Find research datasets worth reusing

Data from: Forecasting landslides using community detection on geophysical satellite data

As a result of extreme weather conditions, such as heavy precipitation, natural hillslopes can fail dramatically; these slope failures can occur on a dry day due to time lags between rainfall and pore-water pressure change at depth, or even after days to years of slow-motion. While the pre-failure deformation is sometimes apparent in retrospect, it remains challenging to predict the sudden transition from gradual deformation (creep) to runaway failure. We use a network science method–multilayer modularity optimization–to investigate the spatiotemporal patterns of deformation in a region near the 2017 Mud Creek, California landslide. We transform satellite radar data from the study site into a spatially-embedded network in which the nodes are patches of ground and the edges connect the nearest neighbors, with a series of layers representing consecutive transits of the satellite. Each edge is weighted by the product of the local slope (susceptibility to failure) measured from a digital elevation model and ground surface deformation (current rheological state) from interferometric synthetic aperture radar (InSAR). We use multilayer modularity optimization to identify strongly-connected clusters of nodes (communities) and are able to identify both the location of Mud Creek and nearby creeping landslides which have not yet failed. We develop a metric, community persistence, to quantify patterns of ground deformation leading up to failure, and find that this metric increases from a baseline value in the weeks leading up to Mud Creek's failure. These methods promise as a technique for highlighting regions at risk of catastrophic failure.

openother-pdJun 2022View details →

Datasets used for the performance evaluation of kataegis detection tools

These two datasets (.csv files) were used for the performance evaluation of katdetectr and other publicly available kataegis detection tools (link to paper, not yet published). The synthetic data was generated using the generateSyntheticData function from the katdetectr package (https://github.com/ErasmusMC-CCBC/katdetectr). Additionally we provide all files and RData objects needed for running the scripts for the performance evaluation which can be found on GitHub at: https://github.com/ErasmusMC-CCBC/evaluation_katdetectr. We present this dataset under the Public Domain Dedication (CC0) waiver.

Supplementary materials for: Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange

Vitamin B1 (thiamin) is a vital nutrient for most cells in nature including marine plankton. Early and recent experiments show that B1 degradation products instead of B1 can support the growth of marine bacterioplankton and phytoplankton. However, the use and occurrence of some degradation products remain uninvestigated – namely N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP) – which has been a focus of plant oxidative stress research. We investigated the relevance of FAMP in the ocean. Experiments and global ocean meta-omic data indicate that eukaryotic phytoplankton, including picoeukaryotes and harmful algal bloom species, use FAMP while bacterioplankton appear more likely to use deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP). Measurements of FAMP in seawater and biomass revealed that it occurs at picomolar concentrations in the surface ocean, heterotrophic bacterial cultures produce FAMP in the dark – indicating non-photodegradation of B1 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton produce intracellular FAMP. Our results require an expansion of thinking about vitamin degradation in the sea, but also the marine B1 cycle – where it is now crucial to consider a new B1-related compound pool (FAMP) – as well as generation (dark degradation – likely via oxidation), turnover (plankton uptake), and exchange of the compound within networks of plankton.

opencc-by-4.0Jun 2023View details →

Reproducibility Report for the paper "Vibration signal-assisted endpoint detection for long-stretch, ultraprecision polishing processes"

This reproducibility report includes the datasets and computer code used for reproducing the results in the paper, Jin, Bukkapatnam, Hayes, and Ding, 2023, “Vibration signal-assisted endpoint detection for long-stretch, ultraprecision polishing processes,” ASME Transactions, Journal of Manufacturing Science and Engineering, Vol.145, pp. 061007.

Accuracy of biomicroscopy, ultrasonography and spectral-domain OCT in detection of complete posterior vitreous detachment

Purpose: To evaluate the accuracy of pre-operative biomicroscopy (BM), ultrasonography (US), and spectral domain optical coherence tomography (SD-OCT) for determining complete posterior vitreous detachment (PVD) confirmed by intraoperative findings of triamcinolone acetonide-assisted pars plana vitrectomy (PPV). Design: This was a prospective, consecutive, interventional case series. Methods: The study included all patients admitted for surgical treatment of epiretinal membrane (ERM) and macular hole (MH). Presence of complete PVD was determined one day before PPV using BM, US, and SD-OCT. Preoperative findings were compared to PVD status determined during PPV. Results: A total of 123 eyes of 123 patients were included in the study. Indications for PPV included ER in 57 (46.34%), full thickness macular hole in 57 (46.34%), and lamelar macular hole in 9 (7.32%) patients. Complete PVD during PPV was observed in 18 (31.58%; 95% CI:18.72–49.91) patients with ERM and 13 (19.7%; 95% CI: 10.49–33.68) patients with MH. Vitreoschisis was present in 30 (24.39%; 95% CI: 15.46–34.82) patients during PPV. The sensitivity of preoperative BM, US, SD-OCT was 48.4% (95% CI: 30.2–66.9), 61.3% (95%CI: 42.2–78.2) and 54.8% (95% CI: 36.0–72.7) respectively. The specificity of preoperative BM, US, SD-OCT was 81.5% (95% CI: 72.1–88.9), 90.2% (95% CI: 82.2–95.4) and 85.9% (95% CI: 77.0–92.3) respectively. With a prevalence of 25.2% of PVD in our sample the positive predictive value of preoperative BM, US, SD-OCT was 46.9% (95% CI: 29.1–65.3), 67.9% (95% CI: 47.6–84.1) and 56.7% (37.4–74.5) respectively. Conclusion: Preoperative BM, US, and SD-OCT are associated with poor sensitivity and a rather good specificity for detecting complete PVD. There is relatively a high percentage of patients with vitreoschisis undergoing vitreoretinal surgery, therefore vitreoretinal surgeons should consider routine usage of triamcinolone in all vitreoretinal cases.

