Contributors: Jesper Rindom Jensen, Sam Karimian-Azari, Jacob Benesty, Mads Christensen
... This dataset contains the code that were used for conducting the experimental evaluations in the paper. Moreover, it contains the speech data used for the evaluation on synthetic data in the manuscript, i.e., to produce the results presented in Figs. 1-3. The evaluation on real data was conducted on data from SMARD (https://www.smard.es.aau.dk/). More specifically, the signals labeled FA0309 and MD2404 in the two scenarios labelled 1011 and 1111 were considered, and, for each scenario, the two ULAs, A and B, were used for the evaluation.
Data for: Where has the city choir gone? Loss of the temporal structure of bird dawn choruses in urban areas
Contributors: Oscar Humberto Marín Gómez, Ian MacGregor-Fors, J. Roberto Sosa López, Wesley Dáttilo, Diego Santiago-Alarcón
... Suplemmentary material for the manuscript “Where has the city choir gone? Loss of the temporal structure of bird dawn choruses in urban areas” Title: dawn_chorus_diversity. Incidence matrices for the recorded assemblages during dawn choruses from heavily-urbanized areas and peri-urban forest. Species richness was compared through rarefaction an confidence intervals (IC84%) and composition between both studied conditions using the βsim index. Title: dawn choruses networks data (dawn_choruses_network_data.zip). Weighted matrices of song duration (s) for each species (columns) in each 5-min time period (rows), from peri-urban forest and heavily urbanised conditions. Negative values in time are relative to sunrise. The network patterns of dawn choruses were assessed using bipartite network analysis through modularity (QuanBiMo) and nestedness (WNODF) metrics. Null model comparisons were used to control estimate the statistical significance with z-score tests. The code are also provided in the folder. Title: niche overlap matrices (niche_overlap_matrices.zip). Matrices of the average peak, low and high song frequencies (kHz) by each species singing in dawn choruses at each 5-min time period, from studied dawn choruses for each survey site and within choruses. Negative values in time are relative to sunrise. The degree of spectral overlap (Czechanowski index) were calculated in EcoSimR 0.1.0 (http://ecosimr.org) contrasted the observed overlap with 1000 randomly generated assemblages using the algorithm RA3 that reshuffles row values to different categories. The code are provided in each folder. Title: phylogenetic structure of bird assemblges recorded during dawn choruses. Incidence matrices for the studied dawn choruses for each survey site and within choruses to calculate the mean nearest taxon distance (MNTD) using the package picante. Positive values of SES (mntd.obsz > 0 and mntd.obsp >0.95) indicate phylogenetic evenness (i.e., co-occurring species more distantly phylogenetically related than expected by chance), while negative values of SES (mntd.obsz 0.05) phylogenetic clustering. A Strict consensus tree (Newick format) of the bird community based on the 1000 trees obtained from birdtree (Ericson All Species) and de code are also included. Example of dawn chorus at peri-urban forest, corresponding to 5 min after and before sunrise. Example of dawn chorus at heavily-urbanized areas, corresponding to 5 min after and before sunrise.
EXD2 protects stressed replication forks and is required for cell viability in the absence of BRCA1/2. Nieminuszczy et al.
Contributors: Jadwiga Nieminuszczy, Ronan Broderick, Marina Bellani, Elizabeth Smethurst, Rebekka Schwab, Veronica Cherdyntseva, Theodora Evmorfopoulou, Yea-Lih Lin, Michal Minczuk, Philippe Pasero
... Original imaging data related to Nieminuszczy et al. "EXD2 Protects Stressed Replication Forks and Is Required for Cell Viability in the Absence of BRCA1/2”, Molecular Cell (2019) DOI:https://doi.org/10.1016/j.molcel.2019.05.026
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