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409 results for “information use”
Modeling plate and spring reverberation using a DSP-informed deep neural network
<p>Accompanying audio samples for the paper:</p> <p>Martínez Ramírez M. A., Benetos, E. and Reiss J. D., “Modeling plate and spring reverberation using a DSP-informed deep neural network” in the IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Barcelona, Spain, May 2020.</p> <p>Dry and wet bass and guitar recordings.</p> <p>Bass and Guitar dry notes are taken from the IDMT-SMT-Audio-Effects dataset. Author: Michael Stein (Fraunhofer IDMT) https://www.idmt.fraunhofer.de/en/business_units/m2d/smt/audio_effects.html</p> <p>Plate Reverb - Bass - recordings are taken from the IDMT-SMT-Audio-Effects dataset. Plate settings are the following:</p> <ul> <li><strong>Smaertelectronix ambience</strong>: ’Gating Amount - 0’, ’Gating Attack" - 10 ms’, ’Gating Release - 10 ms’, ’Decay Time - 2225 ms’, ’Decay Diffusion - 50%’, ’Decay Hold - off’, ’Shape Size - 16%’, ’Shape Predelay - 0 ms’, ’Shape Width - 100%’, ’Shape Quality - 100%’, ’Shape Variation - 0’, ’EQ Bass Frequency - 43 Hz’, ’EQ Bass Gain - −7.8 dB’, ’EQ Treble Frequency - 5044 Hz’, ’EQ Treble Gain - −3.7 dB’, ’Damping Bass Frequency - 158 Hz’, ’Damping Bass Amount - 87%’, ’Damping Treble Frequency - 8127 Hz’, ’Damping Treble Amount - 32%’, ’Dry - −Inf’, ’Wet - 0dB’.</li> </ul> <p>Spring Reverb - Bass and Guitar - recorded from the spring reverb tank<strong>: Accutronics </strong><strong>4</strong><strong>EB</strong><strong>2</strong><strong>C</strong><strong>1</strong><strong>B</strong>: ’Dry Mix - 0%’, ’Wet Mix - 100%’</p> <p>Plate<em> </em>reverb samples correspond to a VST audio plug-in, while spring<em> </em>reverb samples are recorded using an analog reverb tank which is based on 2 springs placed in parallel.</p> <p>The recordings are downsampled to 16 kHz. Also, since the plate reverb samples have a fade-out applied in the last 0.5 seconds of the recordings, we process the spring reverb samples accordingly.</p>
Supplementary Information for: A cautionary note on the use of genotype callers in phylogenomics
<p>Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline, and found that it is very sharp in GATK, while ATLAS maintains a high accuracy even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.</p>
Multi year social stability and social information use in reef sharks with diel fission-fusion dynamics: Raw acoustic detection
<p><span>Animals across vertebrate taxa form social communities and often exist as fission-fusion societies. Central place foragers (CPF) may form social groups, from which they will predictably disperse to forage, either individually or in smaller groups, before returning to fuse with the larger group. However, the function and stability of social associations in predatory fish acting as CPFs is unknown, as individuals do not need to return to a shelter, yet show fidelity to core areas. Using dynamic social networks generated from acoustic tracking data, we document spatially structured sociality in CPF grey reef sharks at a Pacific Ocean atoll. We show that sharks form stable, social groups over multi-year periods, with some dyadic associations consistent for up to four years. Groups primarily formed during the day, increasing in group size before sharks dispersed from the reef to forage at night. Our simulations suggest that multiple individuals sharing a central place and using social information while foraging (i.e. local enhancement), will outperform non-CPF social foragers. We show multiyear social stability in sharks and suggest that social foraging with information transfer could provide a generalisable mechanism for the emergence of sociality with group central place foraging.</span></p>
Data from: Using a multi-isotope approach to inform waterfowl movement in southern Africa
<p>Many far-ranging species depend heavily on relatively small or temporary resources within a heterogeneous landscape. For waterfowl, most species rely on deep, permanent waterbodies as refugia from predators during annual flightless molt periods when synchronous loss and regrowth of the flight feathers occurs. The movements of ducks to and from molt sites are, however, poorly documented for most Afrotropical species and the dependencies of Afrotropical ducks on key sites are unclear, yet this information is integral to conservation and management efforts. We asked whether stable isotopes of wing feathers could be used to determine the molting origins of Afrotropical ducks in southern Africa. We analyzed isotope ratios of carbon, nitrogen, oxygen, and hydrogen in feathers from 4 different species across 5 different sites (wetlands, ponds, lakes) in South Africa, Zimbabwe, Mozambique, and Botswana. We observed differences among sites for all isotopes (<em>P</em> < 0.05), especially δ<sup>13</sup>C and δ<sup>15</sup>N. Based on these differences, we conducted linear discriminant function analysis (LDA) to assess the utility of these isotopes to assign birds to molt locations. We obtained a global classification accuracy = 0.59, although accuracies differed among sites. Our results demonstrate the potential of a multi-isotope approach to discriminate specific molt locations and to provide an initial estimate of molt site. Rigorous documentation of molt site from wing feathers is plausible, but will require large sample sizes, extensive spatial coverage, and careful calibration.</p>
Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis
Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.
