cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.91ht938
title: Data from: Wildlife differentially affect tree and liana regeneration in a tropical forest: an 18‐yr study of experimental terrestrial defaunation versus artificially abundant herbivores

description: 1. Hunting and land use change modify herbivore abundances and cause
 cascading effects in natural ecosystems. The outcomes for vegetation
 depend on changes to specific plant-animal interactions, such as seed
 dispersal or predation, or physical disturbances. 2. We experimentally
 manipulated wildlife populations in a primary lowland forest in Malaysia
 over an 18-yr period (1996-2014) to understand how artificially high or
 low densities of terrestrial wildlife affects tree and liana regeneration.
 Our study site retains a diverse wildlife community and artificially high
 densities of native wild pigs (Sus scrofa) that are sustained by
 crop-raiding in distant oil palm plantations. We used fencing that
 excluded terrestrial animals &gt;1kg to experimentally simulate
 conditions in defaunated forests. These two treatments - abnormally high
 pig abundances in habitat edges and megafauna loss from hunting -
 represent common outcomes in disturbed Southeast Asian forests and are
 characteristic of many forests globally. 3. We focus on trees and lianas
 because they are the two dominant woody lifeforms in tropical forests and
 crucial determinants of forest structure and function. 4. We found that
 liana sapling abundances (30-100 cm height) increased by 86% in unfenced
 control plots with wildlife but were stable in exclosures. In contrast,
 tree abundances did not change in unfenced control plots but increased by
 83% in exclosures without wildlife. Evidence of scaring on surviving stems
 suggested that these inverted outcomes were driven by selective use of
 tree saplings for wild pig nests. Lianas may also have greater tolerance
 to wildlife disturbances. By the end of the study, lianas comprised 38% of
 all saplings in unfenced controls but just 14% in exclosures. 5. We
 conclude that abundant wildlife such as wild pigs may shift understory
 woody communities towards lianas while defaunation may shift it towards
 trees. These results highlight that ecological cascades from hunting or
 land use change can alter plant functional types and reshape to long-term
 patterns of forest succession and change. Managing unnatural wild boar
 populations may be required to conserve native plant communities in both
 their native and exotic ranges, including in South America.
description: Pasoh exclosure
 dataTree and liana saplings
 per replicate in 1996 and 2014 in treatments and controls (standardized to
 25m2 area).Pasoh exclosure summary
 data.csv
DOI: 10.5061/dryad.3kf3gg2
title: Data from: Enamel hypoplasia and dental wear of North American late Pleistocene horses and bison: an assessment of nutritionally-based extinction models

description: Approximately 50,000 – 11,000 years ago many species around the world
 became extinct or were extirpated at a continental scale. The causes of
 the late Pleistocene extinctions have been extensively debated and
 continue to be poorly understood. Several extinction models have been
 proposed, including two nutritionally-based extinction models:
 coevolutionary disequilibrium and mosaic-nutrient models. These models
 draw upon the individualistic response of plant species to climate change
 to present a plausible scenario in which nutritional stress is considered
 one of the primary causes for the late Pleistocene extinctions. In this
 study, we tested predictions of the coevolutionary disequilibrium and
 mosaic-nutrient extinction models through the study of dental wear and
 enamel hypoplasia of Equus and Bison from various North American
 localities. The analysis of the dental wear (microwear and mesowear) of
 the samples yielded results which are consistent with predictions
 established for the coevolutionary disequilibrium model, but not for the
 mosaic-nutrient model. These ungulate species show statistically different
 dental wear patterns (suggesting dietary resource partitioning) during
 preglacial and full-glacial time intervals, but not during the postglacial
 in accordance with predictions of the coevolutionary disequilibrium model.
 In addition to changes in diet, these ungulates, specifically the equid
 species, show increased levels of enamel hypoplasia during the postglacial
 indicating higher levels of systemic stress, a result which is consistent
 with the models tested and with other climate-based extinction models. The
 extent to which the increase in systemic stress was detrimental to equid
 populations remains to be further investigated, but suggests that
 environmental changes during the late Pleistocene significantly impacted
 North American equids.
description: Supplementary Table
 1Microwear data of late
 Pleistocene equid and bison samples studied.Supplementary Table
 2Mesowear data of late
 Pleistocene equid and bison samples studied.Supplementary Table
 3Enamel hypoplasia data
 of late Pleistocene equid and bison samples studied.RAM
 DhPg-8_69-1_anterior-dicomsCT-scan data_RAM DhPg-8
 69.1_anterior dicomsRAM-DhPg-8_69-1_anterior-dicoms.zipRAM DhPg-8_69-1_posterior-dicomsCT-scan data_RAM DhPg-8 69.1_posterior dicomsRAM-DhPg-8_69-1_posterior-dicoms.zipRAM DhPg-8_864CT-scan data_RAM DhPg-8 864_dicomsRAM-DhPg-8_864_dicom.zipRAM DhPg-8_876-1_anterior-dicomsCT-scan data_RAM DhPg-8 876.1_anterior dicomsRAM-DhPg-8_876-1_anterior-dicoms.zipRAM DhPg-8_876-1_posterior dicomsCT-scan data_RAM DhPg-8 876.1_posterior dicomsRAM-DhPg-8_876-1_posterior-dicoms.zipSupplementary File 1_Var_testMATLAB codeSupplementary File 2_Proportion_testMATLAB codeSupplementary File 3_Mean_testMATLAB code
DOI: 10.5061/dryad.4m5d5m9
title: Data from: Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