Multi‐species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds

Aquatic environmental DNA is increasingly used for biodiversity monitoring, such as surveying threatened and invasive species. Mainstreaming these methods in practical applications, however, still requires significant standardisation and optimisation, namely regarding DNA capture methods. Here we evaluated how filter type (standard disc filters vs high-capacity capsules), number of sampling sites, volume of water filtered and environmental factors affected amphibian detection in Mediterranean temporary ponds. The study involved water filtering until clogging at one (capsules) and five (discs) sites from 16 small and shallow ponds, where three urodele and seven anuran species were recorded through sweep-netting and adult observations. Detection probabilities were estimated from site occupancy models based on replicate sampling and from an adaptation of time-to-detection models relating detection probability to volume of water filtered. Discs filtered relatively small volumes (15–1250 mL), with detection probabilities of the two abundant species (Pelobates cultripes, Hyla meridionalis) increasing rapidly with sample size and water volume, reaching almost perfect detection (0.95) at four and seven discs, and 420 mL and 1860 mL, respectively. However, reaching high detection probabilities for rare species (Pelodytes atlanticus, Pleurodeles waltl, Triturus pygmaeus) would require larger sampling effort than that used in our study. Despite filtering much larger volumes (600–5300 mL), filtering with capsules at a single site per pond provided lower detection probabilities for abundant species than filtering with discs at five sites. Rarer species showed no difference between methods, which may be due to small sample sizes and reduced statistical power for species with few detection. The effect of conductivity on species detectability was largely negative, while the influence of water clarity varied across species, and pH had no effects. Overall, our results suggest that eDNA amphibian surveys in Mediterranean temporary ponds need to consider filter clogging, heterogeneous DNA distribution, and highly conductive waters.

Log-based anomaly detection datasets

Dataset for the ICSE'22 paper: Log-based Anomaly Detection with Deep Learning: How Far Are We? If you find the data useful for your research, please cite the following paper: <pre>@inproceedings{le2022log, title={Log-based anomaly detection with deep learning: How far are we?}, author={Le, Van-Hoang and Zhang, Hongyu}, booktitle={Proceedings of the 44th international conference on software engineering}, pages={1356--1367}, year={2022} }</pre>

Deep Learning for Detecting Verticilium Fungus in Olive Trees Using YOLO in UAV Imagery Dataset

Dataset used in the paper entitled "Deep Learning for Detecting Verticillium Fungus in Olive Trees: Using YOLO in UAV Imagery". Contains UAV RGB images of three olive fields located in Greece.

Reduced Graphene Oxide Electrolyte-Gated Transistor Immunosensor with Highly Selective Multiparametric Detection of Anti-Drug Antibodies

Dataset for the publication:  Sensi, M., de Oliveira, R. F., Berto, M., Palmieri, M., Ruini, E., Livio, P. A., Conti, A., Pinti, M., Salvarani, C., Cossarizza, A., Cabot, J. M., Ricart, J., Casalini, S., González-García, M. B., Fanjul-Bolado, P., Bortolotti, C. A., Samorì, P., Biscarini, F., Reduced Graphene Oxide Electrolyte-Gated Transistor Immunosensor with Highly Selective Multiparametric Detection of Anti-Drug Antibodies. Adv. Mater. 2023, 2211352. <a href="https://doi.org/10.1002/adma.202211352">https://doi.org/10.1002/adma.202211352</a> Transfer curves measured with different analytes (used for Figure 3 in the results and discussion section of the publication). In every file are reported the gate-source voltages (VGS) and the average drain-source currents (IDS) after exposure of the gate to ATI (Transfer_ATI-dataset), ATI+TNFa(Transfer_ATI+TNFa-dataset), TNFa(Transfer_TNFa-dataset) at specific concentration. Transfer_control is the dataset for the control experiments, without the probe on gate. EIS (EIS-functionalization-dataset) dataset has been used for the functionalization in figure 2b. In the the file are reported the frequency, the real and the imaginary impedance for each functionalization step (in specific tabs Au, SAM, IFX+ETA). Transfer (Transfer-functionalization-dataset) dataset used for the functionalization in figure 2c. In the the file are reported the VGS and the IDS for each functionalization step (in specific tabs Au, SAM, IFX+ETA).