Data from: Social information use and social learning in non-grouping fishes
Although it is natural to expect that group-living animals will utilize social learning, the expectation for non-grouping species is less clear. Only a few studies have explored the relationship between sociality and social learning. Here we presented 4 non-grouping fish species, fifteenspine sticklebacks (Spinachia spinachia), bullhead sculpins (Cottus gobio), stone loach (Barbatula barbatula) and juvenile European flounders (Platichthys flesus) with social information provided by groups of a shoal-forming heterospecific, the threespine stickleback (Gasterosteus aculeatus). Using a binary choice procedure we allowed individual test subjects to select between simulated prey patches. Although the test subjects could not sample the patches directly they were able to use information generated by the heterospecific demonstrators to select the "richer" of the 2 patches. For comparison we also recorded social information use in 2 shoaling species, threespine, and ninespine sticklebacks (Pungitius pungitius). We saw evidence of social information use and social learning in all 6 species, with no differences seen between social and non-grouping species. We argue that social learning is not likely to be restricted to group-living species, since many solitary species too are regularly exposed to social stimuli from both conspecifics and heterospecifics, and can benefit from using social information. We suggest that researchers have much to learn about the sensory, perceptive, and cognitive mechanisms underlying social learning, and the extent to which these vary (if at all) between grouping and non-grouping species.
Data from: Discrimination of signal carotenoid content using multidimensional chromatic information
Red, orange and yellow carotenoid-based ornaments, which are widely used as sexual signals in many birds, fish and reptiles, are known to exhibit multidimensional chromatic variation as a result of both the concentration and relative proportions of different constituent carotenoids with differing spectral properties. This is thought to reflect intrinsic variation in signaller quality, making it a useful basis for female choice. However, whether females are able to discriminate relevant variation in carotenoid concentration and/or composition independently of each other, and of other phenotypic or behaviour traits, and if so, how this mediates their choice, is poorly understood. Here, female three-spined sticklebacks (Gasterosteus aculeatus) were presented with computer-animated courting males that varied exclusively in the appearance of their carotenoid-based colouration; specifically, each male's signal provided a perceptual match for carotenoid colouration expressed by live males with known underlying carotenoid content, thereby providing a biologically-relevant signal while precluding confounding traits influencing female choice. Females were able to discriminate between prospective mates solely on the basis of perceived variation in the allocation of carotenoids to males' sexual signals, and exhibited a strong preference for males with colouration indicative of higher concentrations of carotenoids in their signal, rather than in response to perceived variation in the relative proportion of constituent carotenoids. This has important implications for our understanding male signalling strategies and the information content of carotenoid-based sexual signals.
Data from: Information use and resource competition: an integrative framework
Organisms may reduce uncertainty regarding how best to exploit their environment by collecting information about resource distribution. We develop a model to demonstrate how competition can facilitate or constrain an individual's ability to use information when acquiring resources. Since resource distribution underpins both selection on information use and the strength and nature of competition between individuals, we demonstrate interdependencies between the two that should be common in nature. Individuals in our model can search for resources either personally or by using social information. We explore selection on social information use across a comprehensive range of ecological conditions, generalising the producer-scrounger framework to a wide diversity of taxa and resources. We show that resource ecology – defined by scarcity, depletion rate, and monopolisability – determines patterns of individual differences in social information use. These differences suggest co-evolutionary processes linking dominance systems and social information use, with implications for the evolutionary demography of populations.
Data from: Information use by humans during dynamic route choice in virtual crowd evacuations
We conducted a computer-based experiment with over 450 human participants and used a Bayesian model selection approach to explore dynamic exit route choice mechanisms of individuals in simulated crowd evacuations. In contrast to previous work, we explicitly explore the use of time-dependent and time-independent information in decision-making. Our findings suggest that participants tended to base their exit choices on time-dependent information, such as differences in queue lengths and queue speeds at exits rather than on time-independent information, such as differences in exit widths or exit route length. We found weak support for similar decision-making mechanisms under a stress-inducing experimental treatment. However, under this treatment participants were less able or willing to adjust their original exit choice in the course of the evacuation. Our experiment is not a direct test of behaviour in real evacuations, but it does highlight the role different types of information and stress play in real human decision-making in a virtual environment. Our findings may be useful in identifying topics for future study on real human crowd movements or for developing more realistic agent-based simulations.
Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex provided that the number of aligned sequences is greater than the average of the lengths of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.
