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opencc-zeroAug 2023View details →

Co-design of a citizen science study: unlocking the potential of eDNA for volunteer freshwater monitoring

<ol> <li>Citizen science is increasingly being promoted as a means of gathering more data to help inform the management of ecosystems. Involving the participants in the design of data collection activities is a form of co-design often proposed by those calling for a translational ecology.</li> <li>In addition, novel monitoring approaches have the potential to improve the quality of data collected by citizen scientists. We explored the potential of environmental DNA (eDNA) for vertebrate (mainly fish) species monitoring through a co-designed catchment monitoring strategy. </li> <li>Having been introduced to the potential of eDNA, citizen scientists designed and executed an eDNA-based survey of a small chalk stream catchment to explore questions of concern.</li> <li>The eDNA monitoring approach provided data about fish and other vertebrate diversity in the catchment which would have otherwise required sampling approaches difficult for citizen scientists. These data give a preliminary answer to some of the citizen scientists' priority questions and are comparable to fish data collected through traditional electrofishing surveys.</li> <li>Recommendations are offered for co-design and the use of novel research techniques by citizen scientists.</li> </ol>

opencc-zeroAug 2023View details →

Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

<div> Salmonids with complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding viability of natural populations. We genotyped adult (n=3,108) and juvenile (n=2,624) samples of anadromous Oncorhynchus mykiss that were collected in the Klickitat River, WA, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources and variation in adult migration timing. Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%) as expected since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other sub-basins, but genetic diversity remains high throughout the sub-basin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations. </div>

opencc-zeroAug 2023View details →

Open‐source workflow approaches to passive acoustic monitoring of bats

<ol> <li>The affordability, storage, and power capacity of compact modern recording hardware has evolved passive acoustic monitoring (PAM) of animals and soundscapes into a non-invasive, cost-effective tool for research and ecological management and is particularly effective for bats and toothed whales that consistently echolocate. The use of PAM at large scales hinges on effective automated detectors and species classifiers which, combined with distance sampling approaches, have enabled species abundance estimation of toothed whales. But standardized, user-friendly, and open-access automated detection and classification workflows are in demand for this key conservation metric to be realized for bats.</li> <li>We used the PAMGuard toolbox including its new deep learning classification module to test the performance of four open-source workflows for automated analyses of acoustic datasets from bats. Each workflow used a different initial detection algorithm followed by the same deep learning classification algorithm and was evaluated against the performance of an expert manual analyst.</li> <li>Workflow performance depended strongly on the signal-to-noise ratio and detection algorithm used: the full deep learning workflow had the best classification accuracy (≤67%) but was computationally too slow for practical large-scale bat PAM. Workflows using PAMGuard's detection module or triggers onboard an SM4BAT or AudioMoth accurately classified up to 47%, 59% and 34%, respectively, of calls to species. Not all workflows included noise sampling critical to estimating changes in detection probability over time, a vital parameter for abundance estimation. The workflow using PAMGuard's detection module was 40 times faster than the full deep learning workflow and missed as few calls (recall for both ~0.6), thus balancing computational speed and performance. </li> <li>We show that complete acoustic detection and classification workflows for bat PAM data can be efficiently automated using open-source software such as PAMGuard and exemplify how detection choices, whether pre- or post-deployment, hardware or software-driven, affect the performance of deep learning classification and the downstream ecological information that can be extracted from acoustic recordings. In particular, understanding, and quantifying detection/classification accuracy and the probability of detection are key to avoid introducing biases that may ultimately affect the quality of data for ecological management. </li> </ol>

opencc-byAug 2023View details →

Population dynamics and seasonal migration patterns of Spodoptera exigua in northern China based on 11 years of monitoring data

The beet armyworm, Spodoptera exigua (Hübner) is an important migratory pest worldwide that has caused serious economic losses in the main crop-producing areas of China. To effectively monitor and control this pest, it is necessary to investigate its interannual and seasonal migration patterns in northern China. In this study, we weekly monitored the population dynamics of S. exigua using sex pheromone traps in Shenyang, Liaoning Province from 2012 to 2022 and simulated the migration trajectories using the HYSPLIT model. Overall, the migration numbers varied significantly among years, with large migrations in 2018 and 2020 that resulted in a total catch of more than 2000 individuals.

Lichens as bioindicators of monitoring of the selective air pollution, Zabrze (Poland) - total carbon (TC) and total sulfur (TS) results.

