cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0440701
title: Manning Park Bear Coexistence Survey Open-Access Data

description: This data was collected in August-September 2023 in EC Manning Park, British Columbia. Our project explored Park visitors' behaviors, behavioral intentions, attitudes, values, and knowledge about coexisting with bears in the Park.
DOI: 10.5281/zenodo.15277842
title: TABLE 1 in New host and locality record for the parasitic isopod Ceratothoa carinata (Bianconi, 1869) (Crustacea: Isopoda: Cymothoidae), with molecular insights into its phylogeography

description: TABLE 1. Sequences of Ceratothoa spp. and Nerocila japonica used in this study with the GenBank accession number, the relevant reference, and locality.
SpeciesGB accession no.referenceLocalityNerocila japonicaLC160331Hata et al. 2017JapanC. arimaeLC159544Hata et al. 2017Nii-jima Island, JapanC. verrucoseLC741985Fujita et al. 2023Seto Inland Sea, JapanC. africanaMK652477Baillie et al. 2019South AfricaC. retusaMK652478Baillie et al. 2019South AfricaC. parallelaMZ127227Bouguerche et al. 2021Mediterranean Sea, AlgeriaC. oxyrrhynchaenaLC626344Saito et al. 2022Sagami Bay, JapanC. carinataOP808334Lumayno et al. 2023Sibuyan Sea, PhilippinesLC160313Hata et al. 2017Tateyama, Chiba, JapanLC160315Hata et al. 2017Iburi Kochi, JapanLC159553Hata et al. 2017Imabari Ehime, JapanLC741987Fujita et al. 2023Seto Inland Sea, JapanLC741986Fujita et al. 2023Seto Inland Sea, JapanLC741977Fujita et al. 2023Seto Inland Sea, JapanLC741976Fujita et al. 2023Seto Inland Sea, JapanLC741960Fujita et al. 2023Seto Inland Sea, JapanLC724050Fujita et al. 2023Seto Inland Sea, JapanLC724049Fujita et al. 2023Seto Inland Sea, JapanPQ764812 (male)Present studyGulf of Oman, IranPQ764811 (female)Present studyGulf of Oman, Iran
description: Published as part of Salari, Mohammad, Khalaji-Pirbalouty, Valiallah, Ranjbar, Mohammad Sharif & Shahdadi, Adnan, 2025, New host and locality record for the parasitic isopod Ceratothoa carinata (Bianconi, 1869) (Crustacea: Isopoda: Cymothoidae), with molecular insights into its phylogeography, pp. 264 in Zootaxa 5621 (2) on page 264, DOI: 10.11646/zootaxa.5621.2.6, http://zenodo.org/record/15262670
DOI: 10.14288/1.0447399
title: Thermal exposure risk in different life stages of Chinook salmon in the Nechako River system, British Columbia

description: Climate change is affecting freshwater systems, leading to increased water temperatures, which is posing a threat to freshwater ecological communities. In the Nechako River, a water management program has been in place since the 1980s to maintain water temperatures at 20°C during the migration of Sockeye salmon. However, the program's effectiveness in mitigating the impacts of climate change on resident species like Chinook salmon's thermal exposure is uncertain. In this study, we utilised the CEQUEAU hydrological model and life stage-specific physiological data to evaluate the consequences of the current program on Chinook salmon's thermal exposure under two contrasting climate change and socio-economic scenarios (SSP2-4.5 and SSP5-8.5). The results indicate that the thermal exposure risk is projected to be above the optimal threshold for parr and adult life stages under both scenarios relative to the 1980s. These life stages could face an increase in thermal exposure ranging from up to 2 and 5 times by 2090s relative to the 1980s during the months they occurred under the SSP5-8.5 scenario, including when the program is active (July 20th to August 20th). Additionally, our study shows that climate change will result in a substantial rise in cumulative heat degree days, ranging from 1.9 to 5.8 times (2050s) and 2.9 to 12.9 times (2090s) in comparison to the 1980s under SSP5-8.5. Our study highlights the need for a holistic approach to review the current Nechako management plan and consider all species in the Nechako River system in the face of climate change.
DOI: 10.14288/1.0436906
title: Poecilia picta female genome assembly files

