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2,107 results for “Spectrum”
The zebra mussel (Dreissena polymorpha) as a model organism for ecotoxicological studies: a prior 1H NMR spectrum interpretation of a whole body extract for metabolism monitoring.
<p>NMR data of the zebra mussel <em>Dreissena polymorpha</em> whole body polar extract metabolome</p> <p>- 1D <sup>1</sup>H annotated spectrum - 600 MHz</p> <p>- 2D <sup>1</sup>H-<sup>1</sup>H JRES spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H COSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H TOCSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 800 MHz</p> <p>- 2D<sup>1</sup>H-<sup>31</sup>P HSQC spectrum - 800 MHz</p> <p>- <sup>1</sup>H annotated spectrum description tables (.xlsx)</p> <p>- Instructions for data visualization in Topspin</p>
Data from: Invertebrate phenology modulates the effect of the leaf economics spectrum on litter decomposition rate across 41 subtropical woody plant species
<ol> <li>Litter quality and decomposers are critical to carbon and nutrient cycling through litter decomposition. However, how relationships between litter quality and invertebrate detritivores change litter mass loss through time is poorly known. Species' initial leaf litter quality, as a legacy of their position on the "leaf economics spectrum" (LES), may determine the invertebrate contribution to litter mass loss. This contribution may change through time, as both population peaks of invertebrate detritivores and litter quality of given species will change through time.</li> <li>Here we introduce invertebrate phenology into a conceptual model of drivers of litter mass loss. We hypothesized that in the early decomposition period, LES can predict litter decomposability with or without a strong invertebrate contribution, i.e., litter with higher nutrient content would decompose faster. But in the later decomposition period, when higher quality litter will already have decomposed too much and lower quality litters have still been less degraded, a strong invertebrate peak would coincide with relatively more consumption of initially lower quality litters; this would lead to a hump-back relationship between leaf litter mass loss and initial LES position in this period.</li> <li>We tested our hypothesis through a one-year field decomposition experiment using leaf litter of 41 woody species in each of two sites in subtropical forest in China; only one of these sites had a strong late peak of leaf litter-feeding moth larvae in the litter layer.</li> <li>LES score of litter species had a positive linear relationship with litter mass loss before the key invertebrate consumer peaks in the litter layer. However, with the invertebrates peaking later into the decomposition process, the invertebrate consumption peaked at initially lower quality litters, which altered the species' decomposability trajectory on the LES, consistent with the hypothesized hump-back relationship between leaf litter mass loss and LES. This phenomenon resulted in a strongly reduced slope of cumulative mass loss on initial LES score across species.</li> <li>Our finding highlights the importance of considering interactions between the timing of detritivore activities and the timing of litter quality for better understanding the relationships between soil animals and ecosystem carbon and nutrient cycling.</li> </ol>
Estimating leaf nitrogen concentration based on the combination with fluorescence spectrum and first-derivative
Leaf nitrogen concentration (LNC) is a major indicator in the estimation of the crop growth status which has been diffusely applied in remote sensing. Thus, it is important to accurately obtain LNC by using passive or active technology. Laser-induced fluorescence (LIF) can be applied to monitor LNC in crops through analyzing the changing of fluorescence spectral information. Thus, the performance of fluorescence spectrum (FS) and first-derivative fluorescence spectrum (FDFS) for paddy rice (Yangliangyou 6 and Manly Indica) LNC estimation was discussed, and then the proposed FS+FDFS was used to monitor LNC by multivariate analysis. The results showed that the difference between FS (R2=0.781, SD=0.078) and FDFS R2=0.779, SD=0.097) for LNC estimation by using the artificial neural network (ANN) is not obvious. The proposed FS+FDFS can improved the accuracy of LNC estimation to some extent (R2=0.813, SD=0.051). Then, principal component analysis was used in FS and FDFS, and extracted the main fluorescence characteristics. The results indicated that the proposed FS+FDFS exhibited higher robustness and stability for LNC estimation (R2=0.851, SD=0.032) than that only using FS (R2=0.815, SD=0.059) or FDFS (R2=0.801, SD=0.065).
