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A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
Detection Histories for Hemlock Woolly Adelgid Infestations at Cadwell Forest in Pelham MA 2008
Monitoring programs increasingly are used to document the spread of invasive species in the hope of detecting and eradicating low-density infestations before they become established. However, interobserver variation in the detection and correct identification of low-density populations of invasive species remains largely unexplored. In this study, we compare the abilities of volunteer and experienced individuals to detect low-density populations of an actively spreading invasive species and we explore how interobserver variation can bias estimates of the proportion of sites infested derived from occupancy models that allow for both false negative and false positive (misclassification) errors. We found that experienced individuals detected small infestations at sites where volunteers failed to find infestations. However, occupancy models erroneously suggested that experienced observers had a higher probability of falsely detecting the species as present than did volunteers. This unexpected finding is an artifact of the modeling framework and results from a failure of volunteers to detect low-density infestations rather than from false positive errors by experienced observers. Our findings reveal a potential issue with site occupancy models that can arise when volunteer and experienced observers are used together in surveys.
Detection Probability of Red Wood Ants in Friedenweiler, Germany 2015
Estimation of population sizes and species ranges is central to population and conservation biology. It is widely appreciated that imperfect detection of mobile animals must be accounted for when estimating population size from presence-absence data. Sessile organisms also are imperfectly detected, but correction for detection probability in estimating their population sizes is rare. We illustrate challenges of detection probability and population estimation of sessile organisms using censuses of red wood ant (Formica rufa-group) nests as a case study. These ants, widespread in the northern hemisphere, can make large (up to 2m tall), highly visible nests. Using data from a two-day mapping campaign by eight individuals of 147 ant nests spread across sixteen 3600-m2 plots in the Black Forest region of southwest Germany, we developed a Bayesian model for quantifying detection probability of sessile organisms. Detection probabilities by individual observers of red wood ant nests ranged from 0.31 – 0.56, and depended on experience of the observers, size and density of nests, and habitat characteristics. Robust estimation of population density of sessile organisms—even highly apparent ones such as red wood ant nests—requires unbiased estimation of detection probability, just as it does when estimating population density of rare or cryptic species.
Ant Resource Detection Distance at the Caxiuana National Forest in Brazil 2017-2018
Environmental change scenarios of low precipitation forecast species loss in tropical regions. These losses can affect generalist species that provide important ecosystem services, such as controlling the rate at which nutrients become available for uptake by other organisms in tropical forests. Here, we use a long-term rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress affects the detection distance of food resources (baits) in a generalist ant guild (number of colonies, richness, and composition) that remove resources on the ground. We found that (i) overall the distance of resource removal by generalist ants did not change with drought; (ii) however, comparing ant species that occurred in drought-induced and control environments, workers walked shorter distances in the drought habitat; (iii) the number of resources detected by ant colonies in the drought-induced habitat decreased by 50%. Although generalist ants are considered resilient to habitat disturbance, the effect of reduced rainfall can negatively affect the services mediated by them. The rate of removal and consumption of resources in tropical forests may be related to abundance of generalist ants; losses in both nest density and walking distances may cause cascading effects on ecosystem processes and the services they mediate.
Confidence in Detection and Discrimination
Open the record for dataset details and reuse information.
