fire. Long-term studies are needed to fully understand regeneration patterns of TMCFs after fires.
DOI: 10.6084/m9.figshare.963411.v1
title: Basin-wide variations in Amazon forest nitrogen-cycling characteristics as inferred from plant and soil <sup>15</sup>N:<sup>14</sup>N measurements

description: <b><i>Background:</i></b> Patterns in tropical forest nitrogen cycling are poorly understood. In particular, the extent to which leguminous trees in these forests fix nitrogen is unclear. <b><i>Aims:</i></b> We aimed to determine factors that explain variation in foliar δ<sup>15</sup>N (δ<sup>15</sup>N<sub>F</sub>) for Amazon forest trees, and to evaluate the extent to which putatively N<sub>2</sub>-fixing Fabaceae acquire nitrogen from the atmosphere. <b><i>Methods:</i></b> Upper-canopy δ<sup>15</sup>N<sub>F</sub> values were determined for 1255 trees sampled across 65 Amazon forest plots. Along with plot inventory data, differences in δ<sup>15</sup>N<sub>F</sub> between nodule-forming Fabaceae and other trees were used to estimate the extent of N<sub>2</sub> fixation. <b><i>Results:</i></b> δ<sup>15</sup>N<sub>F</sub> ranged from −12.1‰ to +9.3‰. Most of this variation was attributable to site-specific conditions, with extractable soil phosphorus and dry-season precipitation having strong influences, suggesting a restricted availability of nitrogen on both young and old soils and/or at low precipitation. Fabaceae constituted fewer than 10% of the sampled trees, and only 36% were expressed fixers. We estimated an average Amazon forest symbiotic fixation rate of 3 kg N ha<sup>−1</sup> year<sup>−1</sup>. <b><i>Conclusion:</i></b> Plant δ<sup>15</sup>N indicate that low levels of nitrogen availability are only likely to influence Amazon forest function on immature or old weathered soils and/or where dry-season precipitation is low. Most Fabaceae species that are capable of nodulating do not fix nitrogen in Amazonia.
DOI: 10.6084/m9.figshare.963409.v1
title: Changes in forest structure and composition after fire in tropical montane cloud forests near the Andean treeline

description: <b><i>Background:</i></b> In tropical montane cloud forests (TMCFs) fires can be a frequent source of disturbance near the treeline. <b><i>Aims:</i></b> To identify how forest structure and tree species composition change in response to fire and to identify fire-tolerant species, and determine which traits or characteristics are associated with fire tolerance. <b><i>Methods:</i></b> Shifts in forest structure and diversity were assessed on 15 paired plots in burnt and unburnt (control) forests, along a fire chronosequence. Species were classified as fire-sensitive, fire survivors or fire thrivers, using a fire tolerance index. Regression and tree analyses were used to determine which traits contributed to the fire tolerance of species. <b><i>Results:</i></b> There were more small- and medium-sized trees in the burnt plots independent of time since the last fire. There were shifts in family importance value and in species diversity among the plots. Of the 73 species analysed there were 39 fire-sensitive species, 19 fire survivors and 14 fire thrivers. Sprouting ability and biomass showed a positive relationship with the fire tolerance of species. <b><i>Conclusions:</i></b> There were immediate as well as long-term (up to 15 years) effects of fire on forest structure and species composition, suggesting that TMCFs take more than 15 years to regenerate from a fire. Long-term studies are needed to fully understand regeneration patterns of TMCFs after fires.
DOI: 10.6084/m9.figshare.963397
title: Comparison of generic force fields for packing of concave molecules

description: Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.
DOI: 10.6084/m9.figshare.963397.v1
title: Comparison of generic force fields for packing of concave molecules

description: Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.
DOI: 10.6084/m9.figshare.963397.v2
title: Comparison of generic force fields for packing of concave molecules

description: Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.
DOI: 10.6084/m9.figshare.963397.v3
title: Comparison of generic force fields for packing of concave molecules

description: Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.
DOI: 10.6084/m9.figshare.963397.v4
title: Comparison of generic force fields for packing of concave molecules

description: Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.
DOI: 10.6084/m9.figshare.963378
title: Density-fitted singles and doubles coupled cluster on graphics processing units

