cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7j699nc
title: Data from: Dual tree complex wavelet transform based signal denoising method exploiting neighbourhood dependencies and goodness of fit test

description: A novel signal denoising method is proposed whereby goodness of fit (GOF)
 test in combination with a majority classifications based neighbourhood
 filtering is employed on complex wavelet coefficients obtained by applying
 dual tree complex wavelet transform (DTCWT) on a noisy signal. The DT-CWT
 has proven to be a better tool for signal denoising as compared to the
 conventional discrete wavelet transform (DWT) owing to its approximate
 translation invariance. The proposed framework exploits statistical
 neighbourhood dependencies by performing the GOF test locally on the
 DT-CWT coefficients for their preliminary classification/detection as
 signal or noise. Next, a deterministic neighbourhood filtering approach
 based on majority noise classifications is employed to detect false
 classification of signal coefficients as noise (via the GOF test) which
 are subsequently restored. The proposed method shows competitive
 performance against the state of the art in signal denoising.
description: DTCWT-GOF-NeighFiltData related to my article titled as "Dual tree complex wavelet transform based signal denoising using Neighbourhood filtering and goodness of fit test". This file contains Matlab signal denoising software and all the signals used in this study.
DOI: 10.5061/dryad.49td812
title: Data from: Maternal provisioning is structured by species’ competitive neighborhoods

description: Differential maternal provisioning of offspring in response to
 environmental conditions has been argued as ‘the missing link’ in plant
 life histories. Although empirical evidence suggests that maternal
 provisioning responses to abiotic conditions are common, there is little
 understanding of how differences in maternal provisioning manifest in
 response to competition. Frequency manipulations are commonly employed in
 ecological studies to assess the strength of interspecific competition,
 relative to intraspecific competition, and we used frequency manipulations
 to test how competition in two soil moisture environments affects maternal
 provisioning of seed mass. Specifically, for 15 pairs comprised from 25
 annual plant species that occur in California, we varied the relative
 frequencies of conspecific to heterospecific competitors from 90%
 (intraspecific competition) to 10% (interspecific competition). We found
 that conspecific frequency affected maternal provisioning (seed mass) in
 12 of the 25 species (8 significantly (P&lt;0.05), four marginally
 significantly (P&lt;0.07)), and that these responses included both
 increased (5 species) and decreased (6 species) seed mass, as well as one
 species with opposing directions of response to conspecific frequency that
 depended on the soil moisture environment. Conspecific frequency also
 affected per capita fecundity (seed number) for 17 of the 25 species (15
 significantly (P&lt;0.05), two marginally significantly
 (P&lt;0.09)), which generally decreased seed number as conspecific
 frequency increased. The direction and magnitude of frequency-dependent
 seed mass depended on the identity of the competitor, even among species
 whose fecundity was not affected by competitor identity; the latter
 finding reveals competitive differences among species that would otherwise
 appear to be competitively equivalent. Our research demonstrates how
 species responses to different competitive environments manifest through
 maternal provisioning, and that these responses alter previous estimates
 of environmentally-determined maternal provisioning and reproductive
 output; future study is needed to understand their combined effects on
 population and community dynamics.
description: alpha only w phylopaper
 seed number dataSeed size/number data
 from portion of experiment where species were grown in pairwise
 competitiondata.lambdaSeed size data when species grown alone at low densities
DOI: 10.5061/dryad.c0kr7
title: Data from: Geographical variation in community divergence: insights from tropical forest monodominance by ectomycorrhizal trees

