cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57707/fmi-b2share.rzm7y-jjn63
title: Data for manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo" by Aakula et al.

description: Data and python code for the manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo", for performing emulator hyperparameter optimization and training. Python file optimize_LSTM_emulator.py can be used either for training an LSTM emulator with predefined hyperparameters or to optimize hyperparameters from a given hyperparameter space. The training data for each fold is included in the files of shape training_data_fold_{}.parquet. The data is obtained from model simulations, including model inputs (meteorological forcings obtained from ERA5 data), model parameters (sampled from distributions defined in the manuscript) and model (BASGRA) outputs. Python file NUTS_calibration.py can be used to calibrate the emulator using the HMC NUTS algorithm against data from the given sites and years. The calibration data for each site is included in the files of shape observed_df_{}.parquet, which include meteorological data (ERA5) of the corresponding site, model parameters on soil properties of the specific site and the measured GPP values. Text file examples.txt gives instructions and examples on running the scripts.
DOI: 10.57707/fmi-b2share.evb3z-d6480
title: Data for manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo" by Aakula et al.

description: Data and python code for the manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo", for performing emulator hyperparameter optimization and training. Python file optimize_LSTM_emulator.py can be used either for training an LSTM emulator with predefined hyperparameters or to optimize hyperparameters from a given hyperparameter space. The training data for each fold is included in the files of shape training_data_fold_{}.parquet. The data is obtained from model simulations, including model inputs (meteorological forcings obtained from ERA5 data), model parameters (sampled from distributions defined in the manuscript) and model (BASGRA) outputs. Python file NUTS_calibration.py can be used to calibrate the emulator using the HMC NUTS algorithm against data from the given sites and years. The calibration data for each site is included in the files of shape observed_df_{}.parquet, which include meteorological data (ERA5) of the corresponding site, model parameters on soil properties of the specific site and the measured GPP values. Text file examples.txt gives instructions and examples on running the scripts.
DOI: 10.5061/dryad.3n5tb2rkm
title: Data for: Effects of nutrient heterogeneity on root foraging and plant growth at the individual and community level

description: Plants can respond to heterogeneous nutrient distribution through
 selective root placement to enhance nutrient uptake. It is believed that
 nutrient heterogeneity can better promote plant growth than homogeneous
 nutrient distribution, but comprehensive analyses are relatively few. We
 meta-analyzed the data from 131 comparative studies and synthesized the
 effects of nutrient heterogeneity on root foraging and plant growth, and
 examined the roles of patch scale and contrast. Plant responses to
 nutrient heterogeneity was phylogenetically conserved, and the response in
 shoot biomass was more correlated with the response in root biomass than
 with root foraging precision. Root precision depended on competition
 status, and plants in interspecific competition had lower precision.
 Community-level responses to nutrient heterogeneity were more significant
 than individual-level responses. With increasing patch scale, root
 foraging precision declined, while overall shoot and root responses of
 individuals increased. Moderate patch contrast significantly increased
 root responses compared to low and high patch contrast. Our results
 indicate that plants optimize nutrient acquisition from heterogeneous
 patches mainly through increasing root growth rate and exploit nutrients
 more effectively at the community than individual level. Patch attribute
 mediation of nutrient heterogeneity effects on plants may help design
 fertilization practices to promote productivity and conserve
 biodiversity.
DOI: 10.5061/dryad.8kprr4xqn
title: Nano-laponite/polymer composite as filtration reducer on water-based drilling fluid and mechanism study

