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10,735 results for “dependability”
Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli
Understanding of the causes by which reproductive isolation arises remains limited. We examine the role of adaptation in driving reproductive isolation among 12 Escherichia coli populations evolved in two different environments. We found that, regardless of whether parents were selected in the same or different environments, the average fitness of recombinants was lower than the expected, consistent with a prevailing influence of incompatibility between independently accumulated mutations. Exceptions to this pattern occurred among recombinants of some parents evolved in different environments. These recombinants were less fit than expected in the selective environment of one parent, but more fit than expected in the selective environment of the other parent. Our results indicate that both parallel and divergent adaptation can quickly lead to intrinsic genetic barriers contributing to the initial stages of speciation and show that these barriers can be complex, for example, depending on the environment in which recombinant offspring are tested.
Data from: Frequency-dependence shapes the adaptive landscape of imperfect Batesian mimicry
Despite more than a century of biological research on the evolution and maintenance of mimetic signals, the relative frequencies of models and mimics necessary to establish and maintain Batesian mimicry in natural populations remains understudied. Here we investigate the frequency-dependent dynamics of imperfect Batesian mimicry, using predation experiments involving artificial butterfly models. We use two geographically distinct populations of Adelpha butterflies that vary in their relative frequencies of a putatively defended model (Adelpha iphiclus) and Batesian mimic (Adelpha serpa). We found that in Costa Rica, where both species share similar abundances, Batesian mimicry breaks down, and predators more readily attack artificial butterfly models of the presumed mimic, A. serpa. In contrast, in Ecuador, where A. iphiclus (model) is significantly more abundant than A. serpa (mimic), both species are equally protected from predation. Our results provide compelling experimental evidence that imperfect Batesian mimicry is frequency-dependent on the relative abundance of models and mimics in natural populations, and contribute to the growing body of evidence that complex dynamics, such as seasonality or the availability of alternative prey, influence the evolution of mimetic traits.
Data from: Comparative phylogeography biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland
The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins. This phylogenetic pattern has not been commonly described in mammals, and we found no evidence for this pattern in the greater mouse deer. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reveals dynamic forested connections throughout Sundaland, and reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos.
Data from: Context-dependent defences in turtle ants: resource defensibility and threat level induce dynamic shifts in soldier deployment
1. Induced defences involve the dynamic deployment of limited and specialized defensive resources across multiple locations, to maximize organismal defensive function and fitness. They have been studied intensively in plants and solitary animals, but the induced defences of complex animal societies are poorly understood by comparison, despite the coordinated defensive actions of these taxa. 2. Here, we ask whether the level of environmental danger induces shifts in the deployment of limited and morphologically specialized soldiers across multiple nests in colonies of the turtle ant Cephalotes rohweri. Specifically, we test whether less defensible nests induce greater soldier deployment, and whether elevated enemy threat induced further increases in deployment, or reduced deployment consistent with a risk-limiting strategy. 3. We used colony-collection data to provide natural ecological context to our experiments, a field experiment to address how nest-entrance defensibility and soldier number impact defensive performance, and laboratory experiments to test whether differences in nest defensibility and threat level induce dynamic shifts in soldier deployment to new nests. 4. Less defensible nests were lost rapidly in our field experiment, irrespective of soldier number, but soldier deployment significantly increased survivorship of more defensible nests. Concordantly, less defensible nests induced the deployment of more soldiers per nest under low threat in laboratory experiments. Nevertheless, high-threat conditions revealed a risk-limiting soldier deployment strategy: with more danger, the number of soldiers per nest was significantly reduced in less defensible nests, as was the overall number of new soldier-defended nests. Total deployment to new nests was also consistently lower under high threat, dropping from 40% to 30% across colonies. 5. Induced soldier-based defences in turtle ants are therefore context-dependent, and dynamically scaled back at multiple levels when the environment is more dangerous. This dynamic, risk-limiting strategy is in strong contrast to stable patterns of soldier production in ants, and to typical task-allocation dynamics in members of the worker caste. Moreover, these findings establish that the evolution of specialized defensive agents can be coupled with sophisticated and inducible deployment strategies in complex social taxa, as we see for organisms at other levels of biological complexity.
Data from: Interspecific variation in conspecific negative density dependence can make species less likely to coexist
Conspecific negative density dependence (CNDD) is thought to promote plant species diversity. Theoretical studies showing the importance of CNDD often assumed that all species are equally susceptible to CNDD; however, recent empirical studies have shown species can differ greatly in their susceptibility to CNDD. Using a theoretical model, we show that interspecific variation in CNDD can dramatically alter its impact on diversity. First, if the most common species are the least regulated by CNDD, then the stabilising benefit of CNDD is reduced. Second, when seed dispersal is limited, seedlings that are susceptible to CNDD are at a competitive disadvantage. When parameterised with estimates of CNDD from a tropical tree community in Panama, our model suggests that the competitive inequalities caused by interspecific variation in CNDD may undermine many species' ability to persist. Thus, our model suggests that variable CNDD may make communities less stable, rather than more stable.
