cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gxd2547qv
title: Changing patterns of the East Asian monsoon drive shifts in migration and abundance of a globally important rice pest

description: Numerous insects including pests and beneficial species undertake
 windborne migrations over hundreds of kilometers. In East Asia,
 climate-induced changes in large-scale atmospheric circulation systems are
 affecting wind-fields and precipitation zones and these, in turn, are
 changing migration patterns. We examined the consequences in a serious
 rice pest, the brown planthopper (BPH, Nilaparvata lugens) in East China.
 BPH cannot overwinter in temperate East Asia, and infestations there are
 initiated by several waves of windborne spring or summer migrants
 originating from tropical areas in Indochina. The East Asian Summer
 monsoon, characterized by abundant rainfall and southerly winds, is of
 critical importance for these northward movements. We analyzed a 42-year
 dataset of meteorological parameters and catches of BPH from a
 standardized network of 341 light-traps in South and East China. We show
 that south of the Yangtze River during summer, southwesterly winds have
 weakened and rainfall increased, while the summer precipitation has
 decreased further north on the Jianghuai Plain. Together, these changes
 have resulted in shorter migratory journeys for BPH leaving South China.
 As a result, immigration levels of pest outbreaks of BPH in the key
 rice-growing area of the Lower Yangtze River Valley (LYRV) have declined
 since 2001. We show that these changes to the East Asian summer monsoon
 weather parameters are driven by shifts in the position and intensity of
 the Western Pacific subtropical high (WPSH) system that have occurred in
 the last 20 years. As a result, the relationship between WPSH intensity
 and BPH immigration that was previously used to predict the size of the
 immigration to the LYRV has now broken down. Our results demonstrate that
 migration patterns of a serious rice pest have shifted in response to the
 climate-induced changes in precipitation and wind pattern, with
 significant consequences for the population management of migratory pests.
description: Daily planthopper catch data from 229 standardized light traps
 located at the plant protection stations of more than 200 counties in
 China were obtained from the National Agro-Tech Extension and Service
 Centre (NATESC), which has been continuously collecting data since
 1977. 
description: The dataset contains two tables/sheets. One table/sheet named
 '5-day BPH catch' includes six columns: SiteID, Longtitude,
 Latitude, Year, Period, No. of catch. Another one named 'annual BPH
 catch' includes four columns: Year, BPH catch in LYRV July, BPH catch
 in LYRV Late Season, BPH catch in NSC May. Information on how the
 measurements were done can be found in the associated manuscript
 referenced above.
DOI: 10.5061/dryad.xsj3tx9kp
title: Soil nutrient dissimilarity and litter nutrient limitation as major drivers of home field advantage in riparian tropical forests

description: Decomposition is a key process driving carbon and nutrient cycling in
 ecosystems worldwide. The home field advantage effect (HFA) has been found
 to accelerate decomposition rates when litter originates from “home” when
 compared to other (“away”) sites. It is still poorly known how HFA plays
 out in tropical, riparian forests, particularly in forests under
 restoration. We carried out three independent reciprocal litter transplant
 experiments to test how litter quality, soil nutrient concentrations and
 successional stage (age) influenced HFA in tropical riparian forests.
 These experimental areas formed a wide gradient of soil and litter
 nutrients, which we used to evaluate the more general hypothesis that HFA
 varies with dissimilarity in soil nutrients and litter quality. We found
 that HFA increased with soil nutrient dissimilarity, suggesting that
 litter translocation uncouples relationships between decomposers and
 litter characteristics; and with litter N:P, indicating P limitation in
 this system. We also found negative HFA effects at a site under
 restoration that presented low decomposer ability, suggesting that forest
 restoration does not necessarily recover decomposer communities and
 nutrient cycling. Within each of the independent experiments, the
 occurrence of HFA effects was limited and their magnitude was not related
 to forest age, nor soil and litter quality. Our results imply that HFA
 effects in tropical ecosystems are influenced by litter nutrient
 limitation and soil nutrient dissimilarity between home and away sites,
 but to further disentangle major HFA drivers in tropical areas, a gradient
 of dissimilarity between litter and soil properties must be implemented in
 future experimental designs.
description: There are two data files, 1)
 soil and litter chemistry, and 2) litter mass loss. Soil and litter
 chemistry were determined for each plot between May and June 2019, in the
 dry season, summing 7 areas x 4 plots = 28 observations. Litter
 decomposition experiments were carried out between August 2019 and
 February 2020, and some samples were retrieved in March 2020 as explained
 in the text. Ash-free dry mass was determined for initial litterbags, as
 well as after retrieval. Data are presented as mass loss in percentage,
 calculated from [1 – (final mass/initial mass)] for each litterbag. Each
 of the three experiments involved litter translocation; therefore, for
 each experiment, there were 3 home areas x 3 away areas x 4 plots = 36
 litterbags for each experiment, totaling 108
 litterbags.
description: The data files are in open-source format (.csv format).
DOI: 10.5061/dryad.bnzs7h4g0
title: A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

