cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8pk0p2nnz
title: Multispecies modelling reveals potential for habitat restoration to re-establish boreal vertebrate community dynamics

description: 1. The restoration of habitats degraded by industrial disturbance is
 essential for achieving conservation objectives in disturbed landscapes.
 In boreal ecosystems, disturbances from seismic exploration lines and
 other linear features have adversely affected biodiversity, most notably
 leading to declines in threatened woodland caribou. Large-scale
 restoration of disturbed habitats is needed, yet empirical assessments of
 restoration effectiveness on wildlife communities remain rare. 2. We used
 73 camera trap deployments from 2015-2019 and joint species distribution
 models to investigate how habitat use by the larger vertebrate community
 (&gt;0.2 kg) responded to variation in key seismic line
 characteristics (line-of-sight, width, density and mounding) following
 restoration treatments in a landscape disturbed by oil and gas development
 in northeastern Alberta. 3. The proportion of variation explained by line
 characteristics was low in comparison to habitat type and season,
 suggesting short-term responses to restoration treatments were relatively
 weak. However, we predicted that lines with characteristics consistent
 with restored conditions would support altered community composition, with
 reduced use by wolf and coyote, thereby indicating that line restoration
 will result in reduced contact rates between caribou and these key
 predators. 4. Our analysis provides a framework to assess and predict
 wildlife community responses to emerging restoration efforts. With the
 growing importance of habitat restoration for caribou and other vertebrate
 species, we recommend longer-term monitoring combined with landscape-scale
 comparisons of different restoration approaches to more fully understand
 and direct these critical conservation investments. Only by combining
 rigorous multispecies monitoring with large-scale restoration will we
 effectively conserve biodiversity within rapidly changing environments.
description: For data collection methods please see the associated paper. The
 raw data from this project was processed through the WildCo labs Singe
 site data processing tool
 (https://github.com/WildCoLab/SingleSiteExploration) - to produce the
 30min independent data given here:
 Algar_2015_2019_30min_Independent_JPE_Beirne_et_al_2021. This data set was
 then processed to give the total observations summary
 (total_observations_JPE_Beirne_et_al_2021), monthly counts summary
 (monthly_counts_JPE_Beirne_et_al_2021) and 6 month counts Y data used in
 the HMSC models (YData_dataframe_format_JPE_Beirne_et_al_2021). Raw
 station data (Raw_station_data_JPE_Beirne_et_al_2021) were standardised
 using the MuMIn package to give the XData used in the analysis
 (XData_JPE_Beirne_et_al_2021). The R code to reproduce the analysis is
 (Community_analysis_JPE_Beirne_at_al_2021) and also stored on GitHub
 (https://github.com/ChrisBeirne/Multispecies_modelling_JPE_Beirne_2021).
DOI: 10.5061/dryad.0rxwdbs1j
title: Data from: Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma

description: Background: Although the effects of macrophages and CD8 T cell
 infiltration on clinical outcomes have been widely reported, the
 association between immunity-associated gene with them for hepatocellular
 carcinoma (HCC) remains unclear. Materials and methods: The ssGSEA served
 for quantifying the macrophages as well as CD8 T cell infiltration in the
 HCC samples obtained from TCGA database. Kaplan-Meier(KM) survival assay
 was used to determine the associations between macrophages and CD8 T cell
 infiltration with OS. LASSO Cox regressive method assisted in developing
 an immune gene signature as well as building a risk score. The performance
 was evaluated by the time-dependent ROC together with the KM survival
 analysis. The ICGC database were adopted for external verification.
 CIBERSORT was applied to the correlation analysis on the immune-related
 signature and the immunocyte infiltration. GSEA were employed exploring
 the underlying molecular mechanisms. Results: Increased CD8+ T cell
 infiltration was associated with longer OS, whereas a greater infiltration
 of macrophages was related to shorter OS. There were 398 differential
 expression genes (DEGs) between the high- and low infiltration groups with
 the “edgeR” package. A prognostic signature consisted of 10 immune genes
 was built in TCGA and examined in ICGC. The uniform cutoff (0.927) was
 adopted for separating sufferers into the high-risk(HR) and low-risk(LR)
 groups. The ROC curves revealed that the AUC data for this signature
 predicting 1,2,3,4 and 5 year were all above 0.7 in both TCGA and ICGC
 cohort and patients in the HR group exhibited evidently weaker prognostic
 results compared with the LR group. The HR group presented evidently
 greater Tregs and Macrophage M0 relative to the LR group, whereas the LR
 group saw the enrichment of CD8 T cells. Conclusion: The immune signature
 associated with macrophages as well as CD8 T cell infiltration has
 reliable prognostic and predictive value for HCC patients.
DOI: 10.5061/dryad.51c59zw91
title: De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea)

