cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mgqnk992r
title: Effects of land clearing for agriculture on soil organic carbon stocks in drylands: A meta-analysis

description: To improve our understanding of clearing natural ecosystems for cropland
 on soil organic carbon stocks in drylands, we searched for related
 peer-reviewed research papers published from 1980 to 2022 on the Web of
 Science (https://www.webofscience.com) and the Scopus Database
 (https://www.scopus.com) (accessed on 30th April 2022). Then, we screened
 papers for integrity, relevance, and scientific merit under the following
 criteria: (1) We made sure all studies were independent and based on
 field-measured data; (2) Each study had to report paired SOC stocks of
 cropland and adjacent natural ecosystems with the same or a similar suite
 of environmental factors; (3) Studies need to explicitly present results
 on SOC stocks or concentrations for certain depths and areas; (4) Studies
 have specified the types of natural ecosystems that were converted to
 cropland, which are used as criteria for defining CNEC types. Finally, we
 winnowed results to a total of 159 scientific journal articles, comprising
 242 sites with 1379 paired soil layer observations from 601 paired soil
 profiles.
DOI: 10.6071/m3dd4f
title: Data and code associated with: Genomic responses to parallel selection in the eelgrass Zostera marina in adjacent bays

description: The extent of parallel genomic responses to similar selective pressures
 depends on a complex array of environmental, demographic, and evolutionary
 forces. Laboratory experiments with replicated selective pressures yield
 mixed outcomes under controlled conditions and our understanding of
 genomic parallelism in the wild is limited to a few well-established
 systems. Here, we examine genomic signals of selection in the eelgrass
 Zostera marina across temperature gradients in adjacent embayments.
 Although we find many genomic regions with signals of selection within
 each bay, there is little overlap at the SNP level across bays. We do find
 overlap at the gene level, potentially suggesting multiple mutational
 pathways to the same phenotype. Using polygenic models we find that some
 sets of candidate SNPs are able to predict temperature across both bays,
 suggesting that small but parallel shifts in allele frequencies may be
 missed by independent genome scans. Together, these results highlight the
 continuous rather than binary nature of parallel evolution in polygenic
 traits and the complexity of evolutionary predictability.
description: See materials and methods in manuscript.
description: See materials and methods in manuscript.
DOI: 10.5061/dryad.x69p8czn6
title: Flowering and fruiting phenology data in Fagaceae in Asia

description: The seasonal timing of flowering and fruiting is crucial for the
 reproductive success of plants and for resource availability to animals.
 Although plants synchronize their reproductive timing to coincide with
 appropriate seasons by responding to environmental cues, seasonal
 variations in temperature and precipitation vary minimally in very wet
 tropical environments. To explore the latitudinal cline in the
 reproductive phenology of the Fagaceae in Asia, we analyzed phenology data
 for a total of 94, 121 and 219 species from Thailand, Malesia and China,
 respectively, in the three genera of Fagaceae, Quercus, Castanopsis, and
 Lithocarpus. We found that Quercus and Castanopsis showed
 flowering peaks in April in China. In Thailand, the peak shifted to an
 earlier month, and the peak disappeared in Malesia. The flowering period
 lengthened with decreasing latitude in the animal-pollinated genera
 Castanopsis and Lithocarpus. However, this was not the case for the
 wind-pollinated genus Quercus. The fruiting period lengthened with
 decreasing latitude in all three genera. We examined the
 relationship between reproductive phenology and climatic factors. The
 combination of monthly temperature and precipitation best explained the
 monthly change in the proportion of flowering and fruiting species in
 China in all three genera. However, climatic factors had almost no impact
 on the predictive ability of the model in Malesia. Our results on
 phenological shifts in the family Fagaceae, from the temperate climates
 and seasonal tropics to the humid tropics, provide valuable information
 for predicting phenological changes in future climate change.
DOI: 10.5281/zenodo.18401936
title: SignBase Version 2.0

description: SignBase Version 2.0 gives meta-information, drawings, and sign sequence codings for 260 mobile artefacts of the Swabian Aurignacian (Upper Paleolithic) archaeological period.
DOI: 10.5281/zenodo.18401937
title: SignBase Version 2.0

description: SignBase Version 2.0 gives meta-information, drawings, and sign sequence codings for 260 mobile artefacts of the Swabian Aurignacian (Upper Paleolithic) archaeological period.
DOI: 10.5061/dryad.08kprr55q
title: Data for: Do ectomycorrhizal exploration types reflect mycelial foraging strategies?

