cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31156957.v1
title: Supplementary Material for: Biocompatibility and Inflammatory Pathways of Silicone Oil in Complex Retinal Detachment: An In Vitro and Clinical Study

description: Introduction: This study aimed to characterize the inflammatory cytokine profile within silicone oil-associated fluid (SOAF) from eyes with complex rhegmatogenous retinal detachment (RRD) treated with silicone oil (SO) tamponade, comparing groups according to tamponade duration. Additionally, we aimed to assess in vitro the emulsification stability of SO in the presence of biological surfactant agents. Methods: This prospective multicenter study included 65 patients with complex RRD who underwent pars plana vitrectomy (PPV) with SO tamponade, divided into two groups according to tamponade duration (&lt;6 months vs ≥6 months), and 30 control eyes that underwent PPV for epiretinal membrane or full-thickness macular hole without SO. SOAF and undiluted vitreous samples were collected and analyzed for cytokine levels (IL-1α, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17, IP-10/CXCL10, IFNγ, TNFα, TGFβ1-3, and MCP-1) using multiplex bead-based immunoassays and ELISA. In vitro emulsification assays were performed using SOs of different viscosities and various biological surfactants. Results: The inflammatory composite score (mean z-score of log10-transformed IL-6, IL-8, and MCP-1) was significantly higher in RRD eyes than in controls (0.78 [0.35-1.16] vs -0.52 [-0.88-0.01]; p &lt; 0.0001), with no significant differences between tamponade-duration groups (0.82 [0.41-1.24] vs 0.76 [0.33-1.13]; p = 0.62). In SOAF, IL-6, IL-8, MCP-1, and TGF-β isoforms were elevated compared with vitreous controls. In vitro assays showed that stable emulsions formed in the presence of proteins (albumin or cell-culture supernatants), whereas lipidic or vitaminic surfactants produced unstable emulsions. Conclusion: Eyes with complex RRD exhibit a sustained pro-inflammatory and pro-fibrotic microenvironment within the perisilicone compartment, independent of tamponade duration. Proteins, particularly albumin, appear to act as key biological surfactants linking inflammation to SO emulsification. These findings highlight the need for targeted anti-inflammatory and anti-fibrotic strategies, as well as standardized tools for detecting subclinical emulsification.
DOI: 10.5061/dryad.b7855
title: Data from: Characterization of microsatellite loci and repeat density in the gooseneck barnacle, Pollicipes elegans, using next generation sequencing

description: Pollicipes elegans is a commercially important and biogeographically
 significant rocky-shore gooseneck barnacle found along the eastern Pacific
 coasts of Peru, El Salvador, and Mexico. Little is known about its
 reproductive biology, and no genetic resources exist despite its growing
 importance as a fisheries species in the region. Next generation
 sequencing methods can provide rapid and cost-effective development of
 molecular markers such as microsatellites, which can be applied to studies
 of paternity, parentage, and population structure in this understudied
 species. Here, we used Roche 454 pyrosequencing to develop microsatellite
 markers in P. elegans and made genomic comparisons of repeat density and
 repeat class frequency with other arthropods and more distantly related
 taxa. We identified 13 809 repeats of 1–6bp, or a density of 9744bp of
 repeat per megabase queried, which was intermediate in the range of
 taxonomic groups compared. Comparison of repeat class frequency
 distributions revealed that P. elegans was most similar to Drosophila
 melanogaster rather than the more closely related crustacean Daphnia
 pulex. We successfully isolated 15 polymorphic markers with an average of
 9.4 alleles per locus and average observed and expected heterozygosities
 of 0.501 and 0.597, respectively. Four loci were found to be out of
 Hardy–Weinberg equilibrium, likely due to the presence of null alleles. A
 preliminary population genetic analysis revealed low but significant
 differentiation between a Peruvian (n = 47) and Mexican (n = 48)
 population (F ST = 0.039) and markedly reduced genetic diversity in Peru.
 These markers should facilitate future studies of paternity, parentage,
 and population structure in this species.
description: Microsatellite genotype
 data for Plough and Marko 2013Microsatellite genotypes
 for the Peru and Mexico sampling sitesMicrosatellite
 data.xlsx
DOI: 10.5061/dryad.51591
title: Data from: Competitive release and outbreaks of non-target pests associated with transgenic Bt cotton