Context-dependent effects of relative temperature extremes on bill morphology in a songbird
<p><span>Species increasingly face environmental extremes. While responses of morphological traits to changes in average environmental conditions are well-documented, responses to environmental extremes remain poorly understood. Bird bills contribute to thermoregulation, with considerable heat loss possible through the bill surface, and with bill morphology shaped by long-term thermal conditions. We used museum specimens to investigate the relationship of bill surface area (SA) in dark-eyed juncos <i>Junco hyemalis</i> to traditional measures of climate (temperature and precipitation) and to a novel measure of short-term relative temperature extremity, which quantifies the degree to which temperature maxima or minima have diverged from the recent five-year norm. We found that bill SA exhibits different patterns of association with relative extremity depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger bill SA at higher relative temperature extremities, we found this to be the case only when the measure of temperature extremity existed in an environmental context that opposed it: relative minimum temperature in a warm climate, or relative maximum temperature in a cool climate. When, instead, environmental context amplified the relative temperature extremity, we found a negative relationship between bill SA and relative temperature extremity. We also found that the strength of associations between bill SA and relative temperature extremity increased as precipitation increased. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments should be of particular concern. Extreme-on-extreme environmental change may produce responses that cannot be predicted from observations in less extreme contexts, which should make it a priority for research on species' responses to climate change as well as trait evolution generally.Species increasingly face environmental extremes. Morphological responses to changes in average environmental conditions are well-documented, but responses to environmental extremes remain poorly understood. We used museum specimens to investigate relationships between a thermoregulatory morphological trait, bird bill surface area (SA), and a measure of short-term relative temperature extremity (RTE), which quantifies the degree that temperature maxima or minima diverge from the five-year norm. Using a widespread, generalist species, <i>Junco hyemalis</i>, we found that SA exhibited different patterns of association with RTE depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger SA at higher RTE, we found this only when the RTE existed in an environmental context that opposed it: atypically cold minimum temperature in a warm climate, or atypically warm maximum temperature in a cool climate. When environmental context amplified the RTE, we found a negative relationship between SA and RTE. We also found that the strength of associations between SA and RTE increased with precipitation. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments may produce responses that cannot be predicted from observations in less extreme contexts.</span></p>
Data from: History-dependent perturbation response in limb muscle
<p>Muscle mediates movement but movement is typically unsteady and perturbed. Muscle is known to behave non-linearly and with history dependent properties during steady locomotion, but the importance of history dependence in mediating muscles function during perturbations remains less clear. To explore muscle's capacity to mitigate perturbations during locomotion, we constructed a series of perturbations that varied only in kinematic history, keeping instantaneous position, velocity and time from stimulation constant. We find that muscle's perturbation response is profoundly history dependent, varying by four fold as baseline frequency changes, and dissipating energy equivalent to ~6 times the kinetic energy of all the limbs in 5 ms (nearly 2400 W Kg<sup>-1</sup>). Muscle's energy dissipation during a perturbation is predicted primarily by the force at the onset of the perturbation. This relationship holds across different frequencies and timings of stimulation. This history dependence behaves like a viscoelastic memory producing perturbation responses that vary with the frequency of the underlying movement. </p>
CODE-RADE dependency graph (14/09/2015)
<p>The dependency graph of the CODE-RADE Continuous Integration service at http://ci.sagrid.ac.za</p> <p> </p> <p>Published 14/09/2015. Incomplete.</p>
Testing sky brightness models against radial dependency: A dense two dimensional survey around the city of Madrid, Spain: SQM data
