cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.js2jx5
title: Occurrence Download

description: A dataset containing 2141 records in GBIF matching the query:
SELECT
 '444' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 47.95259801890024
 AND decimalLongitude &lt;= 56.64958282616588
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 2141 records were derived from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002640-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mpg4f4qxh
title: Data on long-term demographic information for Alliaria petiolata in eastern North America

description: While biological invasions have the potential for large negative impacts
 on local communities and ecological interactions, increasing evidence
 suggests that species once considered major problems can decline over
 time. Declines often appear driven by natural enemies, diseases, or
 evolutionary adaptations that selectively reduce populations of
 naturalized species and their impacts.  Using permanent long-term
 monitoring locations, we document declines of Alliaria petiolata (garlic
 mustard) in eastern North America with distinct local and regional
 dynamics as a function of patch residence time.  Projected
 site-specific population growth rates initially indicated expanding
 populations, but projected population growth rates significantly decreased
 over time and at the majority of sites fell below 1, indicating declining
 populations. Negative soil feedback provides a potential mechanism for the
 reported disappearance of ecological dominance of A. petiolata in eastern
 North America.
description: Standardized long-term data collection in permanent
 0.5m<sup>2</sup> quadrats using multiple locations at a site
 with sites rangin from New Jersey to Illinois in eastern North America. 
 Duration of data collection varied by site but in the longest sites it
 spanned over a decade. Data were collected on important demographic
 parameters for garlic mustard (number of seedlinsg or mature plants, etc.)
 to allow building demographic models to forecast population
 trends.
description: The data we provide in excel is the raw data and all column
 headings are explained in a separate excel file called metadata.
DOI: 10.5061/dryad.xpnvx0kdc
title: Urbanization mediates the effects of water quality and climate on a model aerial insectivorous bird

description: Aerial insectivorous birds have experienced alarming population declines
 in eastern North America. Meanwhile, urbanization continues to increase
 rapidly, with urban land use comprising 69.4 million acres, or 3.6% of
 total land area, in the contiguous United States. Multiple environmental
 changes are associated with urbanization, including alterations to local
 climate, changes in habitat structure, and potential shifts in both
 terrestrial and emergent aquatic flying insects on which aerial
 insectivorous birds rely. Here, we investigated the linkages between
 urbanization, water quality, and Tree Swallow (Tachycineta bicolor)
 reproductive success and body condition at seven river-riparian sites
 representing urban and protected land use in Columbus, Ohio over five
 consecutive years (2014-2018). Tree Swallows at urban and protected sites
 relied on emergent aquatic insects for 37.4 and 30.8% (SD = 28.4 and
 24.1%) of their nutritional subsidies, respectively. Despite the loss of
 environmental quality generally attributed to cities, Tree Swallows
 exhibited greater reproductive success in urban settings where climate was
 more amenable to egg and nestling survival, and the breeding season was
 longer. Urban-nesting Tree Swallows initiated laying 7.9 days earlier and
 fledged 35% more young per nest than those at protected sites. Multiple
 characteristics of urban sites appeared to drive these patterns, including
 differences in mean and extreme air temperatures and measures of water
 quality (e.g., water temperature, nutrient concentrations, turbidity).
 However, chronic effects of elevated Hg concentrations – which were 482%
 greater in adult swallow blood at urban sites than at protected sites
 where swallows exhibited a 17.4% lower trophic position – may disadvantage
 individuals in other ways. Further, although Tree Swallows are a good
 model aerial insectivore bird species, characteristics of urban landscapes
 that benefit Tree Swallows may not advantage other aerial insectivorous
 birds owing to differences in life-history and foraging strategies. These
 findings implicate urbanization, local climate, and water quality as
 important considerations in the conservation of aerial insectivorous
 birds.
DOI: 10.7272/q6sf2tf6
title: Characterization of HIV-induced remodeling reveals differences in infection susceptibility of memory CD4+ T cell subsets in vivo

