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45 results for “Practice Theory”
Database - A Calculus of Tracking: Theory and Practice
<p>A manually curated sample (Top 100 Alexa domains only) of a OpenWPM database obtained from Princeton Web Census (https://webtransparency.cs.princeton.edu/webcensus/). The sample is used to instantiate the model for the paper "<a href="https://petsymposium.org/2021/files/papers/issue2/popets-2021-0027.pdf">A Calculus of Tracking: Theory and Practice</a>" to appear in PETS 2021.</p> <p>Accepted manuscript: https://petsymposium.org/2021/files/papers/issue2/popets-2021-0027.pdf</p> <p>GitHub page: https://github.com/giorgioditizio/calculus_of_tracking</p> <p> </p>
When the practice does not meet the theory: results from an Italian survey on the clini-cal and pathway management of inpatients with decompressive craniectomy or cranioplasty admitted to rehabilitation
<p>Cranioplasty (CP) is supposed to improve the functional outcome of severe acquired brain injury (sABI) patients with decompressive craniectomy (DC). However, ongoing controversies exist regarding its indications, optimum materials, timing, complications, and relationships with hydrocephalus (HC). For these reasons, an International Consensus Conference (ICC) on CP in traumatic brain injury (TBI) was held in June 2018 to issue some recommendations.</p> <p>AIM: To investigate cross-sectionally before the ICC the prevalence of DC/CP in sABI inpatients admitted to neurorehabilitation units in Italy; to assess the perception of Italian clinicians working in the sABI neurorehabilitation settings on the management of inpatients with DC/CP during their rehabilitation stay.</p> <p>DESIGN: Cross-sectional.</p> <p>SETTING AND POPULATION: Physiatrists or neurologists working in 38 Italian rehabilitation centers involved in the care of sABI, giving a pooled sample of 599 inpatients.</p> <p>METHODS: Survey questionnaire consisting of 21 closed-ended questions with multiple-choice answers. Sixteen questions regarded the respondents' opinions and experiences regarding the clinical and management aspects of patients. Survey data were collected via e-mail between April and May 2018.</p>
Data from: Dispersal and diversity in experimental metacommunities: linking theory and practice
There has been a recent rise in the number of experiments investigating the effect of dispersal on diversity, with many of the predictions for these tests derived from metacommunity theory. Despite the promise of linking observed relationships between dispersal and diversity to underlying metacommunity processes, empirical studies have faced challenges in providing robust tests of theory. We review experimental studies that have tested how dispersal affects metacommunity diversity to determine why shortcomings emerge, and to provide a framework for empirical tests of theory that capture the processes structuring diversity in natural metacommunities. We first summarize recent experimental work to outline trends in results and to highlight common methods that cause a misalignment between empirical studies and the processes described by theory. We then identify the undesired implications of three widely used experimental methods that homogenize metacommunity structure or species traits, and present alternative methods that have been used to successfully integrate experiments and theory in a biologically relevant way. Finally, we present methodological and theoretical insights from three related ecological fields (coexistence, food web and priority effects theory) that, if integrated into metacommunity experiments, could help isolate the independent and joint effects of local interactions and dispersal on diversity, and reveal the mechanisms underlying observed dispersal–diversity patterns. Together, these methods can provide stronger tests of existing theory and stimulate new theoretical explorations.
FIGURE 22 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 22. Spectrograms and corresponding oscillograms of the advertisement calls of two anuran species, exemplifying the presence of parallel frequency bands in the spectrogram, although at comparatively low FFT resolution (256; Hanning window function), not representing harmonics, but resulting from a high pulse rate. Left: Section of the advertisement call of Elachistocleis sp., with a pulse rate of 245 pulses/second and a total call duration of 2000‒3040 ms. Right: Advertisement call of Physalaemus albonotatus, with seven recognizable and modulated frequency bands. Its call is exceptionally fastly pulsed, with an approximate rate of 470 pulses/second. Figures modified and data taken from Köhler (2000). Spectrograms and oscillograms produced with CoolEdit Pro.
FIGURE 8 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 8. Comparative oscillograms of notes of four anuran species, illustrating differences in amplitude modulation and respective differences in descriptive terminology, particularly the bioacoustical application of the term pulse as defined herein.
