cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vx0k6djpr
title: Preparation hollow TiO2 microspheres by microwave-assisted method in open system and the research of photocatalytic property of TiO2 microspheres

description: FTIR spectrum was used to identify the functional groups on the carbon
 microspheres after heating under microwave.  New bands
 in comparison with glucose at ~1700 and ~1640 cm-1 were attributed to
 carboxyl groups and aromatic C=C vibrations respectively, supporting the
 concept of aromatization of glucose during microwave-assisted heating. The
 presence of bands of carboxyl (-C=O) groups at ~1700 cm-1 and -OH
 stretching vibration at ~3400 cm-1 indicated that the reactive products
 with a higher abundance of hydroxyl functional groups, such as -COOH, were
 formed under the presence of hydrochloride acid and microwave irradiation.
 The decrease of bands at 1000-1300 cm-1 in carbon microspheres, which
 assigned to the C-OH stretching and -OH bending, also implied the
 condensation reactions and polymerization. All peaks in XRD of the
 calcined TiO2-C could be indexed as anatase phase of TiO2.
description: The X-ray diffraction (XRD) was analyzed with a diffractometer
 (RIGAKU Max-2250PC X-ray diffractometer) employing Cu Ka radiation. The
 data analysis requires the software of MDI jade.  The
 functional groups of carbon spheres was analyzed by using US
 Nicolet/NEXUS-670 FTIR.
DOI: 10.5061/dryad.12jm63xw3
title: Loss of the glucocorticoid receptor causes accelerated reproductive aging in female zebrafish

description: Reproductive decline in mid-adult females isstablished phenotype of the
 aging process. Stress and the rise in glucocorticoids (GCs) accelerate
 reproductive aging, but little is known about the mechanisms involved.
 During stress, GCs activate the glucocorticoid receptor (GR), a
 ubiquitously expressed, ligand-bound transcription factor, to elicit
 physiological changes for restoring homeostasis. Here we tested the
 hypothesis that GC-GR signalling is essential for accelerating
 reproductive aging. To test this, we used a ubiquitous GR knockout (GRKO)
 zebrafish, which is inherently hypercortisolemic, to delineate the role of
 high cortisol and GR signalling on reproductive aging. The loss of GR led
 to premature reproductive aging, including high frequency of typical and
 atypical follicular atresia in vitellogenic oocytes, including yolk
 liquefaction and large inflammatory infiltrates. The reduction in oocyte
 quality was also associated with a decline in ovarian tert expression in
 the adult GRKO fish compared to the early-adult GRKO and adult wildtype
 zebrafish. Accelerated reproductive aging also impacted the progeny,
 including lower breeding success, fecundity, egg fertilization rate, and
 delayed somitogenesis and embryo survival in the adult GRKO fish. We
 adduce that GR signalling is essential for prolonging the reproductive
 life span and improving the egg quality and embryo viability in zebrafish.
DOI: 10.5061/dryad.98sf7m0gz
title: Pleistocene climatic fluctuations promoted alternative evolutionary histories in Phytelephas aequatorialis, an endemic palm from western Ecuador

