cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9zw3r22bk
title: Data from: Combined effect of anthropogenic noise and artificial night lighting negatively affect Western Bluebird chick development

description: Sensory pollutants such as anthropogenic noise and night lighting now
 expose much of the world to evolutionarily novel sound and night lighting
 conditions. An emerging body of literature has reported a variety of
 deleterious effects caused by these stimuli, spanning behavioral,
 physiological, population and community-level responses. However, the
 combined influence of noise and light has received almost no attention
 despite the co-occurrence of these stimuli in many landscapes. Here we
 evaluated the singular and combined effects of these stimuli on Western
 Bluebird (Sialia mexicana) reproductive success using a field-based
 manipulation. Nests exposed to noise and light together experienced less
 predation than control and light-exposed nests, and noise-exposed nests
 experienced less predation than control nests, yet overall nest success
 was only higher in noise-exposed nests compared to light-exposed nests.
 Although exposure to light decreased nestling body condition and evidence
 was mixed for the singular effects of noise or light on nestling size,
 those nestlings exposed to noise and light together were smaller across
 several metrics than nestlings in control nests. Our results support
 previous research on the singular effects of either stimuli, including
 potential benefits, such as reduced nest predation with noise exposure.
 However, our results also suggest that noise and light together can
 negatively affect some aspects of reproduction more strongly than either
 sensory pollutant alone. This finding is especially important given that
 these stimuli tend to covary and are projected to increase dramatically in
 the next several decades.
DOI: 10.5061/dryad.tdz08kpx1
title: Data from: Snakeskin gourami (Trichopodus pectoralis) exhibits XX/XY sex determination and putative young Y chromosome shares sex chromosomal linkage homologies with those of amniotes

description: Snakeskin gourami (Trichopodus pectoralis) is one of the most common
 air-breathing freshwater fish of the Indochina peninsula. It has a high
 meat yield and is one of the top five aquaculture freshwater fish in
 Thailand. However, it takes 2–3 years for adults to reach sexual maturity.
 Snakeskin gourami is not externally sexually dimorphic and its sex
 determination remains unknown, complicating many aspects of broodstock
 management including sex manipulation. Understanding the sex determination
 system will contribute significantly towards full-scale commercialization.
 By  characterizing the sex determination system in snakeskin
 gourami using cytogenetic approaches and Diversity Arrays Technology, we
 identified sex-specific loci in 16 phenotypic sex assignments of snakeskin
 gourami. Of the 39 loci present in all males, 4 male-linked loci reached
 the criteria of moderately sex-linked loci (70:30; males:females and
 80:20; males:females). By contrast, only one female-linked locus was
 detected from moderately sex-linked loci. This suggests that snakeskin
 gourami exhibits an XX/XY sex determination mode. No different chromosomal
 patterns were observed in karyotype, C-banding, and microsatellite repeat
 fluorescence in situ hybridization mapping between males and females, and
 no male-specific loci of 100:0 (males:females) were observed in snakeskin
 gourami. This suggests that the putative Y chromosome is young and the
 non-recombination region is very cryptic. A total of 10.26% male-linked
 loci were involved with the sex developmental pathway in vertebrates and
 5.13% showed partial homology with several amniote sex chromosomal
 linkages. Surprisingly, the hypothesis of an ancestral amniote super-sex
 chromosome with overlaps of partial sex chromosomal linkages was also
 found in teleosts. This approach provides a solid baseline to reveal the
 sex determination mechanism and identify potential sex determination
 regions in teleosts, allowing further investigation of genetic
 improvements in snakeskin gourami.
DOI: 10.5061/dryad.f4qrfj6t7
title: Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling

description: Molecular analysis of DNA left in the environment, known as environmental
 DNA (eDNA), has proven to be a powerful and cost-effective approach to
 infer occurrence of species. Nonetheless, relating measurements of eDNA
 concentration to population abundance remains difficult because detailed
 knowledge on the processes that govern spatial and temporal distribution
 of eDNA should be integrated to reconstruct the underlying distribution
 and abundance of a target species. In this study, we propose a general
 framework of abundance estimation for aquatic systems on the basis of
 spatially replicated measurements of eDNA. The proposed method explicitly
 accounts for production, transport, and degradation of eDNA by utilizing
 numerical hydrodynamic models that can simulate the distribution of eDNA
 concentrations within an aquatic area. It turns out that, under certain
 assumptions, population abundance can be estimated via a Bayesian
 inference of a generalized linear model. Application to a Japanese jack
 mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the
 proposed method gives an estimate of population abundance comparable to
 that of a quantitative echo sounder method. Furthermore, the method
 successfully identified a source of exogenous input of eDNA (a fish
 market), which may render a quantitative application of eDNA difficult to
 interpret unless its effect is taken into account. These findings indicate
 the ability of eDNA to reliably reflect population abundance of aquatic
 macroorganisms; when the “ecology of eDNA” is adequately accounted for,
 population abundance can be quantified on the basis of measurements of
 eDNA concentration.
DOI: 10.5061/dryad.rfj6q577r
title: Data from: Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population

description: Background: Human demand for wheat will continue to increase together with
 the continuous global population growth. Agronomic traits in wheat are
 susceptible to environmental conditions. Therefore, in breeding practice,
 priority is given to QTLs of agronomic traits that can be stably detected
 across multiple environments and over many years. Results: In this study,
 QTL analysis was conducted for eight agronomic traits using an
 introgression line population across eight environments (drought stressed
 and well-watered) for five years. In total, 44 additive QTLs for the above
 agronomic traits were detected on 15 chromosomes. Among these, qPH-6A,
 qHD-1A, qSL-2A, qHD-2D and qSL-6A were detected across seven, six, five,
 five and four environments, respectively. The means in the phenotypic
 variation explained by these five QTLs were 12.26%, 9.51%, 7.77%, 7.23%,
 and 8.49%, respectively. Conclusions: We identified five stable QTLs,
 which includes qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A. They play a
 critical role in wheat agronomic traits. One of the dwarf genes Rht14,
 Rht16, Rht18 and Rht25 on chromosome 6A might be the candidate gene for
 qPH-6A. The qHD-1A and qHD-2D were novel stable QTLs for heading date and
 they differed from known vernalization genes, photoperiod genes and
 earliness per se genes.
description: Extraction of DNA was performed using the CTAB method. Following
 the principle of uniform distribution on the chromosome, 565 simple
 sequence repeat (SSR) markers covering the whole genome of wheat were
 selected based on the high-density microsatellite consensus map [34]. The
 selected SSR markers were screened for polymorphisms between the two
 parents, which yielded 187 polymorphic markers. The polymorphic SSR
 markers were then used to perform a genome-wide screen of the IL
 population.
description: Marker type: 2 for Shaanhan8675;  0 for Lumai14; -1 for missing
 markers
DOI: 10.5281/zenodo.11433237
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - CADIZ - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Cádiz:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5281/zenodo.11433236
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - CADIZ - (June 23 - May 24)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) the andalusian agroclimatic information network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2023, to May 31, 2024, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Cádiz:

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.bg79cnp85
title: Data from: Association of CSF Orexin-A levels and nocturnal sleep stability in patients with hypersomnolence

description: Objective: To evaluate the associations between cerebrospinal
 fluid orexin-A (ORX) levels and markers of nocturnal sleep stability,
 assessed by polysomnography (PSG). Methods: Nocturnal PSG data and ORX
 levels of 300 drug-free subjects (55% men, 29.9±15.5 years, ORX level
 155.1±153.7 pg/ml) with hypersomnolence were collected. Several markers of
 nocturnal sleep stability were analyzed: wake and sleep bouts, sleep/wake
 transitions. Groups were categorized according to ORX levels, in two
 categories (deficient≤110; &gt;110), in tertiles (≤26, ]26;254],
 &gt;254), and compared using logistic regression models. Results were
 adjusted for age, sex and body mass index. Results: We found higher number
 of wake bouts (43 vs 25, p&lt;0.0001), sleep bouts (43 vs 25.5,
 p&lt;0.0001) and index of sleep bouts/hour of sleep time, but lower
 index of wake bouts/hour of waketime (41.4 vs 50.6, p&lt;0.0001) in
 subjects with ORX deficiency. The percentage of wake bouts &lt;30sec
 was lower (51.3 vs 60.8%, p&lt;0.001) and of wake bouts ³1min30sec
 higher (7.7 vs 6.7%, p=0.02) when ORX deficient. The percentage of sleep
 bouts ≤14min was higher (2-5min: 23.7 vs 16.1%, p&lt;0.0001), and of
 long sleep bouts lower (&gt;32min30sec: 7.3 vs 18.3%, p&lt;0.0001)
 when ORX deficient. These findings were confirmed when groups were
 categorized according to ORX tertiles, with a dose-response effect of ORX
 levels in post-hoc comparisons, and in adjusted models. Interpretation:
 This study shows an association between ORX levels and nocturnal sleep
 stabilization in patients with hypersomnolence. Sleep and wake bouts are
 reliable markers of nighttime sleep stability that correlate with CSF ORX
 levels in a dose-dependent manner.
DOI: 10.5061/dryad.crjdfn321
title: Data from: Characterizing niche differentiation among marine consumers with amino acid δ13C fingerprinting