description: The adoption of transgenic Bt cotton has, in some cases, led to
 environmental and economic benefits through reduced insecticide use.
 However, the distribution of these benefits and associated risks among
 cotton growers and cotton-growing regions, has been uneven due in part to
 outbreaks of non-target or secondary pests, thereby requiring the
 continued use of synthetic insecticides. In the southeastern United
 States, Bt cotton adoption has resulted in increased abundance of and
 damage from stink bug pests, Euschistus servus and Nezara viridula
 (Heteroptera: Pentatomidae). While the impact of increased stink bug
 abundance has been well-documented, the causes have remained unclear. We
 hypothesize that release from competition with Bt-susceptible target pests
 may drive stink bug outbreaks in Bt cotton. We first examined the evidence
 for competitive release of stink bugs through meta-analysis of previous
 studies. We then experimentally tested if herbivory by Bt-susceptible
 Helicoverpa zea increases stink bug leaving rates and deters oviposition
 on non-Bt cotton. Consistent with previous studies, we found differences
 in leaving rates only for E. servus, but we found that both species
 strongly avoided ovipositing on H. zea-damaged plants. Considering all
 available evidence, competitive release of stink bug populations in Bt
 cotton likely contributes to outbreaks, though the relative importance of
 competitive release remains an open question. Ecological risk assessments
 of Bt crops and other transgenic insecticidal crops would benefit from
 greater understanding of the ecological mechanisms underlying non-target
 pest outbreaks and greater attention to indirect ecological effects more
 broadly.
description: Competition
 meta-analysis dataData extracted from
 previous papers on competition between stink bug and heliothine
 caterpillar species, used in meta-analysis.meta_analysis_data.csvLeaving rate competition dataData for experiment measuring leaving rates of stink bugs from caterpillar-damaged and undamaged plants.leaving_rate_data.csvStink bug oviposition preference dataData on stink bug oviposition preference between caterpillar-damaged and undamaged cotton plants.oviposition_preference_data.csv
DOI: 10.5061/dryad.st1g8
title: Data from: Shining light on benthic macroalgae: mechanisms of complementarity in layered macroalgal assemblages

description: Phototrophs underpin most ecosystem processes, but to do this they need
 sufficient light. This critical resource, however, is compromised along
 many marine shores by increased loads of sediments and nutrients from
 degraded inland habitats. Increased attenuation of total irradiance within
 coastal water columns due to turbidity is known to reduce species'
 depth limits and affect the taxonomic structure and architecture of
 algal-dominated assemblages, but virtually no attention has been paid to
 the potential for changes in spectral quality of light energy to impact
 production dynamics. Pioneering studies over 70 years ago showed how
 different pigmentation of red, green and brown algae affected absorption
 spectra, action spectra, and photosynthetic efficiency across the PAR
 (photosynthetically active radiation) spectrum. Little of this, however,
 has found its way into ecological syntheses of the impacts of optically
 active contaminants on coastal macroalgal communities. Here we test the
 ability of macroalgal assemblages composed of multiple functional groups
 (including representatives from the chlorophyta, rhodophyta and
 phaeophyta) to use the total light resource, including different light
 wavelengths and examine the effects of suspended sediments on the
 penetration and spectral quality of light in coastal waters. We show that
 assemblages composed of multiple functional groups are better able to use
 light throughout the PAR spectrum. Macroalgal assemblages with four
 sub-canopy species were between 50–75% more productive than assemblages
 with only one or two sub-canopy species. Furthermore, attenuation of the
 PAR spectrum showed both a loss of quanta and a shift in spectral
 distribution with depth across coastal waters of different clarity, with
 consequences to productivity dynamics of diverse layered assemblages. The
 processes of light complementarity may help provide a mechanistic
 understanding of how altered turbidity affects macroalgal assemblages in
 coastal waters, which are increasingly threatened by diminishing light
 quantity and altered spectral distributions through sedimentation and
 eutrophication.
description: Data archive_PLOS
 ONE_7-11-14Primary productivity
 data for macroalgal assemblages, including: P-E curves and action
 spectra
DOI: 10.5061/dryad.344hs
title: Data from: Valuable habitat and low deforestation can reduce biodiversity gains from development rights markets