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Sex chromosome dosage compensation is a model to understand the coordinated evolution of transcription, however, the advanced age of the sex chromosomes in model systems makes it difficult to study how the complex regulatory mechanisms underlying chromosome-wide dosage compensation can evolve. The sex chromosomes of &lt;em&gt;Poecilia picta&lt;/em&gt; have undergone recent and rapid divergence, resulting in widespread gene loss on the male Y, coupled with complete X Chromosome dosage compensation, the first case reported in a fish. The recent de novo origin of dosage compensation presents a unique opportunity to understand the genetic and evolutionary basis of coordinated chromosomal gene regulation. By combining a new chromosome-level assembly of &lt;em&gt;P. picta&lt;/em&gt; with whole-genome bisulfite sequencing and RNA-seq data, we determine that the Yin Yang 1 (YY1) DNA-binding motif is associated with male-specific hypomethylated regions on the X, but not the autosomes. These YY1 motifs are the result of a recent and rapid repetitive element expansion on the &lt;em&gt;P. picta&lt;/em&gt; X Chromosome, which is absent in closely related species that lack dosage compensation. Taken together, our results present compelling support that a disruptive wave of repetitive element insertions carrying YY1 motifs resulted in the remodeling of the X Chromosome epigenomic landscape and the rapid de novo origin of a dosage compensation system.&lt;/p&gt;
DOI: 10.14288/1.0440679
title: Data for: Spillover effects of organic agriculture on pesticide use on nearby fields

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;span lang="EN"&gt;The environmental impacts of organic agriculture are only partially understood and &lt;/span&gt;&lt;span lang="EN"&gt;whether such practices have spillover effects &lt;/span&gt;&lt;span lang="EN"&gt;on pests or pest control activity &lt;/span&gt;&lt;span lang="EN"&gt;on nearby fields remains unknown&lt;/span&gt;&lt;span lang="EN"&gt;. Using &lt;/span&gt;&lt;span lang="EN"&gt;roughly 13,000 field observations per year from 2013-2019 in Kern County, CA , &lt;/span&gt;&lt;span lang="EN"&gt;we estimate that organic crop producers benefit from surrounding organic fields, decreasing overall pesticide use and pesticides targeting insect pests. &lt;/span&gt;&lt;span lang="EN"&gt;&lt;span lang="EN"&gt;Conventional fields, in contrast, tend to increase pesticide use as the area of surrounding organic production increases.&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0440680
title: Repeatability of RRate measurements in children during triage in two Ugandan hospitals

description: &lt;br /&gt;&lt;strong&gt;Background:&lt;/strong&gt; Pneumonia is the leading cause of death in children globally. In low- and middle-income countries the diagnosis of pneumonia relies heavily on an accurate assessment of respiratory rate, which can be unreliable in nurses and clinicians with less advanced training. In order to inform more accurate measurements, we investigate the repeatability of the RRate app used by nurses in district hospitals in Uganda. &lt;br/&gt; &lt;br /&gt;&lt;strong&gt;Methods:&lt;/strong&gt; This planned secondary analysis included 3679 children aged 0-5 years. The dataset had two sequential measurements of respiratory rate using the RRate app. We measured the agreement between respiratory rate observations and clustering around fixed thresholds defined by WHO for fast breathing, which are 60 breaths per minute (bpm) for under two months (Age-1), 50 bpm for two to 12 months (Age-2), and 40 bpm for 12.1 to 60 months (Age-3). We then assessed the repeatability of the paired measurements using the Intraclass Correlation Coefficient (ICC). &lt;br/&gt; &lt;br /&gt;&lt;strong&gt;Results:&lt;/strong&gt; The respiratory rate measurement took less than 15 seconds for 7,277 (98.9%) of the measurements. Despite respiratory rates clustering around the WHO fast-breathing thresholds, the breathing classification based on the thresholds was changed in only 12.6% of children. The mean (SD) respiratory rate by age group was 60 (13.1) bpm for Age-1, 49 (11.9) bpm for Age-2, and 38 (10.1) for Age-3, and the bias (Limits of Agreements) were 0.3 (-10.8 – 11.3), 0.4 (-8.5 – 9.3), and 0.1 (-6.8, 7.0) for Age-1, Age-2, and Age-3 respectively. Most importantly, the repeatability of the two respiratory rate measurements for the 3,679 children was high, with an ICC value (95% CI) of 0.95 (0.94 – 0.95). &lt;br/&gt; &lt;br /&gt;&lt;strong&gt;Discussion:&lt;/strong&gt; The RRate measurements were both efficient and repeatable. The simplicity, repeatability, and efficiency of the RRate app used by healthcare workers in LMICs supports more widespread adoption for clinical use. &lt;br/&gt;
DOI: 10.14288/1.0440931
title: Replication Data for: Overstocking and temporal feed restriction affects dairy cows’ drinking behavior

