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374 results for “Effectiveness Monitoring”
Salmonid habitat use monitoring used to determine effectiveness of habitat improvement projects in the Sacramento River, CA
Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains five datasets. Enclosure Study – Growth Data This dataset covers enclosure studies that examined salmonid growth rates in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Data was collected in July and August 2019 from project sites, constructed habitat project sites, and control sites where no treatment is planned. Six enclosures with juvenile Fall Run Chinook salmon from Coleman National Fish Hatchery were placed in each habitat type. Fish growth was tracked for approximately 6.5 weeks. Annual reports summarize the survey findings. Enclosure Study – Gut Contents Data This dataset covers enclosure studies that examined salmonid growth rates in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Data was collected in July and August 2019 from project sites, constructed habitat project sites, and control sites where no treatment is planned. Six enclosures with juvenile Fall Run Chinook salmon from Coleman National Fish Hatchery were placed in each habitat type. Enclosures remained in the river for approximately 6.5 weeks. At the end of the study, fish were euthanized, and we dissected their guts and enumerated the taxa found. Annual reports summarize the survey findings. Microhabitat Use Data This dataset covers salmonid microhabitat use conducted in the Sacramento River and focused on assessing effectiveness of salmonid habitat improvement projects. Surveys are conducted roughly monthly and include pre-project sites, constructed habitat project sites, and control sites where no treatment is planned. Based upon habitat inventory data, annually identify which habitat units within each side channel will be selected for the collectio
Dataset: Brain negativity as an indicator of predictive error processing: The contribution of visual action effect monitoring
<p>There are two files for each subject:</p> <p>1. sub##_error.dat -> Contains EEG Segments, that were recorded while the subject executed a clear target miss (minimal distance between the center of the ball and target > 12 cm) in the task (segment and electrode information can be found below).</p> <p>2. sub##_hit.dat -> Contains EEG Segments, that were recorded while the subject executed a clear target hit (minimal distance between the center of the ball and the target < 7 cm) in the task (segment and electrode information can be found below).</p> <p><br> The data in the *.dat-files are stored in a two dimensional matrix: n*1400 datapoints x 15 electrodes</p> <p>n represents the number of segments. 1400 datapoints per segment translate to a segment length of 2800 ms (from 600 ms before to 2200 ms after ball release). The ball´s release is located at the 301st datapoint and the feedback was presented at datapoint 726 (850 ms after ball release) in every segment.</p> <p>datapoints: The first dimension (rows) includes the measured neural activations in microvolts. The data is stored vectorized,<br> i.e. hit/error #1 -> row 1 to 1400, hit/error #2 -> row 1401 to 2800, ..., hit/error #n -> (n-1) * 1400 + 1 to n * 1400</p> <p>electrodes: The second dimension (columns) consists of the 15 different electrodes that were used during data recording in this exact order: [F3 Fz F4 C4 Cz C3 P3 Pz P4 VEOGu VEOGo HEOGre HEOGli FCz Mastre]</p>
Data from: The effect of probe density coverage on the detection of oenological tannins in quartz crystal microbalance with dissipation monitoring (QCM-D) experiments
<p>Polyphenols, crucial compounds in grapes, musts, and wines, influence grape ripening, must fermentation, and final wine quality. Current detection methods for polyphenols are expensive, time-consuming, and reliant on specialized laboratories and personnel. This study proposes the use of a functionalized acoustic sensor to address these limitations and efficiently detect oenological polyphenols.</p> <p>The method employs a quartz crystal microbalance with dissipation monitoring (QCM-D) combined with a gelatin-based probe layer to detect the target analyte. The sensor is functionalized by optimizing probe coverage density, accomplished through the use of 12-mercaptododecanoic acid (12-MCA) for probe immobilization onto the gold sensor surface, along with dithiothreitol (DTT) as a reducing and competitive binding agent. Varying concentrations of 12-MCA and DTT allow for control over probe density, with QCM-D measurements demonstrating effective adjustment, ranging from 0.2 × 10^13 to 2 × 10^13 molecules cm^−2. The study also explores the interaction between the probe and tannins, confirming the ability of the sensor to detect them. Notably, lower probe coverage yields higher detection signals when normalized to probe immobilization signals. Additionally, significant alterations in the mechanical properties of the functionalization layer occur after interaction with samples.</p> <p>Combining QCM-D with gelatin functionalization presents promising applications in the wine industry. This approach enables real-time monitoring, requires minimal sample preparation, and offers high sensitivity for quality control purposes.</p>
