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1,709 results for “Reflectivity”
PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts.
PIE LTER, Year 2017-2018, locations, date, sediment concentration and spectral reflectance measurement methods of 40 water samples at Plum Island Sound and deep ocean, Massachusetts
Underlying data for "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?"
<p>This dataset contains code, data, trajectories, and figures used in the article "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?".</p> <p> </p> <p>Contents:</p> <p>code/* - Code used to calculate electric fields from simulation trajectories with either polarizable or additive force fields</p> <p>data/* - Electric fields calculated for the CypA WT cis, WT trans, R55A cis, and R55A trans systems, with AMOEBA, Amber, or Charmm force fields. Each subfolder also includes a set of structural coordinates extracted at 2.5 ns intervals from the first simulation trajectory and used to calculate ONETEP DFT electric fields.</p> <p>figures/* - Underlying data and scripts used to create all figures and movies used in the article.</p> <p>trajectories/* - Simulation trajectories of the CypA WT cis, WT trans, R55A cis, and R55A trans systems</p> <p> </p> <p>Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages and other software used to generate data are available in Dependencies.txt</p>
Data from: Juvenile social dynamics reflect adult reproductive strategies in bottlenose dolphins
The juvenile period is a challenging life history stage, especially in species with a high degree of fission-fusion dynamics, such as bottlenose dolphins, where maternal protection is virtually absent. Here, we examined how juvenile male and female bottlenose dolphins navigate this vulnerable period. Specifically, we examined their grouping patterns, activity budget, network dynamics, and social associations in the absence of adults. We found that juveniles live in highly dynamic groups, with group composition changing every 10 minutes on average. Groups were generally segregated by sex, and segregation was driven by same-sex preference rather than opposite-sex avoidance. Juveniles formed strong associations with select individuals, especially kin and same-sex partners, and both sexes formed cliques with their preferred partners. Sex-specific strategies in the juvenile period reflected adult reproductive strategies, in which the exploration of potential social partners may be more important for males (which form long-term alliances in adulthood) than females (which preferentially associate with kin in adulthood). Females spent more time alone and were more focused on foraging than males, but still formed close same-sex associations, especially with kin. Males cast a wider social net than females, with strong same-sex associations and many male associates. Males engaged in more affiliative behavior than females. These results are consistent with the social bonds and skills hypothesis and suggest that delayed sexual maturity in species with relational social complexity may allow individuals to assess potential associates and explore a complex social landscape without the risks associated with sexual maturity (e.g. adult reproductive competition; inbreeding).
Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species
Aim Biogeographic barriers restrict the movement of individuals, resulting in population divergence, genetic differentiation, endemism and speciation. Yet, some barriers demonstrate unequal effect across species depending on species dispersal, which manifests in varying genetic structure. We test the hypotheses that the genetic structure of four coastal mangrove species would reflect differences in dispersal potential across the Malay Peninsula, a major biogeographic barrier in the Indo-West Pacific region. Location Twelve sites from the east and west coasts of the Malay Peninsula. Taxon Mangrove trees Avicennia alba, Sonneratia alba, Bruguiera gymnorhiza, and Rhizhophora mucronata. Methods For each species, we characterized genetic structure and gene flow using seven to 12 species-specific nuclear microsatellite markers. We tested for east-west genetic differentiation across the peninsula, a stepping-stone migration pattern, and assessed the proportion of recent dispersal and direction of historical migration along the Malacca Strait. Results Significant east-west genetic differentiation across the peninsula was observed in A. alba, S. alba and B. gymnorhiza, and the effect was most pronounced for the two species with lower dispersal potential (A. alba, S. alba). In contrast, the two species with higher dispersal potential (B. gymnorhiza and R. mucronata) exhibited much higher proportion of recent inter-population migration along the Malacca Strait. The signature of historical colonization from refugia in the Andaman Sea (north-to-south migration along the Malacca Strait) predominated for A. alba and S. alba. Historical south-north migration predominated for R. mucronata and B. gymnorhiza. Main conclusions This study is the first to implicate dispersal potential as a causal factor of varying mangrove species genetic structure across a biogeographic barrier. The Malay Peninsula functions as a filter to gene flow rather than a barrier. The genetic structure in mangrove species with a higher dispersal potential is more congruent with contemporary gene flow while that of species with a lower dispersal potential reflects historical processes.Our findings hint at the role of dispersal potential as a predictor of gene flow in mangroves.