description: ·         Ectomycorrhizal exploration types are commonly assumed to denote spatial foraging patterns and resource-related niches of extraradical mycelia. However, empirical evidence of the consistency of foraging strategies within exploration types is lacking. ·         Here, we analysed ectomycorrhizal foraging patterns by incubating root-excluding ingrowth mesh bags filled with six different substrates in mature Picea abies forests. High-throughput sequencing was used to characterize ectomycorrhizal fungal communities in the mesh bags and on adjacent fine roots after one growing season. ·         Contrary to expectations, many ectomycorrhizal genera of exploration types thought to produce little extraradical mycelium colonised ingrowth bags extensively, whereas genera commonly associated with ample mycelial production occurred sparsely in ingrowth bags relative to their abundance on roots. ·         Previous assumptions about soil foraging patterns of exploration types do not seem to hold. Instead, we propose that variation in the proliferation of extraradical mycelium is related to intergeneric differences in mycelial longevity and mobility of targeted resources.
DOI: 10.5061/dryad.jm63xsjf7
title: Variation and association of leaf traits for desert plants in the arid area, northwest China

description: Characterizing variation and association of plant traits is critical for
 understanding plant adaptation strategies and community assembly
 mechanisms. However, little is known about the leaf trait variations of
 desert plants and their association with different life forms. We used
 principal component analysis, Pearson's correlation, phylogenetic
 independent contrasts, linear mixed model, and variance decomposition to
 explore the variation and association of 10 leaf traits in 22 desert
 plants in the arid area of northwest China. We found that: (1) the
 contribution of interspecific variation to the overall variation was
 greater than the intraspecific variation of all the studied leaf traits;
 (2) intraspecific and interspecific variation in leaf traits differed
 among life forms. Some leaf traits, such as tissue density of shrubs and
 specific leaf area of herbs, exhibited greater intraspecific than
 interspecific variation, while other traits exhibited the inverse; (3)
 desert shrubs corroborate the leaf economic spectrum hypothesis and had a
 fast acquisitive resource strategy, but herbs may not conform to this
 hypothesis; (4) there were trade‐offs between leaf traits, which were
 mediated by phylogeny. Overall, our results suggest that interspecific
 variation of leaf traits significantly contributes to the total leaf
 traits variation in desert plants. However, intraspecific variation should
 not be overlooked. There are contrasts in the resource acquisition
 strategies between plants life forms. Our results support understanding of
 the mechanisms underlying community assembly in arid regions and suggest
 that future works may focus on the variation and association of plant
 traits at both intra‐ and interspecific scales.
description: Please refer to the
 README file and subsequent publications. Variation and association of leaf
 traits for desert plants in the arid area, northwest China.
 Ecology and
 Evolution . Accepted.
description: Please refer to the README file and subsequent publications.
 Variation and association of leaf traits for desert plants in the arid
 area, northwest China. Ecology and Evolution . Accepted.
DOI: 10.5061/dryad.wm37pvmr9
title: Public health emergency operations centres in Africa: A cross-sectional study assessing the implementation status of core components and areas for improvement, December 2021

