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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.

FIGURE 18 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 18. Interpretation of advertisement call differences: (A) Spectrograms and oscillograms of calls of two allopatric frog species without any significant differences (evidence for species-level divergence by molecular genetics and tadpole morphology; Vences et al. 2010a). (B) Moderate structural call differences of two allopatric populations currently assigned to the same species. The calls of Blommersia wittei from Sambava and Andrakata are composed of clicking notes of a metallic sound, whereas at Nosy Be, Benavony, and Montagne d'Ambre, notes contain pulses and calls exhibit less distinct inter-note intervals. Spectrograms produced with CoolEdit Pro at Hanning window function, 256 bands resolution.

FIGURE 16 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 16. Spectrograms illustrating qualitative call differences between closely related species (all mantellid frogs from Madagascar). All spectrograms show only a section of a longer series of notes. Gephyromantis eiselti and G. thelenae form a clade together with a third species (Kaffenberger et al. 2011). While G. eiselti emits series of tonal notes, G. thelenae emits much slower series of much longer pulsed notes at similar temperatures. Boophis majori and B. narinsi are sister species (Wollenberg et al. 2011) and differ extremely in note duration and note repetition rate (short clicks vs. long pulsatile sounds). In both cases, the species in each pair occur in syntopy and are extremely similar to each other in adult morphology. Despite distinct qualitative call differences, genetic divergences between each of the two species pairs are remarkably low (p-distances 2.2–3.3% in a fragment of the mitochondrial 16S rRNA gene; Wollenberg & Harvey 2010; Vences et al. 2012a). In such extreme cases of bioacoustical divergence, and if the presence of different call types or recording artifacts can be excluded, bioacoustical data provide conclusive evidence for species level divergence. Recordings from Vences et al. (2006, 2012a); spectrograms made with the R package Seewave (Sueur et al. 2008a) at Hanning windowing function, 512 bands resolution.

FIGURE 9 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 9. Example illustrating the need to consider homology aspects in terminoloy of anuran vocalizations. The calls shown are from four related species of mantellid frogs in the nominal subgenus of the genus Gephyromantis. The four species emit vocalizations consisting of a series of sound units (each corresponding to one expiration), with a defined number of units per series. All spectrograms are to scale; for G. boulengeri, an entire series is shown whereas the remaining spectrograms show parts of a series. In a note-centered terminology, one entire series would be a call, and each sound unit a note. In a call-centered terminology, in G. boulengeri, a series might be defined as one call (because no intervals of full silence occur between sound units), while in G. enki, each sound unit would be a call (separated by wide intervals of silence from the next call) and the series would be a call series. Either definition might be appropriate when looking at a single species, but in a comparative taxonomic study, it is of utmost importance to compare homologous bioacoustical entities and to apply the same name to them; hence, in a call centered approach, also the vocalization of G. boulengeri would need to be dubbed a call series. Spectrograms made with the R package Seewave (Sueur et al. 2008a) at Hanning windowing function, 512 bands resolution. Note that we here refer to homology from the perspective of sound production (one unit corresponding to one expiration) and not from the perspective of signal content of the respective sound unit.

FIGURE 12 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 12. Nightly variation of dominant frequency (A) and call duration (B) in one individual of Leptodactylus syphax. One nocturnal activity phase of ca. 2 hrs of calling (n = 8,106 calls; 29.9 to 31.8 °C). Recording was obtained on 17 November 2014 at the Research Station 'Chiquitos', Bolivia, with a Song Meter SM2 (Wildlife Acoustics; sampling frequency 22,050 Hz; 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 'introductory calls' of a series were excluded). Red lines show smoothed data (Local Polynomial Regression Fitting with span=0.05; M. Jansen & A. Masurowa, unpubl. data).

FIGURE 23 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 23. Spectrograms and oscillograms of calls of the same individual of Bombina bombina recorded at different saturations of the recording levels and different recording distances (Tascam DR-05 digital recorder and a Sennheiser K6/ ME66 microphone; water temperature 22.1 °C; 24 May 2015 at Schorfheide-Chorin Reserve, Germany). Calls were successively recorded from the same individual within a short time period of ca. 30 minutes and each spectrogram thus shows a different call. The upper left spectrogram is from a recording with recording levels in the field deliberately set on oversaturation. The other three spectrograms were analyzed with equalized levels. Note that the number of harmonics is highest in the oversaturated recording, but also depends on recording distance, with the highest-frequency harmonics disappearing with increasing distance. Sounds of birds and insects are visible on the recordings that were not filtered to allow objective comparison. All spectrograms made with the R package Seewave (Sueur et al. 2008a), with settings: Hanning window function, 1024 bands resolution, overlap = 90%.

FIGURE 14 in The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

FIGURE 14. Variation of two call traits within the Madagascar-Comoroan anuran family Mantellidae. (A) Correlation of dominant frequency and maximum male snout-vent length in 155 mantellid species. (B) Variation of note duration (mean, minimum and maximum values) among 171 species of mantellids, ordered by mean note duration (5–20 measurements per species). On Y-axis values are arranged along a logarithmic scale for graphical reasons (but scale shows original values in milliseconds, not log-transformed values). Notes defined following a note-centered scheme (cf. Fig. 7).

opencc-by-4.0May 2023View details →

Data and code for the manuscript "Internal vs Forced Variability Metrics for General Circulation Models Using Information Theory"

Data and code for the manuscript "Internal vs Forced Variability Metrics for General Circulation Models Using Information Theory" published in the Journal of Geophysical Research Oceans.  URL of the manuscript:  https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023JC020101 DOI of the manuscript:  https://doi.org/10.1029/2023JC020101

Artifact: Quick Theory Exploration for Algebraic Data Types via Program Transformations

This is the repeatability package, including the tool (called LemmaCalc) in the paper, the benchmark files, a TheSy binary, Z3 binaries for Linux, and scripts to repeat the experiments. Parts of the paper supported by this artifact: Main results in Fig 1, implementation of Algs 1--3.