description: In vitro studies suggest that CD4+ T cells can exhibit different
 susceptibilities to HIV infection depending on their differentiation or
 activation states, but relatively little is known about the features of
 CD4+ T cells preferentially targeted by HIV in vivo. By applying
 bioinformatics analysis on CyTOF-phenotyped blood specimens from 11
 viremic individuals matched to ART-suppressed specimens from the same
 subjects, we provide an atlas of the phenotypic features of in vivo
 HIV-susceptible cells. The properties of in vivo susceptible cells were
 compared to those of in vitro infected cells to assess which properties of
 in vivo susceptible cells are recapitulated in vitro. Manual gating
 identified Th17 cells and memory CD4+ T cells expressing high levels of
 a4b1 as preferentially targeted for in vivo HIV infection, while memory
 CD4+ T cells of the Tem, Ttm, Th1, and Th1/Th17 subsets were
 preferentially targeted in vitro. PP-SLIDE bioinformatics analysis of the
 datasets revealed that multiple proteins antigens – particularly those
 encoding chemokine and cytokine receptors –were remodeled by HIV during in
 vivo infection, and this was mostly recapitulated in vitro. To identify
 features of HIV-susceptible cells shared between the in vivo and in vitro
 specimens, we implemented unbiased clustering. We identified from both
 specimen types a subset of highly-susceptible Tem-like cells, and
 validated the high susceptibility of this cellular subset. These studies
 provide an in-depth look at the features of HIV-susceptible cells in
 viremic individuals and demonstrate that some – but not all
 – subsets of HIV-susceptible CD4+ T cells characterized in vitro
 can effectively model HIV susceptibility in vivo.
description: FCS files for in vivo and in vitro datasets  for each donor.
 Datasets are provided for uninfected CD4+ T cells, uninfected memory CD4+
 T cells, bystander CD4+ T cells, productively-infected cells, and
 predicted precursor (PRE) cells. Please refer to parent publication for
 details.
DOI: 10.5061/dryad.1g1jwsttq
title: Data from: Latitudinal variation of arrival and breeding phenology of the pied flycatcher Ficedula hypoleuca using large-scale citizen science data.

description: Many species have advanced the timing of annual reproductive cycles in
 response to climatic warming, sometimes leading to asynchrony between
 trophic levels, with negative population consequences. Long-distance
 migratory birds, reliant on short seasonal food pulses for
 breeding, are considered particularly susceptible to such
 disjunction because late arrival may preclude optimal timing of
 egg-laying. It is unknown whether the relative timing of arrival and
 egg-laying is sufficiently plastic, in time and space, to enable an
 adaptive response when arrival times change relative to local food
 resources. We used citizen science data, describing pied
 flycatcher Ficedula hypoleuca arrival and egg-laying dates, to
 explore temporal (2013-2016) and spatial (across Great Britain) variation
 in the phenology of arrival, laying and their difference. To
 assess the long-term trend in arrival and laying at a single location, we
 used data from a long-term field study. The arrival-laying interval was
 consistently shorter in the north, driven by the contrast between spatial
 variation in arrival date and spatial invariance in laying date. To
 understand whether a short arrival-laying interval may have consequences
 for productivity, we assessed the association between this interval and
 clutch size. We found no statistically significant correlation between
 these two variables. To examine long-term changes in arrival and laying
 dates, we focussed on a single location in southwestern England. Both
 dates of first male arrival and first egg laid in a season advanced since
 1986, with no evidence of interval shortening. Together, our results
 demonstrate spatial and annual variation in the arrival-laying interval,
 with no detected effect on fecundity. Thus, the interval from arrival to
 laying is likely dictated by spatially and temporally varying local
 conditions, suggesting these migrant birds may have the ability to adapt
 this interval to align with local conditions and mitigate potential
 mismatch impacts.
description: This file contains the different analyses covering sections 2.1
 to 2.6 of the original paper.  This includes multiple
 datasets including: - processed dataset from database
 BirdTrack (BTO), showcasing presence/absence of Pied Flycatcher on
 checklists across Great Britain between 2013-2016. -
 raw and processed datasets from database Nest Record Scheme (BTO),
 showcasing nests of Pied Flycatcher for the same range and time.
 - geolocator data collected in Devon, UK, with arrival and
 nesting dates, for 2015-2016. - first arrival date and
 first nesting data collected in Devon, UK, from 1986-2018.
 Details of processing are included in the manuscript whenever the
 code is not provided. The code for all the statistical
 analyses is provided.
description: All the ReadMe files are inside of the respective folders with
 instructions of how to use the scripts and with metadata.
DOI: 10.5061/dryad.08kprr51j
title: Forest soil acidification consistently reduces litter decomposition irrespective of nutrient availability and litter type

