cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2b2m
title: Data from: Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems

description: Ancient DNA (aDNA) analysis of lake sediments is a promising tool for
 detecting shifts in past microbial assemblages in response to changing
 environmental conditions. We examined sediment core samples from
 subtropical, freshwater Laguna Blanca (Uruguay), which has been severely
 affected by cultural eutrophication since 1960 and where cyanobacterial
 blooms, particularly those of the saxitoxin-producer Cylindrospermopsis
 raciborskii, have been reported since the 1990s. Samples corresponding to
 ~1846, 1852, 2000 and 2007 A.D. were selected to perform Denaturing
 Gradient Gel Electrophoresis (DGGE) analysis of the 16S-23S rRNA
 intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic
 assemblage composition. Each stratum showed different ITS patterns, but
 the composition of 21st Century samples was clearly different than those
 of mid-19th Century. This compositional change was correlated to shifts in
 sediment organic matter and chlorophyll a content, which were
 significantly higher in recent samples. The presence of
 saxitoxin-producing cyanobacteria was addressed by quantitative real time
 PCR of the sxtU gene involved in toxin biosynthesis. This gene was present
 only in recent samples, for which clone libraries and ITS sequencing
 indicated the presence of Cyanobacteria. Phylogenetic analyses identified
 C. raciborskii only in the 2000 sample, shortly after several years when
 blooms were recorded in the lake. These data suggest the utility of aDNA
 for the reconstruction of microbial assemblage shifts in subtropical
 lakes, at least on centennial scales. The application of aDNA analysis to
 genes involved in cyanotoxin synthesis extends the applicability of
 molecular techniques in paleolimnological studies to include key microbial
 community characteristics of great scientific and social interest.
description: Organic matter and
 chlorophyll a datadata_MO_cloa.xlsfigure_3_treedataNewick file containing the C. raciborskii phylogenetic tree informationDGGE matrix dataPresence/absence of each band in each analyzed sampleRESULT-DGGE.txtqpcr_dataCt data obtained for sxtU gene in 2007 and 2000 samples and for the calibration curve based on the cloned gene used to quantify the number of sxtU copies.
DOI: 10.5061/dryad.88gc4
title: Data from: Stimulation of dopamine D1 receptor improves learning capacity in cooperating cleaner fish

description: Accurate contextual decision-making strategies are important in social
 environments. Specific areas in the brain are tasked to process these
 complex interactions and generate correct follow-up responses. The
 dorsolateral and dorsomedial parts of the telencephalon in the teleost
 fish brain are neural substrates modulated by the neurotransmitter
 dopamine (DA), and are part of an important neural circuitry that drives
 animal behaviour from the most basic actions such as learning to search
 for food, to properly choosing partners and managing decisions based on
 context. The Indo-Pacific cleaner wrasse Labroides dimidiatus is a highly
 social teleost fish species with a complex network of interactions with
 its ‘client’ reef fish. We asked if changes in DA signalling would affect
 individual learning ability by presenting cleaner fish two ecologically
 different tasks that simulated a natural situation requiring accurate
 decision-making. We demonstrate that there is an involvement of the DA
 system and D1 receptor pathways on cleaners' natural abilities to
 learn both tasks. Our results add significantly to the growing literature
 on the physiological mechanisms that underlie and facilitate the
 expression of cooperative abilities.
description: Learning
 dataData set with behaviour
 measures collected during learning tasks. "Treatment" column
 refers to the compound injected. "Sessions to completion" column
 is the number of sessions that were required for the individual to learn
 the task. "Trial score per session" refers to the percentage of
 correct choices made by the individual in a single
 session.Data
 Dryad.xlsx
DOI: 10.5061/dryad.9hr4060
title: Data from: Evaluating a handheld decision support device in pediatric intensive care settings