FIGURE 5 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 5. Spectrograms and oscillograms of anuran advertisement calls conforming to the general sound categories proposed by Beeman (1998) for animals (and slightly modified herein). All graphics produced with the R package Seewave (Sueur et al. 2008a), from recordings of AmphibiawebEcuador.org (Hypsiboas tetete: Hylidae), Dendrobates.org (Andinobates fulguritus: Dendrobatidae), Vences et al. (2006) (Rhombophryne coronata: Microhylidae), Du Preez & Carruthers (2009) (Ptychadena anchietae: Ptychadenidae; Tomopterna marmorata and Amietia angolensis: Pyxicephalidae), Cocroft et al. (2001) (Ceratophrys cornuta: Ceratophryidae), Elliot et al. (2009) (Dryophytes andersonii: Hylidae). All spectrograms at Hanning window function, 512 bands resolution.
FIGURE 3 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 3. Two calls of Dryophytes andersonii (recording taken from Elliot et al. 2009) depicted in exemplary spectrogram, oscillogram and power spectrum, showing units and explaining details and analytical purpose of the graphs. Graphs were produced with the R package Seewave (Sueur et al. 2008a).
FIGURE 2 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 2. Vocal sac variation in anurans. Except for Ceratophrys cranwelli (emitting a warning call with open mouth) and the pictured specimens of Hyperolius (emitting advertisement calls with aggressive components in male-male combat) all pictured specimens are emitting advertisement calls. Phrynobatrachus alleni is suspected to use its yellow vocal sac for visual signalling, and a visual function is also probable for the bright white vocal sacs of the two Guibemantis species, and of other frogs. All hyperoliids (such as Hyperolius viridiflavus shown here) have gular glands on the vocal sac that might have a visual function, in addition to probably producing pheromones (Starnberger et al. 2013). Note that the distinction between vocal sac types is not always clear; for instance, the vocal sacs of Rana temporaria and Boophis tsilomaro can be considered as partially paired subgular and partially paired lateral. All photos by the authors except Trachycephalus typhonius and Pseudopaludicola jaredi (by Daniel Loebmann).
FIGURE 11 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 11. Box plots of Q 10 values reported in the literature for four call traits in 20 different species of amphibians. The red line indicates no temperature effects (Q 10 = 1). CD, call duration; DF, dominant frequency; PR, pulse rate; CR, call rate.
FIGURE 15 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 15. Spectrograms and oscillograms showing intra-specific call variation in two treefrog species from Madagascar, exemplifying the need to account for the possibility of different call / note types and of strong influence of motivation when taxonomically interpreting bioacoustical differences. (A) Males of Boophis at Antsatramidola, Madagascar, were emitting two very different types of calls, one of which might represent a territorial call. However, we never heard the two calls from the same individuals and therefore in the field were convinced of the presence of two morphologically cryptic species. Subsequent genetic study revealed that the individuals were all conspecific with B. tampoka and emitting two different call types (Köhler et al. 2007; Vences et al. 2011). (B) Boophis ankaratra emits long series of notes. Typical note repetition rate is reflected by the call from Manjakatompo, emitted by a male in the presence of several other calling males. At Itremo, during a dry evening, only few specimens were sporadically calling and obviously were in a state of low sexual motivation; despite a slightly higher temperature, note repetition rate was much lower at this occasion. Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.
FIGURE 21 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 21. Spectrograms and oscillograms showing frog advertisement calls with components at frequencies higher than usually reported, partly reaching into the ultrasound spectrum. In these four frog species, the dominant frequency is below 10 kHz but harmonics are visible at much higher frequency. Eleutherodactylus iberia (from Bahia de Taco, Cuba) and Stumpffia sp. [Ca6 Vieites et al. 2009] (from Andasibe, Madagascar) are miniaturized frogs with <11 mm snout-vent length (SVL) whereas Eleutherodactylus [Ca4 Rodríguez et al. 2010b] and Platypelis barbouri are small sized frogs around 20 mm SVL. Note that frequency of the spectrograms goes up to 40 kHz. Eleutherodactylus [Ca4] has almost no frequency components in the ultrasound spectrum, yet frequency reaches distinctly above 10 kHz, much higher than usually reported for frogs. Recordings were made with ultrasound microphone Ultramic200k (Dodotronic, Italy). Graphics produced with the R package Seewave (Sueur et al. 2008a). All spectrograms produced at Hanning window function, 1024 bands resolution. Format of candidate species names follows Padial et al. (2010).