opencc-zeroJul 2023View details →

Data from: Remotely sensed environmental measurements detect decoupled processes driving population dynamics at contrasting scales

The increasing availability of satellite imagery has supported a rapid expansion in forward-looking studies seeking to track and predict how climate change will influence wild population dynamics. However, these data can also be used in retrospect to provide additional context for historical data in the absence of contemporaneous environmental measurements. We used 167 Landsat-5 Thematic Mapper (TM) images spanning 13 years to identify environmental drivers of fitness and population size in a well-characterized population of banner-tailed kangaroo rats (Dipodomys spectabilis) in the southwestern United States. We found evidence of two decoupled processes that may be driving population dynamics in opposing directions over distinct time frames. Specifically, increasing mean surface temperature corresponded to increased individual fitness, where fitness is defined as the number of offspring produced by a single individual. This result contrasts with our findings for population size, where increasing surface temperature led to decreased numbers of active mounds. These relationships between surface temperature and (i) individual fitness and (ii) population size would not have been identified in the absence of remotely sensed data, indicating that such information can be used to test existing hypotheses and generate new ecological predictions regarding fitness at multiple spatial scales and degrees of sampling effort. To our knowledge, this study is the first to directly link remotely sensed environmental data to individual fitness in a nearly exhaustively sampled population, opening a new avenue for incorporating remote sensing data into eco-evolutionary studies.

Embedded machine learning to promote detection of unsafe environments

Datasets used to train and validate the devices and model described in the paper "Embedded machine learning of IoT streams to promote early detection of unsafe environments"

opencc-zeroJul 2023View details →

Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR

Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of Sabella spallanzanii and Bugula neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing in-situ nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and rapid management response to biosecurity threats.

data from Robust multisensory deviance detection in the mouse parietal associative area

This is all the data analysed in the paper "Robust multisensory deviance detection in the mouse parietal associative area." It goes along with the code in https://zenodo.org/record/8189912

opencc-by-4.0Jan 2023View details →

Identifying persistent, mobile and toxic (PMT) organic compounds detected in shale gas wastewater.

Supporting Information (open data) for Identifying persistent, mobile and toxic (PMT) organic compounds detected in shale gas wastewater.

opencc-by-4.0Dec 2019View details →

Figure 1 in Recovery of Sweetpotato Vine Borer, Omphisa anastomosalis (Lepidoptera: Crambidae), in Sweetpotato Fields in Hawaii Through Field Collections and Detection Trapping

Figure 1. Adult female sweetpotato vine borer, Omphisa anastomosalis (Lepidoptera: Crambidae).

opencc-by-4.0Dec 2019View details →

Figure 5. Sweetpotato vine borer shown pupating within a in Recovery of Sweetpotato Vine Borer, Omphisa anastomosalis (Lepidoptera: Crambidae), in Sweetpotato Fields in Hawaii Through Field Collections and Detection Trapping

Figure 5. Sweetpotato vine borer shown pupating within a section of sweetpotato root.

opencc-zeroAug 2023View details →

Detecting regenerating limbs in Hemigrapsus sanguineus based on limb mass

<ol> <li>Regeneration of lost appendages is a gradual process in many species, spreading energetic costs of regeneration through time. Energy allocated to regeneration of lost appendages cannot be used for other purposes and therefore commonly elicits energetic trade-offs in biological processes. </li> <li>We used limb loss in the Asian shore crab Hemigrapsus sanguineus to compare the strength of energetic trade-offs resulting from historic limb losses that have been partially regenerated versus current injuries that have not yet been repaired. Consistent with previous studies, we show that limb loss and regeneration results in trade-offs that reduce reproduction, energy storage, and growth. </li> <li>As may be expected, we show that trade-offs in these metrics from historic limb losses far outweigh trade-offs from current limb losses, and correlate directly with the degree of historic limb loss that has been regenerated. </li> <li>As regenerating limbs get closer to their normal size, these historical injuries get harder to detect, despite the continued allocation of additional resources to limb development. Our results demonstrate the importance of a method for identifying historic appendage losses and of quantifying the amount of regeneration that has already occurred, as opposed to assessing only current injury, to accurately assess the strength of energetic trade-offs in animals recovering from non-lethal injury.</li> </ol>

opencc-by-4.0Aug 2023View details →

Machine Learning Integrated High Quantum Yield Blue Light Carbon Dots for Real-time and On-site Detection of Cr(VI) in Groundwater and Drinking Water

RGB和Kmeans提取后含有Cr(VI)水样的图像数据

opencc-by-4.0Aug 2023View details →

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures"

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures" paper published in doi:10.1038/s41565-023-01489-x