description: Objective: To assess implementation status of Public Health Emergency
 Operations Centres (PHEOCs) in all countries in Africa. Design:
 Cross-sectional. Setting: Fifty-four national PHEOC focal points in Africa
 responded to an online survey between May and November 2021. Included
 variables aimed to assess capacities for each of the four PHEOC core
 components. To assess the PHEOCs’ functionality, criteria were defined
 from among the collected variables by expert consensus based on PHEOC
 operations’ prioritisation. We report results of the descriptive analysis,
 including frequencies of proportions. Results: A total of 51 (93%) African
 countries responded to the survey. Among these, 41 (80%) have established
 a PHEOC. Twelve (29%) of these met 80% or more of the minimum requirements
 and were classified as fully functional. Twelve (29%) and 17 (41%) PHEOCs
 that met 60%–79% and below 60% of the minimum requirements were classified
 as functional and partially functional, respectively. Conclusions:
 Countries in Africa made considerable progress in setting up and improving
 functioning of PHEOCs. One-third of the responding countries with a PHEOC
 have one fulfilling at least 80% of the minimum requirements to operate
 the critical emergency functions. There are still several African
 countries that either do not have a PHEOC or whose PHEOCs only partially
 meet these minimal requirements. This calls for significant collaboration
 across all stakeholders to establish functional PHEOCs in Africa.
description: A standardized self-assessment tool was developed based on Annex
 9 of the PHEOC framework to determine the PHEOC minimum requirements. The
 tool encompasses 31 indicators across the PHEOC core components to assess
 the implementation status and existing capacities.  The response to each
 variable allowed for a yes or no answer and a comment section to provide
 additional information if any. In May 2021, the survey tool was shared
 with MS and was administered via an online KoBo Toolbox and MS completed
 the questionnaire and submitted it online. The online survey questionnaire
 was shared with 54 MS in Africa (47 of the 54 are MS of the WHO African
 Region). Data were collected between May – November 2021.
description: Please see the README document
 (''README_StatusOfPHEOCInAfrica''.txr).
DOI: 10.5061/dryad.kh1893299
title: Brood parasitism risk drives birds to breed near humans

description: Although humans have generally negative effects on wildlife, some animals
 live in close proximity to human residences. Why some animals choose to
 settle near humans remains a long-standing puzzle. Settling near humans or
 in urban environments may be beneficial, because of the availability of
 resources such as food (e.g. supplemental feeding) or suitable nest sites
 (e.g. cavities), or because of reduced predation risk if predators avoid
 settlements. Here, we report on a study of Daurian redstarts Phoenicurus
 auroreus, a common host of the common cuckoo Cuculus canorus, to show that
 settling near humans can also be a strategy employed by hosts to avoid
 brood parasitism. First, redstarts suffered an increased risk of brood
 parasitism with increasing distance from the nearest building. Second,
 redstarts adjusted their nesting location in response to a seasonally
 predictable change in the risk of brood parasitism. Third, experimentally
 simulating the presence of cuckoos during a period when they are naturally
 absent increased the likelihood that redstarts nested indoors or closer to
 human settlements. These findings suggest that redstarts actively choose
 to place their nest in the vicinity of a human residence as a defense
 against cuckoos. Hence, settling near humans may be an anti-parasitism
 strategy in some avian hosts.
DOI: 10.5061/dryad.sn02v6x7h
title: Vehicle pollution is associated with elevated insect damage to street trees

description: 1. Vehicle pollution is a pervasive aspect of anthropogenic change across
 rural and urban habitats. The most common emissions are carbon- or
 nitrogen-based pollutants that may impact diverse interactions between
 plants and insect herbivores. However, the effects of vehicle pollution on
 plant-insect interactions are poorly understood. 2. Here, we combine a
 city-wide experiment across the Sacramento Metropolitan Area and a
 laboratory experiment to determine how vehicle emissions affect insect
 herbivory and leaf nutritional quality. 3. We demonstrate that leaf damage
 to a native oak species (Quercus lobata) commonly planted across the
 western US is substantially elevated on trees exposed to vehicle
 emissions. In the laboratory, caterpillars preferred leaves from
 highway-adjacent trees and performed better on leaves from those same
 trees. 4. Synthesis and applications. Together, our studies demonstrate
 that the heterogeneity in vehicle emissions across cities may explain
 highly variable patterns of insect herbivory on street trees. Our results
 also indicate that trees next to highways are particularly vulnerable to
 multiple stressors, including insect damage. To combat these effects,
 urban foresters may consider planting trees that are less susceptible to
 insect herbivory along heavily traveled roadways.
DOI: 10.5061/dryad.wstqjq2qg
title: Effects of mowing, spring precipitation, soil nutrients and enzymes on grassland productivity