description: Objective: To evaluate end-user acceptance and the effect of a commercial
 handheld decision support device in pediatric intensive care settings. The
 technology, pac2, was designed to assist nurses in calculating medication
 dose volumes and infusion rates at the bedside. Materials and Methods: The
 devices, manufactured by InformMed Inc., were deployed in the pediatric
 and neonatal intensive care units in two health systems. This mixed
 methods study assessed end-user acceptance, as well as pac2’s effect on
 the cognitive load associated with bedside dose calculations and the rate
 of administration errors. Towards this end, data were collected in both
 pre- and post-implementation phases, including through ethnographic
 observations, semi-structured interviews, and surveys. Results: Although
 participants desired a handheld decision support tool such as pac2, their
 use of pac2 was limited. The nature of the critical care environment,
 nurses’ risk perceptions, and the usability of the technology emerged as
 major barriers to use. Data did not reveal significant differences in
 cognitive load or administration errors after pac2 was deployed.
 Discussion and Conclusion: Despite its potential for reducing adverse
 medication events, the commercial standalone device evaluated in the study
 was not used by the nursing participants and thus had very limited effect.
 Our results have implications for the development and deployment of
 similar mobile decision support technologies. For example, they suggest
 that integrating the technology into hospitals’ existing IT infrastructure
 and employing targeted implementation strategies may facilitate nurse
 acceptance. Ultimately, the usability of the design will be essential to
 reaping any potential benefits.
description: pac2DataDRYADDatasets that accompany: Reynolds TL, DeLucia PR, Esquibel KA, Gage T, Wheeler NJ, Randell JA, Stevenson JG, Zheng K. Evaluating a Handheld Decision Support Device in Pediatric Intensive Care Settings. The objective of this study was to evaluate end-user acceptance and the effect of a commercial handheld decision support device in pediatric intensive care settings. The technology, pac2, was designed to assist nurses in calculating medication dose volumes and infusion rates at the bedside.
DOI: 10.5061/dryad.q20p3
title: Data from: Soil nitrogen-cycling responses to conversion of lowland forests to oil palm and rubber plantations in Sumatra, Indonesia

description: Rapid deforestation in Sumatra, Indonesia is presently occurring due to
 the expansion of palm oil and rubber production, fueled by an increasing
 global demand. Our study aimed to assess changes in soil-N cycling rates
 with conversion of forest to oil palm (Elaeis guineensis) and rubber
 (Hevea brasiliensis) plantations. In Jambi Province, Sumatra, Indonesia,
 we selected two soil landscapes – loam and clay Acrisol soils – each with
 four land-use types: lowland forest and forest with regenerating rubber
 (hereafter, “jungle rubber”) as reference land uses, and rubber and oil
 palm as converted land uses. Gross soil-N cycling rates were measured
 using the 15N pool dilution technique with in-situ incubation of soil
 cores. In the loam Acrisol soil, where fertility was low, microbial
 biomass, gross N mineralization and NH4+ immobilization were also low and
 no significant changes were detected with land-use conversion. The clay
 Acrisol soil which had higher initial fertility based on the reference
 land uses (i.e. higher pH, organic C, total N, effective cation exchange
 capacity (ECEC) and base saturation) (P≤0.05–0.09) had larger microbial
 biomass and NH4+ transformation rates (P≤0.05) compared to the loam
 Acrisol soil. Conversion of forest and jungle rubber to rubber and oil
 palm in the clay Acrisol soil decreased soil fertility which, in turn,
 reduced microbial biomass and consequently decreased NH4+ transformation
 rates (P≤0.05–0.09). This was further attested by the correlation of gross
 N mineralization and microbial biomass N with ECEC, organic C, total N
 (R=0.51–0. 76; P≤0.05) and C:N ratio (R=-0.71 – -0.75, P≤0.05). Our
 findings suggest that the larger the initial soil fertility and N
 availability, the larger the reductions upon land-use conversion. Because
 soil N availability was dependent on microbial biomass, management
 practices in converted oil palm and rubber plantations should focus on
 enriching microbial biomass.
description: soil-N cycling rates and
 soil chemical characteristics dataPlease see ReadMe
 file.kallen_PONE_Dryad.xlsx
DOI: 10.5061/dryad.2rn6j99
title: Data from: Proximate mechanisms underlying the rapid modification of phenotypic traits in cane toads (Rhinella marina) across their invasive range within Australia