<p>We present a study of the night sky brightness around the extended<br /> metropolitan area of Madrid using Sky Quality Meter (SQM) photometers. The map is the first to cover the spatial distribution of the sky brightness in the<br /> center of the Iberian peninsula. These surveys are neccessary to test the light<br /> pollution models that predict night sky brightness as a function of the<br /> location and brightness of the sources of light pollution and the scattering of<br /> light in the atmosphere. We describe the data-retrieval methodology, which<br /> includes an automated procedure to measure from a moving vehicle in order to<br /> speed up the data collection, providing a denser and wider survey than previous<br /> works with similar time frames. We compare the night sky brightness map to the<br /> nocturnal radiance measured from space by the DMSP satellite. We find that i) a<br /> single source model is not enough to explain the radial evolution of the night<br /> sky brightness, despite the predominance of Madrid in size and population, and<br /> ii) that the orography of the region should be taken into account when deriving<br /> geo-specific models from general first-principles models. We show the tight<br /> relationship between these two luminance measures. This finding sets up an<br /> alternative roadmap to extended studies over the globe that will not require<br /> the local deployment of photometers or trained personnel.</p>
Action potential dependent sIPSCs from juvenile (P21-30) C57BL/6J male mice
<p>species : Mus musculus</p> <p>sex : male</p> <p>strain : C57BL/6J</p> <p>age : post-natal day 21-30</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from juvenile (P21-30) C57BL/6J male mice. The dataset contains 267 individual events recorded from 3 different neurons (expA1-A3). </p>
Dataset accompanying publication: "Modulation of Cortical Oscillations by Low-Frequency Direct Cortical Stimulation is State-Dependent"
<p>Dataset accompanying publication:</p> <p>"Modulation of Cortical Oscillations by Low-Frequency Direct Cortical Stimulation is State-Dependent", Alagapan, Schmidt, Lefebvre, Hadar, Shin and Frohlich</p> <p>For questions, contact flavio_frohlich@med.unc.edu</p> <p>The mat file consists of the following Matlab variables</p> <ol> <li><strong>Electrode Distance</strong>: 3 x 1 cell array containing the arrays (trial x electrode) of distance from stimulating electrode to recording electrode for the three ECoG participants. (First array corresponds to P001, Second array corresponds to P005 and Third array corresponds to P008)</li> <li><strong>Spectra_Electrode_EC</strong>: 3 x 1 cell array consisting of nTrial x nFreq x nChannels x nEpochs matrices for each subject’s eyes-closed experiment. nTrial corresponds to number of trials, nFreq corresponds to frequencies at which spectral power is calculated, nChannels corresponds to number of electrodes in the analysis and nEpochs corresponds to “Before Stimulation”, “During Stimulation” and “After Stimulation” epochs.</li> <li><strong>Spectra_Electrode_EO</strong>: 3 x 1 cell array consisting of nTrial x nFreq x nChannels x nEpochs matrices for each subject’s eyes-open experiment. The dimensions are the same as above. The first array consists of task-engaged dataset from Participant P001.</li> <li><strong>MI_Summary</strong>: 8 x 1 cell array consisting of 3 x 1 cell arrays of modulation indexes for the three participants. The 8 arrays stand for the modulation indexes in different epochs and different frequencies. Refer <strong>MI_Summary_Names</strong></li> <li><strong>MI_Summary_Names</strong>: 8 x 1 cell array consisting of strings denoting the arrays in <strong>MI_Summary</strong>. <strong>During</strong> in text corresponds to “During Stimulation” epoch and <strong>After</strong> corresponds to “After Stimulation” epoch.</li> <li><strong>f</strong>: Frequencies at which spectral power was estimated.</li> <li><strong>NetworkModel</strong>: Matlab struct containing the time series generated by the network model and corresponding spectra. The <strong>timeseries</strong> consists of 4 columns – 1<sup>st</sup> column corresponds to time, 2<sup>nd</sup> column corresponds to task-engaged state data, 3<sup>rd</sup> column corresponds to eyes-open state data and 4<sup>th</sup> column corresponds to eyes-closed state data. The <strong>spectra </strong>struct consists of spectral powers estimated in the different epochs. 1<sup>st</sup> column of each epoch array corresponds to task-engaged state, 2<sup>nd</sup> column corresponds to eyes-open state and the 3<sup>rd</sup> column corresponds to eyes-closed state.</li> <li><strong>SummationModel</strong>: Matlab struct containing the time series generated by the summation model and the peak values in spectra before and during stimulation by varying the two strength parameters. The columns correspond to stimulation strength while rows correspond to oscillation strength. The oscillation strength parameter was varied from 0.5 to 50 in steps of 0.5 and the stimulation strength parameter was varied from 0.1 to 10 in steps of 0.1. </li> </ol> <p> </p>
Action potential dependent sIPSCs from juvenile (P21-30) C57BL/6J male mice from CA1 pyramidal neurons receiving input from PV+ interneurons
<p>species : Mus musculus</p> <p>sex : male</p> <p>strain : C57BL/6J</p> <p>age : post-natal day 21-30</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from juvenile (P21-30) C57BL/6J male mice and recorded from hippocampal CA1 pyramidal neurons receiving input from parvalbumin positive (PV+) interneurons. The dataset contains 614 individual events recorded from 3 different neurons (expC1-C3).</p>