description: Convergence occurs in both species traits and community structure, but how
 convergence at the two scales influences each other remains unclear. To
 address this question, we focus on tropical forest monodominance, in which
 a single, often ectomycorrhizal (EM) tree species occasionally dominates
 forest stands within a landscape otherwise characterized by diverse
 communities of arbuscular mycorrhizal (AM) trees. Such monodominance is a
 striking potential example of community divergence resulting in
 alternative stable states. However, it is observed only in some tropical
 regions. A diverse suite of AM and EM trees locally codominate forest
 stands elsewhere. We develop a hypothesis to explain this geographical
 difference using a simulation model of plant community assembly.
 Simulation results suggest that in a region with a few EM species (e.g.,
 South America), EM trees experience strong selection for convergent traits
 that match the abiotic conditions of the environment. Consequently, EM
 species successfully compete against other species to form monodominant
 stands via positive plant-soil feedbacks. By contrast, in a region with
 many EM species (e.g., Southeast Asia), species maintain divergent traits
 because of complex plant-soil feedbacks, with no species having traits
 that enable monodominance. An analysis of plant trait data from Borneo and
 Peruvian Amazon was inconclusive. Overall, this work highlights the
 utility of geographical comparison in understanding the relationship
 between trait convergence and community convergence.
description: Tree species traits in
 forest plots in Borneo and PeruSpecific leaf area, leaf
 carbon concentration, leaf nitrogen concentration, leaf C:N ratio, and
 mycorrhizal status of tree species under two soil conditions (less fertile
 sand or more fertile clay) in Borneo and Peru. The data are used for
 Tables 1 and 2 and Figure 6 of the paper. For more detail, see the main
 text of the paper.Fukami.et.al.Borneo.Peru.spmeans.AmNat.csv
DOI: 10.5061/dryad.g08m0
title: Data from: Does older adults' cognitive function disrupt the malleability of their attitudes toward outgroup members?: an fMRI investigation

description: In the current study we examine how individual differences in older
 adults’ global cognitive function impacts the extent to which their
 attitudes toward stigmatized individuals are malleable. Because prior
 research has elucidated the neural processes that are involved in
 evaluating stigmatized individuals who are responsible or not responsible
 for their condition, a cognitive neuroscience approach may be well-suited
 to answer this question. In the current study, 36 older and 17 young
 adults underwent functional magnetic resonance imaging while evaluating
 images of homeless people who were described as being responsible or not
 responsible for their condition. They also indicated how much pity they
 felt for each of the individuals in order to determine the extent to which
 their attitudes were malleable (e.g., more pity for not-responsible as
 compared to responsible individuals). Participants’ cognitive function and
 baseline measure of their attitudes toward stigmatized individuals
 (including homeless individuals) were assessed. Results revealed that
 although older adults’ attitudes were malleable, the extent to which this
 was true varied due to individual differences in their global cognitive
 function. Specifically, the difference in the magnitude of older adults’
 self-reported pity for not-responsible as compared to responsible homeless
 individuals was predicted by their global cognitive function. Moreover,
 the difference in pity that older adults expressed toward not-responsible
 as compared to responsible homeless individuals was related to activity in
 the left insula and the anterior cingulate cortex (regions implicated in
 empathy). These results suggest that attitude malleability is affected by
 individual differences in global cognitive function.
description: Tables_1_2_3_8_PlosONEThe raw behavioral data from which Tables 1-3 were generated and the matrix with the pity-differential scores, attitude scale scores, and peak-based parameter estimates used for the hierarchical regression analysis reported in Table 8.
DOI: 10.6084/m9.figshare.31157293
title: <b>Cognitive Graph SLAM Based on Quantum Graph Neural Networks: Semantic Graph SLAM with Human-Level Spatial Cognition</b>

description: Traditional Simultaneous Localization and Mapping (SLAM) methods are limited in semantic understanding and fail to capture human-level spatial cognition. To address this gap, the study proposes a cognitive graph SLAM framework based on Quantum Graph Neural Networks (QGNN).
DOI: 10.6084/m9.figshare.31157293.v1
title: <b>Cognitive Graph SLAM Based on Quantum Graph Neural Networks: Semantic Graph SLAM with Human-Level Spatial Cognition</b>

description: Traditional Simultaneous Localization and Mapping (SLAM) methods are limited in semantic understanding and fail to capture human-level spatial cognition. To address this gap, the study proposes a cognitive graph SLAM framework based on Quantum Graph Neural Networks (QGNN).
DOI: 10.5061/dryad.2td06
title: Data from: Assessing vulnerability of functional diversity to species loss: a case study in Mediterranean agricultural systems