description: Little research has assessed how the timing and intensity of grazing might
 affect plant biomass, available nutrients, and soil extracellular enzyme
 activity (EEA), and how climate change might influence these responses. We
 tested the effect of two spring precipitation variability (rainfed
 control, -30% of ambient), two mowing intensity (moderate, severe), and
 two mowing season treatments (June, October) on plant and soil properties.
 We detected an interactive effect of precipitation, mowing intensity, and
 mowing season on plant biomass. When plots were mowed at a moderate
 intensity, water reductions had irregular effects on plant biomass
 depending on the mowing season. Plant biomass was also 11% greater in
 plots mowed at moderate than severe intensities. Most soil nutrients were
 unaffected by treatments, except for calcium. Soil EEA was unaffected by
 treatments; however, the activity of a phosphorus (P)-acquisition enzyme
 was ≥4 times greater than the activity of nitrogen (N)- and
 carbon-acquisition enzymes. A substantial amount (adjusted R2= 0.51) of
 plot-to-plot variation in plant biomass was explained by three soil
 properties, especially a N-acquisition enzyme and to a lesser degree by
 plant available P and soil pH. The grassland had a high degree of natural
 buffering capacity as most soil properties were resistant to shifts in
 6-yr spring precipitation and 5-yr simulated grazing intensity and season.
 Grassland plant biomass varied by treatments and was seemingly limited by
 biogeochemical constraints, especially the prevalent need to mobilize P
 and a secondary need to acquire N as plant biomass increased.
description: All data collection and analysis methods are described in,
 "Effects of mowing, spring precipitation, soil nutrients and enzymes
 on grassland productivity".
DOI: 10.25592/uhhfdm.18252
title: Supporting Information for Resource-Efficient Quantum Optimization via Higher-Order Encoding

description: The files GAP.h5, GRAPH_COLORING.h5, and IP.h5 contain all data required to reproduce the figures for the Gate Assignment, Graph Coloring, and Integer Programming problems presented in the manuscript.

Each .h5 file can be opened using the Python package h5py.

Within each .h5 file (one per problem class), the following keys are provided:

• hubo_gate_requirements: A structured array containing the counts of RZ, RX, CNOT, and Hadamard gates, as well as the number of qubits used in the HUBO problem formulation. Using the main script, the number of qubits can be directly mapped to the corresponding problem size.

• qubo_gate_requirements: The same structured array as above, but for the QUBO formulation.

• hubo_nbr_qubits_&lt;x&gt;_depth_&lt;y&gt;: A structured array containing the QAOA parameters (beta and gamma) and the corresponding approximation ratios for QAOA executed on the HUBO formulation with &lt;x&gt; qubits and &lt;y&gt; QAOA layers. For each qubit size &lt;x&gt; and depth &lt;y&gt; described in the main script, a corresponding dataset is provided.

• qubo_nbr_qubits_&lt;x&gt;_depth_&lt;y&gt;: The analogous QAOA data for the QUBO formulation
DOI: 10.5061/dryad.9p8cz8wkt
title: Supplementary data for: New paromomyids (Mammalia, Primates) from the Paleocene of southwestern Alberta, Canada, and an analysis of paromomyid interrelationships