Data from: Defining a spectrum of integrative trait-based vegetation canopy structural types
Vegetation canopy structure is a fundamental characteristic of terrestrial ecosystems that defines vegetation types and drives ecosystem functioning. We use the multivariate structural trait composition of vegetation canopies to classify ecosystems within a global canopy structure spectrum. Across the temperate forest subset of this spectrum we assess gradients in canopy structural traits, characterize canopy structural types (CST), and evaluate drivers and functional consequences of canopy structural variation. We derive CSTs from multivariate canopy structure data, illustrating variation along three primary structural axes and resolution into six largely distinct and functionally relevant CSTs. Our results illustrate that within-ecosystem successional processes and disturbance legacies can produce variation in canopy structure similar to that associated with sub-continental variation in forest types and ecoclimatic zones. The potential to classify ecosystems into CSTs based on suites of structural traits represents an important advance in understanding and modeling structure-function relationships in vegetated ecosystems.
Transcranial Direct Current Stimulation Improves Action-Outcome Monitoring in Schizophrenia Spectrum Disorder
<p>Data set of the publication: Straube, B., van Kemenade, B.M., Kircher, T. & Schülke, R. (2020). Transcranial Direct Current Stimulation Improves Action-Outcome Monitoring in Schizophrenia Spectrum Disorder. <em>Brain Communications.</em> doi: 10.1093/braincomms/fcaa151</p> <p><strong>Abstract</strong></p> <p><strong>Background:</strong> Patients with schizophrenia spectrum disorder (SSD) often demonstrate impairments in action-outcome monitoring. Passivity phenomena and hallucinations, in particular, have been related to impairments of efference copy-based predictions which are relevant for the monitoring of outcomes produced by voluntary action. Frontal transcranial direct current stimulation (tDCS) has been shown to improve action-outcome monitoring in healthy subjects. However, whether tDCS can improve action monitoring in patients with SSD remains unknown.</p> <p><strong>Objective:</strong> We investigated whether tDCS can improve the detection of temporal action-outcome discrepancies in patients with SSD.</p> <p><strong>Methods:</strong> On 4 separate days, we applied sham or left cathodal/right anodal tDCS in a randomised order to frontal (F3/F4), parietal (CP3/CP4) and frontoparietal (F3/CP4) areas of 19 patients with SSD and 26 healthy control (HC) subjects. Action-outcome monitoring was assessed subsequent to 10 min of sham/tDCS (1.5 mA). After a self-generated (active) or externally generated (passive) key press, subjects were presented with a visual outcome (a dot on the screen), which was presented after various delays (0–417 ms). Participants had to detect delays between the key press and the visual consequence. Symptom subgroups were explored based on the presence or absence of symptoms related to a paranoid-hallucinatory syndrome (SSD phs+/phs-).</p> <p><strong>Results:</strong> In general, delay-detection performance was impaired in the SSD compared to the HC group. Interaction analyses showed group-specific (SSD vs HC) and symptom-specific (SSD phs+ vs SSD phs-) tDCS effects. Post-hoc tests revealed that frontal tDCS improved the detection of long delays in active conditions and reduced the proportion of false alarms in undelayed trials of the passive condition in patients. The SSD phs- group benefited especially from frontal tDCS in active conditions, while improvement in the SSD phs+ group was predominantly reflected in reduced false alarm rates in passive conditions.</p> <p><strong>Conclusion:</strong> These data provide some first evidence for the potential utility of tDCS in improving efference copy mechanisms and action-outcome monitoring in SSD. Current data indicate that improving efference copy-related processes can be especially effective in patients with no or few positive symptoms, while intersensory matching (i.e. task-relevant in passive conditions) could be more susceptible to improvement in patients with paranoid-hallucinatory symptoms.</p> <p> </p> <p><strong>Keywords:</strong> transcranial direct current stimulation; action-perception; action feedback; delay detection; schizophrenia.</p> <p> </p>
Data from: The clinical, histological, and genotypic spectrum of SEPN1-related myopathy: a case series