description: In drilling deep complex formations, most drilling fluid additives have
 insufficient temperature and salt tolerance, resulting in the decline of
 drilling fluid performance. This study used 2-acrylamide-2-methylpropane
 sulfonic acid, acrylamide, dimethyl diallyl ammonium chloride, and
 modified nano-laponite to synthesize a nanocomposite filtrate reducer
 (ANDP) with excellent temperature and salt resistance, which can maintain
 the performance of drilling fluid. The structure of ANDP was analyzed by a
 transmission electron microscope and an infrared spectrometer. The thermal
 stability of ANDP was studied by thermogravimetric analysis. The
 performance of ANDP was evaluated in a water-based drilling fluid. The
 mechanism was analyzed per clay-particle size distribution, Zeta
 potential, filter cake permeability, and scanning electron microscopy
 imaging. The results show that ANDP has good thermal stability and
 expected molecular structure. The filtration of freshwater drilling fluid
 after aging at 200°C is 10.4 mL and that of saturated brine drilling fluid
 is 6.4 mL after aging at 150°C. Mechanism analysis suggests that the ANDP
 increases the thickness of clay particle hydration layer and maintains the
 colloidal stability of the drilling fluid. ANDP inhibits the agglomeration
 of clay particles and significantly reduces the filtration by forming
 dense mud cake.
DOI: 10.5061/dryad.47d7wm3gf
title: Temporal stabilizing effects of species richness and seed arrangement on grassland biomass production

description: 1. The extent to which individuals experience inter- and intraspecific
 interactions through their spatial arrangements within diverse plant
 communities, whether because of confounding effects of species richness,
 evenness, or direct changes in species patch sizes on their neighborhood
 relationships, could affect grassland biomass production and its stability
 at community scales. Elucidating the ways in which neighborhood effects
 and species richness contribute to such community responses has important
 implications for how practitioners establish grasslands to meet forage
 production and conservation goals. 2. We assessed the effects of altering
 plant species richness (3 levels: 2, 4, or 8 forage species per plot) and
 seed arrangements (4 levels: species mixed and seeded or seeded in 0.0625
 m2, 0.25 m2, or 1.0 m2 single-species patches while maintaining plot-scale
 species evenness) on aboveground biomass production and its temporal
 stability in developing grasslands seeded with a suite of globally common
 forage species (three legumes, three cool-season grasses, two warm-season
 grasses). 3. Communities seeded with more species and those with their
 seeds arranged into smaller conspecific patches produced more biomass and
 were more temporally stable than those seeded with fewer species and
 larger conspecific patches. The effect of manipulating species
 arrangements is attributable to greater neighborhood scale interspecific
 interactions and stronger complementary effects. Furthermore, seeding
 species into conspecific patches resulted in communities that were 34%
 more productive, that were just as temporally stable, and that had similar
 diversity effects as those seeded with a species mixture, as is common in
 grassland reconstruction efforts. 4. Synthesis: In comparison with
 conventional mixed-seeding methods, seeding grasslands with high species
 richness and small, single-species patches may promote grassland
 reconstruction through increased biomass production, temporal stability,
 and complementarity effects. Our study highlights the importance of
 regulating intraspecific interactions within diverse communities for
 improving grassland biomass production and suggests that efforts to
 reevaluate methods used to establish forage and conservation grasslands
 could result in greater biomass production and stability in these systems.
DOI: 10.5061/dryad.jsxksn0bz
title: A Permian fish reveals widespread distribution of neopterygian-like jaw suspension

description: The actinopterygian crown group (comprising all living ray-finned fishes)
 originated by the end of the Carboniferous. However, most late Paleozoic
 taxa are stem actinopterygians, and broadly resemble stratigraphically
 older taxa. The early Permian †Brachydegma caelatum is notable for its
 three-dimensional preservation and past phylogenetic interpretations as a
 nested member of the neopterygian crown. Here, we use computed
 microtomography to redescribe †Brachydegma, uncovering an unanticipated
 combination of primitive (e.g., aortic canal; immobile maxilla) and
 derived (e.g., differentiated occipital ossifications; posterior stem of
 parasphenoid; two accessory hyoidean ossifications; double jaw joint)
 endoskeletal features relative to most other Paleozoic actinopterygians.
 Some of these features were previously thought restricted to the
 neopterygian crown. The precise phylogenetic position of †Brachydegma is
 unclear, with placements either on the polypterid stem, or as an
 early-diverging stem neopterygian. However, our analyses decisively reject
 previous placements of †Brachydegma in the neopterygian crown. Critically,
 we demonstrate that key-endoskeletal components of the hyoid portion of
 the suspensorium of crown neopterygians appeared deeper in the tree than
 previously thought.
description: This dataset includes an evolving phylogenetic matrix of
 morphological characters. The matrix can be found in .nex and .tnt
 formats. Analyses of this matrix using various algorithms that are part of
 the TNT software, resulted in phylogenetic trees that are also part of
 this dataset. Finally, the tree resulting from a bayesian analysis using
 MrBayes is also included in this dataset. Most trees
 can be opened either on Mesquite or directly with TNT, after loading the
 relevant phylogenetic matrix file.
DOI: 10.5061/dryad.v15dv41z0
title: Experimental evolution of a more restrained clutch size when filial cannibalism is prevented in burying beetles Nicrophorus vespilloides

