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Fig. 1 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 1. Marking scheme for individual identification of Ohlone tiger beetle adults used during the capturerecapture and frequency of capture studies. Some variation in the maculations exists. Numbers on the elytra represent the positions for marking each beetle with a unique identification number. Marks applied to single or multiple locations uniquely identify each marked beetle. For example, beetle #1 would have a mark at the #1 position, beetle #12 would have marks at the #2 and #10 locations, and beetle #147 would have marks at the #7, #40, and #100 locations.
Fig. 4 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 4. Population curves for adult Ohlone tiger beetle generations at Glenwood, Santa Cruz Co., CA. a) Triangular model in 2016, b) Multi-peak model in 2017.
Fig. 3 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 3. Frequency of observed dispersal distances (m) by Ohlone tiger beetle males (bars with vertical lines) and females (bars with horizontal lines).
Fig. 2 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 2. Recapture decay plot of observed Ohlone tiger beetle adult lifespans (i.e., residence) and fitted trend line
Fig. 6 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 6. Inverse correlation between annual (July 1 – June 30) rainfall amounts (cm) and estimated Ohlone tiger beetle (OTB) adult generation population sizes for Moore Creek, Santa Cruz Co., CA.
Fig. 5. Annual Ohlone tiger beetle adult generation population estimates from 2000 through 2017 in Biology and Conservation of Cicindela ohlone Freitag and Kavanaugh (Coleoptera: Carabidae: Cicindelinae), the Endangered Ohlone Tiger Beetle. II. Population Ecology of Adults and Larvae and Recommended Monitoring Methods
Fig. 5. Annual Ohlone tiger beetle adult generation population estimates from 2000 through 2017 at four study sites near Santa Cruz, CA. Horizontal line represents the average generation size of all annual estimates for each site.
Data from: Monitoring soil moisture at the catchment scale – A novel approach combining antecedent precipitation index and radar-derived rainfall data
<p>Knowledge about soil moisture is important for event-based rainfall-runoff models but monitoring conditions at the catchment scale is not a trivial task. Soil moisture is highly variable in space and time, particularly in dry climates with seasonal and spatially heterogeneous rainfall. Point measurements are difficult to upscale, and remotely sensed (RS) data often lack in spatial or temporal resolution for local or regional studies. Longer latency periods – the time required before data becomes available – of some RS data make them less applicable to time-sensitive analyses such as flash flood forecasting. This study evaluated a novel approach for estimating catchment-scale volumetric soil moisture using an antecedent precipitation index (API) -based model. The model was trained and tested using in-situ soil moisture measurements collected during a 3-month field sampling campaign in a 142 km<sup>2</sup><span><span><span><span><span><span><span><span><span> study area in central New Mexico. The calibrated model was applied at the catchment scale to produce soil moisture grids from radar-derived rainfall estimates. Model performance, resolution and latency were compared to satellite-based soil moisture estimates. Benefits of the proposed new method include high spatial resolution (1 × 1 km or less depending on the precipitation data source) and high prediction accuracy (root mean square errors 0.014–0.018 m</span></span></span></span></span></span></span></span></span><sup>3</sup><span><span><span><span><span><span><span><span><span>/m</span></span></span></span></span></span></span></span></span><sup>3</sup><span><span><span><span><span><span><span><span><span>). Given the short latency period for radar-derived rainfall data, the method has potential for use in operational flood risk assessment and forecasting.</span></span></span></span></span></span></span></span></span></p>
Matrix aggregation of species of Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata registered of the Caribbean Sea and Gulf of Mexico region by Ocean Biodiversity Information Systems of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p>This database consists of an aggregation matrix of species from Ocean Biodiversity Information Systems using as geographic filters the Caribbean Sea region (ID 34287) and the Gulf of Mexico region (ID 34287) nomenclature and hierarchical classification of each Phyla from World Register of Marine Species used for the calculation of average taxonomic distinction of species belonging to the Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata associated to Autonomous Reefs Monitoring Structures from the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”</p> <p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>BIS Ocean Biodiversity Information System. Available online: <a href="http://www.iobis.org/">www.iobis.org</a>.</p> <p>Horton, T.; Gofas, S.; Kroh, A.; Poore, G.C.B.; Read, G.; Rosenberg, G.; Stöhr, S.; Bailly, N.; Boury-Esnault, N.; Brandão, S.N.; et al. Improving nomenclatural consistency: A decade of experience in the World Register of Marine Species. <em>Eur. J. Taxon.</em> <strong>2017</strong>, <em>2017</em>, doi:10.5852/ejt.2017.389.</p> <p><span lang="EN-US">was produced in collaboration with the Biodiversidad Marina de Yucatán project. </span><a href="https://www.bdmy.org.mx/carteles-publicaciones/" target="_blank" rel="noopener">https://www.bdmy.org.mx/,</a> Universidad Nacional Autonoma de México and Escuela Nacional de Estudios Superiores</p>