Database of measurements for damage detection of steel beam splice connection by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated splice connection between two steel beams. The data set consists of two parts. The first part of the data set is measurements for six different specimens with wave type impact – short sweep signal with duration 0.05 s. The second part is the measurements during splice connection degradation of one of the specimens with short impulse. The degradation of a connection is presented by four different states of joints. In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>Used materials, methods and results for the second part of the data set is described in Buka-Vaivade, K.; Kurtenoks, V.; Serdjuks, D. Non-Destructive Damage Detection of Structural Joint by Coaxial Correlation Method in 6D Space. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1151. https://doi.org/10.3390/buildings13051151</p>
Database of measurements for damage detection of steel beam splice connections by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated splice connection between two steel beams. The data set consists of measurements for six different specimens with two types of impact – sweep signal with duration 0.5 s and short impulse, during degradation of the splice connections realised by unbolting the bolts in the connections. In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>This database is a continuation of the database Kurtenoks, V., Buka-Vaivade, K., Serdjuks, D., Lapkovskis, V., Mironovs, V., & Podkoritovs, A. (2023). Database of measurements for damage detection of steel beam splice connection by Coaxial Correlation Method in 6-D space (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10077332<br>Suggested by authors data post-processing is described in Buka-Vaivade, K.; Kurtenoks, V.; Serdjuks, D. Non-Destructive Damage Detection of Structural Joint by Coaxial Correlation Method in 6D Space. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1151. https://doi.org/10.3390/buildings13051151</p>
Multi-Class Depression Detection Dataset
<p>This dataset was created as part of the Master's thesis titled "Multi-Class Depression Detection Through Tweets Using Artificial Intelligence." It contains tweets labeled for five types of depression (Bipolar, Major, Psychotic, Atypical, and Postpartum) using lexicons verified by psychiatrists. </p> <p>Purpose: Designed for multi-class classification of depression using AI, focusing on Explainable AI for highlighting key words in the tweets influencing the predictions.<br>Applications: The dataset is suitable for research in natural language processing, sentiment analysis, mental health prediction, and Explainable AI.</p> <p>This dataset is shared under the Creative Commons Attribution 4.0 International (CC BY) license, requiring proper attribution for any use or modification.</p>
Molecular composition of dissolved organic matter in NTL-LTER lakes detected by Fourier-transform ion cyclotron resonance mass spectrometry
The composition of dissolved organic matter (DOM) varies widely in the environment due to distinct sources of the material and subsequent processing. DOM composition drives its reactivity in terms of many processes including photochemical reactions, microbial metabolism, and carbon cycling within water bodies. This study uses ultra-high resolution mass spectrometry via a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) to evaluate DOM composition at the molecular level to determine differences in DOM composition among the NTL-LTER lakes. Whole water samples were collected from the surface of each lake near the shore on August 18th and 19th in 2016 in. Ultraviolet-visible spectra were recorded as light absorbance can also give information about DOM composition. Additionally, concentrations of anions, cations, and pH were measured waters because these can all alter DOM reactivity in the environment. Both water chemistry and DOM composition vary widely among the lakes with the bogs displaying the most terrestrial-like signature in DOM and the oligotrophic lakes show more microbial-like or environmentally processed DOM.
Camera detections of small mammals on the coast of Virginia, 2020-2023
Specially-designed "mousecam" cameras were used to detect and identify small mammals at locations on the coast of Virginia. This dataset contains information on the images, the species observed and the date, time and location of observation. A second table contains information on the identity of the specific camera used and its location. This dataset includes a limited number of miscellaneous images from locations on the mainland as well.
Database of measurements for damage detection of T-type timber structural joint by Coaxial Correlation Method in 6-D space
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned on either side of the investigated joint between two timber beams connected at an angle of 90⁰. Presented data related to seven different states of joints, five load levels, and two type of input signal (short impulse and sweep signal with duration 0.5 seconds). In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p>