description: Increasing land-use intensification is leading to biodiversity losses
 world-wide, which can reduce the functioning of ecosystems. However, it is
 increasingly clear that not all species are equally important for
 ecosystem processes: whereas the loss of a functionally unique species may
 reduce the capacity of the community to perform some functions, losing a
 functionally redundant species should have a much smaller impact.
 Assessing the vulnerability of functional diversity (FD) to species
 extinctions can help to predict the impacts of land-use intensification.
 This approach consists in ranking species according to their risk of
 extinction and then estimating the trajectory followed by FD as species
 are lost from local communities. However, the most widely used FD indices
 are not independent of species richness, being much more sensitive to the
 loss of species in species-poor than in species-rich sites. This may
 result in misleading interpretations, affecting our ability to rank
 communities according to the vulnerability of their FD to species loss, by
 confounding it with the initial level of species richness. Here, we
 propose comparing the trajectory of FD under the most plausible order of
 species loss with that followed under random species losses as an
 effective way to remove the trivial effect of species richness in the
 assessments of vulnerability to species loss. After decoupling
 vulnerability from species richness, we used it to analyse the effect of
 agricultural intensification on the vulnerability of arable plant
 communities in Mediterranean agricultural fields. Our results show that
 management strategies aiming to increase the functionality of these
 systems should focus on intermediately intensified fields, where small
 reductions in the level of intensification are likely to benefit arable
 plant diversity, increasing the number of species and FD and decreasing
 the vulnerability of FD to species losses. Removing the effect of species
 richness is essential to attain unbiased estimations of the vulnerability
 of communities to species loss, especially when species-poor communities
 are considered. Combining vulnerability with information on taxonomic and
 functional diversity appears as a promising tool to inform decision-making
 processes, anticipating the effects of local extinctions.
description: AbundancesSpecies identities and relative abundances of each species on each sampling point of each field.
DOI: 10.5061/dryad.j09v3
title: Data from: Trade-offs in juvenile growth potential vs. shade tolerance among subtropical rainforest trees on soils of contrasting fertility

description: Plant adaptation to gradients of light availability involves a
 well-studied functional trade-off, as does adaptation to gradients of
 nutrient availability. However, little is known about how these two major
 trade-offs interact, and thus, it remains unclear whether and how the
 nature of the growth–shade tolerance trade-off differs on soils of
 contrasting fertility. We asked whether juvenile growth–shade tolerance
 trade-offs differed in slope and elevation between tree assemblages on
 nutrient-rich basalt and nutrient-poor rhyolite soils in an Australian
 subtropical rain forest. We measured the growth of, and the range of light
 environments occupied by, juveniles (40–120 cm tall) of eight basalt
 specialists, six rhyolite specialists, and one generalist that was common
 on both substrates. In situ minimum light requirements were estimated from
 the 5th percentile of the distribution of naturally regenerated juveniles
 in relation to daily light transmittance. Stem growth was measured for
 12–16 months across a wide range of light environments to estimate the
 light compensation point of growth of each species. Light compensation
 points of growth showed nearly a 1 : 1 correspondence with in situ minimum
 light requirements of species, indicating that whole-plant carbon balance
 is a key driver of ecological success in low light. Minimum light
 requirements were negatively correlated with relative growth rate in low
 light, but correlated positively with growth in high light. Soil type had
 no effect on either the slope or the elevation of this trade-off, all
 species aligning around a common growth–shade tolerance trade-off, but our
 results do show a wider range of growth rates and shade tolerance on the
 nutrient-rich basalt soil than on the nutrient-poor rhyolite. Our results
 suggest that adaptation to light availability involves fundamentally
 similar trade-offs on these two substrates of differing fertility.
 However, a wider range of growth rates and shade tolerance on the
 nutrient-rich basalt soil than on the nutrient-poor rhyolite may help to
 explain the higher species richness and greater structural complexity of
 forest stands on the former substrate.
description: Growth, light and trait
 dataRelative growth rate,
 light availability and leaf trait data for saplings growing in subtropical
 rainforest sites in Australia.
DOI: 10.5061/dryad.n3k93
title: Data from: Should mothers provision their offspring equally? A manipulative field test