description: Nitrogen (N), phosphorus (P), and acid deposition are co-occurring in many
 ecosystems, likely with complex interactive effects on litter
 decomposition. Few studies have been conducted to distinguish the
 interactive effects of these three factors on forest litter decomposition.
 Thus, we performed a 5-year litter decomposition experiment with N, P,
 acid addition in a temperate forest of Changbai Mountain in China,
 including four litter types from Pinus koraiensis, Quercus mongolica,
 Tilia amurensis and their mixtures. Our results showed that acid addition
 consistently reduced litter decomposition rate, irrespective of nutrient
 addition or litter types. In contrast, N and P addition had less impact on
 litter decomposition. Litter decomposition rate linearly reduced with
 decreasing soil pH, but positively increased with soil N availability. No
 relationship was found between soil P availability and litter
 decomposition. Soil enzyme activity played a key role in regulating litter
 decomposition response, such as acid phosphatase, xylosidase,
 N-cacetyl-b-D-glucosaminidase and α-1,4 glucosidase. Besides, low-quality
 litter (i.e. high C concentration, C:N and C:P ratio) amplified the
 negative effect of soil acidification on litter decomposition. This study
 suggests that soil acidification consistently decelerates litter
 decomposition in temperate forests, which is independent of soil nutrient
 availability and litter types. The intensifying soil acidification with
 continuous N deposition in the future will greatly reduce litter nutrient
 return to soil, increasing the risk of multiple soil nutrient limitation.
DOI: 10.15468/dl.e3hdfj
title: Occurrence Download

description: A dataset containing 3733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "DatasetKey is Pl@ntNet observations"
 ]
}

 The dataset includes 3733 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002651-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qz612jmd7
title: Data from Stranger Things: Organismal traits of two octocorals associated with singular Symbiodiniaceae in a high-latitude coral community from northern Taiwan

description: Scrutinizing the traits of octocorals that could affect their
 physiological performance becomes increasingly important as several of
 these species are observed to become dominant on reefs pressured by the
 Anthropocene. In the present study, we compare the organismal traits of
 two branching octocorals Litophyton sp. and Stereonephthya sp. commonly
 populating in sympatry the high-latitude coral communities of northern
 Taiwan. Using 13 traits, we describe and compare performance traits in
 these two symbiotic species that we discuss in light of the association
 they maintain with their algal partners. Litophyton sp. and Stereonephthya
 sp. hosted Durusdinium and Gerakladium, respectively. Both genera
 represent singular associations, with the latter further establishing the
 first solid report of Gerakladium in octocorals. Traits distinguished two
 groups explained by the two partnerships considered. Litophyton sp.
 associated with Durusdinium had significantly higher organic matter,
 chlorophyll (chl) a, total lipid and lower chl c/chl a ratio than
 Stereonephthya sp. associated with Gerakladium. The δ15N in the host and
 algae, as well as δ13C in the host were also higher in Litophyton species.
 Although no significant difference was observed in the δ13C of the algae,
 Litophyton sp. presented a significantly higher variance for this trait
 and for chl a content than Stereonephthya species. Altogether, the traits
 examined suggested contrasting performances among the two octocorals. Both
 octocoral species clearly deviate from an autotrophic diet. Litophyton sp.
 appears to complement its heterotrophic diet with photosynthetically
 acquired energy, while Stereonephthya sp. tends to be more specialized and
 benefits relatively little from its symbiotic relationship. Our study
 calls for greater consideration of the individual variation in octocoral
 physiology and in the definition of their ecological strategies.
  