description: 1. Illegal private land deforestation threatens global biodiversity, even
 in areas with native habitat requirements stipulated by law. Compliance
 can be improved by allowing landholders to meet legal reserve requirements
 by buying and selling the rights to have deforested land through a
 Tradeable Development Rights system (TDR). While this policy mechanism may
 prevent native habitat area loss, the spatial pattern of reserved areas
 will shift, creating novel landscape patterns. The resulting altered
 fragmentation and connectivity of habitat will impact biodiversity. TDR
 may also allow landholders to earn rent on land they never intended on
 converting, resulting in additional deforestation elsewhere and net
 habitat loss. 2. We construct a simulation model to explore the potential
 implications for biodiversity when development rights can be traded,
 compared with the landscape resulting from enforced individual compliance
 with deforestation laws. 3. We find that where future deforestation is
 very likely, a TDR market can provide better outcomes for both
 biodiversity and agriculture, resulting in more connected habitat networks
 with larger fragments and fewer edge effects. However, the TDR market can
 be harmful if future deforestation is unlikely, or if one habitat type is
 tightly spatially correlated with high economic returns from agriculture.
 4. Policy implications. Allowing landholders to buy and sell the rights to
 keep more cleared land than legally stipulated will result in transformed
 multi-use landscapes. Losses of native habitat in some areas will be
 offset in others. We conclude that trading forest development rights has
 the potential to improve habitat configurations, but that careful
 consideration should be given to current species distributions and likely
 future deforestation scenarios.
description: R codeR code for all
 simulations and plotsCode for
 publication.zip
DOI: 10.34740/kaggle/dsv/14636414
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.875fb
title: Data from: Hypoxic areas, density-dependence and food limitation drive the body condition of a heavily exploited marine fish predator

description: Investigating the factors regulating fish condition is crucial in ecology
 and the management of exploited fish populations. The body condition of
 cod (Gadus morhua) in the Baltic Sea has dramatically decreased during the
 past two decades, with large implications for the fishery relying on this
 resource. Here, we statistically investigated the potential drivers of the
 Baltic cod condition during the past 40 years using newly compiled
 fishery-independent biological data and hydrological observations. We
 evidenced a combination of different factors operating before and after
 the ecological regime shift that occurred in the Baltic Sea in the early
 1990s. The changes in cod condition related to feeding opportunities,
 driven either by density-dependence or food limitation, along the whole
 period investigated and to the fivefold increase in the extent of hypoxic
 areas in the most recent 20 years. Hypoxic areas can act on cod condition
 through different mechanisms related directly to species physiology, or
 indirectly to behaviour and trophic interactions. Our analyses found
 statistical evidence for an effect of the hypoxia-induced habitat
 compression on cod condition possibly operating via crowding and
 density-dependent processes. These results furnish novel insights into the
 population dynamics of Baltic Sea cod that can aid the management of this
 currently threatened population.
description: Data used in
 GAMsData collected during
 bottom trawl surveys and hydrological surveys in the central Baltic Sea,
 Excel file.Data.xlsx
DOI: 10.5061/dryad.3q7k6
title: Data from: Tasting novel foods and selecting nutrient content in a highly successful ecological invader, the common myna