FIGURE 7 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 7. Concordance and discordance among call centered and note centered approaches to name sound units in anuran vocalizations. The upper two schematic spectrograms show examples where both approaches lead to the same categorization of sounds. (A) A single tonal sound is repeated after regular silent intervals of longer duration than the sounds. There is no defined duration of the series of sounds; if undisturbed, calling could go on for minutes or hours. In both approaches, one sound unit would be a call, and the note-centered approach would define each call consisting of a single note. (B) Series of rapidly repeated sounds, each composed of a series of bursts of sound energy. Because these bursts are <10 ms in duration they are defined as pulses. The call-centered approach does not define each major subunit as call because the silent intervals between them are much shorter than the units themselves; thus, both approaches agree in defining the units as notes. (C) This species emits clearly defined and stereotyped series of sounds, each series being separated by variable intervals from the next series. The note-centered approach defines one coherent entity of sound emission as a call; hence, each sound series unit is a call, and the subunits are notes. In contrast, the call-centered approach defines each sound unit as a call (and each series as a call series) because it is separated from other such units by a long silent interval. (D) This species emits two distinct kinds of pulsatile sound units, of which one is much longer than the other. Because the combination of sounds is emitted as coherent entity, in the note centered approach the entire sound emission is a call and the sound units are notes of two types, of which one is arranged in a series. In the call-centered approach, each sound unit is a call because they are separated by long silent intervals from the next unit. Two call types can be distinguished and one of these is arranged in a call series.
FIGURE 4 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 4. Comparative spectrograms of a call of Dryophytes andersonii, all drawn with Hanning window function, showing the effect of different FFT resolution on the graphic representation of calls. Each spectrogram shows the identical 300 ms section of a recording. Note that with higher FFT settings, the spectral detail of the call representation increases. At lower FFT settings, the temporal pattern of the call is more clearly recognizable. Call recording taken from Elliot et al. (2009). Graphics produced with the R package Seewave (Sueur et al. 2008a).
FIGURE 1 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 1. Inspiratory calling of Bombina bombina (above) and expiratory calling in Pelophylax kl. esculentus (below). Oscillograms show one call and small photos show state of vocal sac at the respective time indicated. Video and sound recorded with a Nikon D750 and processed in Windows Movie Maker software; oscillograms drawn in CoolEdit Pro 2.0 software. Recording of Bombina made at Schorfheide-Chorin Reserve, Germany on 24 May 2015; recording of Pelophylax made at Riddagshausen Reserve, Braunschweig, Germany, on 2 June 2015.
FIGURE 20 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 20. Results of a spectrogram cross-correlation analysis (FFT = 1024, window = Hanning, overlap = 90%) comparing one call of Bombina bombina at Schorfheide-Chorin Reserve, Germany, recorded with four different combinations: Tascam DR05 digital recorder with Sennheiser K6/ME66 microphone (Tascam); Edirol R09 recorder with built-in microphone (Edirol); Sony D6C analog tape recorder (fitted with a type II cassette tape) with Audio Technica ATR6250 external microphone (Sony); and Apple iPhone 6 with built-in microphone (iPhone). Values in the cells represent pairwise pixel-bypixel similarity values between spectrograms, produced from the respective recordings of the same individual call.
FIGURE 6 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 6. Hierarchy of main units and subunits proposed for the description of anuran vocalizations. Call, note and pulse are primary units (in gray boxes). Call is the fundamental unit which might consist of a single note or several notes. In call descriptions, units can consist only of subunits in top-down direction of decreasing hierarchy. Pulses are defined here as the smallest, undividable unit.