description: Within-brood variation in offspring size is universal, but its causes are
 unclear. Theoretical explanations for within-brood variation commonly
 invoke bet-hedging, although alternatives consider the role of sibling
 competition. Despite abundant theory, empirical manipulations of
 within-brood variation in offspring size are rare. Using a field
 experiment, we investigate the consequences of unequal maternal
 provisioning for both maternal and offspring fitness in a marine
 invertebrate. We create experimental broods of siblings with identical
 mean, but different variance, in offspring size, and different sibling
 densities. Overall, more-variable broods had higher mean performance than
 less-variable broods, suggesting benefits of unequal provisioning that
 arise independently of bet-hedging. Complementarity effects drove these
 benefits, apparently because offspring-size variation promotes resource
 partitioning. We suggest that when siblings compete for the same
 resources, and offspring size affects niche usage, the production of
 more-variable broods can provide greater fitness returns given the same
 maternal investment; a process unanticipated by the current theory.
description: Maternal and offspring
 fitness at 8 weeks data
DOI: 10.5061/dryad.25277
title: Data from: Diversity in Müllerian mimicry: the optimal predator sampling strategy explains both local and regional polymorphism in prey

description: The convergent evolution of warning signals in unpalatable species, known
 as Müllerian mimicry, has been observed in a wide variety of taxonomic
 groups. This form of mimicry is generally thought to have arisen as a
 consequence of local frequency-dependent selection imposed by sampling
 predators. However, despite clear evidence for local selection against
 rare warning signals, there appears an almost embarrassing amount of
 polymorphism in natural warning colors, both within and among populations.
 Because the model of predator cognition widely invoked to explain
 Müllerian mimicry (Müller’s “ﬁxed nk” model) is highly simpliﬁed and has
 not been empirically supported; here, we explore the dynamical
 consequences of the optimal strategy for sampling unfamiliar prey. This
 strategy, based on a classical exploration–exploitation trade-off, not
 only allows for a variable number of prey sampled, but also accounts for
 predator neophobia under some conditions. In contrast to Müller’s “ﬁxed
 nk” sampling rule, the optimal sampling strategy is capable of generating
 a variety of dynamical outcomes, including mimicry but also regional and
 local polymorphism. Moreover, the heterogeneity of predator behavior
 across space and time that a more nuanced foraging strategy allows, can
 even further facilitate the emergence of both local and regional
 polymorphism in prey warning color.
description: C++ and R
 codeYou'll find the C++
 code to simulate the evolutionary dynamics of mimetic organisms, and the R
 code used to analyse the outputs (format : .csv) of the
 simulations.Code_Aubier2015.zip
DOI: 10.5061/dryad.89qr5
title: Data from: Positive cytoplasmic UCHL5 tumor expression in gastric cancer is linked to improved prognosis

description: Gastric cancer is the second most common cause of cancer-related mortality
 worldwide. Accurate prediction of disease progression is difficult, and
 new biomarkers for clinical use are essential. Recently, we reported that
 the proteasome-associated deubiquitinating enzyme UCHL5/Uch37 is a new
 prognostic marker in both rectal cancer and pancreatic ductal
 adenocarcinoma. Here, we have assessed by immunohistochemistry UCHL5 tumor
 expression in gastric cancer. The study cohort comprised 650 patients, who
 underwent surgery in Helsinki University Hospital, Finland, between 1983
 and 2009. We investigated the association of cytoplasmic UCHL5 tumor
 expression to assess clinicopathological parameters and patient survival.
 Positive cytoplasmic UCHL5 tumor immunoexpression is linked to increased
 survival of patients with small (&lt;5 cm) tumors (p = 0.001), disease
 stages I-II (p = 0.025), and age 66 years or older (p = 0.037). UCHL5 is
 thus a potential marker in gastric cancer with new prognostic relevance.
description: UCHL5
 GCThis dataset comprises a
 total of 650 patients who underwent gastric cancer
 surgery.Raw
 data UCHL5 gastric cancer.xlsx
DOI: 10.5061/dryad.5r083
title: Data from: Seed polyphenols in a diverse tropical plant community