description: Pleistocene glaciations drove repeated range contractions and expansions
 shaping contemporary intraspecific diversity. Atlantic salmon (Salmo
 salar) in the western and eastern Atlantic diverged &gt;600,000 YBP,
 with the two lineages isolated in different southern refugia during
 glacial maxima, driving trans-Atlantic genomic and karyotypic divergence.
 Here, we investigate genomic consequences of glacial isolation and
 trans-Atlantic secondary contact using 108,870 single nucleotide
 polymorphisms (SNPs) genotyped in 80 North American and European
 populations. Throughout North America, we identified extensive
 inter-individual variation and discrete linkage blocks within and between
 chromosomes with known trans-Atlantic differences in rearrangements:
 Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses
 suggest independence of rearrangements, with Ssa01/Ssa23 showing high
 European introgression (&gt;50%) in northern populations indicative of
 post-glacial trans-Atlantic secondary contact, contrasting low European
 ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population
 diversity suggesting a derived chromosome fusion polymorphism within North
 America. Evidence of potential selection on both genomic regions suggests
 that the adaptive role of rearrangements warrants further investigation in
 Atlantic salmon. Our study highlights how Pleistocene glaciations can
 influence large-scale intraspecific variation in genomic architecture of
 northern species.
description: Salmon genotype
 dataGenotype data for 108K
 SNPs used in the study for Canadian populations of Atlantic salmon. Other
 data used in the study were compiled from other work on Norwegian Atlantic
 salmon (see Barson et al. 2015 Nature for details).Canada_26Pops_Genepop_108K.txt
DOI: 10.5061/dryad.7c702sb
title: Data from: Sucrose and starch intake contribute to reduced alveolar bone height in a rodent model of naturally occurring periodontitis

description: While there is a burgeoning interest in the effects of nutrition on
 systemic inflammatory diseases, how dietary macronutrient balance impacts
 local chronic inflammatory diseases in the mouth has been largely
 overlooked. Here, we used the Geometric Framework for Nutrition to test
 how the amounts of dietary macronutrients and their interactions, as well
 as carbohydrate type (starch vs sucrose vs resistant starch) influenced
 periodontitis-associated alveolar bone height in mice. Increasing intake
 of carbohydrates reduced alveolar bone height, while dietary protein had
 no effect. Whether carbohydrate came from sugar or starch did not
 influence the extent of alveolar bone height. In summary, the amount of
 carbohydrate in the diet modulated periodontitis-associated alveolar bone
 height independent of the source of carbohydrates.
description: Data
 setMain data from which
 analyses in Morimoto et al. 2019. are performed. The file is a .csv
 format. For a full description of the data in each column see the README
 file.Data.Dryad.Upload.csv
DOI: 10.5061/dryad.h3kv180
title: Data from: Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs

description: The release of hatchery-propagated fish and shellfish is occurring on a
 global scale, but the genetic impacts of these practices are often not
 fully understood and rarely monitored. Slow recovery of depleted eastern
 oyster populations in the Chesapeake Bay, USA has prompted a
 hatchery-based restoration program focused in the Choptank River, Maryland
 consisting of the mass release of hatchery-produced juveniles from local,
 wild broodstock. To evaluate potential genetic effects of this program, we
 1) examined changes in genetic diversity (allelic richness,
 heterozygosity) and the effective number of breeders (Nb) over the
 hatchery production cycle with microsatellite-based parentage of natural,
 mass- and controlled-spawned cohorts, and 2) compared genetic diversity
 and effective population size (Ne) of a restored reef to wild source
 populations. Mass-spawned cohorts showed high variance in reproductive
 contribution, particularly among males, leading to a 45% average reduction
 in Nb from spawning adult numbers and higher relatedness–lower magnitude
 reductions in heterozygosity and significant reductions in allelic
 richness were also observed. While controlled-spawns (single male
 fertilizations of pooled eggs) reduced male variance, overall reproductive
 variance (Vk) remained high. Finally, oysters sampled from a restored reef
 displayed comparable Ne, genetic diversity, and relatedness to samples
 from wild populations, with no significant genetic differentiation among
 them. Overall, the hatchery-based results and initial field-based
 population genetic analyses suggest that despite reductions in diversity
 from parents to offspring due to high Vk, enhancement with rotated, wild
 broodstock appears to have maintained genetic diversity in a restored reef
 population compared to proximal wild populations.
description: microsatellite data by
 locus and cohortMicrosatellite genotypes
 (genepop format) for all nine eastern oyster (Crassostrea virginica)
 hatchery cohorts (parents and offspring) from the publication. Alleles are
 represented in three digit format, missing data is represented by
 000000.hatchery_cvirginica
DOI: 10.5061/dryad.n8g5345
title: Data from: Ferula paeoniifolia sp. nov. (Apiaceae) from Sichuan, China

description: Ferula paeoniifolia X. G. Ma & C. Y. Liao sp. nov., from Sichuan
 Province, Southwest China, is described and illustrated. The new species
 is most similar to F. kingdon-wardii Wolff in morphology, but differs
 significantly in its ternate-2-pinnate compound leaves comprising much
 broader leaflets. The key morphological characteristics and nuclear
 ribosomal internal transcribed spacer (ITS) region were also compared
 between F. paeoniifolia and its relatives, which revealed a new species to
 Ferula L.
description: ITS
 sequencesComparison of ITS
 sequencesITS.fas
DOI: 10.6084/m9.figshare.30142385
title: Docetaxel and quercetin-loaded lipid nanocarrier optimized by quality by design for glioblastoma therapy: a ligand-conjugated and therapeutic repurposing approach

description: This study aimed to develop transferrin (Tf)-conjugated nanostructured lipid carrier (NLC) co-loaded with docetaxel (DTX) and quercetin (QUR) for brain delivery via intranasal route as glioblastoma multiforme (GBM) therapy. Molecular docking showed strong binding affinities of DTX and QUR to β-tubulin and PI3K, with docking scores of −7.134/−6.055 kcal/mol and −11.787/−12.830 kcal/mol, respectively. Synergistic effects were confirmed through MTT assay on U87-MG cells. NLCs were prepared using modified emulsiosonication method and optimized via central composite rotatable design, followed by Tf conjugation using carbodiimide chemistry. Optimized NLCs exhibited globule size &lt; 200 nm, a polydispersity index ≡ 0.2, zeta potential between −5 and −25 mV, and entrapment efficiency &gt; 85%. Compared to non-conjugated NLC and (DTX-QUR) suspension (SUS), Tf-(DTX-QUR) NLC showed 3.6- and 5.8-fold decrease in IC<sub>50</sub>, respectively. Cellular uptake studies demonstrated significantly (<i>***p &lt; 0.001</i>) high internalization of Tf-conjugated NLC to U87-MG cells. <i>In vitro</i> release and permeability studies showed 2.8–3.5-fold increase in the release and permeation of the drugs in comparison to (DTX-QUR) SUS. Notably, the nasal ciliotoxicity study indicated no toxicity to the nasal tissues. The results suggested that Tf-conjugated NLC provides a promising noninvasive method for enhancing the delivery of combination, which may improve the effectiveness of GBM treatment.
DOI: 10.6084/m9.figshare.30142385.v1
title: Docetaxel and quercetin-loaded lipid nanocarrier optimized by quality by design for glioblastoma therapy: a ligand-conjugated and therapeutic repurposing approach