description: Water is an essential resource for dairy cows and its consumption is closely linked to feed intake. Social competition can lead to changes in drinking behavior. We studied how the combination of stocking at the drinker (6 or 12 cows per drinker) and temporal feed restriction (14 or 24 h access) impacts drinking in 4 groups of 6 cows each, following a Latin Square design. We recorded drinking behavior and agonistic interactions (i.e., replacements) at the drinker; within each group of 6 focal cows, 2 were identified as most dominant, 2 as most subordinate, and the 2 others as intermediate, based on success when engaged in agonistic interactions at the feeder. Intermediate and subordinate cows drank less water when feed access was restricted (7.9 L/d less ± 5.2). Subordinate cows also spent less time drinking when overstocked (12.5 min/d less ± 6.4). During treatments with more competition, cows, regardless of dominance, shifted and increased their percentages of daily water of 2h and 1h after the morning and afternoon peak of consumption respectively found during control treatment. Our findings provide evidence that feed restriction and overstocking at the drinker changes the drinking behavior of cows with subordinate animals experiencing more pronounced effects.
DOI: 10.14288/1.0440953
title: Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (&lt;em&gt;Menidia menidia&lt;/em&gt;) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.&lt;/p&gt;
DOI: 10.14288/1.0440956
title: Joint environmental and social benefits from diversified agriculture

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Agricultural simplification continues to expand at the expense of more diverse forms of agriculture. This simplification in the form of, for example, intensively-managed monocultures, poses a risk to keeping the world within safe and just Earth system boundaries. Here, we estimate how agricultural diversification simultaneously affects social and environmental outcomes. Drawing from 24 studies in 11 countries across 2,655 farms, we show how five diversification strategies focusing on livestock, crops, soils, non-crop plantings, and water conservation benefit social (human well-being, yields, food security) and environmental (biodiversity, ecosystem services, reduced environmental externalities) outcomes. We find that applying multiple diversification strategies creates more positive outcomes than individual management strategies alone. To realize these benefits, well-designed policies are needed to incentivize the adoption of multiple diversification strategies in unison.&lt;/p&gt;
DOI: 10.14288/1.0440935
title: Replication Data for - Moisture Matters: Determining Which Moisturizer Base Will Affect the Growth of E. Coli and Yeast.

description: Many individuals use moisturizers daily without a second thought. However, immunocompromised people struggle with the risk of contamination when choosing the right cosmetics. The objective of this experiment was to examine the effects of E. coli and yeast on different moisturizer bases: oil, water, and silicone. The hypothesis was that if E. coli and yeast were introduced into three types of moisturizer products, silicone, water, and oil-based, then it was anticipated the E. coli and yeast would develop most in an oil-based product, the least in a silicone-based product, and fairly in a water-based product. To test this hypothesis, agar plates were prepared for bacteria growth. Then, E. coli and yeast were cultured and introduced with sterile filter paper discs containing three types of moisturizer solutions and distilled water as a control. After the incubation period, the growth was measured and recorded in the lab. Data analysis was performed in MS Excel and results were analyzed and visualized. The experiment’s results supported the study’s hypothesis. Both E. coli and yeast developed the most on average in the oil-based moisturizer (E. coli – 8.2mm; yeast - 10.3mm), the least in the silicone-based product (E. coli – 5.4mm; yeast – 5.4mm), and intermediately in the water-based lotion (E. coli - 6.4mm; yeast – 9mm). Interestingly, the control group exhibited that E. coli did not thrive in distilled water (3.5mm), however, yeast generated the most prevalent growth (20.6mm). The study results concluded that immunosuppressed individuals could benefit the most from silicone-based moisturizers as these are the least prone to bacteria and yeast contamination. Also, these users might want to avoid using oil-based moisturizers as this type is the most susceptible to E. coli and yeast contamination. This project could lead to further research about other cosmetic products and their contamination health risks.
DOI: 10.14288/1.0440955
title: Data from: Preparation of isolated guard cells, containing cell walls, from Vicia faba

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Stomatal movement, initiated by specialized epidermal cells known as guard cells (GCs), plays a pivotal role in plant gas exchange and water use efficiency. Despite protocols existing for isolating GCs through proplasting for carrying out biochemical, physiological, and molecular studies, protocols for isolating GCs with their cell walls still intact have been lacking in the literature. In this paper, we introduce a method for the isolation of complete GCs from &lt;em&gt;Vicia faba &lt;/em&gt;and show their membrane to remain impermeable through propidium iodide staining. This methodology enables further in-depth analyses into the cell wall composition of GCs, facilitating our understanding of structure-function relationship governing reversible actuation within cells.&lt;/p&gt;
DOI: 10.14288/1.0441388
title: Optimizing Seagrass Mapping with Remotely Piloted Aircraft Systems and Machine Learning