The Effect of Prescription Drug Monitoring Programs (PDMPs) and Overdose Reversal Drug Accessibility Laws on Opioid Analgesic Mortality in the United States
<p><strong>Purpose: </strong>This analysis focuses on the impact of Prescription Drug Monitoring Programs (PDMPs) and increased layperson access to the overdose reversal drug Naloxone on prescription opioid mortality rates. The prescription opioid mortality rate was analyzed against state laws governing PDMPs and Naloxone accessibility to laypersons to evaluate if there was a correlation between mortality reduction and implementation of the laws.</p> <p>Three main analyses were conducted:</p> <ol> <li>Does a state’s opioid mortality reduction correlate to an effective PDMP and/or Naloxone law?</li> <li>Do states with strong PDMP laws have a corresponding opioid overdose mortality rate reduction?</li> <li>Do states with strong Naloxone accessibility laws have a corresponding opioid overdose mortality rate reduction?</li> </ol> <p><strong>Conclusion:</strong> Patterns show that PDMP and Naloxone accessibility can be successful in reducing mortality rates, but implementations and results vary dramatically between states. Further changes to both PDMPs and Naloxone accessibility are needed for states to see reliable and consistent mortality reductions. Changes to regulations need time to implement and take effect, meaning longer term measurements and data will be required to see if positive impacts can be sustained.</p> <ol> </ol> <p><strong>Data and Datasets:</strong></p> <p>There are three main datasets used in the analysis.</p> <ul> <li>Opioid mortality rate by state from 2006 to 2016. <ul> <li>This datasetis from the CDC website (<a href="https://www.cdc.gov/drugoverdose/data/statedeaths.html">https://www.cdc.gov/drugoverdose/data/statedeaths.html</a>). I used web scraping and regular expression search to extract the data and calculated mortality reduction of each state.</li> <li><em>Mortality reduction formula: (Highest mortality rate) – (2016 mortality rate)</em><br> </li> </ul> </li> <li>PDMP law implementation in each state and its timelinefrom January 1, 1998 to July 1, 2016. <ul> <li>Dataset is from the Prescription Drug Abuse Policy System(<a href="http://pdaps.org./datasets/prescription-monitoring-program-laws-1408223332-1502818372">http://pdaps.org./datasets/prescription-monitoring-program-laws-1408223332-1502818372</a>). This dataset encompasses laws regulating which professions have access to the database and for what purpose, whether practitioners can delegate their access, whether patients can see their own information, and the extent to which access to individually-identified records may be granted for law enforcement purposes.</li> <li>This dataset is not quantitative, but a set of questions on the characteristics of the laws governing the PDMP.I performed the following data preparation to allow for analysis and visualization:</li> <li><em>PDMP law effectiveness calculation:Each question with a “Yes” answer adds one point to the law’s cumulative effectiveness score on the year it was implemented.</em></li> </ul> </li> </ul> <ul> <li>Naloxone accessibility to laypersons law implementation in each state and its timeline from January 1, 2001 to December 31, 2016. <ul> <li>Dataset is also from the Prescription Drug Abuse Policy System (<a href="http://pdaps.org./datasets/laws-regulating-administration-of-naloxone-1501695139">http://pdaps.org./datasets/laws-regulating-administration-of-Naloxone-1501695139</a>).This dataset focuses on state laws that provide civil or criminal immunity to licensed healthcare providers or lay responders for opioid antagonist administration.</li> <li>This dataset is not quantitative, but a set of questions on the characteristics of the laws governing Naloxone accessibility to laypersons. I performed the following data preparation to allow for analysis and visualization:</li> <li><em>Naloxone accessibility law effectiveness calculation:Each question with a “Yes” answer adds one point to the law’s cumulative effectiveness score on the year it was implemented.</em></li> </ul> </li> </ul>
The Effect of Soundscape Composition on Bird Vocalization Classification in a Citizen Science Biodiversity Monitoring Project