description: Aim: Pleistocene (2.58 Ma – 11.7 ka) climatic fluctuations have shaped
 intraspecific genetic patterns worldwide; however, their manifestation in
 many regions remains unknown. In order to determine the impact of
 Pleistocene climatic fluctuations on the tropical rain forests of western
 Ecuador, we explored the evolutionary history of the endemic palm
 Phytelephas aequatorialis. Location: Western Ecuador, northwestern South
 America. Taxon: Phytelephas aequatorialis (Arecaceae). Methods: 176
 nuclear genes were sequenced in 91 individuals for phylogenomic and
 population structure analyses. The time of divergence between identified
 genetic lineages was estimated using a coalescent phylogenomic analysis.
 Paleoecological niche modelling analyses were performed to determine areas
 of historical climatic suitability since the Last Glacial Maximum (LGM; 22
 ka) that potentially acted as forest refugia during the Pleistocene. A
 Wilcoxon test and Pearson correlations were used to explore how current
 levels of genetic diversity (Hs) have been shaped by several paleoclimatic
 and geographic factors. Results: Phylogenomic and population structure
 analyses revealed two genetic lineages with a north-south distribution,
 which diverged 1.14 Ma during the Pleistocene. Two potential Pleistocene
 refugia were identified in the Pacific coast of Ecuador and in the Andean
 foothills of southwestern Ecuador, whose distribution agrees with the
 spatial location of the two lineages. Within the Andean foothills, Hs was
 lower for the southern lineage than for the northern lineage. Hs
 significantly increased with decreasing latitude within the whole species
 distribution. Main conclusions: Pleistocene climatic fluctuations promoted
 intraspecific divergence in P. aequatorialis within the rain forests of
 western Ecuador. The Andean foothills of southwestern Ecuador could be an
 important spot for rain forest evolution because they potentially remained
 climatically suitable through the Pleistocene. Lower genetic diversity in
 the southern lineage, which apparently remained isolated in the Andean
 foothills during glacial cycles, adds evidence to the presence of a forest
 refugium in southwestern Ecuador. The geographic pattern in genetic
 diversity suggests that P. aequatorialis colonized western Ecuador from
 the north. This study supports the role of Pleistocene climatic
 fluctuations in promoting intraspecific divergence, and for the first
 time, we show their impact west of the Andes.
description: Data for phylogenomic analyses in <em>Phytelephas
 aequatorialis</em>. One hundred and seventy six genes were sequenced
 in 91 individuals using the probes from Heyduk et al. (2016). Only the
 loci with at least 75% of their lenght reconstructed in at least 75% of
 individuals we retained. In addition, loci with signs of paralogy were
 removed, leaving 141 usable loci.
DOI: 10.5061/dryad.np5hqbzqv
title: Blastocystis SSU rRNA alignment

description: Blastocystis is a cosmopolitan protist inhabiting the human intestine;
 which prevalence varies between non-industrial and industrialized
 countries. Its role in the human gut ecosystem remains unclear due to
 persisting gaps in knowledge of epidemiology and factors affecting gut
 colonization. The aim of this study was therefore to expand the knowledge
 of the epidemiology of Blastocystis in the gut-healthy humans in one of
 the industrialized European countries, including the distribution of its
 subtypes, the correlation between its occurrence and several factors such
 as lifestyle, contact with animals, age and sex. A total of 288 stool
 samples were obtained from non-symptomatic individuals over the entire
 age-range and 136 samples from animals with which the volunteers were in
 frequent contact. All samples were examined in parallel by PCR and xenic
 culture. Blastocystis was detected in samples from both human and
 non-human hosts. In humans, the overall prevalence was 24% and eight
 subtypes were found, whereas in animals the prevalence was 10% and only
 five subtypes were detected. For factors, there was a higher incidence of
 Blastocystis in individuals traveling outside Europe who were in frequent
 contact with livestock and over 50 years of age. We found no effect on
 gender.
DOI: 10.15468/dl.9vgyg3
title: Occurrence Download

description: A dataset containing 259 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sinojackia"
 ]
}

 The dataset includes 259 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002556-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jwstqjq73
title: Garfagnina goats with Illumina CaprineSNP50 BeadChip

description: The objective of this study was to investigate the genetic diversity of
 the Garfagnina (GRF) goat, a breed that currently risks extinction. For
 this purpose, 48 goats were genotyped with the Illumina CaprineSNP50
 BeadChip and analyzed together with 214 goats belonging to 9 other Italian
 breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG),
 Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT),
 Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and
 Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of
 homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of
 breed traceability via discriminant analysis on principal components
 (DAPC) based on cross-validation. For GRF, an excess of ROH (more than 45%
 in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1
 assembly), which spans the CENPJ (centromere protein) and IL17D
 (interleukin 17D) genes. The same area of excess ROH was also present in
 DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG,
 CCG, and GGT. Admixture analysis revealed a small region of common
 ancestry from GRFshared by BIO, VSS, ARG and CCG breeds. The DAPC model
 yielded 100% assignment success for GRF. Overall, our results support the
 identification of GRF as a distinct native Italian goat breed. This work
 can contribute to planning conservation programmes to save GRF from
 extinction and will improve the understanding of the socio-agro-economic
 factors related with the farming of GRF.
DOI: 10.5061/dryad.6wwpzgmwp
title: Evoregions: mapping shifts in phylogenetic turnover across biogeographic regions