description: We adapt an algorithm for singles and doubles coupled cluster (CCSD) that uses density fitting or Cholesky decomposition (CD) in the construction and contraction of all electron repulsion integrals (ERIs) for use on heterogeneous compute nodes consisting of a multicore central processing unit (CPU) and at least one graphics processing unit (GPU). The use of approximate three-index ERIs ameliorates two of the major difficulties in designing scientific algorithms for GPUs: (1) the extremely limited global memory on the devices and (2) the overhead associated with data motion across the bus. For the benzene trimer described by an aug-cc-pVDZ basis set, the use of a single NVIDIA Tesla C2070 (Fermi) GPU accelerates a CD-CCSD computation by a factor of 2.1, relative to the multicore CPU-only algorithm that uses six highly efficient Intel Core i7-3930K CPU cores. The use of two Fermi GPUs provides an acceleration of 2.89, which is comparable to that observed when using a single NVIDIA Kepler K20c GPU (2.73).
DOI: 10.6084/m9.figshare.963376
title: Similarity transformed equation of motion coupled cluster theory revisited: a benchmark study of valence excited states

description: The similarity transformed equation of motion coupled cluster (STEOM-CC) method is benchmarked against CC3 and EOM-CCSDT-3 for a large test set of valence excited states of organic molecules studied by Schreiber et al. [M. Schreiber, M.R. Silva-Junior, S.P. Sauer, and W. Thiel, J. Chem. Phys. <b>128</b>, 134110 (2008)]. STEOM-CC is found to behave quite satisfactorily and provides significant improvement over EOM-CCSD, CASPT2 and NEVPT2 for singlet excited states, lowering standard deviations of these methods by almost a factor of 2. Triplet excited states are found to be described less accurately, however. Besides the parent version of STEOM-CC, additional variations are considered. STEOM-D includes a perturbative correction from doubly excited determinants. The novel STEOM-H (ω) approach presents a sophisticated technique to render the STEOM-CC transformed Hamiltonian hermitian. In STEOM-PT, the expensive CCSD step is replaced by many-body second-order perturbation theory (MBPT(2)), while extended STEOM (EXT-STEOM) provides access to doubly excited states. To study orbital invariance in STEOM, we investigate orbital rotation in the STEOM-ORB approach. Comparison of theses variations of STEOM for the large test set provides a comprehensive statistical basis to gauge the usefulness of these approaches.
DOI: 10.6084/m9.figshare.963377
title: The eight-valence-electron systems re-examined: convergence of the coupled-cluster series and performance of quasiperturbative methods for quadruple excitations

description: We present the results of a coupled-cluster basis-set convergence study on 12 eight-valence-electron systems. These small systems span a wide range of correlation character (from purely dynamical correlation to pathological static correlation) as well as of chemical bonding (from ionic with some backdonation to quadruple covalent bonding). Indicators such as the correlation entropy and the CASSCF 1-C<sub>0</sub><sup>2</sup>, which primarily sample type A static correlation, are good predictors for the energetic importance of connected quintuple excitations, T<sub>5</sub>, and to a lesser extent of higher order triple excitations, T<sub>3</sub>–(T). The percentage of the total atomisation energy recovered by connected triple excitations, %TAE[(T)], is however a fair predictor for the importance of connected quadruples, T<sub>4</sub>. Of the various ansätze for quasiperturbative connected quadruples, CCSDT(Q)/B appears to be the most robust, even as it is still outperformed by the much more expensive CCSDT(Q)<sub>Λ</sub>.
DOI: 10.6084/m9.figshare.963378.v2
title: Density-fitted singles and doubles coupled cluster on graphics processing units

description: We adapt an algorithm for singles and doubles coupled cluster (CCSD) that uses density fitting or Cholesky decomposition (CD) in the construction and contraction of all electron repulsion integrals (ERIs) for use on heterogeneous compute nodes consisting of a multicore central processing unit (CPU) and at least one graphics processing unit (GPU). The use of approximate three-index ERIs ameliorates two of the major difficulties in designing scientific algorithms for GPUs: (1) the extremely limited global memory on the devices and (2) the overhead associated with data motion across the bus. For the benzene trimer described by an aug-cc-pVDZ basis set, the use of a single NVIDIA Tesla C2070 (Fermi) GPU accelerates a CD-CCSD computation by a factor of 2.1, relative to the multicore CPU-only algorithm that uses six highly efficient Intel Core i7-3930K CPU cores. The use of two Fermi GPUs provides an acceleration of 2.89, which is comparable to that observed when using a single NVIDIA Kepler K20c GPU (2.73).