cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ajbf5d
title: Occurrence Download

description: A dataset listing the 455 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is The Taiwan Breeding Bird Survey Data"
 ]
}

 The dataset's 455 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003005-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gqnk98spc
title: Natural 15N abundance of bulk soil N, ammonium, and nitrate in soil profiles

description: Assessment of nitrogen (N) saturation of forests is critical to evaluate
 how ecosystems will respond to current and future global changes such as N
 deposition. However, quantifying N saturation remains a challenge. We
 developed a conceptual model of N saturation stages in forest ecosystems
 based on i) a hypothetical relative rate of ammonification, nitrification,
 and denitrification, ii) concentrations of ammonium and nitrate in the
 soil, and iii) 15N enrichment pattern of bulk soil N, ammonium, and
 nitrate in the soil profile. We tested the hypotheses using the data from
 the five forests located at five sites across eastern Asia, including one
 boreal forest an dtwo temperate forests in northeastern China, one
 temperate forest in Japan, and one subtropical forest in south China. The
 fraction of nitrate in total inorganic N (TIN) indicated that the sites
 represent an N saturation gradient with one boreal forest being least
 saturated, three temperate forests moderately saturated, and the tropical
 forest most saturated. The δ15N of bulk soil N increased from topsoil to
 subsoil more sharply at N-limited sites than at the N-rich sites along the
 N deposition gradient. We also found distinct 15N enrichment patterns of
 bulk soil N, ammonium, and nitrate in the soil profile across the study
 sites. At the least saturated forest, nitrate was more
 15N-depleted than ammonium only in the organic soil horizon indicating
 limited nitrification while the 15N depletion of nitrate than ammonium was
 observed in the deeper mineral soil in the moderatley and most saturated
 forests. Furthermore, ammonium was more 15N-depleted than bulk
 soil N in the least and moderately saturated forests but more
 15N-enriched than bulk soil N in the most saturated forest. Our study
 suggests that soil profile patterns of δ15N of bulk soil N, ammonium, and
 nitrate provide information about the relative rates of mineralization,
 nitrification, and denitrification, thus can be an additional measure of N
 saturation of forest ecosystem across broad environmental gradients.
DOI: 10.5061/dryad.3r2280ghg
title: Coupled dynamics of the North Equatorial Countercurrent and Intertropical Convergence Zone with relevance to the double-ITCZ problem

description: The North Equatorial Counter Current (NECC) is an important component of
 the tropical Pacific upper-ocean circulation. This current flows against
 easterly trade winds and transports warm water from the Western Pacific
 warm pool eastward. Its core follows the latitudinal position of the
 Intertropical Convergence Zone (ITCZ) – a salient feature of tropical
 atmospheric circulation characterized by convective clouds and intense
 rainfall. The trade winds converge towards the ITCZ, creating a local
 minimum in zonal winds and generating a positive wind stress curl that
 maintains an eastward current despite the westward winds. That the wind
 curl associated with the ITCZ is a critical driver of the NECC is well
 established. However, here we show that the relationship between the ITCZ
 and the NECC is more complex and involves positive feedback: a stronger
 NECC transports warmer water from the western Pacific to the east thus
 increasing SST along its path, intensifying convection within the ITCZ and
 hence strengthening wind stress curl, further strengthening the NECC. We
 refer to this large-scale feedback as the Wind curl - Advection - SST -
 Precipitation (WASP) feedback. To confirm the NECC-ITCZ coupling we
 conduct numerical simulations using a coupled model (CESM) in which we
 progressively strengthen the surface Ekman component of the NECC and
 observe the intensification of the ITCZ and the entire NECC. Consequently,
 a weak NECC leads to a weak ITCZ, which can contribute to the double ITCZ
 problem in climate models, since weak wind convergence north of the
 equator enables stronger convergence to the south.
description: This dataset is the output of the CESM1.2.2.1. We modified the
 viscosity to 0.1, 0.02, 10 and 50 times of the control run along the NECC
 over 130E-90W and 4N-10N. We ran the model for 100
 years and only the last 50 years are collected here.
description: These data are nc files and need to be opened with programs that
 support NetCDF files.
DOI: 10.5061/dryad.ttdz08m0g
title: Data from: Occurrence-habitat mismatching and niche truncation when modelling distributions affected by anthropogenic range contractions

