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958 results for “Data quality”
Long-term water quality monitoring data of Shenzhen Bay
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Water quality data and isotope data of groundwater, river water and seawater in the Pearl River Estuary
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Data from: Manipulation of light spectral quality disrupts host location and attachment by parasitic plants in the genus Cuscuta
Parasitic plants in the genus Cuscuta (dodders) make their living by extracting resources from other plants. While relatively few dodder species are agricultural pests, those that are can be challenging to control, in part due to their intimate physical and physiological association with host plants. Consequently, dodders remain pervasive and economically damaging pests in a variety of crop systems. The development of improved management strategies would be facilitated by greater understanding of the ecological and environmental factors that influence the establishment and perpetuation of dodder infestations. Light cues play an important role in dodder host location and attachment. To better understand the influence of light conditions on parasite ecology, and potential implications for management, we examined how manipulating the ratio of red to far-red wavelengths (R:FR), via both passive filtering of natural sunlight and active spectral manipulation using LEDs, affects host location and host attachment by two dodder species (C. campestris on tomato hosts and C. gronovii on jewelweed). For both host-parasite combinations, host location and subsequent attachment by dodder parasites was dramatically reduced in high R:FR environments compared to control conditions (with R:FR characteristic of sunlight) and low R:FR conditions. Circumnutation by dodder seedlings was also significantly faster under high R:FR. We observed short-term effects of high R:FR on the height and dry mass of tomato host plants (immediately following 7-day exposure), as well as changes in tomato volatile emissions. However, preliminary investigation of long-term effects on host plants suggests that short-term exposure to high R:FR (i.e. during the critical period when dodder seedlings emerge and attach to hosts) has little or no effect on host plant size or fruit yield at the time of harvest. Synthesis and applications. Our findings suggest that spectral manipulation during the early stages of crop plant growth (e.g. via light-filtering row covers), may have significant potential to augment existing methods for managing or preventing dodder infestations in agricultural crops. We discuss potential obstacles to the realization of its potential, as well as next steps toward the development and optimization of spectral manipulation methods for use in agroecosystems.
Data from: Spatiotemporal rank filtering improves image quality compared to frame averaging in 2-photon laser scanning microscopy
Live imaging of biological specimens using optical microscopy is limited by tradeoffs between spatial and temporal resolution, depth into intact samples, and phototoxicity. Two-photon laser scanning microscopy (2P-LSM), the gold standard for imaging turbid samples in vivo, has conventionally constructed images with sufficient signal-to-noise ratio (SNR) generated by sequential raster scans of the focal plane and temporal integration of the collected signals. Here, we describe spatiotemporal rank filtering, a nonlinear alternative to temporal integration, which makes more efficient use of collected photons by selectively reducing noise in 2P-LSM images during acquisition. This results in much higher SNR while preserving image edges and fine details. Practically, this allows for at least a four fold decrease in collection times, a substantial improvement for time-course imaging in biological systems.
Data from: Environmental change mediates mate choice for an extended phenotype, but not for mate quality
Sexual cues, including extended phenotypes, are expected to be reliable indicators of male genetic quality and/or provide information on parental quality. However, the reliability of these cues may be dependent on stability of the environment, with heterogeneity affecting how selection acts on such traits. Here we test how environmental change mediates mate choice for multiple sexual traits, including an extended phenotype – the structure of male-built nests – in stickleback fish. First, we manipulated the dissolved oxygen (DO) content of water to create high or low DO environments in which male fish built nests. Then we recorded the mate choice of females encountering these males (and their nests), under either the same or reversed DO conditions. Males in high DO environments built more compact nests than those in low DO conditions and males adjusted their nest structure in response to changing conditions. Female mate choice for extended phenotype (male nests) was environmentally-dependent (females chose more compact nests in high DO conditions), while female choice for male phenotype was not (females chose large, vigorous males regardless of DO level). Examining mate choice in this dynamic context suggests that females evaluate the reliability of multiple sexual cues, taking into account environmental heterogeneity.