description: This study aimed to develop transferrin (Tf)-conjugated nanostructured lipid carrier (NLC) co-loaded with docetaxel (DTX) and quercetin (QUR) for brain delivery via intranasal route as glioblastoma multiforme (GBM) therapy. Molecular docking showed strong binding affinities of DTX and QUR to β-tubulin and PI3K, with docking scores of −7.134/−6.055 kcal/mol and −11.787/−12.830 kcal/mol, respectively. Synergistic effects were confirmed through MTT assay on U87-MG cells. NLCs were prepared using modified emulsiosonication method and optimized via central composite rotatable design, followed by Tf conjugation using carbodiimide chemistry. Optimized NLCs exhibited globule size &lt; 200 nm, a polydispersity index ≡ 0.2, zeta potential between −5 and −25 mV, and entrapment efficiency &gt; 85%. Compared to non-conjugated NLC and (DTX-QUR) suspension (SUS), Tf-(DTX-QUR) NLC showed 3.6- and 5.8-fold decrease in IC<sub>50</sub>, respectively. Cellular uptake studies demonstrated significantly (<i>***p &lt; 0.001</i>) high internalization of Tf-conjugated NLC to U87-MG cells. <i>In vitro</i> release and permeability studies showed 2.8–3.5-fold increase in the release and permeation of the drugs in comparison to (DTX-QUR) SUS. Notably, the nasal ciliotoxicity study indicated no toxicity to the nasal tissues. The results suggested that Tf-conjugated NLC provides a promising noninvasive method for enhancing the delivery of combination, which may improve the effectiveness of GBM treatment.
DOI: 10.6084/m9.figshare.30329771
title: Design, development and evaluation of rufinamide loaded nanocochleates as delivery vehicle for the treatment of epilepsy

description: Rufinamide is the preferred medication for management Lennox-Gastaut Syndrome (LGS). Its gradual absorption from the gastrointestinal pathway is due to its restricted solubility and slow dissolving rate in gastrointestinal fluids. The restricted bioavailability of Rufinamide leads to inadequate transportation of drug to the brain. This research article explains the formulation of Rufinamide-loaded nanocochleates using liposomes as the core structure. Liposomes were produced via the ethanol injection method and optimized using a Box–Behnken experimental design. The optimization considered three independent factors lipid quantity, cholesterol quantity, and stirring speed and two response parameters: particle size and encapsulation efficiency. The optimized liposomes have a particle size of 130.1 ± 2.2 nm, a zeta potential of −13.3 ± 0.96 mv, an encapsulation efficiency of 86.13 ± 1.46% w/w and a drug release of 86.74 ± 0.87% w/w respectively. The refined liposomes were later transformed into nanocochleates utilizing the trapping process. The nanocochleates were evaluated for several factors including particle size of 157.5 ± 1.4 nm, zeta potential of −19.16 ± 3.02 mv, encapsulation efficiency of 89.78 ± 1.87% w/w and drug release of 80.39 ± 0.73% w/w in over 24 hours. Thus, this innovative method may serve as an improved alternative therapy for Lennox Gastaut Syndrome.
DOI: 10.6084/m9.figshare.30329771.v1
title: Design, development and evaluation of rufinamide loaded nanocochleates as delivery vehicle for the treatment of epilepsy

description: Rufinamide is the preferred medication for management Lennox-Gastaut Syndrome (LGS). Its gradual absorption from the gastrointestinal pathway is due to its restricted solubility and slow dissolving rate in gastrointestinal fluids. The restricted bioavailability of Rufinamide leads to inadequate transportation of drug to the brain. This research article explains the formulation of Rufinamide-loaded nanocochleates using liposomes as the core structure. Liposomes were produced via the ethanol injection method and optimized using a Box–Behnken experimental design. The optimization considered three independent factors lipid quantity, cholesterol quantity, and stirring speed and two response parameters: particle size and encapsulation efficiency. The optimized liposomes have a particle size of 130.1 ± 2.2 nm, a zeta potential of −13.3 ± 0.96 mv, an encapsulation efficiency of 86.13 ± 1.46% w/w and a drug release of 86.74 ± 0.87% w/w respectively. The refined liposomes were later transformed into nanocochleates utilizing the trapping process. The nanocochleates were evaluated for several factors including particle size of 157.5 ± 1.4 nm, zeta potential of −19.16 ± 3.02 mv, encapsulation efficiency of 89.78 ± 1.87% w/w and drug release of 80.39 ± 0.73% w/w in over 24 hours. Thus, this innovative method may serve as an improved alternative therapy for Lennox Gastaut Syndrome.
DOI: 10.5061/dryad.45bp07g
title: Data from: Using 3D modeling and printing to study avian cognition from different geometric dimensions