description: Approaches using microsatellite markers are considered the gold standard
 for modern population-genetic studies. However, though they have found
 application in research into various platyhelminth taxa, they remained
 substantially underutilized in the study of monogeneans. In the present
 study, a newly-developed set of 24 microsatellite markers was used to
 investigate the genetic diversity of the generalist monogenean species
 Dactylogyrus vistulae. The analyzed parasite specimens were collected from
 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas.
 A total of 159 specimens were genotyped at each of the loci and the number
 of alleles per locus ranged from 2 to 16, with a mean number of 6.958
 alleles per locus. Exceptionally high genetic diversity was observed among
 D. vistulae individuals in the southern Balkans (mean NA per locus =
 3.917), suggesting that generalist D. vistulae expanded from the south to
 the north in the Balkans and later putatively into central Europe. The
 initial clustering analysis divided all investigated specimens into three
 major clusters; however, the results of the subsequent analyses revealed
 the existence of various subpopulations, suggesting that the population
 structure of D. vistulae is associated with the diversification of their
 cyprinoid hosts. In addition, the partition of the parasite population was
 observed in regions of the sympatric occurrence of two host species,
 indicating that these hosts may represent a barrier to gene flow, even for
 generalist parasite species.
description: Genotypes were scored using GeneMapper Software version 4.0.
DOI: 10.5061/dryad.8931zcrrj
title: Maps of forest-smallholder homesteads in the Chaco at 10x10km² spatial resolution (1985-2015)

description: The data contained in the three ZIP files represents the following
 information on smallholder homestead distribution and dynamics across the
 Gran Chaco ecoregion: - presence of smallholder homesteads for target
 years in five-year intervals between 1985 and 2015 [% per grid cell] - net
 loss of smallholder homesteads between five-year intervals between 1985
 and 2015 [% per grid cell] - net gain of smallholder homesteads between
 five-year intervals between 1985 and 2015 [% per grid cell] The original,
 digitized point data cannot be made publicly available because it could
 potentially increase the vulnerability of smallholders and/or results in
 (re-)identification of households. The raw data are maintained at the
 Conservation Biogeography Lab at the Geography Department of
 Humboldt-University Berlin (http://hu.berlin/biogeo). Please contact
 Tobias Kuemmerle (tobias.kuemmerle@hu-berlin.de) for more information.
DOI: 10.5061/dryad.j3tx95xfc
title: A novel camera trapping method for individually identifying pumas by facial features