description: Aims: Human-induced pressures such as deforestation cause anthropogenic
 range contractions (ARCs). Such contractions present dynamic distributions
 that may engender data misrepresentations within species distribution
 models. The temporal bias of occurrence data—where occurrences represent
 distributions before (past bias) or after (recent bias) ARCs—underpins
 these data misrepresentations. Occurrence-habitat mismatching results when
 occurrences sampled before contractions are modelled with contemporary
 anthropogenic variables; niche truncation results when occurrences sampled
 after contractions are modelled without anthropogenic variables. Our
 understanding of their independent and interactive effects on model
 performance remains incomplete but is vital for developing good modelling
 protocols. Through a virtual ecologist approach, we demonstrate how these
 data misrepresentations manifest and investigate their effects on model
 performance. Location: Virtual Southeast Asia Methods: Using 100 virtual
 species, we simulated ARCs with 100-year land-use data and generated
 temporally biased (past, recent) occurrence datasets. We modelled datasets
 with and without a contemporary land-use variable (conventional modelling
 protocols) and with a temporally dynamic land-use variable. We evaluated
 each model’s ability to predict historical and contemporary distributions.
 Results: Greater ARC resulted in greater occurrence-habitat mismatching
 for datasets with past bias and greater niche truncation for datasets with
 recent bias. Occurrence-habitat mismatching prevented models with the
 contemporary land-use variable from predicting anthropogenic-related
 absences, causing overpredictions of contemporary distributions. Although
 niche truncation caused underpredictions of historical distributions
 (environmentally suitable habitats), incorporating the contemporary
 land-use variable resolved these underpredictions, even when mismatching
 occurred. Models with the temporally dynamic land-use variable
 consistently outperformed models without. Main conclusions: We showed how
 these data misrepresentations can degrade model performance, undermining
 their use for empirical research and conservation science. Given the
 ubiquity of anthropogenic range contractions, these data
 misrepresentations are likely inherent to most datasets. Therefore, we
 present a three-step strategy for handling data misrepresentations:
 maximise the temporal range of anthropogenic predictors, exclude
 mismatched occurrences, and test for residual data misrepresentations.
description: See dataset notes and methods of the original
 paper.<br><br>Original paper: https://onlinelibrary.wiley.com/doi/10.1111/ddi.13544<br>R codes: https://github.com/Pang-SEH/AnthropogenicRangeContractions-TemporalSamplingBias-SDM-Performance
DOI: 10.5061/dryad.2fqz612q7
title: Stranger danger: A meta-analysis of the dear enemy hypothesis

description: The dear enemy hypothesis predicts that territorial individuals will be
 less aggressive toward known neighbors than to strangers. This hypothesis
 has been well studied and there is a wealth of data demonstrating its
 prevelance among some taxa. However, a quantitative synthesis is needed to
 test the generality of the phenomenon, identify key mechanisms driving the
 behavior, and guide future research. Here we made a comprehensive
 collection of Dear Enemy data from 138 studies representing 105 species
 spread over eight taxonomic classes. The associated paper finds that Dear
 Enemy is a common phenomenon but drivers of this phenomenon are still
 understudied and current knowledge is unable to disentangle competing
 hypotheses of drivers of this behavior.
description: This data was collected from 138 unique studies of Dear Enemy
 behavior. Data was collected from several sequential literature searches
 on Science Direct and Google Scholar. Our initial search in Science direct
 using search term “<i>dear enemy</i>” in journals related to
 Agricultural and Biological Sciences, Earth and Planetary Sciences, and
 Environmental Science resulted in 221 unique hits. Later searches
 in Google Scholar using the key words <i>neighbor
 </i>or<i> neighbour</i> and “<i>dear
 enemy</i>” yielded 712 and 68425 studies respectively.
 We excluded studies if the dear enemy hypothesis, neighbor-stranger
 discrimination, or nasty neighbor phenomenon were not mentioned in the
 abstract, if the study did not directly test individual territorial
 responses to conspecifics or if measures of variance were missing. We
 contacted authors to acquire data whenever possible. Data was extracted
 with Data thief or from tables.
description: We have included a README for the data
 set: Stranger_Danger_Data_README.txt and a README for the code:
 README.txt
DOI: 10.5061/dryad.wm37pvmp7
title: Data from: Prenatal acoustic programming of mitochondrial function for high temperatures in an arid-adapted bird