description: Rubiaceae is among the most species-rich, morphologically and
 geographically diverse plant families. Phylogenies have been inferred for
 many different groups across the family, however these have mostly relied
 on few genomic and plastid loci, as opposed to large-scale genomic data.
 Target enrichment provides the ability to generate sequence data for
 hundreds to thousands of phylogenetically informative, single-copy loci,
 which often leads to improved phylogenetic resolution at both shallow and
 deep taxonomic scales; however, a publicly accessible Rubiaceae-specific
 probe set that allows for comparable phylogenetic inference across clades
 is lacking. Here, we use publicly accessible genomic resources to identify
 putatively single copy nuclear loci for target enrichment in two Rubiaceae
 tribes: Hillieae (Cinchonoideae) and Palicoureeae+Psychotrieae
 (Rubioideae). We sequenced 2270 exons corresponding to 1059 supercontigs
 in our target clades, and generated in silico target enrichment sequences
 for other Rubiaceae taxa using our designed probe set. Our probe set,
 which we call Rubiaceae 2270, was effective for targeting loci in species
 across and even outside of Rubiaceae. This probe set will
 facilitate phylogenomic studies in Rubiaceae and advance systematics and
 macroevolutionary studies in the family.
description: # A target enrichment probe set for resolving phylogenetic relationships
 in the coffee family,Rubiaceae Publicly accessible genomic resources were
 used to identify putatively single copy nuclear loci for target enrichment
 in two Rubiaceae tribes: Hillieae (Cinchonoideae) and
 Palicoureeae+Psychotrieae (Rubioideae). ## Description of the Data and
 file structure 2270_Rubiaceae_exons.fasta is a file containing the 2,270
 individual exons identified in this study.
DOI: 10.5061/dryad.t76hdr84r
title: Microhabitat data of bryophyte occurrences in and near Sequoia National Park at varying elevations

description: On the western slope of California's Sierra Nevada, bryophytes were
 studied from the foothills (summers dry; winters mild) to the alpine zone
 (summers short; winters with snow cover).  Plots of 25 m2 were
 chosen from 380 to 3,578 meters above sea level. Within each of the 253
 plots, bryophyte species and their abundance were recorded along with
 microsite wetness, shadiness, incline, and the type of
 substrate.  Data was used to assess changes in species richness
 and abundance across elevations and microhabitat characteristics.
  
description: Plots of 25 m<sup>2</sup> were chosen from 380 to 3578 m a.s.l. Within each of 253 plots, bryophyte species and their abundance were recorded along with microsite wetness, shadiness, incline, and substrate type. In addition to recording bryophyte occupancy of microhabitats, we also recorded whether each microhabitat category was present or absent in the plot, regardless of whether it was occupied by any bryophytes. This was our reference site data on microhabitat availability.
DOI: 10.5061/dryad.r2280gbhk
title: Phylogenomic data of Litsea complex based on genome-wide single-nucleotide variants (SNVs) and plastomes

description: In this study, we focus on the Litsea complex (Lauraceae), a key lineage
 with dominant species of evergreen broadleaved forests (EBLFs) in East
 Asia to gain insights into how evergreen versus deciduous trait shifted,
 providing insights into the origin and historical dynamics of EBLFs in
 East Asia under Cenozoic climate change. We reconstructed a robust
 phylogeny of the Litsea complex using  genome-wide
 single-nucleotide variants (SNVs) and plastomes. Finally, the dataset of
 phylogenomic matrices was generated, including five genome-wide SNVs
 dataset and plastomes matrix used for phylogenetic analysis.
DOI: 10.5061/dryad.8pk0p2ns7
title: The ginseng transcriptome, ginsenoside and environmental factors dataset