Data from: Honey bees flexibly use two navigational memories when updating dance distance information
Honey bees can communicate navigational information which makes them unique amongst all prominent insect navigators. Returning foragers recruit nest mates to a food source by communicating flight distance and direction using a small scale walking pattern: the waggle dance. It is still unclear how bees transpose flight information to generate corresponding dance information. In single feeder shift experiments, we monitored for the first time how individual bees update dance duration after a shift of feeder distance. Interestingly, the majority of bees (86%) needed two or more foraging trips to update dance duration. This finding demonstrates that transposing flight navigation information to dance information is not a reflexive behavior. Furthermore, many bees showed intermediate dance durations during the update process, indicating that honey bees highly likely use two memories: (i) a recently acquired navigation experience and (ii) a previously stored flight experience. Double shift experiments, in which the feeder was moved forward-backward, created an experimental condition in which honey bee foragers did not update dance duration; suggesting the involvement of more complex memory processes. Our behavioral paradigm allows the dissociation of foraging and dance activity and opens a possibility to study the molecular and neural processes underlying the waggle dance behavior.
Supplementary Information "Fabrication and characterization of narrow wavelength phosphors of Tb-doped yttrium-silicon-aluminum oxynitride using spray pyrolysis"
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ADVANTAGES OF USING INFORMATION COMMUNICATION TECHNOLOGIES IN THE EDUCATIONAL PROCESS
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Supporting information, WRF output, and processed WRF files used for the generation of the manuscript "Observational and modelling analysis of Canada's only F5/EF5 tornado"
<p>WRF simulation output and processed files used to generate the figures and calculations in the manuscript "Observational and modelling analysis of Canada's only F5/EF5 tornado". Two zipped folders are attached, one is from the original control simulation with the microphysics scheme on (MP), and the other is from the experimental simulation with the microphysics scheme turned off (NOMP).</p><p>Each simulation zipped folder includes sub-directories containing the processed observed and simulated surface station data, surface wet-bulb potential temperature, cross sections (the MP simulation only), and convective parameter fields at 2100 UTC 22 June 2007.</p><p>A supplemental material in the form of a movie showing the radar observation between 2000 UTC 22 June 2007 and 0000 UTC 23 June 2007 is also attached. See the manuscript's Figure 5 caption for more information on the data shown in the animation.</p>
SPECIFIC FEATURES OF USING GRAPHIC INFORMATION PROCESSING TECHNOLOGY
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Supplementary information to "ScRNA-IMM: Single-cell RNA-Seq Imputation method using Mean/Median Imputation"
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Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise.
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Dataset for "Reconstruction of Excitation Waves from Mechanical Deformation using Physics-Informed Neural Networks"
<p>Archive consisting of the synthetic datasets used in "Reconstruction of Excitation Waves from Mechanical Deformation using Physics-Informed Neural Networks" (<a title="https://doi.org/10.1038/s41598-024-67597-3" href="https://doi.org/10.1038/s41598-024-67597-3" target="_blank" rel="noreferrer noopener"><span>https://doi.org/10.1038/s41598-024-67597-3</span></a>) as well as the results after PINN optimization. Datasets include the electrical simulation data, generated active tension and resulting deformation. The PINN_results.zip file covers all results discussed in the paper. Short txt files give more information on the data format. The code used to create the synthetic dataset, construct and optimize the PINNs, and generate the figures from the paper can be found on <a href="https://gitlab.com/heartkor/scripts-2d-deformation-pinn">https://gitlab.com/heartkor/scripts-2d-deformation-pinn</a>.</p>
Data from: Interindividual variation in the use of social information during learning in honeybees
<p class="MsoNoSpacing">Slow-fast differences in cognition among individuals have been proposed to be an outcome of the speed-accuracy trade-off in decision-making. Based on the different costs associated with acquiring information via individual and social learning, we hypothesized that slow-fast cognitive differences would also be tied to the adoption of these different learning modes. Since foragers in honeybee colonies likely have both these information acquisition modes available to them, we chose to test them for inter-individual differences in individual and social learning.</p> <p class="MsoNoSpacing">Individual honeybees foragers were presented with a learning task: making a choice between two types of flowers one rewarding (offering sucrose) and one unrewarding (offering water). This task was presented twice: 1) the bee was alone (individual learning) and 2) there was a social cue (model bee) on the correct color. For every individual, the raw data consisted of 20 successive choices between rewarding and unrewarding flowers in each of the two learning tasks. From these data, learning curves were constructed by calculating an accuracy index as the proportion of correct choices for rewarding in the 4 visits up to and including that visit, and a logisitc function was fit to the accuracy index. From this logistic function we calculated individual learning parameters: maximum individual learning score, individual learning rate, maximum social learning score, social learning rate. </p> <p class="MsoNoSpacing">Our results support the existence of a speed-accuracy trade-off in both the individual and the social learning contexts. However, the trade-off is steeper during individual learning, which was slower than social learning but led to higher accuracy. Most importantly, our results also show that bees which attained high accuracy on the individual learning task had low accuracy on the social learning task and vice versa.</p>
Supplementary information for "GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability"
<p>GROMACS inputs for the performance benchmarks in the manuscript.</p>
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Allen Brain Atlas
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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.
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