<p>This archive includes sound clips (.wav files) and associated mel-scale spectrograms of bird vocalizations for 54 species in Sonoma County, California, USA. These data were used for training and validating convolutional neural network (CNN) models for bird species detection. We also include xeno-canto training and validation mel spectrograms used to pretrain CNNs. Details on these data are explained in the paper by Clark et al. (2023) titled "The effect of soundscape composition on bird vocalization classification in a citizen science biodiversity monitoring project". These data are available for use without restrictions, with no warranty on data quality or utility for a given application. We request that any work that does use these data cite the Clark et al. (2023) paper.<br> <br> Clark, M.L., Salas, L., Baligar, S., Quinn, C., Snyder, R.L., Leland, D., Schackwitz, W., Goetz, S.J., Newsam, S. (2023). The effect of soundscape composition on bird vocalization classification in a citizen science biodiversity monitoring project. <em>Ecological Informatics</em>. <a href="https://doi.org/10.1016/j.ecoinf.2023.102065">https://doi.org/10.1016/j.ecoinf.2023.102065</a></p> <p>Associated code for training CNN models, performing inference, and applying post-classification corrections can be found in the GitHub archive <a href="https://github.com/pointblue/Soundscapes2Landscapes/tree/master/CNN_Bird_Species">https://github.com/pointblue/Soundscapes2Landscapes/tree/master/CNN_Bird_Species</a></p> <p>Raw sound data from the Soundscapes to Landscapes project are available upon request: Dr. Matthew Clark, matthew.clark@sonoma.edu</p> <p>These data were collected as part of the Soundscapes to Landscapes project (<a href="https://soundscapes2landscapes.org/">soundscapes2landscapes.org</a>), funded by NASA’s Citizen Science for Earth Systems Program (CSESP) 16-CSESP 2016-0009 under cooperative agreement 80NSSC18M0107.<br> <br> ----------------------------<br> This depository includes the following archives:</p> <ul> <li> <p>mel_specs.zip: contains 2-sec mel spectrograms split into training (“tr”), validation (“val”), testing (“test”) data for each target bird species (n = 54) used to fine-tune the CNNs. Select spectrogram files are appended with “aug” if they are augmented versions for the training data.</p> </li> <li> <p>wav.zip: contains the associated wav-format sound recordings used to generate the training, validation, testing mel spectrograms found in mel_specs.zip.</p> </li> <li> <p>Xeno-canto_pretrain.tar: contains 2-sec mel spectrograms split into training and validation data for 40 bird species used for CNN pre-training that were generated using a warbleR segmentation methodology described in the paper. The sound files used to generate these mel spectrograms came from the Kaggle competition, <a href="https://www.kaggle.com/datasets/imoore/xenocanto-bird-recordings-dataset">https://www.kaggle.com/datasets/imoore/xenocanto-bird-recordings-dataset</a><br> Mel spectrogram naming reflects the XC number used for cataloging on Xeno-canto in the format XC123456_2.png. The six numbers following the XC characters can be used to search for unique recordings on Xeno-canto (<a href="https://xeno-canto.org/">https://xeno-canto.org/</a>) using the search query “nr:123456” in the search tool or queried using the Xeno-canto API (<a href="https://xeno-canto.org/explore/api">https://xeno-canto.org/explore/api</a>). Unique recording names can be extracted from the mel spectrogram filenames.</p> </li> <li> <p>soundscape_test_wavs.zip: the wav-format sound recordings used to perform soundscape testing.</p> </li> </ul>
Throw trap and electrofishing data collected during 1996–2022 from the Everglades, Florida, United States for the publication "Contrasting invasion histories and effects of three non-native fishes observed with long-term monitoring data"
This dataset was used to analyze the effects of three non-native fishes in the Florida Everglades for a publication in the journal Biological Invasions. The dataset incorporates plot-level mean densities (# of individuals per square meter) of common aquatic animals collected during 1996–2022 from 17 sites across three regions of the Everglades: Taylor Slough, Shark River Slough, and Water Conservation Area 3A. Prey species included are nine common small fishes and three common decapod species (two crayfish species and grass shrimp). The dataset includes throw trap data on three predator taxa: African Jewelfish (Hemichromis letourneuxi), Mayan Cichlids (Mayaheros uruphthalmus), and sunfishes (Lepomis spp.). Annual indices of mean wet season electrofishing catch-per-unit-effort of Asian Swamp Eels (Monopterus albus/javanesis), Mayan Cichlids, sunfishes, and the three other large 'top predator' fishes (Amia calva, Lepisosteus platyrhincus, Micropterus salmoides) are included for plots where electrofishing was performed from 1997-2021. Hydrologic measures used in analyses and R code used to conduct analyses are also included.