description: Camera traps (CTs), used in conjunction with capture-mark-recapture
 analyses (CMR; photo-CMR), are a valuable tool for estimating abundances
 of rare and elusive wildlife. However, a critical requirement of photo-CMR
 is that individuals are identifiable in CT images (photo-ID). Thus,
 photo-CMR is generally limited to species with conspicuous pelage patterns
 (e.g., stripes or spots) using lateral-view images from CTs stationed
 along travel paths. Pumas (Puma concolor) are an elusive species for which
 CTs are highly effective at collecting image data, but their suitability
 to photo-ID is controversial due to their lack of pelage markings. For a
 wide range of taxa, facial features are useful for photo-ID, but this
 method has generally been limited to images collected with traditional
 handheld cameras. Here we evaluate the feasibility of using puma facial
 features for photo-ID in a CT framework. We consider two issues: 1) the
 ability to capture puma facial images using CTs, and 2) whether facial
 images improve human ability to photo-ID pumas. We tested a novel CT
 accessory that used light and sound to attract the attention of pumas,
 thereby collecting face images for use in photo-ID. Face captures rates
 increased at CTs that included the accessory (n = 208, χ2 = 43.23, P ≤
 0.001). To evaluate if puma faces improve photo-ID, we measured the
 inter-rater agreement of 5 independent assessments of photo-ID for 16 of
 our puma face capture events. Agreement was moderate to good (Fleiss’
 kappa = 0.54, 95% CI = 0.48–0.60), and was 92.90% greater than a
 previously published kappa using conventional CT methods. This study is
 the first time such a technique has been used for photo-ID, and we believe
 a promising demonstration of how photo-ID may be feasible for an elusive
 but unmarked species.
description: Raw detections of pumas were collected using camera traps with
 and without an 'attention caller device' (ACD) to capture puma
 face images. Data include the time and camera site ID of detection, and
 whether the detection was at an ACD site. Detection data was further
 processed to include if the puma's face was captured, as well as
 behavioral reactions of pumas. To generate the daily
 detection data, raw image data was processed in R to create a sitewise
 record of capture counts for each day of deployment. Columns also include
 whether the site used an ACD, whether the site was a community scrape
 site, and the age in days of the scent lure placed at sites.
 The interrater agreement data was collected with an online
 application that was distributed to 5 independent users who rated 120 puma
 face image comparisons, giving each comparison a same (1) or different (0)
 rating.
DOI: 10.5061/dryad.bvq83bk98
title: Natural history of a bighorn sheep pneumonia epizootic

description: A respiratory disease epizootic at the National Bison Range (NBR) in
 Montana in 2016-2017 caused an 85% decline in the bighorn sheep
 population, documented by observations of its unmarked but individually
 identifiable members, the subjects of an ongoing long-term study. The
 index case was likely one of a small group of young bighorn sheep on a
 short-term exploratory foray in early summer of 2016. Disease subsequently
 spread through the population, with peak mortality in September and
 October and continuing signs of respiratory disease and sporadic mortality
 of all age classes through early July 2017.  Body condition
 scores and clinical signs suggested that the disease affected ewe groups
 before rams, although by the end of the epizootic ram mortality (90% of
 71) exceeded ewe mortality (79% of 84). Microbiological sampling 10 years
 to 3 months prior to the epizootic had documented no evidence of infection
 or exposure to Mycoplasma ovipneumoniae at NBR, but during the epizootic a
 single genetic strain of Mycoplasma ovipneumoniae was detected in affected
 animals. Retrospective screening of domestic sheep flocks near the NBR
 identified the same genetic strain in one flock, presumptively the source
 of the epizootic infection. Evidence of fatal lamb pneumonia was observed
 during the first two lambing seasons following the epizootic but was
 absent during the third season following the death of the last identified
 M. ovipneumoniae carrier ewe.  Monitoring of life history traits
 prior to the epizootic provided no evidence that environmentally and/or
 demographically induced nutritional or other stress contributed to the
 epizootic.  Furthermore, the epizootic occurred despite proactive
 management actions undertaken to reduce risk of disease and increase
 resilience in this population. This closely observed bighorn sheep
 epizootic uniquely illustrates the natural history of the disease
 including the (presumptive) source of spillover, course, severity, and
 eventual pathogen clearance.
description: Laboratory testing conducted by the Washington Animal Disease
 Diagnostic Laboratory (aerobic bacteriology, cELISA serology for M.
 ovipneumoniae antibodies, realtime PCR for M. ovipneumoniae), or the TEB
 lab (realtime PCR for M. ovipneumoniae, DNA sequencing of M. ovipneumoniae
 MLST loci.)
description: Please see Dryad_README.txt file.
DOI: 10.5281/zenodo.18398024
title: EATR: Emotion-Aware Temporal Reinforcement Learning Datasets for Multi-Device Recommendation

description: This repository contains datasets used in the research article“Emotion-Aware Temporal Reinforcement Learning for Serendipitous Recommendations in Multi-Device Environments”.