Super-resolved Reflectance Confocal Microscopy 3D reconstruction of a Diatom shell
<p>These movies present back-to-back the performance in term of resolution of both standard reflectance confocal microscopy and super-resolved rescanned reflectance confocal microscopy. One movie is a 3D stack angular rotation, the other is a Zstack. </p> <p> </p>
Super-resolved Reflectance Confocal Microscopy data on Diatom shells and live MEF cells
<p>This dataset is linked to a paper submission in Open Research Europe. It contains the RAW data of confocal reflectance super-resolved point spread function, diatom shell zstack and time lapse imaging of a living Mouse Embryonic Fibroblast cell. </p>
Super-resolved Reflectance Confocal Microscopy time-lapse imaging of a living MEF cell lamellipod
<p>This movies presents a time-lapse of a label-free living Mouse embryonic fibroblast cell observed with super-resolved rescanned reflectance confocal microscopy.. </p>
Floral spectral reflectance data for: Floral color properties of serpentine seep assemblages depend on community size and species richness
<p>Functional traits, particularly those that impact fitness, can shape the ecological and evolutionary relationships among coexisting species of the same trophic level. Thus, examining these traits and properties of their distributions (underdispersion, overdispersion) within communities can provide insights into key ecological interactions (e.g., competition, facilitation) involved in community assembly. For instance, the distribution of floral colors in a community may reflect pollinator-mediated interactions between sympatric plant species, and the phylogenetic distribution of color can inform how evolutionary contingencies can continue to shape extant community assemblages. Additionally, the abundance and species richness of the local habitat may influence the type or strength of ecological interactions among co-occurring species. To evaluate the impact of community size and species richness on mechanisms shaping the distribution of ecologically relevant traits, we examined how floral color (defined by pollinator color vision models) is distributed within co-flowering assemblages. We modeled floral reflectance spectra of 55 co-flowering species using honeybee (<i>Apis mellifera</i>) and syrphid fly (<i>Eristalis tenax</i>) visual systems to assess the distributions of flower color across 14 serpentine seep communities in California. We found that phylogenetic relatedness had little impact on the observed color assemblages. However, smaller seep communities with lower species richness were more overdispersed for flower color than larger, more species-rich communities. Results support that competitive exclusion could be a dominant process shaping the species richness of flower color in smaller-sized communities with lower species richness, but this is less detectable or overwhelmed by other processes at larger, more speciose communities.</p>
Dataset: The role of social costs as a mechanism enforcing the honesty of ultraviolet-reflecting signals in a lizard
<p>Here are the data associated with the study entitled "The role of social costs as a mechanism enforcing the honesty of ultraviolet-reflecting signals in a lizard<strong>"</strong> authored by Anna Kawamoto, Jean-François Le Galliard, and Arnaud Badiane and published in <em>Biological Journal of the Linnean Society</em>.</p> <p>Four different data sets are provided and the Notes.xlsx file explains the content of these data sets.</p> <p>We also added three short videos showing typical lizards' behaviours scored in this study.</p> <p> </p>
Supplementary Data for Remote soil moisture measurement from drone-borne reflectance spectroscopy: Applications to hydroperiod measurement in desert playas
<p>This supporting dataset includes:</p> <p>• Ground-based reflectance measurements for the two plume-crossing transects (AHT3 and AHT4). Data show reflectance by wavelength at each scan position.</p> <p>• Reduced data records (RDR) showing GPS position data for the drone and the associated reflectance measurement, by wavelength, averaged over 1 second intervals for the three mapping sorties, AHS4, 5, and 7.</p> <p>• The sample datasheet showing ground-based and lab-base measurements of the sampling transects.</p>