description: The over-production of offspring is commonly associated with high hatching
 failure and a mechanism for dispensing with surplus young. We used
 experimental evolution of burying beetle populations Nicrophorus
 vespilloides to determine causality in these correlations. We asked: does
 eliminating the mechanism for killing ‘spare’ offspring cause the
 evolution of a more restrained clutch size, and consequently select for
 reduced hatching failure? N. vespilloides typically over-produces eggs but
 kills 1st instar larvae through partial filial cannibalism during brood
 care. We established replicate evolving populations that either could
 practice filial cannibalism (Full Care) or could not, by removing parents
 before their young hatched (No Care). After 20+ generations of
 experimental evolution, we measured clutch size and hatching success. We
 found that No Care females produced fewer eggs than Full Care females when
 allowed to breed on a small corpse, a finding not explained by differences
 in female quality. On larger corpses, females from both populations laid
 similar numbers of eggs. Furthermore, hatching success was greater in the
 No Care populations on small corpses. Our results suggest that the
 adaptive over-production of offspring depends on a mechanism for
 eliminating surplus young and that killing offspring, in turn, relaxes
 selection against hatching failure.
description: Data were collected from experimentally evolving populations of
 <em>Nicrophorus vespilloides</em>. Please see
 "Experimental evolution of a more restrained clutch size when filial
 cannibalism is prevented in burying beetles Nicrophorus vespilloides"
 for complete details.
DOI: 10.5061/dryad.jwstqjqbs
title: Data from: Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils

description: Arctic soils are marked by cryoturbic features, which impact
 soil-atmosphere methane (CH4) dynamics vital to global climate regulation.
 Cryoturbic diapirism alters C/N chemistry within frost boils by
 introducing soluble organic carbon and nutrients, potentially influencing
 microbial CH4 oxidation. CH4 oxidation in soils,
 however, requires a spatio-temporal convergence of ecological factors to
 occur. Spatial delineation of microbial activity with respect to these key
 microbial and biogeochemical factors at relevant scales is experimentally
 challenging in inherently complex and heterogeneous natural soil matrices.
 This work aims to overcome this barrier by spatially linking microbial
 CH4 oxidation with C/N chemistry and metagenomic characteristics.
 This is achieved by using positron-emitting radiotracers to visualize
 millimeter-scale active CH4 uptake areas in Arctic soils with and
 without diapirism. X-ray absorption spectroscopic speciation of active and
 inactive areas shows CH4 uptake spatially associates with greater
 proportions of inorganic N in diapiric frost boils. Metagenomic analyses
 reveal Ralstonia pickettii associates with
 CH4 uptake across soils along with pertinent CH4 and
 inorganic N metabolism associated genes. This study highlights the
 critical relationship between CH4 and N cycles in Arctic soils, with
 potential implications for better understanding future climate.
 Furthermore, our experimental framework presents a novel, widely
 applicable strategy for unraveling ecological relationships underlying
 greenhouse gas dynamics under global change.
DOI: 10.5061/dryad.0cfxpnw4s
title: Data and code for: Uncovering commercial activity in informal cities