FIGURE 19 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 19. Comparison of the recording performance of four different recorder/microphone combinations on a set of nine advertisement calls of one individual of Bombina bombina at Schorfheide-Chorin Reserve, Germany. All recordings were made simultaneously at the same recording distance, and same calls were thus compared. Call variables were automatically assessed using SoundRuler software (see text for details on the methods employed). Recording equipment as follows: Tascam DR-05 digital recorder/Sennheiser K6+ME66 microphone; Edirol R09 recorder with built-in microphone; Macintosh iPhone 6 with built-in microphone and recording software; Sony D6C cassette tape recorder with Audiotechnica external microphone (recordings digitized with CoolEdit Pro software at sampling rate of 44.1 kHz). Rise time is the time from the start of a call to the point where it reaches the maximum amplitude. Shape-on is the ratio between the rise time and the total duration of a call. Other call properties as defined in the text. Boxplots show median (middle line), first and third quartiles (upper and lower box limits), and non-outlier range (whiskers).
FIGURE 13 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 13. Comparative spectrograms and oscillograms exemplifying the effect of hybridization on the call structure of anurans. The two tree frogs Phyllomedusa distincta (diploid) and P. tetraploidea (tetraploid) co-occur and hybridize in Ribeirão Branco, south of São Paulo state, Brazil, producing triploid hybrids (3n = 39) (Haddad et al. 1994; Gruber et al. 2013). Their advertisement calls are of similar structure and indistinguishable to the human ear, but have subtle quantitative differences (Student's t-Test = 11.06; p <0.0001): 6–11 notes (7.8 ± 1.02; n = 31 calls from 3 males) in P. distincta, 8–17 notes (12.8 ± 2.4; n = 58 calls from 8 males) in P. tetraploidea (4n). An intermediate range of 6–16 notes (9.7 ± 1.9; n = 78 calls from 9 males) is found in triploid hybrids (3n). Recordings obtained in the hybridization zone (Ribeirão Branco, São Paulo, Brazil) using a Nagra E tape recorder and a Sennheiser ME80 microphone, at air temperatures varying from 14.5 to 21 o C. All recorded specimens were karyotyped to confirm their identities. Spectrograms made with the R package Seewave (Sueur et al. 2008a) with Hanning window function at 512 bands FFT resolution.
FIGURE 10 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 10. Individual, intraspecific and interspecific call trait variation in Leptodactylus spp. exemplified by the trait call duration. (A) Individual variation in call duration during one night in individual A (one nightly calling activity phase of ca. 1 hrs of calling; N = 4,401 calls; 18 November 2014; 29.1 to 29.4 °C); (B) Intraspecific variation: comparison of call durations of three individuals during each one night of calling (individual A: see above; individual B: n = 22,472 calls, ca. 5:20 hrs of calling, 27 November 2014, 23.0 to 23.4 °C; individual C: n = 15,561, 2:50 hrs of calling, 14 November 2014, 22.7 to 23.4 °C); (C) Interspecific variation: comparison of Kernel density estimates of call durations of three sympatric species (L. syphax: same three individuals as above, n = 38,434 calls; L. mystacinus: one individual, ca. 3:20 hrs of calling, n = 49,573, 24 January 2012, 25.1 to 25.9 °C; L. vastus, one individual, ca. 1:10 hrs of calling, n = 3,649 calls, 16 November 2014, 25.2 to 26.4 °C). All recordings were done at the Research Station 'Chiquitos', Bolivia, with Song Meters SM2 (Wildlife Acoustics) respectively Olympus DM-550 recorders (sampling frequency 22.05 kHz; 16-bit resolution), and afterwards analyzed with software Raven Pro, version 1.4 (Bioacoustics Research Program 2011) using implemented amplitude detectors; statistics were done with R; only calls with high amplitude were considered (i.e., less intense 'initial calls' of a series were excluded; M. Jansen, unpublished data).
FIGURE 17 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice
FIGURE 17. Interpretation of advertisement call differences: (A) Example showing spectrograms and oscillograms with distinct qualitative call differences of two frogs in sympatry (syntopy), providing evidence for species-level divergence, despite a comparatively low level of genetic divergence (Köhler et al. 2010). (B) Example showing distinct and constant quantitative call differences of two frogs in sympatry (syntopy), providing clear indication of species-level divergence, corroborated by high genetic divergence (Vences et al. 2010b). Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.
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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)
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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.