Data from: Resource quality affects weapon and testis size and the ability of these traits to respond to selection in the leaf-footed cactus bug, Narnia femorata
The size of weapons and testes can be central to male reproductive success. Yet, the expression of these traits is often extremely variable. Studies are needed that take a more complete organism perspective, investigating the sources of variation in both traits simultaneously and using developmental conditions that mimic those in nature. In this study, we investigated the components of variation in weapon and testis sizes using the leaf-footed cactus bug, Narnia femorata (Hemiptera: Coreidae) on three natural developmental diets. We show that the developmental diet has profound effects on both weapon and testis expression and scaling. Intriguingly, males in the medium-quality diet express large weapons but have relatively tiny testes, suggesting complex allocation decisions. We also find that heritability, evolvability, and additive genetic variation are highest in the high-quality diet for testis and body mass. This result suggests that these traits may have an enhanced ability to respond to selection during a small window of time each year when this diet is available. Taken together, these results illustrate that normal, seasonal fluctuations in the nutritional environment may play a large role in the expression of sexually selected traits and the ability of these traits to respond to selection.
Data from: Masculinisation of gene expression is associated with male quality in Drosophila melanogaster
The signature of sexual selection has been revealed through the study of differences in patterns of genome-wide gene expression, both between the sexes and between alternative reproductive morphs within a single sex. What remains unclear, however, is whether differences in gene expression patterns between individuals of a given sex consistently map to variation in individual quality. Such a pattern, particularly if found in males, would provide unambiguous evidence that the phenotypic response to sexual selection is shaped through sex-specific alterations to the transcriptome. To redress this knowledge gap, we explored whether patterns of sex-biased gene expression are associated with variation in male reproductive quality in Drosophila melanogaster. We measured two male reproductive phenotypes, and their association with sex-biased gene expression, across a selection of inbred lines from the Drosophila Genetic Reference Panel. Genotypes with higher expression of male-biased genes produced males exhibiting shorter latencies to copulation, and higher capacity to inseminate females. Conversely, female-biased genes tended to show negative associations with these male reproductive traits across genotypes. We uncovered similar patterns, by reanalysing a published dataset from a second D. melanogaster population. Our results reveal the footprint of sexual selection in masculinising the male transcriptome.
Data from: Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat (Capra hircus)
The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat (Capra hircus). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.
Data from: Taxon-level assessment of the data collection quality in Atlas Florae Europaeae: insights from the case of Rosa (Rosaceae) in Eastern Europe
<p>By the method of data re-collection and re-assessment, we tested the completeness of distribution areas of the species and species aggregates of <i>Rosa</i> in Eastern Europe as mapped in volume 13 of <i>Atlas Florae Europaeae</i>, and discussed insights into the issues connected with the data. We have found many new occurrences which are additions to the published maps: 1068 records of species and 570 records of species aggregates. The new occurrences are listed with references to the sources, and the updated AFE maps are provided. The greatest increase by new native occurrences was revealed for the species that are widespread or taxonomically complicated, and by new alien occurrences for the species that expand their secondary distribution areas. The mapping work published in 2004 is considered good, with minor omissions caused by possible oversights and incomplete sampling. The majority of new additions originated in the period after the original data collection. Nearly the same amount of new data originated from larger and smaller herbarium collections, underlining the value of small collections for chorological studies. We found that only ca. 20% of new records based on herbarium specimens have been published, thus highlighting the need of data papers for publication of distributional data. The greatest increase by new records based on herbarium specimens was found for insufficiently studied territories (Belarus, central, northern and eastern parts of Russia), whereas the same level of increase for the territories with reasonably good coverage (Latvia) was achieved by observations. We conclude that the overall sparsity of published records in Eastern Europe was caused by a lower level of data collection rather than by the poor data availability, and that floristic surveys based on herbarium specimens cannot compete in speed and density of records with observation-based surveys, which may become the main source of distributional information in the future.</p>
Raw data- IDENTIFICATION PERFORMANCE DURING QUARANTINE BY COVID 19 PANDEMIC: INFLUENCE OF EMOTIONAL VARIABLES AND SLEEP QUALITY
<p>The raw data supporting the conclusions of this article</p>
Figure 9 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 9 - Timeline. We will prepare and update the Web app (Aim 2) as we develop it for use in annotating gold standard audio data (Aim 1) and as we get feedback on its use in connection with Amazon's Mechanical Turk (Aim 2). Year 2 will consist primarily of testing the aggregation of annotated audio data for further analysis (Aim 2), to train an automated approach (Exploratory Aim), and to publish and present our findings.