description: Sound is an essential source of information in many taxa and can notably
 be used by embryos to program their phenotypes for postnatal environments.
 While underlying mechanisms are mostly unknown, there is growing evidence
 for the implication of mitochondria – main source of cellular energy (i.e.
 ATP) – in developmental programming processes. Here, we tested whether
 prenatal sound programs mitochondrial metabolism. In the arid-adapted
 zebra finch, prenatal exposure to “heat-calls” – produced by parents
 incubating at high temperatures – adaptively alters nestling growth in the
 heat. We measured red blood cell mitochondrial function, in nestlings
 exposed prenatally to heat- or control-calls, and reared in contrasting
 thermal environments. Exposure to high temperatures always reduced
 mitochondrial ATP production efficiency. However, as expected to reduce
 heat production, prenatal exposure to heat-calls improved mitochondrial
 efficiency under mild heat conditions. In addition, when exposed to an
 acute heat-challenge, LEAK respiration was higher in heat-call nestlings,
 and mitochondrial efficiency low across temperatures. Consistent with its
 role in reducing oxidative damage, LEAK under extreme heat was also higher
 in fast-growing nestlings. Our study, therefore, provides the first
 demonstration of mitochondrial acoustic sensitivity, and brings us closer
 to understanding the underpinning of acoustic developmental programming
 and avian strategies for heat adaptation.
description: <strong>Variable names</strong>
 ch:
 chick identity date / dateJD: sampling
 and mitochondrial measurement date / date in Julian days
 idclutch / idnest /
 idnest_num: nest of origin (genetic) / foster nest / simpler
 label for foster nest tray: prenatal playback
 (A= heat-calls, B= control-calls) from: experimental
 conditions (nest= in-nest, chamber= heat-challenge)
 mNT /
 NT3hsamp: average nest temperature from hatching to D12
 during daytime (=12D-Tnest) / nest temperature 3h before sampling (=
 AM-Tnest) chamber_maxTemp: max
 temperature experienced in the heat-challenge (2 birds stopped at 42, all
 others at 44°C) mNT_dev / NT3h_dev: for
 heat-challenged birds only, temperature deviations experienced from the
 nest (chamber_maxTemp - mNT / chamber_maxTemp - NT3hsamp)
 broodSize: brood size
 (number of chicks in the rearing nest) routineTP to fcr_retsTP:
 mitochondrial respiration rates and FCRs. Rates are corrected by total
 protein (TP) content. FCRs do not need normalisation (they are
 ratios). growth: mass gained (g)
 between D7 and D12 massD12: mass (g) at
 D12
DOI: 10.5061/dryad.stqjq2c4d
title: Has long-distance flight ability been maintained by pigeons in highly insular habitats?

description: Aim: A reduction in dispersal ability has been thought to be a general
 trend for island land birds because of their physical isolation
 to a limited area, scarcity of predators, and ability to forage without
 flight in island habitats. However, recent studies have indicated
 that long-distance dispersal among island habitats may be
 maintained in island pigeon populations, which may be related to unstable
 food resource availability on a single island. Here, we investigated
 whether pigeons could maintain their long-distance dispersal ability to
 move among islands within the archipelago, even in highly insular
 conditions, by comparing two subspecies of Japanese wood pigeon (Columba
 janthina) distributed on islands with different levels of
 insularity. Location: The Ogasawara, Izu and Nansei Islands in the
 north-western Pacific Ocean Taxon: Japanese wood pigeon (Columba janthina)
 Methods: We compared morphological traits related to dispersal potential
 between the two subspecies: C. j. janthina and C. j. nitens. We
 performed phylogenetic and population genetic analyses based on genomic
 markers to indirectly assess dispersal ability via the rate of gene flow
 and determine how long C. j.nitens in a more insular habitat have been
 isolated for a long time. Results: C. j. nitens had a wing shape that was
 better suited for long-distance flight than that of C. j. janthina. Both
 subspecies maintained sufficient gene flow among the islands within their
 habitat archipelagos, with no evidence of isolation by distance. The
 divergence time of the two subspecies was 0.67 million years ago, which
 was sufficient to reduce dispersiveness compared to other cases of island
 land birds.  Main conclusion: We showed that long-distance flight
 can be maintained under highly insular conditions despite
 long-term isolation from the ancestral populations. This indicates that
 the strategy of maintaining dispersal ability may also be
 possible in island systems, where organisms have repeatedly and
 globally shown reduced dispersal ability. Although further
 studies are required to reveal its evolutionary processes, our
 study provides an exceptional case for island birds' biogeography.
DOI: 10.5061/dryad.xksn02vh7
title: Metabolic phenotype mediates the outcome of competitive interactions in a response-surface field experiment