description: 1. Biogeographic regionalization offers context to the geographical
 evolution of clades. The positions of bioregions inform both the spatial
 location of clusters in species distribution and where their most
 important boundaries are. Nevertheless, defining bioregions based on
 species distribution alone only incidentally recover regions that are
 important during the evolution of the focal group. The extent to which
 bioregions correspond to centers of independent diversification depends on
 how clusters of species composition naturally reflect the radiation of
 single clades, which is not the case when mixed colonization occurred. 2.
 Here, we showed that using phylogenetic turnover based on fuzzy sets,
 instead of species composition, led to adequate detection of
 evolutionarily important bioregions, that is, regions that account for the
 independent diversification of lineages. Mapping those evoregions in the
 phylogenetic tree quickly reveals the timing and location of major shifts
 of biogeographic regions. Moreover, evolutionary transition zones are
 easily mapped, and permits the recognition of regions with high
 phylogenetic overlap. 3. Our results using the global radiation of rats
 and mice (Muroidea) recovered four evoregions—three major evolutionary
 arenas corresponding to the Neotropics, a Nearctic-Siberian, and a
 Paleotropical-Australian evoregion, and a fourth and fuzzy Afro-Palearctic
 evoregion. Transition zones among evoregions were minimized when compared
 to other methods considering or not phylogenetic information, that is, the
 affiliation of cells to their assigned region was higher using evoregions
 than other approaches. Such higher affiliation values result from the
 lower phylogenetic overlap within evoregions, as expected when single
 radiations are accounted for as best as possible. 4. Evoregions is a
 useful framework whenever the question is related to the identification of
 the most important centers of a group’s diversification history and its
 evolutionary transitions zones.
DOI: 10.5061/dryad.v15dv41tq
title: Degradation of gaseous unsymmetrical dimethylhydrazine by vacuum ultraviolet coupled with MnO2

description: In this study, α-, β-, and δ-MnO2 were prepared by a uniform hydrothermal
 method and then coupled with vacuum ultraviolet (VUV) for the degradation
 of gaseous unsymmetrical dimethylhydrazine (UDMH). The performance in the
 remove of UDMH, by-products distribution and mechanistic insights were
 systematically investigated. The catalysts were characterized by X-ray
 diffraction (XRD), N2 adsorption/desorption, Field Emission Scanning
 Electron Microscopy (FE-SEM), Raman, thermal gravimetric (TG), X-ray
 photoelectron spectroscopy (XPS) and Fourier-transform infrared (FTIR) to
 investigate the factors affecting the catalytic activity. The results
 showed that O2 and H2O were essential for the remove of UDMH . The
 integrated process considerably improved the remove and mineralization of
 UDMH by ozone catalytic oxidation . There were more reactive oxygen
 species generated in the integrated process. The catalytic activity of the
 prepared catalysts following the order: δ-MnO2 &gt;α-MnO2
 &gt;β-MnO2. δ-MnO2 displayed the highest remove rate of 100% and CO2
 concentration of 42 ppmv. The good performance of δ-MnO2 was attributed to
 high specific surface area and surface oxygen vacancies.
description: <strong>XRD data</strong><br> The raw data of
 XRD patterns belong to MnO<sub>2 </sub>(Fig.2).
 <strong>N<sub>2 </sub>adsorption-desorption
 isotherms</strong><br> N<sub>2</sub>
 adsorption−desorption isotherms of α-, β- and δ-MnO<sub>2
 </sub>(Fig.3). <strong>Raman
 Spectroscopy</strong><br> Raman spectra of α-, β- and
 δ-MnO<sub>2</sub> (Fig.5).
 <strong>FTIR spectroscopy</strong><br> FTIR
 spectra of α-, β-, δ-MnO<sub>2</sub> and
 α-MnO<sub>2</sub> after the reaction (Fig.6).
 <strong>TG</strong><br> TG analyses curves of
 α-, β-, and δ-MnO<sub>2</sub> (Fig.7).
 <strong>XPS</strong><br> Mn
 2p<sub>2/3</sub>, Mn 3s and O 1s XPS spectra of α-, β-, and
 δ-MnO<sub>2</sub> (Fig.8).
 <strong>Degradation of UDMH</strong><br> The
 data and calculations of the degradation of UDMH and the concentration of
 CO<sub>2</sub> in the continuous flow fixed-bed steel
 reactor. <strong>GC-MS
 spectra</strong><br> GC-MS spectra of organic products from
 (a) VUV photolysis and (b) VUV/MnO<sub>2</sub> process
 (Fig.12).
DOI: 10.5061/dryad.1g1jwstt5
title: R code for Snyder, Ellner, and Hooker, "Time and chance: using age partitioning to understand how luck drives variation in reproductive success"