description: Ginseng is a world-renowned and precious Chinese herbal medicine. Its
 practical components have apparent effects on alleviating sub-health and
 rehabilitation. In our study, we conducted WGCNA bioinformatics analysis
 and verified it using transcriptome expression, saponin phenotype, and
 environmental factors data. We found the basic rule of typical saponins
 accumulation mediated by transcriptome expression profiles through the
 effect of some typical environmental factors and built a prediction model
 that makes biological sense. Using relevant data, we can further analyze
 the relationship between the change in environmental factors and the
 accumulation of effective components of ginseng, which lays a foundation
 for the establishment of a digital ginseng model more in line with the
 growth and development characteristics of ginseng. This data set involves
 the transcriptome expression of 42 ginseng samples, the content of
 saponins, the expression of 11 key enzyme genes associated with saponin
 Rb1 and typical ecological factors at the same time.
DOI: 10.5061/dryad.sj3tx968p
title: Different assembly mechanisms of leaf epiphytic and endophytic bacterial communities underlie their higher diversity in more diverse forests

description: Plant microbiomes are known to influence host fitness and ecosystem
 functioning, but mechanisms regulating their structure are poorly
 understood. Here, we explored the assembly mechanisms of leaf
 epiphytic and endophytic bacterial communities using a subtropical forest
 biodiversity experiment. Both epiphytic and endophytic bacterial diversity
 increased as host tree diversity increased. However, the increased
 epiphytic diversity in more diverse forests was driven by greater
 epiphytic diversity (i.e., greater α diversity) on individual trees,
 whereas the increased endophytic diversity in more diverse forests was
 driven by greater dissimilarity in endophytic composition (i.e., greater β
 diversity) among trees. Mechanistically, responses of epiphytes to changes
 in host diversity were consistent with mass effects, whereas responses of
 endophytes were consistent with species sorting. Synthesis: These results
 provided novel experimental evidence that biodiversity declines of plant
 species will lead to biodiversity declines of plant-associated
 microbiomes, but the underlying mechanism may differ between habitats on
 the plant host.
DOI: 10.5061/dryad.tqjq2bw3v
title: Data from: Nest building in titmice Paridae: Selectivity in bryophyte use

description: In many bird species, reproductive success is dependent on nest quality.
 However, detailed data on nest composition are scarce, and quantitative
 analyses have generally used only rough categories, without species
 identification. Bryophytes dominate the nests of many passerine bird
 species, but little is known about whether birds have preferences for
 certain species. In this study, we determined the bryophyte species
 composition in nests of blue tits Cyanistes caeruleus and great tits Parus
 major in a forest near Oslo, Norway. We also sampled the abundance of the
 bryophyte species in plots on the forest floor surrounding a subset of the
 great tit nests. Blue tits and great tits both used 15 bryophyte species
 as nest materials, mainly the same pleurocarpous species but in different
 proportions. The tits preferred highly branched bryophyte species, i.e.
 Pleurozium schreberi, Rhytidiadelphus squarrosus and Sanionia uncinata,
 but avoided common forest-floor bryophyte species that are sparsely
 branched. Great tits clearly collected bryophyte species selectively. We
 also found that bryophyte species content in great tit nests in the same
 nest box in different years was very similar. Our results also indicated
 that the great tits collected bryophyte nest materials close to their
 nests, mostly within 5 m, supporting the view that collecting nest
 materials is costly. We review several hypotheses to explain why the tits
 prefer certain species of bryophytes as nest materials. These include
 handling costs and their suitability as structural materials. We recommend
 field experiments to test specific hypotheses, and to study whether
 preferences are heritable.
description: The data was collected in a forest nearby Oslo SE Norway and
 consists of two main types of data (but with derived files): bryophyte
 species composition of 69 nests of blue- and great tit and data on the
 bryophyte species composition, sampled in 167 plots, surrounding nine
 trees with nest boxes. Where the bryophyte species composition of these
 nests was recorded in two different years. For further details, please
 read the readme files and the published paper.
description: All files are txt-files and can be opened in most softwares.
DOI: 10.5061/dryad.4f4qrfjgx
title: Data from: The Competitive exclusion – tolerance rule explains habitat partitioning among co-occurring species of burying beetles