Data for PASP paper: Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation

High-resolution figures for paper "Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation", accepted for publication in The Publications of the Astronomical Society of the Pacific (PASP).

Resultados da aplicação das técnicas codificação aberta e axial (Grounded Theory)

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Dataset for "The Operator Product Expansion for Radial Lattice Quantization of 3D φ4 Theory"

<h2>Description of the data</h2>This dataset is supplement to the paper "The Operator Product Expansion for Radial Lattice Quantization of 3D φ4 Theory". It contains <ul><li>the raw data for the partial wave expansion coefficients of the scalar four-point amplitude in the interacting theory for different lattice refinements. The corresponding files are named Rawdata_L=_.json.</li><li>the fit results going into the model averaged lattice results for the OPE coefficients and scaling dimensions of the interacting theory. The corresponding files are named ModelAveraging_L=_.csv.</li><li>the synthetic lattice data for the free theory at different lattice refinements L and cylinder lengths L_t. The corresponding files are named free_cj_L_Lt_.dat.</li></ul><h3>Rawdata_L=_.json</h3>The Rawdata_L=_.json files contain data for the partial wave expansion coefficients c_j of the antipodal conformal four-point amplitude that were computed as described in Section IV of the paper. They are given for even j up to j=20 for different values of the lattice refinement L. The first two entries in each file are the value of the lattice refinement L as well as the length of the cylinder L_t.  Thereafter, the partial wave coefficients "c_j" are given for different j as a function of lattice cylinder time t. For each j, we store a list of c_j(t), with the first entry corresponding to t=0, the second to t=1 etc. up until t=L_t/2. Note that the range of t-values is only half of the cylinder length. This is because we used periodic boundary conditions in our simulations and combined the entries for the corresponding times t and L_t-t.  "c_j_err" then gives the statistical errors of the partial wave expansion coefficients c_j for the different values of j, again as a function of t, starting with t=0 and ending at t=L_t/2+1.Lastly, c_conv contains the covariance matrix of the data. Here, we give the covariance matrix of the c_j data for all j, which we have concatenated for this purpose, starting with c_0 at t=0, running to c_0 at t=L_t/2+1 and then continuing with c_2 at t=0 etc until reaching c_20 at t=L_t/2+1. Thus, the entry with index (i, j) will give the covariance of c_{i integer division by L_t/2+1} at time t = i mod L_t/2+1 with c_{j integer division by L_t/2+1} at time t = j mod L_t/2+1. (Especially, the square roots of the diagonal entries give a concatenated list of c_j_err for all j.)<h3>ModelAveraging_L_.csv</h3>The ModelAveraging_L=_.csv files contain tables of the fit results that go into the final model averaged fit results shown in the paper, i.e. the fits that pass all employed cuts making sure the fits are physical, the parameters are constrained and the fits have an adequate model probability. For a detailed description of the fitting procedure and the employed cuts, see Section IV of the paper. Each line of the CSV file should contain 21 entries, separated by commas. Each line corresponds to one fit, and the fits are given in descending order of model probability. For each fit, we give<ul><li>"t_0_min": the firstf timeslice we include in this fit for c_0</li><li>"t_2_min": the first timeslice we include in this fit for c_2</li><li>"chi2_dof": the reduced chi^2 value of this fit</li><li>"AIC": the value of the Akaike Information Criterion for this fit</li><li>"prob": the model probability of this fit</li><li>"fe": the fit value for the OPE coefficient f^2_σσε</li><li>"fe_err": the fitting error for the OPE coefficient f^2_σσε</li><li>"De": the fit value for the scaling dimension ∆_ε</li><li>"De_err": the fitting error for the scaling dimension ∆_ε</li><li>"fT": the fit value for the OPE coefficient f^2_σσT</li><li>"fT_err": the fitting error for the OPE coefficient f^2_σσT</li><li>"DT": the fit value for the scaling dimension ∆_T</li><li>"DT_err": the fitting error for the scaling dimension ∆_T</li><li>"fep": the fit value for the OPE coefficient f^2_σσε'</li><li>"fep_err": the fitting error for the OPE coefficient f^2_σσε'</li><li>"Dep": the fit value for the scaling dimension ∆_ε'</li><li>"Dep_err": the fitting error for the scaling dimension ∆_ε'</li><li>"fTp": the fit value for the OPE coefficient f^2_σσT'</li><li>"fTp_err": the fitting error for the OPE coefficient f^2_σσT'</li><li>"DTp": the fit value for the scaling dimension ∆_T'</li><li>"DTp_err": the fitting error for the scaling dimension ∆_T'</li></ul><h3>free_cj_L_Lt_.dat</h3>Finally, in the free_cj_L_Lt_.dat files, we give the synthetic lattice data for the free theory calculated on our simplicial lattices by inversion of the quadratic action as described in Section VI of the paper. This data does not have errors, so we simply give the data for the free partial wave expansion coefficients c_j(t) as a function of the lattice time t. For each combination of L and L_t we supply a separate file, with the values of L and L_t written in the filename after the corresponding letter. Each file has 3 columns, the first one indicating the value of j, the second one the time t and the last one the value for c_j(t). The columns are separated by " ". Note that for the free theory, we only calculated c_j(t) for j up to 12.

opencc-by-4.0Nov 2023View details →

Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach

This repository contains i. optimized geometry of the cis and trans retinal, ii. figure labelling the internal coordinates of retinal.