Predicting Photosynthetic Capacity in Tobacco (Nicotiana tabacum) Using Shortwave Infrared Spectral Reflectance
<p>These files contains the data used for analysis in the (currently under-review) publication "<strong>Predicting Photosynthetic Capacity in Tobacco (</strong><strong><em>Nicotiana tabacum</em></strong><strong>) Using Shortwave Infrared Spectral Reflectance" </strong> in the Journal of Experimental Botany. </p>
Data from: Holocene lake phosphorus species and primary producers reflect catchment processes in a small, temperate lake
<p>This palaeo data set consists of a Holocene record from a small, temperate lake (Lake Fuglsø, Denmark). It comprises radiocarbon (<sup>14</sup>C)-dating, pollen, X-ray fluorescence scanning, carbon and nitrogen (contents and stable isotopes), phosphorus (P) pools (from sequential P extraction and <sup>31</sup>P nuclear magnetic resonance spectroscopy), pigment, diatom, and plant macrofossil data. Our multi-proxy palaeolimnological study aimed to investigate how natural processes and anthropogenic land-use changes have affected sedimentary P forms and primary producers. We found three periods of human impact: (1) low disturbance from domestic grazing during the Early/Mid Neolithic (~3600 – ~2600 BC), (2) higher disturbance because of animal husbandry and some grain cultivation during the Late Bronze and Pre-Roman Iron Age (~800 BC – AD ~100) and (3) strong disturbance caused by domestic grazing, intensified crop cultivation and, in particular, by retting of fibre plants during the Middle Ages and Renaissance (AD ~1000 – ~1700). Cultural eutrophication during the latter phase caused unprecedented changes in the lake, including altered species composition, high production and strongly accelerated sediment accumulation rates. Generally, catchment deforestation was related to elevated proportions of metal (iron, aluminium, calcium)-bound P forms in the sediment, while high tree cover correlated with elevated proportions of P forms associated with organic material ("organic" P, humic-bound P, refractory organic P) and loosely bound P. During phases with forest in the catchment, silicon (Si) inputs to the lake were insufficient and diatom frustules were mostly absent in the sediments. In contrast, diatoms thrived in the lake when the landscape was open and erosional Si influx was high. This study is the first to show long-term (~eight millennia) and recurring Si limitation of diatoms, a finding that may explain the absence of diatoms in sediment records of other sites too. In summary, human land-use with preceding deforestation accelerated the transport of nutrients and elements from the terrestrial to the aquatic environment, leading to substantial and irreversible changes in Lake Fuglsø. Our study is a good example of the tight links between catchment processes and lake status, indicating that catchment dynamics should be considered in lake restoration projects, particularly for lowland lakes with high catchment:lake area ratios.</p>
Data from: Tooth fracture frequency in gray wolves reflects prey availability
Exceptionally high rates of tooth fracture in large Pleistocene carnivorans imply intensified interspecific competition, given that tooth fracture rises with increased bone consumption, a behavior that likely occurs when prey are difficult to acquire. To assess the link between prey availability and dental attrition, we documented dental fracture rates over decades among three well-studied populations of extant gray wolves that differed in prey:predator ratio and levels of carcass utilization. When prey:predator ratios declined, kills were more fully consumed, and rates of tooth fracture more than doubled. This supports tooth fracture frequency as a relative measure of the difficulty of acquiring prey, and reveals a rapid response to diminished food levels in large carnivores despite risks of infection and reduced fitness due to dental injuries. More broadly, large carnivore tooth fracture frequency likely reflects energetic stress, an aspect of predator success that is challenging to quantify in wild populations.