description: 1. Polyphenols are one of the most common groups of secondary metabolites
 in plants and thought to play a key role in enhancing plant fitness by
 protecting plants against enemies. Although enemy-inflicted mortality at
 the seed stage can be an important regulator of plant populations and a
 key determinant of community structure, few studies have assessed
 community-level patterns of polyphenol content in seeds. 2. We describe
 the distribution of the main seed polyphenol groups across 196 plant
 species on Barro Colorado Island (Panama) and community-level patterns in
 two aspects of their biological activity (protein precipitation and
 oxidative capacity). Taking advantage of substantial variation in
 morphological and ecological traits in the studied plant community, we
 test for correlations and trade-offs between seed polyphenols and
 non-chemical plant traits hypothesised to make plant species more or less
 likely to invest in polyphenol production. 3. The majority of species have
 polyphenols in their seeds. The incidence and concentrations of
 polyphenols were related to a set of non-chemical plant traits.
 Polyphenols were most likely to be present (and where present, to be
 expressed in high concentrations) in species with large seeds, short seed
 dormancy times, low investment in mechanical seed defences, high wood
 density, high leaf mass per area, tough leaves, and slow growth rates. 4.
 Synthesis: Our study reveals a potential trade-off between chemical and
 mechanical seed defences and shows that plant species that invest in
 physical defences at later life stages (high wood density and tough
 leaves) tend not to invest in physical defences of seeds but instead
 produce secondary metabolites likely to act as seed defences. Overall, our
 results conform to predictions from the resource availability hypothesis,
 which states that species in resource-limited environments (such as
 slow-growing shade-tolerant tree species) will invest more in defences
 than fast-growing pioneer species.
description: BCI_polyphenols_traitdataData on seed polyphenols and non-chemical seed and plant traits for 196 species on Barro Colorado Island, Panama.Gripenberg et al. 2017_traitdata.csv
DOI: 10.5061/dryad.bv2g720
title: Data from: Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high-latitudes

description: At high-latitude, climatic shifts hypothetically drove episodes of
 divergence during isolation in glacial refugia, or ice-free pockets of
 land that enabled terrestrial species persistence. Upon glacial recession,
 populations can expand and often come into contact, resulting in admixture
 between previously isolated groups. To understand how recurrent periods of
 isolation and contact have impacted evolution at high latitudes, we
 investigated introgression in the stoat (Mustela erminea), a Holarctic
 mammalian carnivore, using whole-genome sequences. We identify two
 temporally isolated introgression events coincident with large-scale
 climatic shifts: contemporary introgression in a mainland contact zone and
 ancient contact ~ 200 km south along North America’s North Pacific Coast.
 Repeated episodes of gene flow highlight the central role of cyclic
 climates in structuring high-latitude diversity, through refugial
 divergence and subsequent introgressive hybridization. Introgression
 followed by allopatry (e.g., insularization) may contribute to expedited
 divergence of island taxa experiencing substantial glacial flux.
description: Tar ball of genome .fq
 files of Mustela erminea (N=10)Tar ball of genome ,fq
 files of Mustela erminea, representing specimens from Museum of
 Southwestern Biology (MSB) with catalog number: 152905 (ME01), 221783
 (ME02), 199855 (ME03), 43333 (ME04), 145234 (ME05), 148962 (ME06), 149365
 (ME07), 144524 (ME08), 215111 (ME09), 248153 (ME10).ermineGenome_fq_files.tar.gzTar ball of mitochondrial genome .fq files of Mustela erminea (N=10)Tar ball of mitochondrial genome ,fq files of Mustela erminea, representing specimens from Museum of Southwestern Biology (MSB) with catalog number: 152905 (ME01), 221783 (ME02), 199855 (ME03), 43333 (ME04), 145234 (ME05), 148962 (ME06), 149365 (ME07), 144524 (ME08), 215111 (ME09), 248153 (ME10).ermineMitogenome_fq_files.gz