<p><b><span>Objective: </span></b><span>To clarify the prevalence, long-term natural history and severity determinants of SEPN1-related myopathy (SEPN1-RM), we analyzed a large international case series. </span></p> <p><b>Methods: </b>Retrospective clinical, histological and genetic analysis of 132 pediatric and adult patients (2-58 years) followed-up for several decades.</p> <p><b><span>Results: </span></b><span>The clinical phenotype was marked by severe axial muscle weakness, spinal rigidity and scoliosis (86.1%, from 8.9±4 years), with relatively-preserved limb strength and previously-unreported ophthalmoparesia in severe cases. All patients developed respiratory failure (from 10.1±6 years), 81.7% requiring ventilation while ambulant. Histopathologically, 79 muscle biopsies showed large variability, partly determined by site of biopsy and age. Multi-minicores were the most common lesion (59.5%), often associated with mild dystrophic features and occasionally with eosinophilic inclusions. Identification of 65 SEPN1 mutations, including 32 novel ones and the first pathogenic CNV, unveiled exon 1 as the main mutational hotspot and revealed the first genotype-phenotype correlations, bi-allelic null mutations being significantly associated with disease severity (<i>p</i>=0.017). SEPN1-RM was more severe and progressive than previously thought, leading to loss of ambulation in 10% cases, systematic functional decline from the end of the third decade and reduced lifespan even in mild cases. The main prognosis determinants were scoliosis/respiratory management, <i>SEPN1</i> mutations and body mass abnormalities, which correlated with disease severity. Finally, we propose a set of severity criteria, provide quantitative data for outcome identification and establish a need for age stratification.</span></p> <p><b><span>Conclusion</span></b><span>: Our results inform clinical practice, improving diagnosis and management, and represent a major breakthrough for clinical trial readiness in this not-so-rare disease.</span></p>
Towards resolving the complex paramagnetic NMR spectrum of small laccase: Assignments of resonances to residue specific nuclei
<p>NMR dataset as TopSpin (Bruker Corporation) files for the article titled "Towards resolving the complex paramagnetic NMR spectrum of small laccase: Assignments of resonances to residue specific nuclei" (https://doi.org/10.5194/mr-2020-31).</p>
Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in mycosis fungoides and Sezary syndrome
<p>T-cell non-Hodgkin's lymphomas (NHL) develop following transformation of tissue resident T-cells. We performed a meta-analysis of mutational catalogues derived from whole exome sequencing data from 403 patients with eight subtypes of T-cell NHL to identify mutational signatures and recurrent gene mutations associated with specific causal peaks within these signatures. Signature 1, indicative of age-related deamination, was prevalent across all T-cell NHL subtypes, reflecting the derivation of these malignancies from memory T-cell subsets. Adult T-cell leukemia-lymphoma (ATLL) was specifically associated with signature 17, which was found to strongly correlate with the IRF4 K59R mutation that is exclusive to ATLL. Signature 7, implicating UV exposure as a potential initiating factor was uniquely identified in cutaneous T-cell lymphoma, contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4+ T-cells isolated from blood suggesting extensive re-circulation of these T-cells through both skin and blood and strongly implicating a role for UV in the pathogenesis of cutaneous T-cell lymphoma.</p>
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9% of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after 10 replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
Structural defence is coupled with the leaf economic spectrum across saplings of spiny species
<p>Given that the rate of resource capture constrains plant growth and defence, understanding the linkage between the leaf economic spectrum (LES) and defence and how it contributes to growth is central to predicting species performance. In spite of the prevalence of spiny plants in many plant communities, little is known about how the LES relates to defence and growth rate across these species. We grew 42 spiny species, from diverse environments, under common garden conditions for 15 weeks and measured LES (leaf N, SLA and assimilation rate), defence and growth traits. We assessed general relationships between LES and growth rate and tested whether structural defences (spines, leaf fibre and lignin content) and quantitative chemical defences (condensed tannins) are linked to the LES and growth and if different spine types (i.e. leaf spines, stipular spines, prickles and thorns), with distinct anatomical origins, partition out across the LES. We observed two independent trait axes that together explained ~68% of trait variation across species. The first axis showed that structural defences (spines, leaf fibre and lignin content) trade off with leaf productivity along the LES. Axis 2 revealed that condensed tannins is orthogonal and less integrated with the LES-structural defence axis. Bivariate trait analyses disclosed positive covariations between LES traits and sapling growth rate. All structural defence traits were negatively related to sapling growth. Across spine types, species with leaf spines were associated with the conservative end of the LES, characterized by high structural defences and lower leaf productivity relative to other spine types. Our study shows that the LES and structural defences are coupled in spiny species such that constitutive growth – defence strategies range from fast-growing species with low allocation to defences to slow-growing species that invest heavily in structural defences (dominated by leaf spiny species).</p>
Data from: Non-linear effect of sea ice: Spectacled Eider survival declines at both extremes of the ice spectrum
Understanding the relationship between environmental factors and vital rates is an important step in predicting a species' response to environmental change. Species associated with sea ice are of particular concern because sea ice is projected to decrease rapidly in polar environments with continued levels of greenhouse gas emissions. The relationship between sea ice and the vital rates of the Spectacled Eider, a threatened species that breeds in Alaska and Russia and winters in the Bering Sea, appears to be complex. While severe ice can impede foraging for benthic prey, ice also suppresses wave action and provides a platform on which eiders roost, thereby reducing thermoregulation costs. We analyzed a 23-year mark-recapture dataset for Spectacled Eiders nesting on Kigigak Island in western Alaska, and tested survival models containing different ice and weather-related covariates. We found that much of the variation in eider survival could be explained by the number of days per year with >95% sea ice concentration at the Bering Sea core wintering area. Furthermore, the data supported a quadratic relationship with sea ice rather than a linear one, indicating that intermediate sea ice concentrations were optimal for survival. We then used matrix population models to project population trajectories using General Circulation Model (GCM) outputs of daily sea ice cover. GCMs projected reduced sea ice at the wintering area by year 2100 under a moderated emissions scenario (RCP 4.5) and nearly ice-free conditions under an unabated emissions scenario (RCP 8.5). Under RCP 4.5, stochastic models projected an increase in population size until 2069 coincident with moderate ice conditions, followed by a decline in population size as ice conditions shifted from intermediate to mostly ice-free. Under RCP 8.5, eider abundance increased until 2040 and then decreased to near extirpation toward the end of the century as the Bering Sea became ice-free.
Figure 3 in Behavior notes and prey spectrum of three species of the bee-hunting wasp Trachypus Klug (Hymenoptera: Apoidea)
Figure 3. Trachypus taschenbergi biology. (A) female carrying a prey (Paratrigona subnuda drone) near the nest entrance. (B) female exiting the nest; (C-E) a female trying to enter an occupied nest and being expelled by a female that was inside the nest.
Figure 1 in Behavior notes and prey spectrum of three species of the bee-hunting wasp Trachypus Klug (Hymenoptera: Apoidea)
Figure 1. Study site. (A) Curitiba, Paraná, Brazil, (B) land cover (modified from Pereira et al., 2020), (C) original sampling sites (modified from Michener et al., 1958).
Figure 2 in Behavior notes and prey spectrum of three species of the bee-hunting wasp Trachypus Klug (Hymenoptera: Apoidea)
Figure 2. Rose diagrams for seasonal activities of (A) Trachypus elongatus and (B) Trachypus taschenbergi, considering the number of female observations per day of fieldwork. Months are treated as sectors of 30 degrees each, with January corresponding to 0 and December to 330.
Data from: Within-species patterns challenge our understanding of the Leaf Economics Spectrum
The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive datasets of trait variation within species, across species, and across communities, we analyzed whether and at what scales 'leaf economics spectrum' (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families, between genera in a family). However, we found that trait covariation shows distinct taxonomic scale-dependence, with some trait correlations showing opposite signs within versus across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy.