description: Competition and metabolism should be linked. Intraspecific variation in
 metabolic rates and, hence, resource demands covary with competitive
 ability. The effects of metabolism on conspecific interactions, however,
 have mostly been studied under laboratory conditions. We used a
 trait-specific response-surface design to test for the effects of
 metabolism on pairwise interactions of the marine colonial invertebrate,
 Bugula neritina in the field. Specifically, we compared the performance
 (survival, growth, and reproduction) of focal individuals, both in the
 presence and absence of a neighbour colony, both of which had their
 metabolic phenotype characterised. Survival of focal colonies depended on
 the metabolic phenotype of the neighbouring individual, and on the
 combination of both the focal and neighbour colony metabolic phenotypes
 that were present. Surprisingly, we found pervasive effects of neighbour
 metabolic phenotypes on focal colony growth and reproduction, though the
 sign and strength of these effects showed strong microenvironmental
 variability. Overall, we find that the metabolic phenotype changes the
 strength of competitive interactions, but these effects are highly
 contingent on local conditions. We suggest future studies explore how
 variation in metabolic rate affects organisms beyond the focal organism
 alone, particularly under field conditions.
description: We characterised the metabolic phenotype of individuals of the
 marine colonial invertebrate, <em>Bugula neritina</em> and,
 using a trait-specific response-surface design, created pairs of
 individuals that differed in their metabolic rates. We then followed the
 performance of all individuals throughout their lives to determine the
 effects of metabolism on competitive interactions in the field (note that
 we treated both colonies as the focal and neighbour colony to test for
 reciprocal interactions). Specifically, we followed the survival,
 growth, and fecundity (reproductive output) of each individual by checking
 colony absence/presence and counting the number of bifurcations (colony
 size, later converted to zooid number) and the number of ovicells
 (external offspring bearing brood chambers; every ovicell contains a
 single larva) every two weeks over a period of six months.
DOI: 10.48733/ifjpan/rncelu
title: AFM-IR insights into cell wall remodeling and protein reorganization in Candida auris versus Candida albicans - research data

description: This dataset includes averaged AFM-IR and FT-IR spectra of Candida auris and Candida albicans from the manuscript “AFM-IR insights into cell wall remodeling and protein reorganization in Candida auris versus Candida albicans”. Two files are provided, containing separated and averaged spectra of cells (AFM-IR) and colonies (FT-IR).
DOI: 10.5061/dryad.crjdfn35j
title: Structural model of PORCN .cif and .pdb files

description: Wnt signaling is essential for normal development and is a therapeutic
 target in cancer. The enzyme PORCN, or porcupine, is a membrane-bound
 O-acyltransferase (MBOAT) that is required for the post-translational
 modification of all Wnts, adding an essential mono-unsaturated palmitoleic
 acid to a serine on the tip of Wnt hairpin 2. Inherited mutations in PORCN
 cause focal dermal hypoplasia, and therapeutic inhibition of PORCN slows
 the growth of Wnt-dependent cancers. Here, based on homology to mammalian
 MBOAT proteins we develop and validate a molecular structural model of
 PORCN. The model accommodates palmitoleoyl-CoA and Wnt hairpin 2 in two
 tunnels in the conserved catalytic core, shedding light on the catalytic
 mechanism. The model predicts how previously uncharacterized human
 variants of uncertain significance can alter PORCN function. Drugs
 including ETC-159, IWP-L6 and LGK-974 dock in the PORCN catalytic site,
 providing insights into PORCN pharmacologic inhibition. This structural
 model provides mechanistic insights into PORCN substrate recognition and
 catalysis as well as the inhibition of its enzymatic activity and can
 facilitate the development of improved inhibitors and the understanding of
 disease relevant PORCN mutants.
description: The homology model of PORCN was generated as described in Yu et
 al. bioRxiV 2021 and Journal of Cell Science.
description: These files can be opened with structure visualization programs
 such as PyMol and Chimera.
DOI: 10.5061/dryad.j3tx95xfs
title: Dataset of distribution and trait of small mammals in Mt. Liangshan