description: Biological invasions often involve rapid modification of phenotypic
 traits, presumably in response to the host of novel pressures to which an
 invader is exposed, but the proximate basis for those changes remains
 unclear. Phenotypic changes may be generated by environmental factors (E),
 genetic factors (G), or the interaction between these two processes (GE).
 To explore this issue, we obtained eight clutches of the cane toad
 (Rhinella marina) from three regions across its invaded range within
 Australia, and raised the offspring under standard conditions (diet and/or
 exercise level manipulations) to clarify the proximate underpinnings of
 geographic divergence in phenotypic traits. Our results demonstrate that
 phenotypic variation among Australia cane toad populations are affected by
 genetics and environment, and an interaction of these two processes. Some
 traits (e.g., sprint distance) differed among populations, suggesting a
 heritable basis. Other traits (e.g., relative heart mass) were affected by
 experimental treatments but not by population. Intriguingly, other traits
 (e.g., growth rate) were affected by interactions between Population of
 Origin and experimental treatments. The relative importance of G, E and GE
 differs among traits, but all three mechanisms have contributed to the
 rapid phenotypic divergence observed across the Australian range of
 invasive cane toads.
description: Stuartetal_2018_CaneToad_DataUploadSummary data for variables described in the manuscript "Proximate mechanisms underlying the rapid modification of phenotypic traits in cane toads (Rhinella marina) across their invasive range within Australia, Stuart, Katarina, Shine, Richard, Brown, Greg"
DOI: 10.5061/dryad.mn40k
title: Data from: Intergenerational trade-off for water may induce a mother-offspring conflict in favour of embryos in a viviparous snake

description: Parent-offspring conflicts are likely to occur when resources are limiting
 either at pre- or postnatal stages due to intergenerational trade-offs
 over resources. Current theory posits that such conflicts may influence
 the evolution of parental allocation as well as reproductive modes. While
 energy allocation to the offspring has received considerable attention,
 the distribution of water – another potentially limited vital resource to
 both the mother and offspring – and the resulting outcomes remain grossly
 understudied. Here, we explored the intergenerational trade-off related to
 water resources in the viviparous aspic viper (Vipera aspis) by examining
 the effects of water deprivation on female physiology (body mass,
 haematocrit, and osmolality), water transfer to developing embryos, and
 reproductive performance. As a result of water deprivation, females became
 dehydrated, with the effects more pronounced in pregnant compared to
 non-reproductive females. Among pregnant females, the impacts of water
 deprivation on water balance were correlated with fecundity. In contrast,
 water deprivation had no effect on water transfer to the offspring or on
 reproductive performance. Our results demonstrate that, under
 water-constraining conditions, female water balance is compromised in
 favour of the developing embryos, highlighting a significant
 intergenerational trade-off for water. Although ectothermic reptiles are
 particularly tolerant in water balance perturbations, our results suggest
 that, like energy, water can be a conflicting resource between mother and
 offspring. Parent-offspring conflict over water should therefore be
 further investigated to better understand reproductive modes and
 reproductive trade-offs in terrestrial organisms.
description: Female physiology and
 reproductive performance datasheetFile containing
 measurements of female physiology and reproductive
 performanceFemale physiology and
 reproductive performance.txtNeonate
 morphologyFile containing
 measurements of neonate morphologyneonate
 morphology.txt
DOI: 10.5061/dryad.m9m4f
title: Data from: Donald’s ideotype and growth redundancy: a pot experimental test using an old and a modern spring wheat cultivar

description: Human selection for high crop yield under water-limited conditions should
 have led modern cereal cultivars to invest less in root biomass, be it
 unconsciously. To test this hypothesis we conducted a pot experiment with
 two spring wheat cultivars, one old and one modern, both widely grown in
 the semi-arid regions of China. Using the replacement series method
 introduced by de Wit, we showed that the older landrace (Monkhead) was
 significantly more competitive than the more-modern cultivar (92-46).
 However, when grown in pure stand, old Monkhead had grown root biomass 3.5
 times modern 92-46, whereas modern 92-46 gained a 20% higher grain yield.
 We also found modern 92-46 significantly increased root biomass per plant
 and root allocation (i.e., root biomass/total individual biomass) as its
 frequency in mixtures decreased, whereas old Monkhead did not respond in a
 similar way. This result suggests that the roots of modern cultivars may
 have gained an ability to recognize neighboring root systems and show more
 plastic self-restraining response to intra-cultivar competition.
description: Data for two spring
 wheat varieties in a de Wit series of competitionPot experiment conducted
 in the Botanical Garden of Beijing Normal University.Zhu&Zhang_PLOS
 ONE_data.docx
DOI: 10.5061/dryad.gt3m1
title: Data from: Cell compartmentation of ultraviolet-absorbing compounds: an underexplored tool related to bryophyte ecology, phylogeny and evolution