Difference in effect of pheromone for monitoring the European spruce bark beetle
<p>In recent decades there have been an increasing number of outbreaks of the European spruce bark beetle (<i>Ips typographus</i>) in Europe. A large amount of sanitary felling has taken place, with significant economic and ecological consequences. In order to anticipate such large-scale outbreaks, an effective monitoring system should be set up. One important aspect of monitoring is the decision on which pheromone to use. We suggest a framework for selecting an effective pheromone with few side effects and implemented it on five different pheromones under different disturbance conditions: Pheroprax, IT Ecolure, Ipstyp, Ipsowit and Typosan. We set 50 traps in two areas with sites that were disturbed and undisturbed by wind storms. We collected bark beetles from traps every one to two weeks from the end of March until the end of September in 2019. We investigated the number of bark beetles caught, bark beetle dynamics, amount of bycatch and predators, the taxonomic groups of the bycatch and the overall costs of the monitoring system. We found that Pheroprax, IT Ecolure and Ipsowit caught the most bark beetles and best showed the population dynamics. There was a low amount of bycatch (less than 6% of the total catch) and predators (a few individuals), but some groups seem to prefer certain pheromones. The cost of the pheromones increased with their effectiveness. However, pheromone costs are low relative to the personnel costs involved in setting traps and collecting bark beetles. The framework and the results will help professionals to decide which pheromones to purchase for their bark beetle monitoring system.</p>
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction.
AdaptFerm: Bioprocess Monitoring Using FTIR spectroscopy: Insights into Substrate Effects and Domain Adaptation
<h2> </h2> <h2><strong>1. Introduction</strong></h2> <p>The AdaptFerm dataset is designed to support the development of a monitoring framework for lactic acid production fermentation using Fourier Transform Infrared (FTIR) spectroscopy. Its primary goal is to facilitate the control strategies for continuous fermentation processes to maximize the lactic acid production. The AdaptFerm encompasses data from two distinct batch fermentation environments: one employing simple sugar (glucose) as the substrate and the other utilizing complex sugars derived from bio-waste. The study focuses on developing accurate predictive models for glucose and lactic acid concentrations, with an emphasis on applying classical machine learning techniques and enhancing domain generalization capabilities.</p> <h2><strong>2. Prediction Model for Different Substrate Environments</strong></h2> <p>The chemical composition of substrates are presented in <a title="Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates" href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">Table 1 [1]</a>. The dataset is utilized to train and test models within the same substrate domain. For instance, data from a single fermentation environment (e.g., glucose substrate) is used for both training and testing phases. The applied machine learning models showed accurate prediction within the same domain <a title="Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates" href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">[1]</a>. For more details on the methods applied, please refer to the following link: <a title="Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates" href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">https://doi.org/10.1016/j.heliyon.2024.e38791</a>. In this study, the MIR results correspond to the AdaptFerm dataset. The spectra of the glucose and biowaste hydrolysate fermentation process are presented in <a title="Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates" href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">Figure 3</a> and <a title="Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates" href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">Figure 4</a>.