Database of Incidence per reef and región of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>This database contains information of specimens of the cryptofauna assemblages identified by experts of each Phyla per reef and región and is a complementary material of the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”. For the present research, animals of the appropriate species and quality were selected and the minimum number required to obtain scientifically valid results were considered, all animals were anesthetized and deposited in National Collections: Colección Regional de Crustáceos de la Península de Yucatán (SEMARNAT number: YUC-CC-255-11), Colección Regional de Moluscos de la Península de Yucatán (SEMARNAT number: YUC. -INV-240-01-11), Colección Regional de Equinodermos de la Península de Yucatán (SEMARNAT number: DGVS-CC-307-18), Colección Regional de Ascidias de la Península de Yucatán (SEMARNAT number: DGVS-CC-306-18), Colección Regional de Briozoos de la Península de Yucatán (SEMARNAT number: DGVS-CC-308-18), Colección Regional de Cnidarios de la Península de Yucatán (SEMARMAT number: YUC-CC-254-11), Colección Regional de Policládidos de la Península de Yucatán (105 Collection CONABIO) and Colección Nacional del Phyla Porifera “Gerardo Green” of Universidad Nacional Autónoma de México, Facultad de Ciencias, Sisal, Mexico (UMDI-Sisal) and within accordance with scientific collection permits: PPF/DGOPA: 295/17, 300/17, 294/17, 293/17, PPF/DGOPA-076/19 issued by Mexico’s State Secretaria de Agricultura, Ganaderia, Desarrollo Rural, Pesca y Alimentación (SAGARPA).</p> <p><strong>CC-BY-NC-N</strong></p>
Quantitatively Monitoring the Resilience of Patterned Vegetation in the Sahel
Processed monthly Sentinel-2 image data for 42 patterned vegetation sites across the Sahel. Data includes RGB images, greyscale NDVI images and binary BWNDVI sub-images. These sub-images contain black pixels for vegetation and white pixels for soil, with 289 sub-images corresponding to a single image. Sentinel images are provided by Copernicus and accessed via Google Earth Engine.
City scale particulate matter monitoring using LoRaWAN based air quality IoT devices
<p>Air Quality (AQ) is a very topical issue for many cities and has a direct impact on citizen health. The AQ of a large UK city is being investigated using low-cost Particulate Matter (PM) sensors, and the results obtained by these sensors have been compared with government operated AQ stations. In the first pilot deployment six AQ Internet of Things (IoT) devices have been designed and built, each with four different low-cost PM sensors, and they have been deployed at two locations within the city. These devices are equipped with LoRaWAN wireless network transceivers to test city scale Low-Power Wide Area Network (LPWAN) coverage. The study concludes that i) the physical device developed can operate at a city scale ii) some low-cost PM sensors are viable for monitoring AQ and for detecting PM trends iii) LoRaWAN is suitable for city scale sensor coverage where connectivity is an issue. Based on the findings from this first pilot project a larger LoRaWAN enabled AQ sensor network is being deployed across the city of Southampton in the UK.</p>
Tropical Forest Monitoring: Challenges and Recent Progress in Research
<p>Data accompanying: </p> <p><em>Remote Sens.</em> <strong>2021</strong>, <em>13</em>(12), 2252; <a href="https://doi.org/10.3390/rs13122252">https://doi.org/10.3390/rs13122252</a></p>
Monitoring small mammal abundance using NEON data: Are calibrated indices useful?
<p>Small mammals are important to the functioning of ecological communities with changes to their abundances used to track impacts of environmental change. While capture-recapture estimates of absolute abundance are preferred, indices of abundance continue to be used in cases of limited sampling, rare species with little data, or unmarked individuals. Improvement to indices can be achieved by calibrating them to absolute abundance but their reliability across years, sites, or species is unclear. To evaluate this, we used the US National Ecological Observatory Network (NEON) capture-recapture data for 63 small mammal species over 46 sites from 2013–2019. We generated 17,155 absolute abundance estimates using capture-recapture analyses and compared these to two standard abundance indices, and three types of calibrated indices. We found that neither raw abundance indices nor index calibrations were reliable approximations of absolute abundance, with raw indices less correlated with absolute abundance than index calibrations (raw indices overall R<sup>2</sup> < 0.5, index calibration overall R<sup>2</sup> > 0.6). Performance of indices and index calibrations varied by species, with those having higher and less variable capture probabilities performing best. We conclude that indices and index calibration methods should be used with caution with a count of individuals being the best index to use, especially if it can be calibrated with capture probability. None of the indices we tested should be used for comparing different species due to high variation in capture probabilities. Hierarchical models that allow for sharing of capture probabilities over species or plots (i.e., joint likelihood models) may offer a better solution to mitigate the cost and effort of large-scale small mammal sampling while still providing robust estimates of abundance.</p>
Ultrahigh-responsivity waveguide-coupled optical power monitor for Si photonic circuits operating at near-infrared wavelengths
<p>The simulation code and script of Lumerical for the Simulation in the Supplementary figures: Fig. S4 and Fig. S5.</p>
#DeOlhoNosCorais: a polygonal annotated dataset to optimize coral monitoring