description: Over the course of individual lifetimes, luck usually explains a large
 fraction of the between- individual variation in lifespan or lifetime
 reproductive output (LRO) within a population, while  variation in
 individual traits or “quality” explains much less. To understand how,
 where in the life cycle, and through which demographic processes luck
 trumps trait variation, we show how to partition by age the contributions
 of luck and trait variation to LRO variance, and how to quantify three
 distinct components of luck. We apply these tools to several empirical
 case studies. We find that luck swamps effects of trait variation at all
 ages, primarily due to randomness in individual state dynamics (“state
 trajectory luck”). Luck early in life is most important. Very  early state
 trajectory luck generally determines whether or not an individual ever
 breeds, likely by ensuring that they are not dead or doomed quickly. Less
 early luck drives variation in success among those breeding at least once.
 Consequently, the importance of luck often has a sharp  peak early in
 life, or two peaks. We suggest that ages/stages where the importance luck
 peaks  are potential targets for interventions to benefit a population of
 concern, different from those  identified by eigenvalue elasticity
 analysis.
description: R code
description: The code should be self-contained.
DOI: 10.5061/dryad.rfj6q578c
title: Effect of Light Wavelength on Soybean Growth and Development in a Context of Speed Breeding

description: Soybean breeding involves crossing and inbreeding for multiple generations
 to develop genetically-stable lines. The long generation times and the
 absence of easily-scalable double-haploid technologies cause early
 generations to be the major bottleneck in soybean breeding. Here we tested
 the effect of red and blue lights (RB) and full spectrum white lights (FS)
 generated by light emitting diode (LED) panels, coupled with 12 h light
 (29 °C) / 12 h darkness (27 °C) photothermal conditions, on the growth and
 development of soybean lines and breeding materials of diverse maturity
 groups in a context of speed breeding. We observed that RB light, when
 compared to FS light, reduced plant height by an average of 17.3 cm but
 did not affect vegetative biomass, pods and seeds per plants, nor the
 ability to meet a minimum of one seed per plant. Overall, the RB light
 treatment reduced days after planting (DAP) to physiological maturity (R7)
 by 1.5 d as compared to FS. The period between planting and the harvest of
 seeds (cycle time) of mid- and late-maturity soybean ranged from 63 to 81
 d in the greenhouse, as compared to approximately 120 d typically observed
 in field conditions. Also, DAP to R7 was dependent on soybean maturity
 group. The use of RB lights, coupled with photothermal conditions herein
 reported, would allow to advance up to 5 generations of US-adapted soybean
 under a controlled environment, instead of the 1-3 generations currently
 possible. This methodology is simple and easily scalable for it maintains
 stable growing conditions throughout the crop cycle and it allows for
 simultaneous planting and harvesting within the same growth room. This
 could have a significant impact in genetic gain of U.S. soybean breeding
 programs.
DOI: 10.5061/dryad.pg4f4qrmn
title: Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate

description: 1. Degree of reproductive synchronization in prey is hypothesized as a
 predator defense strategy reducing prey risk via predator satiation or
 predator avoidance. Species with precocial young, especially those exposed
 to specialist predators, should be highly synchronous to satiate predators
 (predator satiation hypothesis), while prey with nonprecocial (i.e.,
 altricial) young, especially those exposed to generalist predators, should
 become relatively asynchronous to avoid predator detection (predator
 avoidance hypothesis). The white-tailed deer (Odocoileus virginianus) in
 North America is an example of a nonprecocial ungulate that uses the hider
 strategy early in life; its primary predator (coyote; Canis latrans) is a
 generalist, making white-tailed deer a good model species to test the
 predator avoidance hypothesis. 2. We used birth dates and known fates of
 white-tailed deer neonates (n=1032) across nine study sites varying in
 relative synchrony and predator assemblages to test the predator avoidance
 hypothesis. We predicted that relative birthing asynchrony of the
 population would increase relative survival at the population level;
 therefore, at the individual scale, neonate birth date nearer to mean
 birthing date in a respective population would not influence individual
 survival. 3. Coyotes were responsible for the majority of predation
 events, and survival of those neonates increased the closer the individual
 was born to peak birthing season in each respective population. Also, at
 the population level, reproductive asynchronization negatively affected
 survival. 4. Contrary to the predator avoidance hypothesis, our data
 indicate patterns in neonate survival for white-tailed deer better support
 the predator satiation hypothesis at the individual and population level.
 Additionally, coyotes may present a selective force great enough to shift
 reproductive synchrony such that predator satiation may become a feasible
 defense strategy for neonates at local spatial scales. 5. Our results
 indicate that synchronizing reproduction may still be the most effective
 strategy to reduce individual predation risk from generalist predators,
 particularly when the window of heightened resource availability to the
 prey is narrow.
DOI: 10.5061/dryad.cjsxksn48
title: Data for: Intraspecific variation in responses to aposematic prey in a jumping spider (Phidippus regius)