description: Knowledge of the spatial organisation of economic activity within a city
 is key to policy concerns. However, in developing cities with high levels
 of informality, this information is often unavailable. Recent progress in
 machine learning together with the availability of street imagery offers
 an affordable and easily automated solution. Here we propose an algorithm
 that can detect what we call visible firms using street view imagery.
 Using Medellín, Colombia as a case study, we illustrate how this approach
 can be used to uncover previously unseen economic activity. This dataset
 contains the data and code required to replicate our analysis for the
 manuscript: "Uncovering commercial activity in informal cities."
description: The dataset contains has two components. More information on both
 of them is found in the corresponding README files. 
 Code and data related to detecting visible firms in Medellin.
 Random locations were sampled from the street grid of
 the city. A model was trained on the google street view images
 corresponding to them. The model code is in the folder best_model, and the
 location coordinates are found in the data folder.
 The predictions of the model are found in the prediction tab,
 and the corresponding metrics are found in the main folder.
 Code and data for the analysis of the
 spatial distribution found with the model presented in 1. 
 Data on the location of all detections in the city of
 Medellin. Code to recreate the analysis/figures in
 the paper.
DOI: 10.5061/dryad.8cz8w9gss
title: Appendices of basal Anseriformes from the early Paleogene of North America and Europe

description: We describe nearly complete skeletons of basal Anseriformes from the
 Latest Paleocene to the early Eocene of North America and Europe.
 Collectively, these birds appear to be representative of anseriforms near
 the divergence of Anhimae and Anseres, but their exact positions relative
 to these clades remains uncertain. A new family, Anachronornithidae nov.
 fam., is erected on the basis of one of these, Anachronornis anhimops nov.
 gen., nov. gen. et sp., to which the others cannot be confidently
 assigned. The new fossils augment a growing collection of early
 Pan-Anseriformes, which in their diversity do not paint an unambiguous
 picture of phylogeny or character state evolution on the path to or within
 crown-Anseriformes. Anachronornis nov. gen. is similar in some aspects of
 both cranial and postcranial anatomy to other well-represented early
 Paleogene Anseriformes and members of Anseres, such as Presbyornis
 Wetmore, 1926. However, it exhibits a more landfowl-like bill, like that
 of Anhimae and unlike the spatulate bill of Anseres. Additional specimens
 of similar basal Anseriformes of uncertain affinities from the early
 Eocene of North America and Europe further complicate interpretation of
 character state polarity due to the mosaicism of primitive and derived
 characters they exhibit.
description: Appendices include input files in nexus format (i.e., data
 matrices, executable commands, and constraint trees) for phylogenetic
 parsimony analysis (including bootstrap) and Kishino-Hasegawa tests in
 PAUP and Bayesian phylogenetic anlysis in MrBayes. Appendices also include
 output files (i.e., results) of these analyses and .tre files that can be
 opened with Figtree. Also included are Appendices of shared characters and
 apomorphies for each of seven datasets.
description: All included files can be opened with MSword or any text editor.
 Many of these are executable files that can be opened and run in PAUP,
 MrBayes, and Figtree.
DOI: 10.5061/dryad.ncjsxksx2
title: Location of 82 methane point sources in Shanxi, China

description: These data were generated to investigate the coal mine methane (CMM)
 emitters. GF-5B provided hyperspectral cubes, and a matched filter
 algorithm was used to obtain the XCH4 enhancement maps. The methane plumes
 were extracted by visual interpretation and these high spatial resolution
 images. Some of the results were assessed using on-site measurements to
 confirm the ability to detect the methane emission sources by
 hyperspectral cubes. The location of point sources detected is provided in
 .kmz format.
description: According to the satellite data documentation, the hyperspectral
 data needs radiometric calibration and RPC Orthorectification.
 All bands between 2200 and 2360 nm were selected to retrive XCH4
 enhancements.
description: # Location of 82 point sources in Shanxi, China
 [https://doi.org/10.5061/dryad.ncjsxksx2](https://doi.org/10.5061/dryad.ncjsxksx2) This is the location of 82 detected point sources in Shanxi, China by GF5B satellite. The hyperspectral data is processed by the Matched Filter method. The methane plumes were extracted by visual interpretation and these high spatial resolution images. ## Description of the data and file structure The location of point sources detected is provided in .kmz format, which can be accessed via Google Earth ([https://earth.google.com/web/](https://earth.google.com/web/)).
DOI: 10.5061/dryad.brv15dvbx
title: Use of cenotes and the cave environment by mammals on the Yucatán Peninsula, Mexico