description: Studying animal cognition is meaningful because it helps us understand how
 animals adapt to the natural environment. Many birds build nests, clean
 their nests and reject foreign objects from their nests, which provide an
 optimal opportunity for studying their cognition toward foreign objects in
 nests. However, hand-made models used in previous studies have many
 deficiencies that considerably constrain our capacity to understand the
 evolution of avian cognition of foreign objects because they are
 unquantifiable and dependent on different features. We established a 3D
 modeling and printing method to manipulate one geometric dimension of a
 model while controlling for others, which allowed us to investigate avian
 cognition for different dimensions independently. Here we introduce this
 method, conduct an empirical study as an example, and discuss its
 applications to further studies.
description: data_figure 1 &
 3Data
 for figure 1 and figure 3data_figure
 4Data
 for figure 4
DOI: 10.5061/dryad.qm5m0s5
title: Data from: Is the keystone role of figs maintained across a gradient of increasing human disturbance?

description: Fig trees provide important resources to tropical animals, but is their
 keystone role affected by human disturbance? In Sri Lanka, we found that
 more bird species were found in close association with fruiting figs in
 urban areas, suggesting their role is accentuated there, and justifying
 their planting. their planting.
description: Data1Peabotuwageetal,BirdSpeciesBird species, their diets and the habitats in which they were detected.Data2Peabotuwageetal,FigTreesThe characteristics of the fig tree species in the different habitats.Data3Peabotuwageetal,LocationsThe coverage of different vegetation types at tree and non-tree locations in the different habitats.
DOI: 10.5061/dryad.nn430n6
title: Data from: Predicting evolutionary potential: a numerical test of evolvability measures

description: Despite sophisticated mathematical models, the theory of microevolution is
 mostly treated as a qualitative rather than a quantitative tool. Numerical
 measures of selection, constraints, and evolutionary potential are often
 too loosely connected to theory to provide operational predictions of the
 response to selection. In this paper, we study the ability of a set of
 operational measures of evolvability and constraint to predict short‐term
 selection responses generated by individual‐based simulations. We focus on
 the effects of selective constraints under which the response in one trait
 is impeded by stabilizing selection on other traits. The conditional
 evolvability is a measure of evolutionary potential explicitly developed
 for this situation. We show that the conditional evolvability successfully
 predicts rates of evolution in an equilibrium situation, and further that
 these equilibria are reached with characteristic times that are inversely
 proportional to the fitness load generated by the constraining characters.
 Overall, we find that evolvabilities and conditional evolvabilities
 bracket responses to selection, and that they together can be used to
 quantify evolutionary potential on time scales where the G‐matrix remains
 relatively constant.
description: READMER-code and
 R-dataPlease see README for
 description of data files and code.Hansen_Solvin_Pavlicev_Evolution_2019_data_and_code.zip
DOI: 10.5061/dryad.bd10668
title: Data from: Fish culling reduces tapeworm burden in Arctic charr by increasing parasite mortality rather than by reducing density‐dependent transmission

description: 1. Two common Dibothriocephalus (formerly Diphyllobothrium) tapeworm
 species were significantly reduced by experimental culling of their fish
 host Arctic charr (Salvelinus alpinus) in a subarctic lake. 2. Between
 1984 and 1991, funnel traps were used to cull ~ 35 metric tons of Arctic
 charr, reducing charr density by ~ 80%. As charr densities decreased,
 tapeworm prevalence and then intensity also declined over the following
 three decades, with D. dendriticus (formerly dendriticum) responding
 faster than D. ditremus (formerly ditremum). The two main hypotheses for
 how culling a host can decrease parasitism are reductions in parasite
 transmission due to reduced host density and reductions in parasite
 survival through increases in host mortality rates. 3. We found little
 evidence that charr density was the main driver for reduced parasite
 transmission. Instead, decreased survivorship in charr, initially, through
 fishing-induced changes in charr age structure, and later through
 increased predation rates by brown trout, led to increased parasite
 mortality. Although brown trout, which increased significantly after fish
 culling, are also hosts, they are often too big for the final host birds
 to eat, thus becoming parasite sinks. 4. Synthesis and applications: Fish
 populations with heavy parasite burdens constitute a management problem.
 Our results show how fish culling reduce indirectly transmitted parasites
 through increased parasite mortality. Managing overcrowded fish
 populations by culling can produce two desirable outcomes: an increase in
 fish growth rates and reduced parasite burdens.
description: Henriksen_et_al_dibothriocephalus_dataData used to produce figure 1 and 2 in manuscript.dibothriocephalus_data.csvHenriksen_et_al_individual_fish_dataData used for GLS and logistic regression analysis.individual_fish_data.csv