description: Organismal trait data for <i>Litophyton </i>sp.
 (n=10) and <i>Stereonephthya </i>sp. (n=10) colonies sampled
 in April 2019 at Bitou (-10 m), TAIWAN Detailed methods
 are available in Hsu et al. (2020). Frontiers in Marine
 Science. doi: 10.3389/fmars.2020.606601
description: The source code for data analysis is available at
 https://github.com/vianneydenis/stranger-things.git
DOI: 10.5061/dryad.66t1g1k0z
title: Data from: Detection of the elusive dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)

description: Monitoring large marine mammals is challenging due to their low abundances
 in general, an ability to move over large distances and wide geographical
 range sizes.  The distribution of the pygmy (Kogia breviceps) and
 dwarf (Kogia sima) sperm whales is informed by relatively rare sightings,
 which does not permit accurate estimates of their distribution ranges.
 Hence, their conservation status has long remained Data Deficient (DD) in
 the Red list of the International Union for Conservation of Nature (IUCN),
 which prevent appropriate conservation measures. Environmental DNA (eDNA)
 metabarcoding uses DNA traces left by organisms in their environments to
 detect the presence of targeted taxon, and is here proved to be useful to
 increase our knowledge on the distribution of rare but emblematic
 megafauna. Retrieving eDNA from filtered surface water provides the first
 detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo
 island (Colombia). Environmental DNA collected during oceanic missions can
 generate better knowledge on rare but emblematic animals even in regions
 that are generally well sampled for other taxa.
description: Post-processed eDNA metabarcoding data identified as marine
 mammals in Malpelo
DOI: 10.5061/dryad.fttdz08r6
title: Evaluation of foliar fungus-mediated interactions with below- and aboveground enemies of the invasive plant Ageratina adenophora

description: Plant–fungal associations are frequently key drivers of plant invasion
 success. Foliar fungi can benefit their invasive hosts by enhancing growth
 promotion, disease resistance and environmental stress tolerance. However,
 the roles of foliar fungi may vary when a given invasive plant faces
 different stresses. In this study, we designed three independent
 experiments to evaluate the effects of a foliar fungus, Colletotrichum
 sp., on the growth performance of the invasive plant Ageratina adenophora
 under different soil conditions, as well as the responses of A. adenophora
 to the foliar fungal pathogen Diaporthe helianthi and to herbivory. We
 found that the soil type was the most influential factor for the growth of
 A. adenophora. The role of the foliar fungus Colletotrichum sp. varied in
 the different soil types but generally adversely affected leaf development
 in A. adenophora. Colletotrichum sp. may be a weak latent foliar pathogen
 that can enhance the pathogenicity of D. helianthi on leaves of A.
 adenophora and marginally reduce signs of herbivory by natural insects in
 the wild on A. adenophora seedlings.In general, the benefits of the foliar
 fungus Colletotrichum to the fitness of A. adenophora are not significant
 in the context of this experimental design. However, our data highlight
 the need to consider both aboveground and belowground biota in different
 soil habitats when evaluating the effects of foliar fungi.
DOI: 10.5061/dryad.41ns1rnc8
title: Data from: A unified framework for quantifying land carbon sequestration