Data from: Demographic model selection using random forests and the site frequency spectrum
Phylogeographic data sets have grown from tens to thousands of loci in recent years, but extant statistical methods do not take full advantage of these large data sets. For example, approximate Bayesian computation (ABC) is a commonly used method for the explicit comparison of alternate demographic histories, but it is limited by the "curse of dimensionality" and issues related to the simulation and summarization of data when applied to next-generation sequencing (NGS) data sets. We implement here several improvements to overcome these difficulties. We use a Random Forest (RF) classifier for model selection to circumvent the curse of dimensionality and apply a binned representation of the multidimensional site frequency spectrum (mSFS) to address issues related to the simulation and summarization of large SNP data sets. We evaluate the performance of these improvements using simulation and find low overall error rates (~7%). We then apply the approach to data from Haplotrema vancouverense, a land snail endemic to the Pacific Northwest of North America. Fifteen demographic models were compared, and our results support a model of recent dispersal from coastal to inland rainforests. Our results demonstrate that binning is an effective strategy for the construction of a mSFS and imply that the statistical power of RF when applied to demographic model selection is at least comparable to traditional ABC algorithms. Importantly, by combining these strategies, large sets of models with differing numbers of populations can be evaluated.
Perceived gender ratings for high and low scorers on the Autism-spectrum Quotient consistent with the extreme male brain account of autism
<p>Software required: SPSS</p> <p>'Male faces data_final.sav' and 'Female faces data_final.sav' contain masculinity (for male faaces) and femininity (for female faces) ratings of face photographs. Each photograph is labelled as a variable (top row, third cell onwards) and subsequent rows represent ratings provide by each rater (E.g., first row of data represents ratings provided by rater for each of the photograph presented to him/her). 'Male voices data_final.sav' and 'Female voices data_final.sav' contain masculinity (for male voices) and femininity (for female voices) ratings of voice recordings. Data layout is the same as face data described above. Click on variable tab for details on each variable. 'AQ_rating_corr_face.sav' and 'AQ_rating_corr_voice.sav' contain mean ratings of male and female faces and voices, and their respective AQ scores.</p>
0-D BiOeconomic mArine Trophic Size-spectrum (BOATS) model (review version)
<p>This is version 1.0 of the BiOeconomic mArine Trophic Size-spectrum (BOATS) model, a bioenergetically-constrained coupled fisheries-economics model for global studies of harvesting and climate change. The code is written in MATLAB version R2012a. This release contains the zero-dimensional version of the code that models a single oceanic grid cell. This release is part of the peer review for the journal Geoscientific Model Development, which was published as Carozza et al. (2016) [Carozza, D. A., Bianchi, D., and Galbraith, E. D.: The ecological module of BOATS-1.0: a bioenergetically constrained model of marine upper trophic levels suitable for studies of fisheries and ocean biogeochemistry, Geosci. Model Dev., 9, 1545-1565, doi:10.5194/gmd-9-1545-2016, 2016.].</p>
The Legal Spectrum
<p>The Legal Spectrum shows legal information on the range from closed to open. While contracts (or other voluntarily entered agreements) are often closed or shared, legislation and case law are - or at least should be - available to the general public without restrictions. </p> <p>The Legal Spectrum is based on the Data Spectrum, originally published by the Open Data Institute (ODI).</p>
Spectrum usage in Madrid (20150331) when some DVB-T channels were switched off
<p>This dataset represents the spectrum usage in Madrid city on 31st of March 2015 between 02:00 am and 04:00 am. Some DVB-T channels stopped transmitting (~800-860MHz) to make room for 4G networks. The spectrum was scanned using a RTL-SDR device connected to a RPi unit.</p> <p>The dataset is a CSV file with the following structure. Pear each line you have:</p> <p>TimeStamp (seconds) , frequency(Hz) , Signal Power (dB)</p>
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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.