Database of measurements for damage detection of panel-to-panel moment joints in timber structures by Coaxial Correlation Method
<p>This database includes series of measurements of the structure's response taken in six-dimensional space using two 6D sensors, coaxially positioned in two different ways on either side of the investigated panel-to-panel connection. Presented data related to ten different states of joints, two load levels, and two type of input signal (short impulse and sweep signal with duration 0.5 seconds with frequency range from 10 Hz to 2000 Hz). In the "<strong>Read_me_first.pdf</strong>" is described the experiment, the format of .csv files names and files' structure.</p><p>Used materials, methods and results for the case of static load equal to 151.8 kg with sweep-type input signal, and T2 scheme of sensors placement is described in Kurtenoks, V.; Kurajevs, A.; Buka-Vaivade, K.; Serdjuks, D.; Lapkovskis, V.; Mironovs, V.; Podkoritovs, A.; Vilnitis, M. The Quality Assessment of Timber Structural Joints Using the Coaxial Correlation Method. <i>Buildings</i> <strong>2023</strong>, <i>13</i>, 1929. https://doi.org/10.3390/buildings13081929</p>
Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms (supplementary material)
<p>Supplementary material for Sawi et al., 2023, <i>Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms </i>(The Seismic Record). Catalog of repeating earthquakes in sequences on a 10-km long segment of the San Andreas Fault in California from 1984-2019. </p><p> </p><p><strong>Catalog Header</strong></p><p>YR/MO/DY...........Date of event</p><p>HR/MN/SC...........Time of event</p><p>LAT/LON/DEP........Location of event</p><p>EX/EY/EZ...........Relative location uncertainty (in m)</p><p>MAG................NCSN magnitude</p><p>evID.................NCSN event ID</p><p>seqID................Repeating earthquake sequence ID</p><p>isRESp............Is quasi-periodic RES (bool)</p><p> </p><p><strong>References: </strong></p><p>Sawi T., Waldhauser F., Holtzman B. K., Groebner, N. (2023) Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms. The Seismic Record. </p><p>Waldhauser, F., and Schaff, D. P. (2021). A Comprehensive Search for Repeating Earthquakes in Northern California: Implications for Fault Creep, Slip Rates, Slip Partitioning, and Transient Stress. J Geophys Res B Solid Earth, 126(11), 1–22. <a href="https://doi.org/10.1029/2021JB022495">https://doi.org/10.1029/2021JB022495</a></p>
ColoPola: A dataset of colorectal cancer polarimetric images (Mueller matrix elements) for colorectal cancer detection
<p><strong>ColoPola</strong> dataset is <strong>Colo</strong>rectal cancer <strong>Pola</strong>rimetric images dataset</p> <p>The dataset consists of 572 slices (specimens) with 20,592 images, 284 slices of which were designated as cancer samples and 288 as normal samples.</p> <p>Each sample has 36 polarimetric images (i.e., HH, HV, HP, HM, HR, HL, VH, VV, VP, VM, VR, VL, PH, PV, PP, PM, PR, PL, MH, MV, MP, MM, MR, ML, RH, RV, RP, RM, RR, RL, LH, LV, LP, LM, LR, and LL).</p> <p>Each folder in the <strong>ColoPola</strong> dataset consists of 36 polarimetric images. Each image is 1280x1024 pixels in size and was created in the TIF file format (HH.tif, HV.tif, ..., LL.tif). </p>
A collection of datasets for software vulnerability detection
<p>This is a collection of datasets that are used for AI-based software vulnerability detection. All the datasets are in the .csv format and each row represents a sample. Each dataset includes a set of functions written in C and the target of each function is either 0 (non-vulnerable) or 1 (vulnerable).</p> <ol> <li><strong>data_C_Lin2017_test.csv:</strong> <ul> <li>Reference paper: <a href="https://dl.acm.org/doi/10.1145/3133956.3138840">Vulnerability Discovery with Function Representation Learning from Unlabeled Projects</a>, 2017.</li> <li>Data source on GitHub: <a href="https://github.com/DanielLin1986/function_representation_learning">https://github.com/DanielLin1986/function_representation_learning</a></li> <li>This dataset includes 44 vulnerable and 577 non-vulnerable functions from the LibPNG project.</li> </ul> </li> <li><strong>data_C_LineVul_test.csv:</strong> <ul> <li>Reference paper: <a href="https://ieeexplore.ieee.org/document/9796256">LineVul: A Transformer-based Line-Level Vulnerability Prediction</a>, 2022.</li> <li>Data source on Hugging Face: <a href="https://huggingface.co/datasets/Partha117/LineVul_Test_Dataset">https://huggingface.co/datasets/Partha117/LineVul_Test_Dataset</a></li> <li>This dataset includes 1055 vulnerable and 17809 non-vulnerable functions.</li> </ul> </li> <li><strong>data_C_PrimeVul_test.csv:</strong> <ul> <li>Reference paper: <a href="https://arxiv.org/abs/2403.18624">Vulnerability Detection with Code Language</a><br><a href="https://arxiv.org/abs/2403.18624">Models: How Far Are We?</a> 2024.</li> <li>Data source on GitHub: <a href="https://github.com/DLVulDet/PrimeVul">https://github.com/DLVulDet/PrimeVul</a></li> <li>From the data source, the primevul_test.jsonl was used to created this dataset.</li> <li>This dataset includes 695 vulnerable and 25213 non-vulnerable functions.