description: Mammals are important sources of nutrients to cave ecosystems, and in some
 circumstances, caves may be an essential resource for mammals. Few
 studies, however, have focused on the use of caves by terrestrial mammals.
 We used camera traps at 17 cenotes on the Yucatán Peninsula to determine
 patterns of use by mammals. Eighteen non-volant mammal taxa were
 identified using cenotes, the most commonly occurring being lowland paca
 (Agouti paca), opossums (Didelphis spp.), white-nosed coati (Nasua
 narica), gray fox (Urocyon cinereoargenteus), tayra, (Eira barbara) and
 gray four-eyed opossum (Philander opossum); collectively these taxa
 accounted for 76% of all mammal records. We also recorded several felids
 using cenotes, including jaguar (Panthera onca) and puma (Puma concolor).
 Activity patterns at cenotes usually matched normal activity schedules but
 some species were nocturnal in the forest but diurnal at cenotes. Mammals
 mostly accessed cenotes to drink, but a range of activities were recorded
 including foraging, nesting, mating, resting and bathing.
description: We had four study sites
 comprising a total of 17 cenotes. At each cenote, cameras (ScoutGuard
 SG-680V; infra-red flash; programmed to take 1-min long videos when
 triggered, at high sensitivity and with no ‘quiet time’ between triggers)
 were positioned in order to best capture visitations by mammals; this
 typically involved placing one or more cameras at (1) the entrance(s) to
 the cenote, (2) along sections of dry cave leading to water and (3) at the
 point where the dry cave ends and the aquifer begins. Cameras were focused
 on locations most likely to permit animals to easily access water. The
 number of cameras placed within each cenote was influenced by the
 complexity of the site in terms of the width of the entrance, number of
 entrances and the breadth of the dry cave-water interface.
 Photos were sorted by
 species at each camera location and processed using the ‘CameraSweet’
 camera trapping analysis software (https://smallcats.org/camerasweet/). We considered independent events to be those where 30 or more minutes had elapsed between successive photos of the same species at the same camera.
description: These data only show independent records; the location of animals
 in terms of which cenote they appeared at has not been included. The
 dataset would therefore be useful to examine activity patterns in the
 forests around cenotes ('Jungle) or within cenotes
 ('Cenote'), or to examine activity patterns of mammals within
 the forests of the Yucatán Peninsula. Mammals codes should be easily
 interpreted based on the list of mammals seen during the study, published
 in the full paper by Vernes and Devos (2022).
DOI: 10.5061/dryad.j0zpc86h0
title: Tree-ring stable isotopes suggest an increase in Asian monsoon rainfall at 4.2 ka BP

description: A synthesis of stable oxygen isotope records from tree rings and
 speleothems does not support a significant hydroclimate transition in our
 study region around 4.2 ka, nor the notion that this rapid climate
 deterioration should be regarded as generalized climatic transition from
 the mid to late Holocene. 
description: Comparison of normalized speleothem δ<sup>18</sup>O
 records (thin line) from different parts of southern China spanning 5–3
 ka. Each record is interpolated annually, and then
 their linear trends are removed before normalization. A 100-yr low-pass
 filter is applied to each series to highlight centennial fluctuations. The
 grey bar covers the period 3.97–4.26 ka. A regional composite and 95% CIs
 (yellow shading) for southern China is shown, which is derived by
 averaging the six higher-resolution normalized speleothem
 δ<sup>18</sup>O series from Dongge Cave, Xianglong Cave, Wuya
 Cave, Sanbao Cave 43, Heshang Cave and Shennong Cave using Z-score method.
 Each of the six speleothem records has a temporal resolution better than
 20 years, at least 5 U-Th ages and dating precision higher than 60-yr
 average age error (2σ) in the 5–3 ka interval. A 100-point low-pass filter
 (heavy line) is applied in each normalized series to highlight
 low-frequency variability.