description: Seagrass meadows play a vital role in the protection of coastlines and support productive habitats for marine life, unfortunately, seagrasses are experiencing declines due to climate change and human activities. Gathering accurate data on their spatial extent is essential for coastal management, yet traditional field methods are costly and impractical over large areas. Remotely piloted aircraft systems (RPAS) offer a flexible and cost-effective alternative for collecting imagery, though a standardized method for detecting seagrass meadows in British Columbia (BC) has yet to be established. Coastal dynamics associated with seagrass habitat such as tidal conditions and growing season limits the extent to which seagrass can be accurately detected. In this study, I test a methodology for seagrass detection and evaluate how detection accuracy is impacted by tidal conditions, growing season, and the incorporation of multispectral sensors. Specifically, I compare classifications of two eelgrass (Zostera marina) sites in the Gulf Islands (Sidney and Moresby) in southwestern BC. I employed a Random Forest Classifier and compared the incorporation of near-infrared and red-edge wavelengths to traditional red-green-blue (RGB) imagery to explore potential improvements in eelgrass detection. This achieved overall accuracies up to 95%. RGB images captured at low and high tide in July and August performed better than images captured in June and at medium tide. Imagery captured at medium tide exhibited the most variability in accuracy. The addition of multispectral imagery did not significantly improve eelgrass detection for these two sites and should be further tested over a greater sample size. The results of this analysis intend to contribute to the development of a provincial seagrass mapping methodology, supporting eelgrass monitoring and conservation in BC.
DOI: 10.14288/1.0441389
title: Exploring Potential Benefits of Visualizing Canopy Cover Change in 3D Gaming Engine Environment

description: This research explores the innovative use of a 3D gaming engine, Minetest, for visualizing changes in canopy cover change at the University of British Columbia (UBC) campus, addressing the pressing challenge of urban expansion on green spaces. We compared and visualized canopy height change for UBC campus in both 2D traditional environment and 3D gaming engine environment and we revealed a consistency between the spatial patterns of canopy cover change observed in both environments. Our findings indicate 3D environment provided multi-dimensional insights into canopy cover changes, offering decision-makers more straightforward and transparent insight than traditional maps can achieve in an immersive and interactive environment. We observed there is a significant change in canopy cover with 25 percent loss in total where Wesbrook community area experienced the most significant canopy cover loss in past 5 years due to rapid urban development. Our findings goes beyond merely presenting geographic maps and attributes from a 3D voxel game perspective. Instead, it will serve as a useful tool and references for UBC decision makers and planners to inform management plan on the pathway of building a green, well-planned community.
DOI: 10.14288/1.0441390
title: Monitoring mangrove reforestation in Madagascar with Sentinel 2 derived spectral indices

description: Mangroves play a crucial role in carbon sequestration, coastal protection, and biodiversity. The efficacy of mangrove reforestation projects is important for environmental management and conservation efforts around the world. This study evaluates the use of spectral indices derived from Sentinel-2 data to monitor mangrove reforestation. Specifically, Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index 2 (EVI-2), Red Edge Normalized Difference Vegetation Index (RedEdge NDVI), and Mangrove Vegetation Index (MVI) were analyzed across two study areas: Tsimipaika Bay and Assassin's Bays. Our findings indicate that all four indices were capable of detecting change in mangrove reflectance, but differed in their relative efficacy. The research underscores the complex interaction between mangrove growth, reforestation area size, and the effectiveness of different spectral indices in remote sensing. Recommendations for future studies include refining data extraction methods to enhance change detection and to consider seasonal variations to mitigate the influence of vegetation saturation. This study contributes to the optimization of monitoring strategies for mangrove reforestation, offering insights into the scalability and applicability of remote sensing techniques in conservation efforts.
DOI: 10.14288/1.0441539
title: Hotspot analysis for mangrove restoration suitability

description: This research paper presents a globally replicable methodology for subnational hotspot analysis of mangrove restoration suitability. The study utilized Central America as a focal area and employed a two-phase workflow involving scripted analysis in RStudio and non-scripted application of QGIS geoprocessing tools and qualitative assessment. Approaches to spatially defining mangrove areas for analysis were examined, including global administrative zones, buffering around mangrove areas of loss, and manual boundary selection. Specific datasets for restoration suitability indicators such as mangrove loss, population distribution, poverty metrics, soil organic carbon, protected areas and others were evaluated for effectiveness. Key findings included high restoration suitability in Nicaragua and Honduras, consistent underestimation of mangrove loss to aquaculture conversion, and varying effectiveness of protected areas between countries and designation types. The discussion section expands on the effectiveness of different indicators, compares mangrove delineation methods from the literature, emphasizes the usefulness of screening processes, and suggests future directions for restoration hotspot analysis. Overall, this research presents a flexible hotspot analysis methodology suitable for restoration practitioners operating within common constraints such as open-source software and freely accessible data.