</li> </ul> </li> <li><strong>data_C_Choi2017_test.csv:</strong> <ul> <li>Reference paper: <a href="https://www.ijcai.org/proceedings/2017/0214.pdf">End-to-End Prediction of Buffer Overruns from Raw Source Code</a><br><a href="https://www.ijcai.org/proceedings/2017/0214.pdf">via Neural Memory Networks</a>, 2017.</li> <li>Data source on GitHub: <a href="https://github.com/mjc92/buffer_overrun_memory_networks">https://github.com/mjc92/buffer_overrun_memory_networks</a></li> <li>From GitHub, all the data in trainnig_100.txt, test_1_100.txt, test_2_100.txt,test_3_100.txt,test_4_100.txt, and corresponding _labels.txt files are combined to create this dataset.</li> <li>This dataset includes 7054 vulnerable and 6946 non-vulnerable functions.</li> </ul> </li> <li><strong>data_C_Devign_test.csv:</strong> <ul> <li>Reference paper: <a href="https://proceedings.neurips.cc/paper_files/paper/2019/file/49265d2447bc3bbfe9e76306ce40a31f-Paper.pdf">Devign: Effective Vulnerability Identification by Learning Comprehensive Program Semantics via Graph Neural Networks</a>, 2019</li> <li>Data source on Hugging Face: <a href="https://huggingface.co/datasets/claudios/code_x_glue_devign">https://huggingface.co/datasets/claudios/code_x_glue_devign</a></li> <li>From Hugging Face, all the data in train, validation, and test are combined to create this dataset.</li> <li>This dataset includes 12460 vulnerable and 14858 non-vulnerable functions.</li> </ul> </li> <li><strong>data_C_Ours_{train,test}.csv:</strong> <ul> <li>This dataset is manually collected from projects on GitHub that have registered CVEs into NVD from 2002 to 2023. The 6,766 non-vulnerable code functions are extracted from the <a href="https://dl.acm.org/doi/10.1145/3607199.3607242">DiverseVul dataset</a> to increase the code diversity. </li> <li>This training set includes 5413 vulnerable and 5413 non-vulnerable functions.</li> <li>The test set includes 1353 vulnerable and 1353 non-vulnerable functions.</li> </ul> </li> </ol>
RoHuCAD: Robots and Humans Collaborative Anomaly Detection
<h1>RoHuCAD: Robots and Humans Collaborative Anomaly Detection</h1> <p>RoHuCAD is a dataset of human-robot collaboration in a robotic workshop (check <code>workshop_layout.png</code>). Two robots (collaborative manipulator - cobot, autonomous mobile robot - AMR) assist three human operators in assembly of electronic devices.</p> <p>There are two 8-min long recordings in the dataset. They mostly follow the same scenario, with slightly different anomalies. The data is in ROS Noetic rosbag format.</p> <h2>Included data </h2> <ul> <li>RGBD camera data (color + depth) <ul> <li>3 cameras: <a href="https://www.intelrealsense.com/depth-camera-d435i/">Intel Realsense D435i</a></li> <li>color and depth data at 6 frames per second</li> <li>Intrinsic calibration data</li> <li>Extrinsic calibration data (positions and orientations)</li> </ul> </li> <li>Information about positions of robots <ul> <li>AMR: <a href="https://www.ez-wheel.com/en/development-kit-for-agv-and-amr">Ez-Wheel SWD® Starter Kit</a></li> <li>Cobot: <a href="https://www.universal-robots.com/products/ur10-robot/">Universal Robots UR10e</a></li> </ul> </li> </ul> <h2>Annotations</h2> <p>Annotations of specific anomalies are included (CSV file with columns: event_id, tstart, tend, event_type, person_id, camera_id)</p> <ul> <li>Gestures / poses <ul> <li>BENT</li> <li>T-POSE (hands horizontally to the sides)</li> <li>L+R-UP (both hands up)</li> <li>RH-UP (right hand up)</li> <li>LH-UP (left hand up)</li> <li>SQUAT</li> <li>HI-POSE (waving)</li> </ul> </li> <li>Unsafe behaviour <ul> <li>Human in robot working area</li> <li>Standing back to (moving) robot</li> <li>Looking at phone</li> <li>Human in the way of AMR</li> </ul> </li> <li>Normal activities <ul> <li>Assembling/Working</li> <li>Loading/unloading AMR</li> </ul> </li> </ul> <h2>ROS topics</h2> <ul> <li><code>/tf </code></li> <li><code>/tf_static</code></li> <li><code>/joint_states</code></li> <li>cam_ws2_box <ul> <li><code>/cam_ws2_box/color/camera_info</code></li> <li><code>/cam_ws2_box/color/image_raw/compressed</code></li> <li><code>/cam_ws2_box/depth_registered/camera_info</code></li> <li><code>/cam_ws2_box/depth_registered/image_rect_raw</code></li> </ul> </li> <li>cam_ta2_ws2 <ul> <li><code>/cam_ta2_ws2/color/camera_info</code></li> <li><code>/cam_ta2_ws2/color/image_raw/compressed</code></li> <li><code>/cam_ta2_ws2/depth_registered/camera_info</code></li> <li><code>/cam_ta2_ws2/depth_registered/image_rect_raw</code></li> </ul> </li> <li>cam_ta1_ws2 <ul> <li><code>/cam_ta1_ws2/color/camera_info</code></li> <li><code>/cam_ta1_ws2/color/image_raw/compressed</code></li> <li><code>/cam_ta1_ws2/aligned_depth_to_color/camera_info</code></li> <li><code>/cam_ta1_ws2/aligned_depth_to_color/image_raw</code></li> </ul> </li> </ul> <h2>Acknowledgement</h2> <p>The work leading to these results has received funding from the European Union’s Horizon Europe research and innovation programme within the ULTIMATE project under the Grant Agreement no 101070162.</p>
Appendix - Potential COVID-19 test fraud detection: Findings from a pilot study comparing conventional and statistical approaches