description: 1. Excessive exposure to ultraviolet (UV) radiation can be harmful to
 photosynthetic organisms, that most frequently respond with the
 accumulation of protective UV-absorbing compounds (UVACs). UVACs location
 in different cell compartments can influence their preferential protective
 role as antioxidants and/or UV screens. However, the phylogenetic,
 ecological and evolutionary implications of UVACs compartmentation has
 been little studied, particularly in bryophytes. 2. We analysed UVACs in
 the methanol-soluble and -insoluble fractions (SUVACs and IUVACs,
 respectively) in extracts of 87 bryophytes belonging to their three
 evolutionary lineages: 22 liverworts, 64 mosses and 1 hornwort. Assuming
 that the cell wall-bound IUVACs are more effective UV screens than the
 mainly vacuolar SUVACs, thus conferring a higher UV tolerance, we
 evaluated whether UVACs levels and compartmentation were related to: 1)
 the bryophyte phylogeny down to the Order level; and 2) the bryophyte
 ecological attributes, including sun exposure and Ellenberg indicator
 values (numerical system classifying species’ habitat along gradients of
 environmental factors). A similar phylogenetic and ecological analysis was
 conducted on the sclerophylly index (the ratio between the dry mass and
 the surface area of the bryophyte shoot). 3. Mosses showed lower SUVACs
 but higher IUVACs and total UVACs, together with higher IUVAC/SUVAC
 ratios, than liverworts. Thus, mosses would better tolerate UV radiation
 than liverworts, which matches well with their general ecological
 preferences. As bryophytes were the earliest diverging land plants, we
 could infer that the different UVACs compartmentation between mosses and
 liverworts could have influenced their ecological segregation upon plant
 land colonization. 4. UVACs compartmentation also differed between the two
 major moss lineages (acrocarpous and pleurocarpous), while the
 anatomically peculiar Sphagnales were the best characterized Order. 5.
 There were not solid relationships between UVACs and the ecological
 attributes considered. Hence, UVACs might be mainly constitutive in
 bryophytes, depending more on the species phylogeny than on the habitat
 occupied in nature. 6. Liverworts were less sclerophyllous than mosses,
 and, as in tracheophytes, water restrictions and high sun exposures
 increased sclerophylly. 7. In conclusion, UVACs compartmentation
 represents an ecophysiological trait useful to understand the bryophyte
 ecophylogeny, because different compartmentation modalities seem to imply
 different UV adaptations and tolerance.
description: Table 1. Data of the 87
 bryophytes used in this study.DataTable1Dryad.csvTable 2. Data of an additional set of species collected in diverse places and dates.DataTable2Dryad.csv
DOI: 10.5061/dryad.s3t53
title: Data from: The evolution of sexes: a specific test of the disruptive selection theory

description: The disruptive selection theory of the evolution of anisogamy posits that
 the evolution of a larger body or greater organismal complexity selects
 for a larger zygote, which in turn selects for larger gametes. This may
 provide the opportunity for one mating type to produce more numerous,
 small gametes, forcing the other mating type to produce fewer, large
 gametes. Predictions common to this and related theories have been
 partially upheld. Here, a prediction specific to the disruptive selection
 theory is derived from a previously published game-theoretic model that
 represents the most complete description of the theory. The prediction,
 that the ratio of macrogamete to microgamete size should be above three
 for anisogamous species, is supported for the volvocine algae. A fully
 population genetic implementation of the model, involving mutation,
 genetic drift and selection, is used to verify the game-theoretic
 approach, and accurately simulates the evolution of gamete sizes in
 anisogamous species. This model was extended to include a locus for gamete
 motility, and shows that oogamy should evolve whenever there is costly
 motility. The classic two-fold cost of sex may be derived from the fitness
 functions of these models, showing that this cost is ultimately due to
 genetic conflict.
description: anisogamyFortran 90 code for population genetic simulation of the evolution of anisogamy.oogamyFortran 90 code for population genetic simulation of the evolution of oogamy.
DOI: 10.5061/dryad.q1791
title: Data from: Habitat restoration benefits wild bees: a meta-analysis