Figure 2 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 2 - Mockup of audio recording annotation tool – Step 1: Selection. This figure shows a mockup of what an audio annotation Web application tool could look like. In this first step, (A) the Worker presses the Play icon to listen to the voice recording, (B) selects a problematic segment by clicking and dragging the mouse over the waveform, and (C) replays the recording if necessary and selects other problematic segments.
Figure 5 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 5 - DARPA-funded seedling project. This schematic represents our DARPA-funded seedling project to assess the feasibility of collecting phone voice recordings from PD patients for use in a competition.
Figure 4 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 4 - Audio recording annotation tool – Step 3: Rating. Following Figures 2 and 3, here the Worker rates how serious the problem is that is affecting the highlighted segment of the recording. In this example, the Worker indicates that the background noise (wind) is not good, but that it doesn't interfere with his/her ability to hear the voice in the recording.
Figure 7 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 7 - Example mPower patient voice data. In the mPower app, PD patients are prompted to perform the voice activity three times per day: once before taking their medication, a second time when they feel they are at their best after taking their medication, and a third "random" time. This figure shows example voice data for a single patient on medication (top) and at a "random" time, very likely off medication (bottom). On the left are waveforms, showing the acoustic voice signal over time (0-10 seconds), from which one can clearly see that the patient's voice trailed off to a minimum (bottom left) compared to after medication (top left). On the right are spectrograms, representing signal amplitude at different frequencies (0-5 kHz) over time (0-10 seconds). The spectrogram after medication (top right) has more uniform frequency bands across the recording compared to the rather "muddled" spectrogram recorded at the random time (bottom right).
Figure 3 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 3 - Audio recording annotation tool – Step 2: Annotation. Following Figure 2, here the Worker selects one or more categories describing why the highlighted segment in the audio waveform is problematic. In this example, there was a lot of background noise (wind).
Figure 6 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848
Figure 6 - Android and iOS Parkinson app screenshots. Top: Android PD app screenshots showing instructions for the phonation (voice) task. Bottom: mPower PD app screenshots. Each participant in the mPower study is prompted to perform a voice activity three times a day. The rightmost screenshot demonstrates the visual feedback that is provided during audio recording, to try to keep the voice at the best amplitude for recording.
Open government data and big data from a quality perspective
<p>This dataset contains information about the documents and the analysis categories related to open government data and big data from a quality perspective.</p>
Lupi et al data for Disentangling water quality indices to enhance the valuation of divergent ecosystem services PNAS
<p>State dataset for PNAS article, in press, Lupi, F., J.A. Herriges, R.J. Stevenson, and H. Kim. <em>In Press</em>, Disentangling water quality indices to enhance the valuation of divergent ecosystem services. <em>Proceedings of the National Academy of Science.</em></p>
Data Set Generated by the Fuzzy Model Constructed to Describe Execution Tracing Quality
<p>The uploaded data set was generated by the fuzzy model published in T. Galli, F. Chiclana, and F. Siewe. Genetic algorithm-based fuzzy inference system for describing execution tracing quality. Mathematics, 9(21), 2021. ISSN 2227-7390. doi: https://doi.org/10.3390/ma th9212822. URL https://www.mdpi.com/2571-5577/4/1/20.</p> <p>The goal of the data generation is to make the published model available in the form of data points in a 5D space, which facilitates the construction of simpler models to approximate the original model. The names of the columns in the .csv file constitute the quality properties of execution tracing: (1) accuracy, (2) legibility, (3) implementation, and (4) security, while column (5) contains execution tracing quality derived from the fuzzy model. The indices in brackets show the column indices in the .csv file.</p> <p>All variables lie in the continuous range [0, 100], where 100 means the best possible quality value and 0 the complete lack of quality or the lack of the given quality property. While generating the data, the inputs were increased by a step-size 5 and the model's output was collected, i.e. 4 inputs, from including 0 to 100 with 21 data points (21^4 = 194481).</p> <p> </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.