<p>The methods and results of the publication "COVID-19 test fraud detection: Findings from a pilot study comparing conventional and statistical approaches" are described in more detail in this appendix. The R-syntax for the calculation is provided, as well as a pseudo data set with which the syntax can also be tested.</p>
Dataset of "Anomaly Detection in Industrial Networks: Current State, Classification, and Key Challenges"
<p>Industrial networks are adapted to their specific requirements, especially in terms of industrial processes. To ensure sufficient security in these networks, it is necessary to set and use security policies that complement government regulations, recommendations, and relevant security standards. This paper aims to provide an in-depth analysis of the anomalies occurring within the networks and propose a structure for collecting valuable data from the experimental site based on dividing anomalies into three main categories:<br>security, operational, and service anomalies (and regular traffic recognition). We present a proof-of-concept solution/design aggregating data in industrial networks for advanced anomaly classification. Multiple data sources such as industrial communication, sensor data (additional sensors controlling device behavior), and HW status data are used as data sources. A total of three scenarios (using a physical testbed) were implemented, where we achieved an accuracy of 0.8540/0.9972 in advanced anomaly classification.</p>
A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians: Supplemental Files
<p><strong>Supplementary Fig. S1</strong>: θ<sub>evo</sub> calculated for each analyzed edge for specific OXPHOS complexes. Analyses were performed as in fig. 1F, except that SPCSs calculated from mtDNA-encoded protein positions in Complex I, Complex III, Complex IV, or Complex V were used to generate θevo values.</p> <p><strong>Supplementary Fig. S2</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 2A, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p><strong>Supplementary Fig. S3</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median confidence intervals). Analysis was performed as in (<em>A</em>) fig. 2B or (<em>B</em>) fig. 2C, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S4</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 3A, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V subunits.</p> <p><strong>Supplementary Fig. S5</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by lower 90% median confidence limit). Analysis was performed as in fig. 3B, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S6</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by upper 90% median confidence limit). Analysis was performed as in fig. 3C, except that θ<sub>evo</sub> values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p>---</p> <p><strong>Supplementary File 1</strong>: All predicted protein substitutions along all edges at positions containing less than 2% gaps across input and ancestral sequences are listed, along with associated taxonomy information, TSS, and branch length. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 2</strong>: The TSS calculated for each mitochondrial protein alignment position. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 3</strong>: SPCS and θevo outputs are provided for analyses across all mitochondria-encoded positions, as well as for focused analyses of specific OXPHOS complexes and individual proteins.</p> <p><strong>Supplementary File 4</strong>: A GenBank flat file containing RefSeq entries for mammalian mtDNAs, as well as the entry for the reptile Anolis punctatus.</p> <p><strong>Supplementary File 5</strong>: A maximum likelihood inferred tree generated by a RAxML-NG analysis of concatenated and aligned protein coding sequences from mammalian and Anolis punctatusmtDNAs.</p> <p><strong>Supplementary File 6</strong>: Bootstrap replicates were generated from the alignment of concatenated protein coding sequences. Felsenstein’s Bootstrap Proportions (Felsenstein 1985) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 7</strong>: Bootstrap replicates were generated using concatenated mammalian mtDNA coding sequences. Transfer Bootstrap Expectations (Lemoine 2018) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 8</strong>: PAGAN tree output produced using aligned amino acid sequences and the rooted maximum likelihood inferred tree as input.</p>
SQLite database to accompany the paper, "Statistical learning mitigation of false positives from template-detected data in automated acoustic wildlife monitoring"
<p>This dataset is a SQLite database that accompanies methods and analysis described in the paper, "Statistical learning mitigation of false positives from template-detected data in automated acoustic wildlife monitoring" (Balantic & Donovan 2019, Bioacoustics, https://www.tandfonline.com/doi/full/10.1080/09524622.2019.1605309). </p> <p>A Github repository containing code for using the SQLite database also accompanies this paper at: <a href="https://github.com/cbalantic/false-positive-mitigation">http://github.com/cbalantic/false-positive-mitigation</a></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.