description: 1.Pollinator conservation is of increasing interest in light of managed
 honeybee (Apis mellifera) declines, and declines in some species of wild
 bees. Much work has gone into understanding the effects of habitat
 enhancements in agricultural systems on wild bee abundance, richness, and
 pollination services. However, the effects of ecological restoration
 targeting “natural” ecological endpoints (e.g., restoring former
 agricultural fields to historic vegetation types or improving degraded
 natural lands) on wild bees have received relatively little attention,
 despite their potential importance for countering habitat loss. 2.We
 conducted a meta-analysis to evaluate the effects of ecological
 restoration on wild bee abundance and richness, focusing on unmanaged bee
 communities in lands restored and managed to increase habitat availability
 and quality. Specifically, we assessed bee abundance and/or richness
 across studies comparing restored vs. unrestored treatments and studies
 investigating effects of specific habitat restoration techniques, such as
 burning, grazing, invasive plant removal and seeding. 3.We analysed 28
 studies that met our selection criteria: these represented 11 habitat
 types and 7 restoration techniques. Nearly all restorations associated
 with these studies were performed without explicit consideration of
 habitat needs for bees or other pollinators. The majority of restorations
 targeted plant community goals, which could potentially have ancillary
 benefits for bees. 4.Restoration had overall positive effects on wild bee
 abundance and richness across multiple habitat types. Specific restoration
 actions, tested independently, also tended to have positive effects on
 wild bee richness and abundance. 5.Synthesis and applications. We found
 strong evidence that ecological restoration advances wild bee
 conservation. This is important given that habitat loss is recognized as a
 leading factor in pollinator decline. Pollinator responses to land
 management are rarely evaluated in non-agricultural settings and so
 support for wild bees may be an underappreciated benefit of botanically
 focused management. Future restoration projects that explicitly consider
 the needs of wild bees could be more effective at providing nesting,
 foraging and other habitat resources. We encourage land managers to design
 and evaluate restoration projects with the habitat needs of wild bee
 species in mind.
description: JAE_Tonietto&LarkinST1All citations for articles included in the meta-analysis with: categorical response and test variables, restoration subgroup category assignment (see Figures 1, 2) and effect size calculations (Hedge's d) with the variance of Hedge's d, and 95% confidence intervals.
DOI: 10.5061/dryad.cr24d
title: Data from: Seasonal patterns of hormones, macroparasites, and microparasites in wild African ungulates: the interplay between stress, reproduction, and disease

description: Sex hormones, reproductive status, and pathogen load all affect stress.
 Together with stress, these factors can modulate the immune system and
 affect disease incidence. Thus, it is important to concurrently measure
 these factors, along with their seasonal fluctuations, to better
 understand their complex interactions. Using steroid hormone metabolites
 from fecal samples, we examined seasonal correlations among zebra and
 springbok stress, reproduction, gastrointestinal (GI) parasite infections,
 and anthrax infection signatures in zebra and springbok in Etosha National
 Park (ENP), Namibia, and found strong seasonal effects. Infection
 intensities of all three GI macroparasites examined (strongyle helminths,
 Strongyloides helminths, and Eimeria coccidia) were highest in the wet
 season, concurrent with the timing of anthrax outbreaks. Parasites also
 declined with increased acquired immune responses. We found hormonal
 evidence that both mares and ewes are overwhelmingly seasonal breeders in
 ENP, and that reproductive hormones are correlated with immunosuppression
 and higher susceptibility to GI parasite infections. Stress hormones
 largely peak in the dry season, particularly in zebra, when parasite
 infection intensities are lowest, and are most strongly correlated with
 host mid-gestation rather than with parasite infection intensity. Given
 the evidence that GI parasites can cause host pathology, immunomodulation,
 and immunosuppression, their persistence in ENP hosts without inducing
 chronic stress responses supports the hypothesis that hosts are tolerant
 of their parasites. Such tolerance would help to explain the ubiquity of
 these organisms in ENP herbivores, even in the face of their potential
 immunomodulatory trade-offs with anti-anthrax immunity.
description: Cizauskas et al 2015
 Hormones Parasites DataThese data include
 parasite, immune, and hormone data for wild plains zebra (Equus quagga)
 and springbok (Antidorcas marsupialis) in Etosha National Park,
 Namibia.