description: Invasion success is dependent on the ability of a species to discover and
 exploit novel food resources. Within this context, individuals must be
 willing to taste novel foods. They must also be capable of evaluating the
 nutritional content of new foods, and selecting their relative intake in
 order to fulfil their nutritional needs. Whereas the former capacity is
 well studied, little is known about the latter capacity. First, using the
 common myna as a model avian invader species, we quantified the
 willingness of mynas to taste novel foods relative to familiar ones. Mynas
 readily tasted high protein (HP) novel foods and consumed them in higher
 quantities compared to a familiar food. Data showed that at three
 different levels – mixes, ingredients and macronutrients – intake could
 not be explained by a random model. In experiment 2, we confirmed that
 mynas were making their selection based on protein (P) content rather than
 a selection for novelty per se. When given the choice of three equally
 unfamiliar foods, mynas again ate disproportionately from the high protein
 relative to high lipid and high carbohydrate foods. Analysis revealed that
 mynas consumed amounts of protein that were closer to the ones in their
 natural diet. Finally, in experiment 3, we measured inter-individual
 variation in innovation and exploration propensities, and examined
 associations with inter-individual variation in consumption of specific
 macronutrients. This analysis revealed that individuals that selected HP
 pellets were more exploratory and individuals that selected HC pellets
 were quicker to solve the innovative foraging task. These findings
 indicate that not only the willingness to taste novel foods, but also the
 capacity to evaluate their nutritional content, might be central to the
 myna's substantial ecological success.
description: Data for experiments 1,
 2 and 3.Data collected on
 captive birds. Dataset 1 = Experiment 1: total amount of foods,
 ingredients, and nutrients consumed over 3 days. Mix 1 = Dog pellet (DP),
 Mix 2 = Dog pellet and Wombaroo (W), Mix 3 = Dog pellet + Wombaroo + Eggs
 & Biscuits (EB). P = protein, L = lipid, and C = carbohydrate. Dataset
 2 = Experiment 2: total amount of artificial pellets consumed over 3 days.
 P = protein, L = lipid, and C = carbohydrate. Dataset 3 = Experiment 3:
 behavioural data for innovation test (innovation score = latency to solve
 - latency to first contact task) and exploration test (exploration score =
 PC1 scores from variables compiled in PCA).All_data.xlsx
DOI: 10.5061/dryad.6t066
title: Data from: A voyage to Terra Australis: human-mediated dispersal of cats

description: Background. Cats have been transported as human commensals worldwide
 giving rise to many feral populations. In Australia, feral cats have
 caused decline and extinction of native mammals, but their time of
 introduction and origin is unclear. Here, we investigate hypotheses of cat
 arrival pre- or post-European settlement, and the potential for admixture
 between cats of different invasion events. We analyse the genetic
 structure and diversity of feral cats from six locations on mainland
 Australia, seven Australian islands and samples from Southeast Asia and
 Europe using microsatellite and mitochondrial DNA data. Results.Our
 results based on phylogeographic model selection are consistent with a
 European origin of cats in Australia. We find genetic distinctiveness of
 Australian mainland samples compared with Dirk Hartog Island, Flinders
 Island, Tasman Island and Cocos (Keeling) Island samples, and genetic
 similarities between some of the island populations. Historical records
 suggest that introduction of cats to these islands occurred at the time of
 European exploration and/or in connection with the pearling, whaling and
 sealing trades early in the 19th century. On-going influx of domestic cats
 into the feral cat population is apparently causing the Australian
 mainland populations to be genetically differentiated from those island
 populations, which likely are remnants of the historically introduced cat
 genotypes. Conclusion. A mainly European origin of feral cats in
 Australia, with possible secondary introductions from Asia following the
 initial establishment of cats in Australia is reasonable. The islands
 surrounding Australia may represent founding populations and are of
 particular interest. The results of the study provide an important
 timeframe for the impact of feral cats on native species in Australia.
description: Origin_struc_resubmissionmicrosatellite markers in genepop2 format, with 10 loci
DOI: 10.5061/dryad.t4660
title: Data from: Caregivers' attitude towards people with mental illness and perceived stigma: a cross-sectional study in a tertiary hospital in Nepal