description: Marine food webs are highly compartmentalized and characterizing the
 trophic niches among consumers is important for predicting how impact from
 human activities affect the structuring and functioning of marine food
 webs. Biomarkers such as bulk stable isotopes have proven to be powerful
 tools to elucidate trophic niches, but they may lack in resolution,
 particularly when spatio-temporal variability in a system is high. To
 close this gap, we investigated whether carbon isotope (δ13C )
 patterns of essential amino acids (EAAs), also termed d13CAA fingerprints,
 can characterize niche differentiation in a highly dynamic marine system.
 Specifically, we tested the ability of d13CAA fingerprints to
 differentiate trophic niches among six functional groups and ten
 individual species in the Baltic Sea. We also tested whether fingerprints
 of the common zooplanktivorous fishes, herring and sprat, differ among
 four Baltic Sea regions with different biochemical conditions and
 phytoplankton assemblages. Additionally, we investigated how these results
 compared to bulk C and N isotope data for the same sample set. We found
 significantly different d13CAA fingerprints among all six functional
 groups. Species differentiation was in comparison less distinct, due to
 partial convergence of the species’ fingerprints within functional groups.
 Herring and sprat displayed region specific d13CAA fingerprints indicating
 that this approach could be used as a migratory marker. Niche metrics
 analyses showed that bulk isotope data had a lower power to differentiate
 between trophic niches than 13CAA fingerprinting. We conclude that d13CAA
 fingerprinting has a strong potential to advance our understanding of
 ecological niches, and trophic linkages from producers to higher trophic
 levels in dynamic marine systems. Given how management practices of marine
 resources and habitats are reshaping the structure and function of marine
 food webs, implementing new and powerful tracer methods are urgently
 needed to improve the knowledge base for policy makers.
description: Baltic Sea fish samples collected during the cruise AL476 with
 the research vessel ALKOR in April 2016. All tissue samples were freeze
 dried. Samples for d13C amino acid analysis were first hydrolyzed in 6 N
 HCl at 110°C for 20 h before derivatizing the amino acids to
 <i>N</i>-acetyl methyl esters. The samples were analysed at
 the Leibniz Laboratory at Kiel University. Elemental
 content and bulk isotope values were determined at the Stable Isotope
 Facility of the Experimental Ecology Group, GEOMAR, Kiel.
description: The isotope ratios are expressed relative to international
 standards; Vienna Pee Dee Belemnite (VPDB) for carbon and atmospheric air
 for nitrogen.
DOI: 10.5061/dryad.p8cz8w9ms
title: Raw data used in A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factor

description: The biomass ratio of herbivores to primary producers reflects the
 structure of a community. Four primary factors have been proposed to
 affect this ratio, including production rate, defense traits and nutrient
 contents of producers, and predation by carnivores. However, identifying
 the joint effects of these factors across natural communities has been
 elusive, in part because of the lack of a framework for examining their
 effects simultaneously. Here, we develop a framework based on
 Lotka-Volterra equations for examining the effects of these factors on the
 biomass ratio. We then utilize it to test if these factors simultaneously
 affect the biomass ratio of freshwater plankton communities. We found that
 all four factors contributed significantly to the biomass ratio, with
 carnivore abundance having the greatest effect, followed by producer
 stoichiometric nutrient content.  Thus, the present framework
 should be useful for examining the multiple factors shaping various types
 of communities, both aquatic and terrestrial.
DOI: 10.5061/dryad.r2280gb9x
title: Molecular systematics and taxonomic overview of the bird’s nest fungi (Nidulariaceae)