description: Habitat partitioning among co-occurring, ecologically similar species is
 widespread in nature and thought to be an important mechanism for
 coexistence. The factors that cause habitat partitioning, however, are
 unknown for most species. We experimentally tested among three alternative
 hypotheses to explain habitat partitioning among two species of
 co-occurring burying beetle (Nicrophorus) that occupy forest (N.
 orbicollis) and wetland (N. hebes) habitats. Captive experiments revealed
 that the larger N. orbicollis (forest) was consistently dominant to N.
 hebes (wetland) in competitive interactions for carcasses that they
 require for reproduction. Transplant enclosure experiments in nature
 revealed that N. hebes had poor reproductive success whenever the dominant
 N. orbicollis was present. In the absence of N. orbicollis, N. hebes
 performed as well, or better, in forest versus its typical wetland
 habitat. In contrast, N. orbicollis performed poorly in wetlands
 regardless of the presence of N. hebes. These results support the
 Competitive exclusion – tolerance rule where the competitively dominant N.
 orbicollis excludes the subordinate N. hebes from otherwise suitable or
 preferable forest habitat, while the subordinate N. hebes is uniquely able
 to tolerate the challenges of breeding in wetlands. Transplant experiments
 further showed that carcass burial depth – an important trait thought to
 enhance the competitive ability of the dominant N. orbicollis – is costly
 in wetland habitats. When in the presence of N. hebes, N. orbicollis
 buried carcasses deeper; deeper burial is thought to provide a competitive
 advantage in forests, but further compromised the reproductive success of
 N. orbicollis in wetlands. Overall, results provide evidence that the
 Competitive exclusion – tolerance rule underlies habitat partitioning
 among ecologically similar species, and that the traits important for
 competitive dominance in relatively benign environments are costly in more
 challenging environments, consistent with a trade-off.
description: # Data from: The Competitive exclusion – tolerance rule explains habitat
 partitioning among co-occurring species of burying beetles
 [https://doi.org/10.5061/dryad.4f4qrfjgx](https://doi.org/10.5061/dryad.4f4qrfjgx) ## Description of the data and file structure See Readme.txt file. Version 2 published on 11 Oct 2023 includes updated R code. ## Code/Software See R code file.
DOI: 10.5061/dryad.612jm647c
title: DMID14-0100: A randomized, controlled Phase 1b trial of the Sm-TSP-2 vaccine for intestinal schistosomiasis ELISA results

description: Recombinant Schistosoma mansoni Tetraspanin-2 formulated on Alhydrogel
 (Sm-TSP-2/Alhydrogel) is being developed to prevent intestinal and hepatic
 disease caused by S. mansoni. The tegumentary Sm-TSP-2 antigen was
 selected based on its unique recognition by cytophilic antibodies in
 putatively immune individuals living in areas of ongoing S. mansoni
 transmission in Brazil, and preclinical studies in which vaccination with
 Sm-TSP-2 protected mice following infection challenge. 
description: A randomized, observer-blind, controlled, Phase 1b clinical trial
 was conducted in 60 healthy adults living in a region of Brazil with
 ongoing <em>S. mansoni</em> transmission. In each cohort of 20
 participants, 16 were randomized to receive one of two formulations of
 <em>Sm</em>-TSP-2 vaccine (adjuvanted with Alhydrogel only, or
 with Alhydrogel plus the Toll-like receptor-4 agonist, AP 10-701), and 4
 to receive Euvax B<sup>TM</sup> hepatitis B vaccine.
 Successively higher doses of antigen (10 µg, 30 µg, and 100 µg) were
 administered in a dose-escalation fashion, with progression to the next
 dose cohort being dependent upon evaluation of 7-day safety data after all
 participants in the preceding cohort had received their first dose of
 vaccine. Each participant received 3 intramuscular injections of study
 product at intervals of 2 months and was followed for 12 months after the
 third vaccination. IgG and IgG subclass antibody responses to
 <em>Sm</em>-TSP-2 were measured by qualified indirect ELISAs
 at pre- and post-vaccination time points through the final study
 visit.
DOI: 10.5281/zenodo.18402445
title: Molecular Docking of Opiates: Achieving binding energies exceeding –20 kcal/mol

description: The structure has an unprecedented triple viscous and massive grip and all-pervasive architecture, exceeding the binding energy of known opioids and botulinum toxin:

OC(COc1cccc2ccccc12)C(C(O)COc3cccc4ccccc34)N5CCOCCOCCOCCOCCOCCOCC5
DOI: 10.5281/zenodo.18402446
title: Molecular Docking of Opiates: Achieving binding energies exceeding –20 kcal/mol

description: The structure has an unprecedented triple viscous and massive grip and all-pervasive architecture, exceeding the binding energy of known opioids and botulinum toxin:

OC(COc1cccc2ccccc12)C(C(O)COc3cccc4ccccc34)N5CCOCCOCCOCCOCCOCCOCC5
DOI: 10.5061/dryad.2547d7wvw
title: AutoMate: a dataset and learning approach for automatic mating of CAD assemblies

description: Assembly modeling is a core task of computer aided design (CAD),
 comprising around one third of the work in a CAD workflow. Optimizing this
 process therefore represents a huge opportunity in the design of a CAD
 system, but current research of assembly based modeling is not directly
 applicable to modern CAD systems because it eschews the dominant data
 structure of modern CAD: parametric boundary representations (BREPs). CAD
 assembly modeling defines assemblies as a system of pairwise constraints,
 called mates, between parts, which are defined relative to BREP topology
 rather than in world coordinates common to existing work. We propose
 SB-GCN, a representation learning scheme on BREPs that retains the
 topological structure of parts, and use these learned representations to
 predict CAD type mates. To train our system, we compiled the first
 large-scale dataset of BREP CAD assemblies, which we are releasing along
 with benchmark mate prediction tasks. Finally, we demonstrate the
 compatibility of our model with an existing commercial CAD system by
 building a tool that assists users in mate creation by suggesting mate
 completions, with 72.2% accuracy.
description: The Automate dataset contains 451,967 unique CAD parts, 255,211
 CAD assemblies, and 1,292,016 unique mates scraped from public OnShape
 documents.   The data was
 collected using Onshape's API and pre-processed to detect and remove
 duplicate and corrupted parts.  
 Assembly data was processed to flatten sub-assembly hierarchies
 and to reference deduplicated parts.  
 Mates were processed to remove duplicates up to identical
 parts, mate types, and mating coordinate frames.
   Document names have been edited to
 make them compatible with most file systems, and code to convert back to
 the original Onshape names is provided.
description: Assembly information is stored as JSON files, and parts are
 stored as both Parasolid (requiring the Parasolid kernel) and STEP files
 (an open-standard which can be read by most CAD software, including the
 open-source OpenCascade project and related open source projects such as
 FreeCAD). Metadata about parts, assemblies, and mates is stored as Apache
 parquet files, an open format which can be read by a variety of packages
 including pandas. Python code is provided to look-up
 the originating Onshape documents.
DOI: 10.5061/dryad.5dv41ns9t
title: Data for: Genetics of continuous colour variation in a pair of sympatric sulphur butterflies

description: Continuous colour polymorphisms can serve as a tractable model for the
 genetic and developmental architecture of traits, but identification of
 the causative genetic loci is complex due to the number of individuals
 needed, and the challenges of scoring continuously varying traits. Here we
 investigated continuous colour variation in Colias eurytheme and C.
 philodice, two sister species of sulphur butterflies that hybridise in
 sympatry. Using Quantitative Trait Locus (QTL) analysis of 483 individuals
 from interspecific crosses and a high-throughput method of colour
 quantification, we found that two interacting large effect loci explain
 around 70% of the heritable variation in orange-to-yellow chromaticity.
 Knockouts of red Malphighian tubules (red), a candidate gene at the
 primary QTL likely involved in endosomal maturation, resulted in
 depigmented wing scales showing disorganised pterin granules. The Z sex
 chromosome contains a large secondary colour QTL that includes the
 transcription factor bric-a-brac (bab), which we show can act as a
 modulator of orange pigmentation in addition to its previously-described
 role in specifying UV-iridescence. We also describe the QTL architecture
 of other continuously varying traits, and that wing size maps to the Z
 chromosome, supporting a Large-X effect model where the genetic control of
 species-defining traits is enriched on sex chromosomes. This study sheds
 light on the genetic architecture of a continuously varying trait and
 illustrates the power of using automated measurement to score phenotypes
 that are not always conspicuous to the human eye.
description: We scanned the dorsal and ventral surface of forewings and hindwings from seven broods (705 individuals), with an Epson Perfection V600 scanner with a 24-colour correction card and greyscale standards. Data tables describing images, along with code used for QTL analysis, is also included.
description: All code is in R or bash (open source). All images are TIFs.