The datasets include:(i) a synthetic emotion-aware multi-device interaction dataset designed for affective and temporal reinforcement learning,(ii) anonymized and aggregated cross-device temporal interaction logs representing realistic smart-environment usage patterns.

All datasets are fully anonymized, contain no personally identifiable information, and are released to support reproducibility and future research in affect-aware recommender systems.
DOI: 10.5281/zenodo.18398023
title: EATR: Emotion-Aware Temporal Reinforcement Learning Datasets for Multi-Device Recommendation

description: This repository contains datasets used in the research article“Emotion-Aware Temporal Reinforcement Learning for Serendipitous Recommendations in Multi-Device Environments”.

The datasets include:(i) a synthetic emotion-aware multi-device interaction dataset designed for affective and temporal reinforcement learning,(ii) anonymized and aggregated cross-device temporal interaction logs representing realistic smart-environment usage patterns.

All datasets are fully anonymized, contain no personally identifiable information, and are released to support reproducibility and future research in affect-aware recommender systems.
DOI: 10.15468/dl.hsjnc2
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Korea, Republic of",
 "TaxonKey is Aster koraiensis",
 "Year 1000-2006"
 ]
}

 The dataset includes 127 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002931-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p5hqbzkqc
title: Patterns and processes in the history of body size in turritelline gastropods, Jurassic-to-Recent

description: Body size is an important trait with implications for energy use and
 ecology as well as generation time and evolutionary rates. Turritelline
 gastropods are widely distributed through geologic time and space, making
 them an excellent group for evaluating macroevolutionary patterns. To
 evaluate the pattern of body size change in turritelline gastropods, we
 compiled a dataset of shell lengths of 316 species of turritelline
 gastropods spanning the Jurassic to Recent. Type specimens were almost
 always significantly larger than specimen distributions from the same
 species. We found that 1) turritelline gastropod size was inversely
 correlated with latitude, a trend likely driven by the Neogene-Recent
 diversification of small-bodied Southern Hemisphere taxa. A time series
 model was applied to distinguish among three possible macroevolutionary
 patterns: unbiased random walk (no directional trend), biased random walk
 (directional trend), and stasis (no net change). We found that 2)
 turritelline gastropods have experienced stasis in body size throughout
 their evolutionary history, adding to the growing literature documenting
 directionless body size trends in marine invertebrate clades. Stasis of
 geographically widespread clades may be the result of ecological
 variability across the environmental range occupied by the group or
 differential diversification into opposing environments. Turritelline
 life-history patterns, especially their reproductive strategy that
 combines a short lifespan and decline in growth rate around 1 year of age
 to reallocate energy to reproduction, might circumvent selection for
 longevity and larger size while further decrease in minimum size is likely
 limited by feeding efficiency and anti-predatory defense. The expectation
 that species or clades should continue to evolve to occupy larger size
 classes conflicts with the evolutionary advantages of small size, which in
 turritelline gastropods include high generational turnover and larger
 population sizes that yield opportunities for genetic variance.
description: Methods are detailed in the associated Paleobiology article.
description: Software: R Microsoft word, excel-
 alternative Google workspace
DOI: 10.5061/dryad.3n5tb2rjb
title: Survival data of five artificial morphs with different transparency characteritics

description: Fieldwork data of artificial prey survival of five different morphs with
 differences in their transparent element characteristics: O (opaque, 0
 transparency), SW (small transparent windows), LW (large transparent
 windows), BE (large windows touching one prey edge) and B3E (large windows
 touching 3 prey edges). The experiment was performed in in two forests in
 southern France with evergreen and white oaks as predominant tree
 vegetation: La Rouvière forest (43.65°N, 3.64°E) and a large natural
 wooded area of the Montpellier Zoological Park (43.64°N, 3.87°E), for
 three 1-week sessions at each place. Artificial prey survival was
 monitored from predation by bird local communities once per day for four
 consecutive days. Morph order was randomized within blocks of 25
 artificial prey, with 5 items per morph per block. Non-attacked prey were
 considered censoring data.
DOI: 10.15468/dl.n4wxhm
title: Occurrence Download