description: Land ecosystems offer an effective nature-based solution to climate change
 mitigation by absorbing approximately 30% of anthropically emitted carbon.
 This absorption is primarily based on constraints from atmospheric and
 oceanic measurements while quantification from direct studies of the land
 carbon cycle itself displays great uncertainty. The latter hinders
 prediction of the future fate of the land carbon sink. Here, we show a
 unified framework for quantifying land carbon sequestration. The framework
 unifies all carbon cycle processes under a theory of dynamic
 disequilibrium and all models with one matrix equation to represent a
 nonautonomous compartmental system. While carbon input and residence
 (transit) time have been used to quantify carbon storage capacity at
 dynamic equilibrium, we introduce the third quantity, carbon storage
 potential that integrates fluxes and timescales, to define dynamic
 disequilibrium of land carbon cycle under global change. The carbon
 storage potential is presently not directly measurable. Its estimation
 requires the integration of multiple data sets with models. We urge the
 research community to convert the existing models and develop new models
 in the matrix form before we can fully identify sources of uncertainty in
 model predictions, evaluate relative values of various data sets, and
 improve the accuracy of quantification of land carbon sequestration.
DOI: 10.5061/dryad.zkh18938n
title: Nicotinamide riboside and pterostilbene cooperatively delay motor neuron failure in ALS SOD1G93A mice

description: Oxidative stress-induced damage is a major mechanism in the
 pathophysiology of amyotrophic lateral sclerosis (ALS). A recent human
 clinical trial showed that the combination of nicotinamide riboside (NR)
 and pterostilbene (PT), molecules with potential to interfere in that
 mechanism, was efficacious in ALS patients. We examined the effect of
 these molecules in SOD1G93A transgenic mice, a well-stablished model of
 ALS. Assessment of neuromotor activity and coordination was correlated
 with histopathology, and measurement of proinflammatory cytokines in the
 cerebrospinal fluid. Cell death, Nrf2- and redox-dependent enzymes and
 metabolites, and sirtuin activities were studied in isolated motor
 neurons. NR and PT increased survival and ameliorated ALSassociated loss
 of neuromotor functions in SOD1G93A transgenic mice. NR and PT also
 decreased the microgliosis and astrogliosis associated with ALS
 progression. Increased levels of proinflammatory cytokines were observed
 in the cerebrospinal fluid of mice and humans with ALS. NR and PT
 ameliorated TNFα-induced oxidative stress and motor neuron death
 in vitro. Our results support the involvement of oxidative stress,
 specific Nrf2-dependent antioxidant defenses, and sirtuins in the
 pathophysiology of ALS. NR and PT interfere with the mechanisms leading to
 the release of proapoptotic molecular signals by mitochondria, and also
 promote mitophagy
DOI: 10.5061/dryad.573n5tb63
title: No impact of neonicotinoids on male solitary bees Osmia cornuta under semi-field conditions

description: The ubiquitous use of agrochemicals is one driver for the ongoing loss of
 insect biomass and diversity. Data show that field-realistic
 concentrations of neonicotinoid insecticides can negatively affect both
 population density and the fitness of solitary bees. However, the
 underlying mechanisms for these effects remain poorly understood. Here,
 using an established semi-field experimental set-up and Osmia cornuta as a
 solitary bee model, we examined the effects of field-realistic
 concentrations of a common neonicotinoid insecticide (clothianidin) on
 male larvae and adults. Besides measuring lethal (i.e., overwintering
 success and adult survival) and sub-lethal endpoints (i.e., emergence mass
 and emergence duration), we examined, for the first time, potential
 effects on the male reproductive physiology of a solitary bee (i.e., sperm
 quantity and viability). The data revealed no significant effects on any
 of the measured response variables. This may be due to the low degree of
 clothianidin exposure (0.56 ng g−1) and/or the apparent low susceptibility
 of solitary bee larvae to neonicotinoids. Furthermore, it is conceivable
 that ideal foraging conditions, combined with optimal weather and lack of
 other environmental stressors, may have improved the ability of bees to
 cope with the insecticide. To reliably assess and understand the
 environmental hazards of agrochemicals, a holistic approach, including
 laboratory, semi-field, and field data is required. Knowledge of
 underlying mechanisms will help to mitigate the current global declines of
 insect populations.