</p> <h2><strong>3. Domain Adaptation</strong></h2> <p>The dataset was also used to address the challenge posed by shifts in FTIR data when substrates change. Transitioning from simple sugar (glucose) to complex sugar (bio-waste) causes significant variations in the FTIR spectra, making it difficult for models trained on glucose fermentation data to maintain prediction accuracy in the complex sugar fermentation environment. This results in reduced robustness and performance when applied to out-of-distribution data. To address these challenges, we explore methods that improve the generalization ability and robustness of models in such scenarios without using labels from complex sugar fermentation <a title="Domain-Invariant Monitoring for Lactic Acid Production: Transfer Learning from Glucose to Bio-Waste Using Machine Learning Interpretation" href="https://dx.doi.org/10.2139/ssrn.5012080" target="_blank" rel="noopener">[2]</a>. It shows the application of machine learning interpretation to find domain invariant features for glucose and lactic acid. For more details on the methods applied, please refer to the following link: <a title="Domain-Invariant Monitoring for Lactic Acid Production: Transfer Learning from Glucose to Bio-Waste Using Machine Learning Interpretation" href="https://dx.doi.org/10.2139/ssrn.5012080" target="_blank" rel="noopener">https://dx.doi.org/10.2139/ssrn.5012080</a>. The code is available at <a title="ShapFS" href="https://github.com/shl-shawn/ShapFS" target="_blank" rel="noopener">https://github.com/shl-shawn/ShapFS</a>.</p> <h2><strong>4. Real-World Use Cases</strong></h2> <h3><strong>4.1. Regression Task</strong></h3> <p>AdaptFerm serves as a benchmark for machine learning model applications in fermentation processes, specifically for predicting glucose and lactic acid concentrations, measured in g/L (grams per liter), while considering issues of out-of-distribution generalization.</p> <h3><strong>4.2. Domain Adaptation Regression Task</strong></h3> <p>The dataset is also suitable for evaluating different domain adaptation methods. In particular, the glucose substrate fermentation data can be used as the source domain, while the complex sugar fermentation data from bio-waste serves as the target domain. For semi-supervised domain adaptation approaches, it is recommended to use the initial data points (i.e., those collected at the beginning of the fermentation process) from the target domain, as the dataset is organized chronologically by collection day. These approaches aim to improve the robustness of models by transferring knowledge across domains and mitigating the effects of out-of-distribution data.</p> <h3><strong>4.3. Anomaly Detection</strong></h3> <p>The dataset can be used to train anomaly detection models to identify outliers or deviations from normal fermentation behavior. This could be valuable in industrial bioprocessing, where early detection of issues like contamination or process failure is crucial. Techniques like Isolation Forests, One-Class SVM, or Autoencoders could be applied to identify unusual patterns in FTIR spectra.</p> <h3><strong>4.4. Classification Task</strong></h3> <p>Although the main task is regression, the dataset could also be used in classification tasks by discretizing the concentrations of glucose and lactic acid into categories (e.g., low, medium, high). This would allow for the application of classification algorithms like Support Vector Machines (SVM), Random Forests, or Neural Networks for predicting the fermentation phase or identifying specific operational conditions.</p> <h3><strong>4.5. Transfer Learning</strong></h3> <p>Given the nature of the domain adaptation approach in this dataset, transfer learning models can be explored. Models pre-trained on glucose fermentation data can be fine-tuned on complex sugar fermentation data, enabling quicker model convergence and improved performance in data-scarce environments.</p> <h3><strong>4.6. Multi-Task Learning</strong></h3> <p>In a multi-task learning scenario, models could simultaneously predict both glucose and lactic acid concentrations from the same FTIR data. This could help in improving model accuracy by leveraging shared representations across the two tasks.