description: Secondary and plantation forests are the main alternative forests
 remaining after the deforestation of primary forests. Understanding the
 conservation value of secondary and plantation forests is
 important for biological conservation. To explore the impact of forest
 conversion on biodiversity, we compared multiple diversity metrics
 (taxonomic, phylogenetic, and functional diversity) and the community
 structure of small mammals in the primary, secondary, and plantation
 forests in Mt. Liangshan, Sichuan Province, China. The dataset
 describes the distribution, morphological traits, and other traits of
 small mammals.
description: The distribution data of small mammal were depends on whether we
 catch it or not in primary, secondary, and plantation forests. The
 morphological trait data of a species was calculated as the average value
 of all its captured individuals, and other trait data were compiled from
 Elton Traits 1.0
DOI: 10.5061/dryad.pg4f4qrqt
title: Early onset of adult deafness in the Rhodesian Ridgeback is associated with in-frame deletion in the EPS8L2 gene

description: Domestic dogs exhibit diverse types of both congenital and non-congenital
 hearing losses. Rhodesian Ridgebacks can suffer from a progressive hearing
 loss in the early stage of their life, a condition known as early onset of
 adult deafness (EOAD), where they lose their hearing ability within 1-2
 years after birth. In order to investigate the genetic basis of this
 hereditary hearing disorders, we performed a genome-wide association study
 (GWAS) by using a sample of 23 affected and 162 control Rhodesian
 Ridgebacks. We identified a genomic region on canine chromosome 18 (CFA18)
 that is strongly associated with EOAD, and our subsequent targeted Sanger
 sequencing analysis identified a 12-bp inframe deletion in EPS8L2
 (CFA18:25,868,739-25,868,751 in the UMICH_Zoey_3.1/canFam5 reference
 genome build). Additional genotyping confirmed a strong association
 between the 12-bp deletion and EOAD, where all affected dogs were
 homozygous for the deletion, while none of the control dogs was a deletion
 homozygote. A segregation pattern of this deletion in a 2-generation
 nuclear family indicated an autosomal recessive mode of inheritance. Since
 EPS8L2 plays a critical role in the maintenance and integrity of the inner
 ear hair cells in humans and other mammals, the inframe deletion found in
 this study represents a strong candidate causal mutation for EOAD in
 Rhodesian Ridgebacks. Genetic and clinical similarities between childhood
 deafness in humans and EOAD in Rhodesian Ridgebacks emphasizes the
 potential value of this dog breed in translational research in hereditary
 hearing disorders.
description: In order to recruit EOAD-affected and normal hearing dogs, we
 conducted an online survey in 2020 to private dog owners of Rhodesian
 Ridgebacks who agreed to participate in scientific research. DNA was
 extracted from buccal swab samples collected by dog owners and extracted
 by Illumina, Inc. Genotypes of the dogs were collected by using custom
 Illumina Canine high-density SNP arrays.
DOI: 10.5281/zenodo.18398297
title: Microglia sense fungal infections through capsular components from capillary-bound Cryptococcus neoformans via endothelial nucleotide signaling

description: The Flow cytometry files associated with the publication. Staining and gating strategy has been discribed in the article.
DOI: 10.5281/zenodo.18398298
title: Microglia sense fungal infections through capsular components from capillary-bound Cryptococcus neoformans via endothelial nucleotide signaling

description: The Flow cytometry files associated with the publication. Staining and gating strategy has been discribed in the article.