Action potential dependent sIPSCs from juvenile (P21-30) C57BL/6J male mice CA1 pyramidal neurons receiving input from PV+ and CCK+ interneurons
<p>species : Mus musculus</p> <p>sex : male</p> <p>strain : C57BL/6J</p> <p>age : post-natal day 21-30</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from juvenile (P21-30) C57BL/6J male mice and recorded from hippocampal CA1 pyramidal neurons receiving input from parvalbumin positive and cholecystokinin positive (CCK+) interneurons. The dataset contains 2130 individual events recorded from 3 different neurons (expD1-D3).</p>
Supplementary material: Modeling and Compensating Temperature-dependent Non-uniformity Noise in IR Microbolometer Cameras
<p><strong>Abstract</strong>: Images rendered by uncooled microbolometer-based infrared (IR) cameras are severely degraded by the spatial non-uniformity (NU) noise. The NU noise imposes a fixed-pattern over the true images, and the intensity of the pattern changes with time due to the temperature instability of such cameras. In this paper, we present a novel model and a compensation algorithm for the spatial NU noise and its temperature-dependent variations. The model separates the NU noise into two components: a constant term, which corresponds to a set of NU parameters determining the spatial structure of the noise, and a dynamic term, which scales linearly with the fluctuations of the temperature surrounding the array of microbolometers. We use a black-body radiator and samples of the temperature surrounding the IR array to offline characterize both the constant and the temperature-dependent NU noise parameters. Next, the temperature-dependent variations are estimated online using both a spatially uniform Hammerstein-Wiener estimator and a pixelwise least mean squares (LMS) estimator. We compensate for the NU noise in IR images from two long-wave IR cameras. Results show an excellent non-uniformity correction performance and a root mean square error of less than 0.25◦C, when array’s temperature varies approximately 15◦C.</p>
Action potential dependent sIPSCs from 3-4 months old C57BL/6J X SJL female mice hippocampus CA1 pyramidal cell
<p>species : Mus musculus</p> <p>sex : female</p> <p>strain : C57BL/6J X SJL</p> <p>age : 3 - 4 months</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from 3-4 months old C57BL/6J X SJL female mice . The dataset contains 701 individual events recorded from 7 different neurons (expB1-B7).</p>
Action potential dependent sIPSCs from 3-4 months old Tg2576 female mice
<p>species : Mus musculus</p> <p>sex : female</p> <p>strain : Tg2576</p> <p>age : post-natal day 90 - 120</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from 3-4 months old Tg2576 (carrying the Amyloid Precursor Protein KM670/N671L Swedish mutation) female mice. The dataset contains 1000 individual events recorded from 10 different neurons (expE1-E10)<strong>.</strong></p>
Results for paper "Energy dependent mesh adaptivity of discontinuous isogeometric discrete ordinate methods with dual weighted residual error estimators"
<p>This spreadsheet contains the results used to generate the plots in the paper "Energy dependent mesh adaptivity of discontinuous isogeometric discrete ordinate methods with dual weighted residual error estimators".</p>
Gaze-dependent Coding of Somatosensory Reach Targets after Effector Movement: Testing the Impact of Online Information, Movement Timing, and Target Distance
<p>The uploaded files contain data as SPSS data files (.sav) and tab delimited (.csv) textfiles as well as the respective variable desriptions as images (.png). In particular, I uploaded 1) the raw data, 2) the means of reach errors which we analyzed by repeated-measures ANOVA, and 3) the means of ellipse sizes on which repeated-measures ANOVA of precision were based.</p> <p>After publication of the article, I also uploaded the reported analyses and corresponding datafiles (plus some more material) here: </p> <p>https://doi.org/10.5281/zenodo.821307</p>
A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling
<p>seq.fasta and P96787_1UAZ.fasta are the input files for I-TASSER suite.</p> <p>The command of running I-TASSER suite:<br> path-to-I-TASSER-dir/I-TASSERmod/runI-TASSER.pl -pkgdir path-to-I-TASSER-dir -libdir path-to-I-TASSER-lib-dir -seqname P96787 -datadir path-to-workdir -outdir path-to-outdir -java_home /usr/ -restraint2 P96787_1UAZ.fasta</p> <p>For detailed data please refer to I-TASSER documentation.</p> <p>The P96787_1UAZ_IT.zip is an archieve with I-TASSER output for the best achaerhodopsin-3 prediciton.</p> <p>SCRIPTS_GENERAL.zip contains all the scripts for the structure postprocessing: addition of hydrogen atoms,<br> chromophore insertion and equilibration, internal waters addition.</p> <p>P96787_wi.pdb is a final prepared structure.</p> <p>Input files for spectra calculations are rhodopsin_gaussian.inp and rhodopsin_orca.inp.</p> <p> </p>
Supplementary information for: "A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling".
<p>This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling.</p> <p>Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.</p>
ScienceDex guides
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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.