Total carbon (TC) and total sulfur (TS) contents were measured using an Eltra CS-500 IR-analyzer with a TIC module. TC was determined using an infrared cell detector on CO2 gas, which was evolved by combustion under an oxygen atmosphere. Calibration was made by means of the Eltra standards 2.27 % S and 45.14 % C.  Dr Ewa Szram, employed at the Institute of Earth Sciences, Faculty of Natural Sciences, Silesian University in Katowice, carried out the project. This research was funded by the National Science Centre, Poland MINIATURA-6 2022/06/X/ST10/00338 “Lichens as bioindicators of monitoring of the selective air pollution”

Lichens as bioindicators of monitoring of the selective air pollution, Zabrze (Poland) - XRF analysis results.

XRF analyses were performed by the BRUKER S8 TIGER series 2 WD-XRF spectrometer with a 1kW Rh X-ray tube. The system is equipped with five analyzing crystals (LiF200, PET, XS–55, LIF-220  & Ge) and two detectors (flow and scintillation counter). The samples were measured by best detection mode (18min analysis time), and the results were evaluated in Quant-Express (fundamental parameters) and SPECTRAplus Software. Dr Ewa Szram, employed at the Institute of Earth Sciences, Faculty of Natural Sciences, Silesian University in Katowice, carried out the project. This research was funded by the National Science Centre, Poland MINIATURA-6 2022/06/X/ST10/00338 “Lichens as bioindicators of monitoring of the selective air pollution”

Dataset from structural health monitoring of a steel bridge in Sweden

The dataset consists of sensor data from the Vänersborg Bridge in Sweden, comprising 64 bridge opening events registered as accelerations, strains, inclinations, and weather conditions. Data from before, during, and after a verified fracture are provided. The sample of raw data captured the same bridge opening event multiple times over the monitoring duration. Classifying data before and after damage enables the development and verification of routines for novelty detection.

Lichens as bioindicators of monitoring of the selective air pollution, Zaabrze (Poland) - chromatograms of GC-MS

Detailed geochemical analyses were performed on 21 powdered samples after their extraction using ultrasound Elmasonic Easy with a dichloromethane (DCM) and methanol (MeOH) mixture (1:1 vol). Extracts were separated into aliphatic-, aromatic-, semipolar- and polar fractions by column chromatography. Silica-gel was first activated at 120 °C for 24 h, cooled, and poured into Pasteur pipettes. Foour eluents were used for fraction collection, namely, n-pentane for the aliphatic fraction, n-pentane and DCM (7:3) for the aromatic fraction, acetone and DCM (1:1) for the semipolar fraction, and DCM and methanol (1:1) for the polar fraction. The semipolar - and polar fraction was derivatized with MTBSTFA (N-tertbutyldimethylsilyl-N-methyltrifluoroacetamide). Samples were derivatized with MTBSTFA dissolved in super-dehydrated n-hexane, and heated at 70 °C for 3 h. The composition of the separated extracts was analyzed by gas chromatography–mass spectrometry (GC–MS) using an Agilent gas chromatograph 7890A coupled with a mass spectrometer 5975C XL MDS. A DB-5UI column was applied (60 m × 250 μm id, 0.25 μm stationary phase film), with He (purity of 99.9999%) as a carrier gas. The experimental conditions were as follows: injection volume of 1 μL; split/splitless mode; initial temperature of 45 ◦C (isothermal for 1 min); heating rate up to 100 ◦C at 20 ◦C/min, then 3 ◦C/min to 280 ◦C for 66.25 min. The mass spectrometer worked in electron ionization (EI) mode at 70 eV in full scan mode and scanned from 50 to 650 Da. Dr Ewa Szram, employed at the Institute of Earth Sciences, Faculty of Natural Sciences, Silesian University in Katowice, carried out the project. This research was funded by the National Science Centre, Poland MINIATURA-6 2022/06/X/ST10/00338 “Lichens as bioindicators of monitoring of the selective air pollution”

Time series of flow measurement and water quality monitoring at a large combined sewer overflow in Berlin