description: Aposematic signals often allow chemically defended prey to avoid attack
 from generalist predators, including jumping spiders. However, not all
 individual predators in a population behave in the same way. Here, in
 laboratory trials, we document that most individual Phidippus
 regius jumping spiders attack and reject chemically defended
 milkweed bugs (Oncopeltus fasciatus), immediately releasing them unharmed.
 However, a small number of individuals within the population kill and
 completely consume these presumably toxic prey items. This phenomenon was
 infrequent with only 14% of our sample (17/122) consuming the milkweed
 bugs over the course of the study. Individuals that killed and consumed
 bugs often did so repeatedly; specifically, individuals that consumed a
 bug in their first test were more likely to kill a bug in their second
 test and also tended to consume them again. We explored what might drive
 some (but not all) individuals to consume these bugs and found that
 neither sex, sexual maturity, body size, laboratory housing type, nor
 being wild‐caught or being laboratory‐reared, predicted milkweed bug
 consumption. Consuming bugs had no negative effects on spider mass or body
 condition; contrary to expectations, individuals that consumed milkweed
 bugs actually gained more body mass and increased in body condition. We
 discuss potential behavioural and physiological variation between
 individuals that may drive these rare behaviours and the implications for
 the evolution of prey defences.
description: Find details about methods and statistical analyses in the
 manuscript text: Powell, E. & Taylor, L. (2020). Intraspecific
 variation in responses to aposematic prey in a jumping spider
 (<em>Phidippus regius</em>).
 <em>Ethology</em>.
DOI: 10.5061/dryad.6q573n5wz
title: Supplementary material - measuring atrophy in the behavioral variant of frontotemporal dementia: a multicenter study

description: Objective: To test the hypothesis that accesible and
 reproducible measures of atrophy may have high clinical utility
 for the study of patients with the behavioral variant of
 frontotemporal dementia (bvFTD), we determined the diagnostic and
 prognostic value of six previously-validated visual atrophy scales (VAS)
 and the Magnetic Resonance Parkinsonism Index (MRPI). Methods: We
 gathered data from 235 patients with bvFTD and 225 age- and
 MRI-matched healthy controls from three centers. One hundred
 twenty-one bvFTD participants had underlying frontotemporal lobar
 degeneration (bvFTD-FTLD) and nineteen did not have FTLD (bvFTD-noFTLD).
 Blinded clinicians applied VAS and the MRPI was calculated with a
 fully-automated approach. Cortical thickness and subcortical gray matter
 volumes were also calculated for comparison. We used linear mixed
 and Cox regression models to evaluate the ability of atrophy measures to
 predict clinical deterioration and survival. Results: The bvFTD
 atrophy score (sum of atrophy scores in orbitofrontal, anterior cingulate,
 anterior temporal, medial temporal lobe and frontal insula regions) was
 usefull to discriminate bvFTD-FTLD from healthy controls (AUROC=.930;
 95%CI, .903 to .957) and bvFTD-FTLD from bvFTD-noFTLD (AUROC=.880; 95%CI,
 .787 to .972) and had similar accuracy than cortical thickness and
 subcortical gray matter volumes. MRPI was increased in patients with bvFTD
 with underlying 4R tauopathies. The bvFTD atrophy score was an independent
 predictor of clinical deterioration and survival in bvFTD.
 Conclusions: In bvFTD, the bvFTD atrophy score can
 increase the diagnostic certainty of underlying FTLD and predict disease
 progression. Moreover, the MRPI can identify bvFTD participants
 with an increased risk of underlying 4R tauopathies.