description: Fungi in the Nidulariaceae, otherwise known as ‘bird’s nest fungi’, are
 among the least studied groups of Agaricomycetes (Basidiomycota). Bird’s
 nest fungi are globally distributed and typically grow on woody debris or
 animal dung as saprotrophs. This group of fungi is morphologically
 diverse, and ca. 180 different species have been described. Phylogenetic
 relationships of bird’s nest fungi were investigated with Maximum
 Likelihood and Bayesian analyses of four commonly used loci (ITS, LSU,
 tef, and rpb2). The family was resolved as a monophyletic group with
 Psathyrellaceae and Squamanitaceae as potential sister taxa. Specimens
 identified as Cyathus and Crucibulum formed well-supported clades. Nidula
 and Nidularia together are monophyletic. Two Mycocalia species studied are
 on their own separate branches. Misidentifications were detected in most
 genera. Common bird’s nest fungi species have global geographical
 distributions whereas rarer species may have more limited ranges. Our data
 also indicate that basic morphological characters of bird’s nest fungi
 have likely been lost or gained multiple times. The relationships among
 genera of bird’s nest fungi remain largely unresolved and the sister
 lineage of bird’s nest fungi is still unclear. Further studies with data
 from rare species and additional informative loci are needed to resolve
 the topology of this family and to identify a sister group with more
 certainty. We also provide a detailed morphological comparison to
 differentiate the five currently accepted genera of Nidulariaceae.
description: Specimens of Nidulariaceae fungi were obtained through three
 different methods: fresh field collections, contributions from citizen
 scientists and traditional herbarium loans.
DOI: 10.5061/dryad.0p2ngf1xg
title: The structural determinants of PH domain-mediated regulation of Akt revealed by segmental labeling

description: Akt is a critical protein kinase that governs cancer cell growth and
 metabolism. Akt appears to be autoinhibited by an intramolecular
 interaction between its N-terminal pleckstrin homology (PH) domain and
 kinase domain, which is relieved by C-tail phosphorylation, but the
 precise molecular mechanisms remain elusive. Here we use a combination of
 protein semisynthesis, NMR, and enzymological analysis to characterize
 structural features of the PH domain in its autoinhibited and activated
 states. We find that Akt autoinhibition depends on the length/tension of
 the PH-kinase linker. We identify a role for a dynamic short segment in
 the PH domain that appears to regulate autoinhibition and PDK1-catalyzed
 phosphorylation of Thr308 in the activation loop. We determine that Akt
 allosteric inhibitor MK2206 drives distinct PH domain structural changes
 compared to baseline autoinhibited Akt. These results highlight how the
 conformational plasticity of Akt governs the delicate control of its
 catalytic properties.
DOI: 10.15468/dl.p6nctw
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000048784, K-M000067398, K-M000067641, K-M000067663, K-M000067683, K-M000067702, K-M000067721, K-M000068133, K-M000068172, K-M000154491, K-M000154496, K-M000154498, K-M000154504, K-M000154545, K-M000154564, K-M000792615, K-M000874863, K-M001043816, K-M000977665, K-M000708856, K-M000985086, K-M000836464, K-M000770345, K-M000766417, K-M000764800, K-M000985087, K-M001043634, K-M001043637, K-M000067665, K-M000836457, K-M000836466, K-M000897934, K-M000067646, K-M000979287, K-M000707000, K-M001043815)"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002395-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1zcrjdfpw
title: Data from: Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment

description: Microplastics are recognized as an emerging contaminant worldwide.
 Although microplastics have been shown to strongly affect organisms in
 aquatic environments, less is known about whether and how microplastics
 can affect different taxa within a soil community, and it is unclear
 whether these effects can cascade through soil food webs. By conducting a
 microplastic manipulation experiment, i.e. adding low-density polyethylene
 fragments in the field, we found that microplastic addition significantly
 affected the composition and abundance of microarthropod and nematode
 communities. Contrary to soil fauna, we found only small effects of
 microplastics on the biomass and structure of soil microbial communities.
 Nevertheless, structural equation modeling revealed that the effects of
 microplastics strongly cascade through the soil food webs, leading to the
 modification of microbial functioning with further potential consequences
 on soil carbon and nutrient cycling. Our results highlight that taking
 into account the effects of microplastics at different trophic levels is
 important to elucidate the mechanisms underlying the ecological impacts of
 microplastic pollution on soil functioning.