The table contains 3 years CSO monitoring time series, already split in 22 separated CSO events. All details about the monitoring set up in the papers and reports indicated below. Fields: <ul> <li>evtID: event ID</li> <li>myDateTime; date/time</li> <li>v: m/s velocity</li> <li>Q: m³/s flow</li> <li>TSS: mg/l TSS concentration</li> <li>COD: mg/l COD concentration</li> <li>CODf: mg/l dissolved COD concentration</li> <li>EC: µS/cm electric conductivity</li> <li>NH4_N: mg/l NH4_N concentration</li> </ul> TSS and COD have been measured with a spectrometer using a linear local calibration as presented in Lepot et al., 2016. ore information about the monitoring set up in  Sandoval, S., Torres, A., Pawlowsky-Reusing, E., Riechel, M., Caradot, N. (2013): The evaluation of rainfall influence on CSO characteristics: the Berlin case study. Water Science & Technology Vol. 68 (12): 2683-2690 10.2166/wst.2013.524 Caradot, N. (2012): Continuous Monitoring of Combined Sewer Overflows in the Sewer and the Receiving River: Return on Experience. Kompetenzzentrum Wasser Berlin gGmbH; MIA-CSO Project Report Riechel, M., Matzinger, A., Pawlowsky-Reusing, E., Sonnenberg, H., Uldack, M., Heinzmann, B., Caradot, N., von Seggern, D., Rouault, P. (2016): Impacts of combined sewer overflows on a large urban river - Understanding the effect of different management strategies. Water Research 105: 264-273 10.1016/j.watres.2016.08.017 Caradot, N., Sonnenberg, H., Riechel, M., Matzinger, A., Rouault, P. (2013): The influence of local calibration on the quality of UV-VIS spectrometer measurements in urban stormwater monitoring. Water Practice & Technology Vol 8 (No 3-4): 417-425 10.2166/wpt.2013.042 Lepot, M., Torres, A., Hofer, T., Caradot, N., Gruber, G., Aubin, J.-B., Bertrand-Krajewski, J.-L. (2016): Calibration of UV/Vis spectrophotometers: A review and comparison of different methods to estimate TSS and total and dissolved COD concentrations in sewers, WWTPs and rivers. Water Research 101 (15 September 2016): 519-534 10.1016/j.watres.2016.05.070

opencc-by-4.0Feb 2023View details →

The application of unmanned aerial vehicle (UAV) surveys and GIS to the analysis and monitoring of recreational trail conditions - dataset

This dataset contains data used to test the protocol for high-resolution mapping and monitoring of recreational impacts in protected natural areas (PNAs) using unmanned aerial vehicle (UAV) surveys, Structure-from-Motion (SfM) data processing and geographic information systems (GIS) analysis to derive spatially coherent information about trail conditions (Tomczyk et al., 2023). Dataset includes the following folders: <ol> <li>Cocora_raster_data (~3GB) and Vinicunca_raster_data (~32GB) - a very high-resolution (cm-scale) dataset derived from UAV-generated images. Data covers selected recreational trails in Colombia (Valle de Cocora) and Peru (Vinicunca). UAV-captured images were processed using the structure-from-motion approach in Agisoft Metashape software. Data are available as GeoTIFF files in the UTM projected coordinate system (UTM 18N for Colombia, UTM 19S for Peru). Individual files are named as follows [location]_[year]_[product]_[raster cell size].tif, where: <ul> <li>[location] is the place of data collection (e.g., Cocora, Vinicucna)</li> <li>[year] is the year of data collection (e.g., 2023)</li> <li>[product] is the tape of files: DEM = digital elevation model; ortho = orthomosaic; hs = hillshade</li> <li>[raster cell size] is the dimension of individual raster cell in mm (e.g., 15mm)</li> </ul> </li> <li> Cocora_vector_data. and Vinicunca_vector_data – mapping of trail tread and conditions in GIS environment (ArcPro). Data are available as shp files. Data are in the UTM projected coordinate system (UTM 18N for Colombia, UTM 19S for Peru). </li> </ol> Structure-from-motio n processing was performed in Agisoft Metashape (<a href="https://www.agisoft.com/">https://www.agisoft.com/</a>, Agisoft, 2023). Mapping was performed in ArcGIS Pro (<a href="https://www.esri.com/en-us/arcgis/about-arcgis/overview">https://www.esri.com/en-us/arcgis/about-arcgis/overview</a>, Esri, 2022). Data can be used in any GIS software, including commercial (e.g. ArcGIS) or open source (e.g. QGIS). Tomczyk, A. M., Ewertowski, M. W., Creany, N., Monz, C. A., & Ancin-Murguzur, F. J. (2023). The application of unmanned aerial vehicle (UAV) surveys and GIS to the analysis and monitoring of recreational trail conditions. International Journal of Applied Earth Observations and Geoinformation, 103474. doi:<a href="https://doi.org/10.1016/j.jag.2023.103474"> https://doi.org/10.1016/j.jag.2023.103474</a>

Supplementary material to 'Subglacial volcano monitoring with fibre-optic sensing: Grímsvötn, Iceland'

This supplementary material contains a video with impressions of the fieldwork, that was part of the work published in the article ' Subglacial volcano monitoring with fibre-optic sensing: Grímsvötn, Iceland' in Volcanica.