Anuran limbs reflect microhabitat and distal, later-developing bones are more evolutionarily labile
Tetrapod limbs have been used as a model system to investigate how selective pressures and constraints shape morphological evolution. Anurans have had many independent transitions to various microhabitats, allowing us to dissect how these factors influence limb morphology. Furthermore, anurans provide a unique system to test the generality of developmental constraints proposed in mammals, namely that later-developing limb bones are under less constraint and show more variation. We used micro-computed tomography scans of 236 species from 52 of 55 families, geometric morphometrics, and modern phylogenetic comparative methods to examine how limb bones are related to microhabitat, phylogeny, allometry, and developmental timing. Although there was significant phylogenetic signal, anuran limb shape showed a relationship with microhabitat and to a lesser extent, body size. We found that distal bones had higher evolutionary rates than proximal bones, providing evidence that developmental constraints are reduced in later-developing bones. Distal bones also showed increased selection related to allometry and microhabitat, providing an additional explanation for higher evolutionary rates. By looking at the evolution of limb shape across a diverse clade, we demonstrated that multiple factors have shaped anuran limbs and that greater evolutionary lability in later-developing limb bones is likely a general trend among tetrapods.
Photochemical Reflectance Index (PRI) captures the ecohydrological sensitivity of a semi-arid mixed conifer forest
The Photochemical Reflectance Index (PRI) corresponds to the de-epoxidation state of the xanthophyll cycle and is one of the few pigment-based vegetation indices sensitive to rapid plant physiological responses. As such, new remotely-sensed PRI products present opportunities to study diurnal and seasonal processes in evergreen conifer forests, where complex vegetation dynamics are not well reflected by the small annual changes in chlorophyll content or leaf structure. Because PRI is tied explicitly to short and long term changes in xanthophyll pigments which are responsible for regulatig stress, this study characterized PRI in a semi-arid, sub-alpine mixed conifer forest, in order to assess its potential as a proxy for water stress by extension of its association with photoprotection. To determine the sensitivity of PRI to seasonal changes in ecohydrological variability and gross primary productivity, canopy spectral measurements were combined with eddy covariance flux and sap flow methods. Seasonally, there was a significant relationship between PRI and sap flow velocity (R2=0.56), and multiple linear regression analysis demonstrated the PRI response to dynamic water and energy limitations in this system. Although PRI was an effective indicator of stomatal response to ecohydrological constraints on a seasonal time scale, top-of-canopy leaf-level gas exchange, chlorophyll fluorescence, and hyperspectral reflectance measurements suggest that diurnal PRI saturates under conditions of severe light stress. This research indicates that remotely-sensed PRI has potential to fill spatial and temporal gaps in the ability to distinguish how water availability influences carbon dynamics of forested ecosystems.
Messinian vegetation and climate of the intermontane Florina-Ptolemais-Servia Basin, NW Greece: How well do plant fossils reflect past environments?
The late Miocene is marked by pronounced environmental changes and the appearance of strong temperature and precipitation seasonality. Although environmental heterogeneity is to be expected during this time, it is challenging to reconstruct palaeoenvironments using plant fossils. We investigated leaves and dispersed spores/pollen from 6.4–6 Ma strata in the intermontane Florina-Ptolemais-Servia Basin (FPS) of NW Greece. To assess how well plant fossils reflect the actual vegetation of the FPS, we assigned fossil-taxa to biomes providing a measure for environmental heterogeneity. Additionally, the palynological assemblage was compared to pollen spectra from modern lake sediments to assess biases in spore/pollen representation in the pollen record. We found a close match of the Vegora assemblage with modern Fagus–Abies forests of Turkey. Using taxonomic affinities of leaf fossils, we further established close similarities of the Vegora assemblage with modern laurophyllous oak forests of Afghanistan. Finally, using information from sedimentary environment and taphonomy, we distinguished local and distantly growing vegetation types. We then subjected the plant assemblage of Vegora to different methods of climate reconstruction and discussed their potentials and limitations. Leaf and spore/pollen records allow accurate reconstructions of palaeoenvironments in the FPS, whereas extra-regional vegetation from coastal lowlands is likely not captured.