description: Background: Mental illness is stigmatized in most of the communities and
 people with such illness are often subjected to defame. Stigma impairs an
 individual’s and their caregiver’s physical, social and emotional
 wellbeing, and health-seeking behavior. Sufficient literature on how often
 the caregivers of people with mental illness from low and middle-income
 countries are stigmatized and how they perceive people with mental illness
 is unavailable. In this study, we examined caregivers’ attitude towards
 people with mental illness and perceived stigma. Methods: We conducted
 face-to-face interviews with 170 caregivers in an outpatient clinic of a
 hospital in Nepal using a structured questionnaire. We calculated median
 and inter-quartile range of the attitude and perceived stigma scores. To
 assess the correlates, Kruskal Wallis H test and Mann Whitney U test were
 carried out. Results: Overall median score for the domains: attitude
 (score range: 18–90) and perceived stigma (score range: 12–60) were 42 and
 28 respectively, inter-quartile range being 8 each. Attitude score
 differed significantly by the sex of caregiver (p&lt;0.05),
 educational status of caregiver (p&lt;0.001), sex of patient
 (p&lt;0.05) and type of mental illness (p&lt;0.05). Perceived
 stigma score varied significantly by caregiver’s sex (p&lt;0.05),
 marital status (p&lt;0.001), educational status (p&lt;0.001),
 occupation (p&lt;0.05), relation with the patient (p&lt;0.005) and
 use of alternative treatment modalities (p&lt;0.05). Conclusion: Sex
 of participant, educational status, sex of patient and type of mental
 illness were the correlates of attitude towards mental illness. Similarly,
 sex of participant, marital status, educational status, occupation,
 caregiver’s relation with patient and use of alternative treatment
 modalities were correlates of perceived stigma. Findings of this study
 suggest that interventions targeting these high-risk populations might be
 beneficial to help build a positive attitude and overcome the perceived
 social stigma.
description: Dataset-
 Caregivers' StigmaThis file contains the
 data form the study "Caregivers’ Attitude towards People with Mental
 Illness and Perceived Stigma: A Cross-Sectional Study in A Tertiary
 Hospital in Nepal"
DOI: 10.48420/31150573
title: Computational data for: Markovian approach <i>N</i>-photon correlations beyond the quantum regression theorem

description: This repository contains computer generated data and figures for the publication "Markovian approach to <i>N</i>-photon correlations beyond the quantum regression theorem" by M. Salamon <i>et al. </i>(https://doi.org/10.1103/pgk3-b57l).The data was generated by numerically solving for the steady-state of the combined emitter-sensors system using Python 3.11, as outlined in the associated publication.Data for Fig. 2 is saved as .dat plain text files with comma-separated variables in two columns: frequencies and intensities. Comments in the header begin with '#'. There are 3 data files corresponding to data generated with the sensor method, QRT and TEMPO.<br>Data for Fig. 3 is saved as NumPy .npz binary files. Arrays labelled 'x' and 'y' correspond to a grid of frequency values and arrays labelled 'z' correspond to second-order coherence data [g<sup>(2)</sup>(0)]. There are two data files: one includes phonon interactions and the other does not.<br>Folder 'Plotting scripts' contains Python scripts that allow for reproducing Figures 2 and 3a), 3b), and Figure S1 of the associated article.
DOI: 10.48420/31150573.v1
title: Computational data for: Markovian approach <i>N</i>-photon correlations beyond the quantum regression theorem

description: This repository contains computer generated data and figures for the publication "Markovian approach to <i>N</i>-photon correlations beyond the quantum regression theorem" by M. Salamon <i>et al. </i>(https://doi.org/10.1103/pgk3-b57l).The data was generated by numerically solving for the steady-state of the combined emitter-sensors system using Python 3.11, as outlined in the associated publication.Data for Fig. 2 is saved as .dat plain text files with comma-separated variables in two columns: frequencies and intensities. Comments in the header begin with '#'. There are 3 data files corresponding to data generated with the sensor method, QRT and TEMPO.<br>Data for Fig. 3 is saved as NumPy .npz binary files. Arrays labelled 'x' and 'y' correspond to a grid of frequency values and arrays labelled 'z' correspond to second-order coherence data [g<sup>(2)</sup>(0)]. There are two data files: one includes phonon interactions and the other does not.<br>Folder 'Plotting scripts' contains Python scripts that allow for reproducing Figures 2 and 3a), 3b), and Figure S1 of the associated article.