Forestry and Biodiversity monitoring in Lithuania with hyperspectral camera and UAV

Acquisition dates: to be updated. Location: Scots pine and mixed forest in Lithuania Camera data:  Spectral Range  400 – 1000 nm Spectral sampling  2.68 nm Spectral resolution  5.5 nm Fore lens focal length  15 mm Field of view  38 deg Spectral bands  224 Spatial pixels  1024 Flight altitude: 70 m Spatial resolution: 0.05 m/pixel    The dataset consists of pine tree forest hyperspectral imaging data acquired with a UAV on several dates.  The data from each UAV flight are given as a separate dataset.  Each dataset consists of raw and processed hyperspectral imaging data. The raw data include calibration images of white reference and dark background, raw hyperspectral images, and information on the UAV flight path.  TheSPECIM CaliGeoPRO software was used to process raw images into hyperspectral data cubes, which are provided in the format ENVI standard.  Each flight data will come as a separate hyperlink to the storage. zip file structure (folders): calibration - holds the radiometric calibration ENVI type file (raster of size 1x1024) capture - raw camera capture data, navigation files, log file. metdata, results - config and empty folder out - holds generated ENVI data cube raster file. Download: <a href="https://icaerus-data-1.s3.eu-central-1.amazonaws.com/Uzkresti_miskai_new_fl7_20230510_151005.zip">https://icaerus-data-1.s3.eu-central-1.amazonaws.com/Uzkresti_miskai_new_fl7_20230510_151005.zip</a>

Effectiveness of self-management of medication and self-monitoring of blood pressure, diet, and physical exercise on blood pressure in patients with poorly controlled hypertension (MEDICHY study): randomized and controlled trial

Dataset study medichy ISRCTN144433778

Monitoring of Russian universal scientific libraries

The results of an analysis of the websites of 50 regional universal scientific libraries of Russia (the main innovators in library services to the regions), the purpose of which was to identify problems in reflecting library, information and other services, are presented. As part of the study, free and paid services offered online and offline were analyzed and a rating of the most common types was given.

opencc-by-3.0-usDec 2022View details →

Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP

This dataset corresponds to the research manuscript entitled "Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP"

opencc-zeroSep 2023View details →

Monitoring mesophotic scleractinian corals using an underwater mini-ROV to sample eDNA

Mesophotic coral ecosystems (MCEs) are light-dependent tropical or subtropical communities occurring at depths of 30 to 150 m. We recently devised a coral-specific environmental DNA (eDNA) barcoding method that can identify 36 scleractinian genera in shallow reefs by sampling ~1L of surface seawater. If eDNA barcoding is combined with sampling using underwater mini-Remote Operated Vehicles (mini-ROVs), it may be possible to survey mesophotic corals more easily and broadly. Around the Zamami Islands, in Okinawa, Japan, seawater was collected 1–2 m above the bottom at six locations 20–80 m below the surface and subjected to coral-specific eDNA amplification. Metabarcoding analyses showed that (a) eDNA from ~0.5 L seawater was sufficient to identify genera and to yield comparative ratios of genera at these sites; (b) Acropora dominates shallow reefs and upper ridges of slopes, while other genera including Porites, Pocillopora and Polyphyllia are more abundant at mesophotic sites; (c) one site showed a gradient in which Acropora was replaced by Plesiastrea at increasing depths. Although further technical improvements are required, the use of eDNA and underwater mini-ROVs may permit monitoring of mesophotic corals more broadly and easily.

opencc-zeroSep 2023View details →

Data from: Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions

Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods have left DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scaled community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant derived eDNA analysis for large-scale biodiversity assessments that include information about community level interactions.

opencc-zeroSep 2023View details →

Monitoring data for oyster reefs and nearby controls, including high frequency environmental parameters, carbonate chemistry, oyster growth, and other data

Data for Oyster reefs' control of carbonate chemistry - implications for oyster reef restoration in estuaries subject to coastal ocean acidification.

opencc-by-4.0Oct 2023View details →

Experimental Validation of Automated OMA and Mode Tracking for Structural Health Monitoring of Transmission Towers

This dataset is part of the Smart Tower Project and is intended to accompany academic publications entitled "Experimental Validation of Automated OMA and Mode Tracking for Structural Health Monitoring of Transmission Towers". It provides valuable data under high wind excitation conditions and is beneficial for researchers in the field of structural dynamics and Structural Health Monitoring (SHM). The dataset includes high-resolution accelerometer data and estimated modal parameters, along with part of the code script used for analysis. Dataset Components: <ol> <li> Raw Accelerometer Data (April Month): High-resolution time-series accelerometer data recorded during April, under high wind excitation conditions. The data is sampled at a rate of 250 Hz. The data is organized in dd/YYYYmmdd_HHMMSS.tdms <ul> <li>Format: TDMS</li> </ul> </li> <li> Modal Parameters: Resonance frequencies estimated over the entire monitoring period from 29/03/2023 to 25/06/2023. <ul> <li>Format: Parquet</li> </ul> </li> </ol>