</p> <h3><strong>4.7. Feature Selection</strong></h3> <p>The FTIR spectral data contains a large number of features (wavelengths), and feature selection techniques such as Recursive Feature Elimination (RFE), Lasso regression, or mutual information could be applied to identify the most relevant wavelengths for predicting glucose and lactic acid concentrations, improving model performance and interpretability.</p> <h2><strong>5. Dataset Structure and Meta Information</strong></h2> <p>The dataset is organized into four Excel files, corresponding to two main fermentation domains (different substrates) and two key process variables:</p> <p><strong>a) Simple Sugar Substrate</strong><br>This domain contains data for the fermentation process using glucose as the substrate to produce lactic acid. It includes two files—one for glucose concentrations and one for lactic acid concentrations. Both are measured in g/L.</p> <p><strong>b) Complex Sugar Substrate</strong><br>This doman contains data for the fermentation process using bio-waste as the substrate to produce lactic acid. Similar to the previous domain, it includes two files—one for glucose concentrations and one for lactic acid concentrations. Both are measured in g/L.</p> <p>Each file is structured as follows:</p> <ul> <li>The first column contains the<strong> </strong>sample ID, which serves as the timeline of measurements (Sample ID 1 represents the first measurement in the fermentation process).</li> <li>From the second column onwards, the FTIR data is provided, covering the spectral range from 549.6 cm-1 to 3999.6 cm-1 comprising 3,579 features.</li> <li>The final column contains the ground truth data, the chemical measurements of fermentation variables such as glucose and lactic acid concentrations, both measured in g/L.</li> </ul> <h2><strong>6. Conclusion</strong></h2> <p>The AdaptFerm features FTIR spectra data from two distinct fermentation environments: simple sugar (glucose) and complex sugar (bio-waste). The dataset is designed to be used in regression tasks, including domain adaptation, and can be applied in machine learning model development for fermentation process monitoring, with a focus on enhancing model robustness and handling out-of-distribution data. This dataset provides a valuable resource for exploring<strong> </strong>domain shift and improving the robustness of machine learning models in bioengineering and fermentation processes. It enables further research into domain generalization techniques and offers a wide range of possibilities for machine learning applications.</p> <h2>References</h2> <p> [1] Arman Arefi, Barbara Sturm, Majharulislam Babor, Michael Horf, Thomas Hoffmann, Marina Höhne, Kathleen Friedrich, Linda Schroedter, Joachim Venus, Agata Olszewska-Widdrat, Digital model of biochemical reactions in lactic acid bacterial fermentation of simple glucose and biowaste substrates, Heliyon, Volume 10, Issue 19, 2024, e38791, ISSN 2405-8440, DOI: 10.1016/j.heliyon.2024.e38791, <a href="https://doi.org/10.1016/j.heliyon.2024.e38791" target="_blank" rel="noopener">https://doi.org/10.1016/j.heliyon.2024.e38791</a>.</p> <p>[2] Majharulislam Babor, Shanghua Liu, Arman Arefi, Agata Olszewska-Widdrat, Barbara Sturm, Joachim Venus, and Marina M.-C. Höhne, Domain-Invariant Monitoring for Lactic Acid Production: Transfer Learning from Glucose to Bio-Waste Using Machine Learning Interpretation. Available at <a href="https://dx.doi.org/10.2139/ssrn.5012080" target="_blank" rel="noopener">http://dx.doi.org/10.2139/ssrn.5012080.</a></p>
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
<p>1. Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling as a cost-effective population-wide genetic monitoring approach. Genetic non-invasive sampling has, however, known limitations which may impact the accuracy of downstream genetic analyses.</p> <p>2. Here, using high quality SNP data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures.</p> <p>3. We found that genetic non-invasive sampling at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled.</p> <p>4. We show that genetic non-invasive sampling at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.</p>
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
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Difference in effect of pheromone for monitoring the European spruce bark beetle
Open the record for dataset details and reuse information.