Data from: Apparent annual survival estimates of tropical songbirds better reflect life history variation when based on intensive field methods
Aim: Adult survival is central to theories explaining latitudinal gradients in life history strategies. Life history theory predicts higher adult survival in tropical than north temperate regions given lower fecundity and parental effort. Early studies were consistent with this prediction, but standard-effort netting studies in recent decades suggested that apparent survival rates in temperate and tropical regions strongly overlap. Such results do not fit with life history theory. Targeted marking and resighting of breeding adults yielded higher survival estimates in the tropics, but this approach is thought to overestimate survival because it does not sample social and age classes with lower survival. We compared the effect of field methods on tropical survival estimates and their relationships with life history traits. Location: Sabah, Malaysian Borneo. Time period: 2008–2016. Major taxon: Passeriformes. Methods: We used standard-effort netting and resighted individuals of all social and age classes of 18 tropical songbird species over 8 years. We compared apparent survival estimates between these two field methods with differing analytical approaches. Results: Estimated detection and apparent survival probabilities from standard-effort netting were similar to those from other tropical studies that used standard-effort netting. Resighting data verified that a high proportion of individuals that were never recaptured in standard-effort netting remained in the study area, and many were observed breeding. Across all analytical approaches, addition of resighting yielded substantially higher survival estimates than did standard-effort netting alone. These apparent survival estimates were higher than for temperate zone species, consistent with latitudinal differences in life histories. Moreover, apparent survival estimates from addition of resighting, but not from standard-effort netting alone, were correlated with parental effort as measured by egg temperature across species. Main conclusions: Inclusion of resighting showed that standard-effort netting alone can negatively bias apparent survival estimates and obscure life history relationships across latitudes and among tropical species.
Data for: Variability in thermal and phototactic preferences in Drosophila may reflect an adaptive bet-hedging strategy
<p>Data and code for "Variability in thermal and phototactic preferences in <em>Drosophila</em> may reflect an adaptive bet-hedging strategy." </p> <p>.zip file contains .mats with data, a LabView .vi for the acquisition instrument, and Matlab .m analysis and visualization scripts. </p> <p>The included index.html file acts as a readme and contains descriptions of all other files and links.</p>
Data for Manuscript "Changes in P300 Latency and Amplitude Reflect Expertise Acquisition in a Football Visuomotor Learning Task"
<p>Open-access data for the manuscript "Changes in P300 Latency and Amplitude Reflect Expertise Acquisition in a Football Visuomotor Learning Task". Includes:</p> <p>Grand Average dEEG file containing data from all days and all conditions. .csv file outputs used for all analyses. .rmd file detailing the statistical workflow used to obtain the stats presented in the manuscript.</p>
Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences
<p>The dataset and code used for the publication of "<a href="https://www.biorxiv.org/content/10.1101/2024.11.12.623335v1" target="_blank" rel="noopener"><strong>Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences</strong></a>".</p> <div> <div><strong>Data path</strong></div> <div> <ol> <li>derivatives (./data/derivatives/): preprocessed data. <ul> <li>meg_quat-tsss-withEOG_100hz_0d3-40: meg data preprocessed at 100 Hz filtered between 0.3 and 40 Hz.</li> <li>FreeSurfer: anatomy data preprocessed</li> </ul> </li> <li>behavior_data (./behavior_data/)</li> <li>stimuli (./exp_procedure/material/): exp stimuli and procedure</li> <li>features (./data/features/): calculated phonological and linguistic features.</li> </ol> </div> <strong>Code path</strong></div> <div><br> <div>Preprocessing<strong>:</strong></div> <div> <ol> <li>[preprocessing.py]: preprocessing of behavior and MEG data.</li> <li>[recon.py]: reconstruction of T1 .niift data into surface data in FreeSurfer.</li> <li>[analysis_stimuli.ipynb]: preprocessing and feature extraction of stimuli.</li> </ol> </div> Analysis</div> <div> <ul> <li>[analysis_meg.ipynb]: spectral, time course, and RSA analysis.</li> </ul> </div>
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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.