<p>The first version of the #DeOlhoNosCorais dataset was built in collaboration with the Laboratory of Marine Ecology (LECOM) at the Federal University of Rio Grande do Norte (UFRN). The dataset contains images extracted from social networks with the hashtag “#DeOlhoNosCorais” and images provided by the LECOM. It contains 1411 images and 21 classes. Each image has two labels, its major class and the segmentation map. The labeling was performed by the LECOM researchers using the Labelme tool. The duplicate images were removed using the FiftyOne tool. </p> <p>One of the objectives of the dataset is to measure the viability to use machine learning to speed up the processing of analyses of the images extracted from the Instagram. So, the extra images taken by divers from the researcher group were used to augmented the train set. The Instagram images were divided into train, validation, and test accordingly to their date. The rules for the division was:</p> <ul> <li>Train set: images dated until 12/31/2019 + extra images from LECOM-UFRN</li> <li>Validation set: images dated between 01/01/2019 to 06/30/2019</li> <li>Test set: images dated between 07/01/2019 to 08/24/2021</li> </ul> <p>The test set includes an interval of 2 years, due to the drop in the number of posts during the Covid-19 pandemic.The full dataset folder contains the raw labeling using the Labelme. The experiments folder contains treated datasets for the following tasks:</p> <ul> <li>Full images classification</li> <li>Sub images classification</li> <li>Binary semantic segmentation</li> <li>Binary object detection</li> </ul> <p>In addition, the experiments folder has an extra data from the Pacific Labeled Corals (PLC). The extra data contains 12 classes of the 20 present in the PLC, and the images patches were extracted centered in the labeled pixels with size of 224 x 224.</p>
Dataset for puplication: Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing 1H-1H TOCSY NMR
<p>Data set used in the publication: <strong>Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing <sup>1</sup>H-<sup>1</sup>H TOCSY NMR. </strong></p> <p>Abstract: In this work, the dynamic evolution of adipose tissue-derived human MSCs (AT-derived hMSCs) after fourteen days of cultivation, adiobocytes and osteocytes differentiation has been inspected based on 2D NMR TOCSY using machine learning techniques. Multi-class classification in addition to novelty detection of metabolites was established based on the profile of a control hMSCs sample at four days cultivation and successively detect the absence and the abundance of metabolites in differentiated MSCs following a set of <sup>1</sup>H-<sup>1</sup>H TOCSY profiles. The uploaded files are:</p> <p>File: metabolites_names.xlsx contain the names of the used metabolites.</p> <p>File: metabolites.xlsx</p> <p> column 1: metabolite abbreviation</p> <p>column 2: 2D NMR TOCSY horizontal and vertical frequencies of metabolites in the control group at 4 days cultivation (Ct d4)</p> <p>column 3: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of cultivation (Ct d14)</p> <p>column 4: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of differentiation into adipocytes (AT d14)</p> <p>column 5: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after14 days of differentiation into osteocytes (OS d14)</p> <p>column 6: 2D NMR TOCSY horizontal and vertical standard frequencies of all metabolites measured at broadband high resolution 600.13 MHz NMR</p>
Long-term snow chemical composition monitoring - Ariebreen glacier (Hornsund) - raw data
<p>Since 2020, snow samples have been taken from the Ariebreen glacier several times a season during the accumulation season. The snow samples are collected in polyethylene sterile bags and transported to the Polish Polar Station Hornsund. After melting at room temperature, they are analysed in the chemical laboratory of the Polish Polar Station for pH, conductivity and chemical composition (major ions).<br> <br> Site Information Ariebreen - 0.5 km long glacier between Skoddefjellet and the northern part of Ariekammen, southernmost in Wedel Jarlsberg Land.</p> <p>Presented data from 2020 to 2022</p> <p>The data has not been checked, which means that it is raw data.</p> <p>Principal investigator (PI) Adam Nawrot</p>
Development and validation of an eDNA protocol for monitoring endemic Asian Spiny Frogs in the Himalayan region of Pakistan
<p>Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (<em>Allopaa hazarensis</em>) and Murree Hills Frog (<em>Nanorana vicina</em>). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both <em>A. hazarensis</em> and <em>N. vicina</em> than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for <em>A. hazarensis</em>. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.</p>
Figure 1 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit
Figure 1. Botujuru Private Natural Heritage Preserve location and the respective collecting sites.
Experimental and Computational Dataset for ""Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide hybridization onto gaps and overhangs"
<p>Binding of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. The templates in these reactions often contain adjacent duplex segments that stabilize base pair formation to single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to the<br> experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide<br> hybridization using steady-state and temperature-jump infrared spectroscopy. Thermodynamic results indicate that duplex segments adjacent to overhangs and gaps stabilize dinucleotide binding<br> through a combination of coaxial stacking interactions and additional factors that remain unclear. All-atom molecular dynamics simulations indicate potential structural differences between the<br> dinucleotide-gap complexes and canonical duplexes that may contribute to binding stability. We demonstrate time-resolved measurements of dinucleotide dehybridization and observe timescales ranging from 200 ns to 40 µs depending on the template and temperature. Together, our work provides an initial step for predicting the binding stability and kinetics of short DNA and RNA duplex segments onto various type of nucleic acid templates</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.