description: Paromomyidae are one of several families of plesiadapiforms that
 flourished during the Paleocene in North America soon after the extinction
 of non-avian dinosaurs some 66 million years ago. Although they are often
 among the best-represented plesiadapiforms in mammalian faunas in both
 North America and Europe, the early history of paromomyids is poorly
 understood, and their fossil record at higher latitudes is comparatively
 depauperate. We report here on the discovery of two new species of
 paromomyids from Paleocene deposits in southwestern Alberta: Edworthia
 greggi new species is the second known species of the basal paromomyid
 Edworthia Fox, Scott, and Rankin, whereas Ignacius glenbowensis new
 species is among the most abundantly represented species of Ignacius
 Matthew and Granger. These new discoveries document for the first time
 parts of the upper dentition of Edworthia, and the new species of Ignacius
 represents the first new, pre-Clarkforkian species of the genus to be
 described in nearly one hundred years. A comprehensive phylogenetic
 analysis of nearly all known paromomyid taxa (including the new species
 described herein) recovered both species of Edworthia near the base of the
 paromomyid tree in a polytomy with Paromomys depressidens, and a
 paraphyletic Ignacius. The new paromomyids from Alberta not only increase
 the known taxonomic diversity of Edworthia and Ignacius, but also add
 significantly to knowledge of the dental anatomy of these poorly known
 genera, and further add to a uniquely Canadian complement of Paleocene
 plesiadapiforms.
description: The supplementary data includes the Character List, Character
 taxon matrix, and a figure showing the branch support from the Cladistic
 analysis.  As stated in the paper, these data were analyzed as
 follows:  A parsimony analysis was conducted using PAUP
 4.0*a165 (Swofford, 2002) using the following steps: 1)
 Set Ukhaatherium nessovi as the only outgroup (Data&gt;Define
 Outgroup…), 2) set selected characters as ordered
 (Data&gt;Set Character Types; turn the following characters into
 ordered: 1, 12, 18, 31, 67, 72, 73, 83, 86, 92, and 93),
 3) accept ordered characters (click ‘Done’),
 4) set the type of analysis (Analysis&gt;Heuristic
 search), 5) set the maximum number of trees to be saved
 to 1000 (General &gt; SetMaxTrees &gt; 1000);
 6) set the number of replicates (reps) at 1000 holding 1000 trees
 at each step), 7) run the analysis (click
 OK). The supplementary data also includes individual
 measurements for specimens of <em>Edworthia greggi</em> n. sp.
 and <em>Ignacius glenbowensis</em> n. sp.
description: The files are submitted as .txt and .xlsx files.  The .txt files
 can be opened with any text editor.  The .xlsx file can be opened in
 Excel.
DOI: 10.25592/uhhfdm.18251
title: Supporting Information for Resource-Efficient Quantum Optimization via Higher-Order Encoding

description: The files GAP.h5, GRAPH_COLORING.h5, and IP.h5 contain all data required to reproduce the figures for the Gate Assignment, Graph Coloring, and Integer Programming problems presented in the manuscript.

Each .h5 file can be opened using the Python package h5py.

Within each .h5 file (one per problem class), the following keys are provided:

• hubo_gate_requirements: A structured array containing the counts of RZ, RX, CNOT, and Hadamard gates, as well as the number of qubits used in the HUBO problem formulation. Using the main script, the number of qubits can be directly mapped to the corresponding problem size.

• qubo_gate_requirements: The same structured array as above, but for the QUBO formulation.

• hubo_nbr_qubits_&lt;x&gt;_depth_&lt;y&gt;: A structured array containing the QAOA parameters (beta and gamma) and the corresponding approximation ratios for QAOA executed on the HUBO formulation with &lt;x&gt; qubits and &lt;y&gt; QAOA layers. For each qubit size &lt;x&gt; and depth &lt;y&gt; described in the main script, a corresponding dataset is provided.

• qubo_nbr_qubits_&lt;x&gt;_depth_&lt;y&gt;: The analogous QAOA data for the QUBO formulation
DOI: 10.25592/uhhfdm.18242
title: Dataset: Scholia Reference Symbols in Organon Manuscripts

description: Supplementary dataset for MA thesis submitted to the Asia–Africa Institute. For review by Thesis advisor and submission.
DOI: 10.25592/uhhfdm.18241
title: Dataset: Scholia Reference Symbols in Organon Manuscripts

description: Supplementary dataset for MA thesis submitted to the Asia–Africa Institute. For review by Thesis advisor and submission.