Effects of soil preservation for biodiversity monitoring using environmental DNA
Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
Data from high throughput SNP-chip as cost effective new monitoring tool for assessing invasion dynamics in the comb jelly Mnemiopsis leidyi
<p class="MsoNormal"><span>High throughput low-density SNP arrays provide a cost-effective solution for population genetic studies and monitoring of genetic diversity as well as population structure commonly implemented in real time stock assessment of fish species. However, the application of high throughput SNP arrays for monitoring of invasive species has so far not been implemented. We developed a species-specific SNP array for the invasive comb jelly <em>Mnemiopsis leidyi</em> based on whole genome resequencing data. Initially, </span><span>a total of</span><span> </span><span>1,</span><span>395</span><span> </span><span>high quality </span><span>SNPs</span><span> were identified</span><span> </span><span>u</span><span>sing stri</span><span>ngent</span><span> filtering criteria</span><span>. From those, 192 assays were designed and validated, resulting in the final panel of 116 SNPs. Markers were diagnostic between the northern and southern <em>M. leidyi</em> lineages and highly polymorphic to distinguish populations. Despite using a reduced representation of the genome, our SNP panel yielded comparable results to using a whole genome resequencing approach (832,323 SNPs), recovering similar values of genetic differentiation between samples and detecting the same clustering groups when performing Structure analyses. The resource presented here provides a cost-effective, high throughput solution for population genetic studies, allowing to routinely genotype large number of individuals. Monitoring of genetic diversity and effective population size estimations in this highly invasive species will allow for the early detection of new introductions from distant source regions or hybridization events. Thereby, this SNP chip represents an important management tool in order to understand invasion dynamics and </span><span>opens the door for implementing such methods for a wider range of alien invasive species.</span></p> <div></div>
Monitoring GPS-collared moose by ground versus drone approaches: efficiency and disturbance effects
<p>Efficient wildlife management requires precise monitoring methods, e.g., to estimate population density, reproductive success, and survival. Here, we compared the efficiency of the drone (equipped with an RGB camera) and ground approaches to detect and observe GPS-collared female moose (<em>Alces alces</em>) and their calves. Moreover, we quantified how drone (n = 42) and ground (n = 41) approaches affected moose behavior and space use (n = 24 individuals). The average time used for drone approaches was 17 minutes compared to 97 minutes for ground approaches, with drone detection probability being higher (95% of adult female moose and 88% of moose calves) compared to ground approaches (78% of adult females and 82% of calves). Drone detection success increased at lower drone altitudes (50-70 m). Adult female moose left the site in 35% of drone approaches (with > 40% of those moose becoming disturbed once the drone hovered < 50 m above ground) compared to 56% of ground approaches. We failed to find short-term effects (3-h after approaches) of drone approaches on moose space use, but moose moved > 4-fold greater distances and used larger areas after ground approaches (compared to before the approaches had started). Similarly, longer-term (24-h before and after approaches) space use did not differ between drone approaches compared to days without known disturbance, but moose moved comparatively greater distances during days of ground approaches. In conclusion, we could show that drone approaches were highly efficient in detecting adult moose and their calves in the boreal forest, being faster and less disturbing than ground approaches, making them a useful tool to monitor and study wildlife.</p>
Monitoring the effect of water erosion on soil surface microtopography using Lidar
<p>This dataset contains three dimensional (3D) reconstructions of laboratory soil surfaces eroding under rainfall simulation experiments. Experiments were conducted using the Walnut Gulch Rainfall Simulator at the USDA-ARS Southwest Watershed Research Center in Tucson, Arizona. A terrestrial laser scanner was used to collect soil surface 3D data.</p>
Assessment of the Effectiveness of Coarse Resolution Fire Products in Monitoring Long-term Changes in Fire Regime within Protected Areas in South Africa
<p>The dataset includes fire histrory (shapefiles with data perimeters for 2003-2020) within 3 protected areas in South Africa, Blyde, Manyeleti, and Songimvelo.</p>
Phytoplankton Dataset: Supporting HAB monitoring based on cost-effective open-hardware solutions
<p>ASTRAL Phytoplankton monitoring dataset which has supported technology validation based on images from single-specie phytoplankton sample and prototype deployment within IMTA labs</p>
Microplastic Dataset: Supporting microplastic monitoring based on cost-effective open-hardware solutions
<p>ASTRAL Dataset related to microplastic monitoring based on the open-hardware initiative PlanktoScope</p>
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
<p>Dataset study medichy ISRCTN144433778</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.