description: A dataset containing 39789 records in GBIF matching the query:
SELECT
 '465' 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;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= -93.54013222947316
 AND decimalLongitude &lt;= -81.82717519335071
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 39789 records were derived from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002943-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8934t
title: Cargo routing and disadvantaged communities

description: Freight is fundamental to economic growth, however, the trucks that haul
 this freight are pollution intensive, emitting criteria pollutants and
 greenhouse gases at high rates. The increasing volume and time-sensitivity
 of freight demand over the past decade has encouraged carriers to take the
 fastest route, which is often not an eco-friendly route. The increase in
 urban freight movement has thus brought along negative externalities such
 as congestion, emissions, and noise into cities. Alternative fuel
 technologies, such as electric trucks and hydrogen-fuel trucks can
 significantly reduce freight-related emissions. However, despite their
 lower operational costs, the high purchase cost and consequent longer
 payback periods compared to traditional vehicles, have resulted in slow
 adoption rates. Since the need to reduce global greenhouse gas emissions
 and local criteria pollutants is immediate, accounting for externalities
 in carriers’ tactical and operational decision-making in the form of
 eco-routing can bring about desired reductions in emissions. The
 objectives of this work are to explore the possibilities and potential of
 eco-routing from the perspective of the carrier, in terms of cost-benefits
 and trade-offs, and from the perspective of the regulator, in terms of
 network-wide effects and policy initiatives that could encourage carriers
 to eco-route. This study evaluates reduction in global greenhouse
 emissions and local criteria pollutants, with a particular focus on direct
 impacts on disadvantaged communities in the Southern California
 Association of Governments (SCAG) region.
description: This study develops two
 analytical tools -<br> 1. Point-to-Point Routing tool (PPR) to
 evaluate private impacts of eco-routing for a carrier hauling diesel
 trucks in the SCAG region.<br> 2. multi-class Traffic Assignment by
 Paired Alternative Segments (mTAPAS) to evaluate network-wide effects of
 system-wide freight eco-routing. These two tools employ
 -<br> 1. Southern California Association of Governments (SCAG)
 region network and its attributes<br> 2. Califronia Communities
 Environmental Health Screening Tool (CalEnviroScreen)
 The SCAG network can be requested via SCAG data
 services program, while the CalEnviroScreen tool can be obtained
 from the California Office
 of Environmental Health Hazard Assessment website.
description: Please view the README.txt file for information on the uploaded
 dataset.
DOI: 10.5061/dryad.g4f4qrfr1
title: The contributions of lightning to biomass turnover, gap formation, and plant mortality in a tropical forest

description: Lightning is a common source of disturbance, but its ecological effects in
 tropical forests are largely undescribed. Here we quantify the
 contributions of lightning strikes to forest turnover and plant mortality
 in a lowland Panamanian forest using a real-time lightning monitoring
 system. We examined 2195 lightning-damaged trees distributed among 93
 different strikes. None exhibited scars or fires. On average, each strike
 disturbed 451 m2 (95% CI: 365-545 m2), created canopy gaps of 304 m2 (95%
 CI 198-454 m2), and caused 7.36 Mg of woody biomass turnover (CI:
 5.36-9.65 Mg). Cumulatively, we estimate that lightning strikes in this
 forest create canopy gaps equaling 0.39% of forest canopy area,
 representing 20.1% of annual gap area formation, and are responsible for
 16.1% of total woody biomass turnover. Trees, lianas, herbaceous climbers,
 and epiphytes were killed by lightning at rates 8-29 times greater than
 their baseline mortality rates in undamaged control sites. The likelihood
 of lightning-caused death was higher for trees, lianas, and herbaceous
 climbers than for epiphytes, and high liana mortality suggests that
 lightning is an important driver of liana turnover. These results indicate
 that lightning influences gap dynamics, plant community composition, and
 carbon storage capacity in some tropical forests.