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ADAR1 Links R-Loop Homeostasis to ATR Activation in Replication Stress Response
<p>Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.</p>
Data and R-code to reproduce analyses in: A Picture is Worth a Thousand Dollars: A photographic approach to studying color in anoles
<p>Data archive for MS: </p> <p><strong>A Picture is Worth a Thousand Dollars: A photographic approach to studying color in anoles</strong></p> <p>by Jacobs J, Salazar, J, and Winchell K.</p> <p>Archive includes 5 files:</p> <p>1. archived R markdown script (archiveddewlap_final.Rmd) with all analyses from the manuscript executable with the additional archived files (#3-5 below)</p> <p>2. pdf version of R markdown script with code and output (archiveddewlap_final.pdf)</p> <p>3. csv of dewlap color data from photographs (dewlap_archivedata_v1.csv)</p> <p>4. csv of metadata of population identity, SVL, and mass for all lizards (speciesbypopulation.csv)</p> <p>5. compressed file containing three folders: Bahamas specs, DR specs, and Jamaica specs, which include all spectral files for all lizards in the analysis (specs.zip)</p>
Supplementary material 2 from: Cumming RT, Le Tirant S, Linde JB, Solan ME, Foley EM, Eulin NEC, Lavado R, Whiting MF, Bradler S, Bank S (2023) On seven undescribed leaf insect species revealed within the recent "Tree of Leaves" (Phasmatodea, Phylliidae). ZooKeys 1173: 145-229. https://doi.org/10.3897/zookeys.1173.104413
All sampled specimens are listed with their collection data, deposition location, and GenBank accession numbers for the generated sequences.
i, Heterodontosaurus tucKi. j, Stegosaurus stenops. k, Protoceratops andrewsi. l, Iguanodon bernissartensis. m, Limusaurus inextricabilis. n, Deinocheirus mirificus. o, ErliKosaurus andrewsi. p, Citipati osmolsKae. q, Gobipteryx minuta. r in New reptile shows dinosaurs and pterosaurs evolved among diverse precursors
i, Heterodontosaurus tucKi. j, Stegosaurus stenops. k, Protoceratops andrewsi. l, Iguanodon bernissartensis. m, Limusaurus inextricabilis. n, Deinocheirus mirificus. o, ErliKosaurus andrewsi. p, Citipati osmolsKae. q, Gobipteryx minuta. r, Gallus gallus.
CROSMOD project "Crop Stress Monitoring in the semi-arid context of Doukkala, Morocco" supported by ESA and AUC in the framework of EO AFRICA R&D Facility
<p>The CROSMOD project “Crop Stress Monitoring in the semi-arid context of Doukkala, Morocco” supported by ESA and AUC in the framework of EO AFRICA R&D Facility, aimed at developing a procedure for crop yield estimates and extreme events crops shocks monitoring or pest and diseases by integrating multiple satellite data and water-energy-crop modelling, able to support farmers precision agriculture for the case of the Doukkala Irrigation area in Morocco. <strong>The project was run by: Chiara Corbari and Nicola Paciolla from Politecnico di Milano (Italy); and Fatima-ezzahra Elghandour and Youssef Houali from Chouaib Doukkali University (Morocco).</strong></p> <p>The dataset report the results from the three case studies, which are cultivated fields with alfalfa, sugar beet and wheat in Morocco (LE, H, net radiation, land surface temperature, ET, potential irrigation, LAI, soil moisture) generated from FEST-EWB-SAFY model.</p> <p>The crop-energy-water balance FEST-EWB-SAFY model (Corbari et al., 2022) couples the distributed energy-water balance FEST-EWB (Corbari et al, 2011), which allows computing continuously in time and distributed in space both soil moisture and evapotranspiration fluxes, and the SAFY (Duchemin et al, 2008), simple model for yield prediction and plant development. FEST-EWB is based on the system of energy-water balances equations which are written in terms of a LST that allows closing the energy balance equation, so that this model internal variable can be directly compared with EO LST for model parameters calibration (Corbari & Mancini, 2014). The crop growth simple model (SAFY) (Duchemin et al, 2008) simulate yield and LAI prediction based on light-use efficiency theory with leaf partitioning function.</p> <p><strong>The code was developed by Chiara Corbari and Nicola Paciolla from Politecnico di Milano (Italy).</strong></p> <p>[1] Corbari, C., Ravazzani, G. and Mancini, M. (2011), A distributed thermodynamic model for energy and mass balance computation: FEST–EWB. Hydrol. Process., 25: 1443-1452. <a href="https://doi.org/10.1002/hyp.7910">https://doi.org/10.1002/hyp.7910</a></p> <p>[2] Corbari, C., Ben Charfi, I., Al Bitar, A., Skokovic, D., Sobrino, J.A., Perelli, C., Branca, G., Mancini, M. (2022), A fully coupled crop-water-energy balance model based on satellite data for maize and tomato crops yield estimates: The FEST-EWB-SAFY model, Agr. Wat. Man., 272: 107850. <a href="https://doi.org/10.1016/j.agwat.2022.107850%5Cn">https://doi.org/10.1016/j.agwat.2022.107850\n</a></p> <p>[3] Corbari, C., Mancini, M., 2014. Calibration and validation of a distributed energy water balance model using satellite data of land surface temperature and ground discharge measurements. J. Hydrometeorol. 15, 376–392. <a href="https://doi.org/10.1175/JHM-D-12-0173.1">https://doi.org/10.1175/JHM-D-12-0173.1</a></p> <p>[4] Duchemin, B., Maisongrande, P., Boulet, G., Benhadj, I., 2008. A simple algorithm for yield estimates: Evaluation for semi-arid irrigated winter wheat monitored with green leaf area index. Environ. Modell. Softw. 23(7), 876-892. <a href="https://doi.org/10.1016/j.envsoft.2007.10.003">https://doi.org/10.1016/j.envsoft.2007.10.003</a></p>
CIFAR-10-R dataset
<p>Towards Realistic Out-of-Distribution Detection: A Novel Evaluation Framework for Improving Generalization in OOD Detection:</p> <p>This paper presents a novel evaluation framework for Out-of-Distribution (OOD) detection that aims to assess the performance of machine learning models in more realistic settings. We observed that the real-world requirements for testing OOD detection methods are not satisfied by the current testing protocols. They usually encourage methods to have a strong bias towards a low level of diversity in normal data. To address this limitation, we propose new OOD test datasets (CIFAR-10-R, CIFAR-100-R, and ImageNet-30-R) that can allow researchers to benchmark OOD detection performance under realistic distribution shifts. Additionally, we introduce a Generalizability Score (GS) to measure the generalization ability of a model during OOD detection. Our experiments demonstrate that improving the performance on existing benchmark datasets does not necessarily improve the usability of OOD detection models in real-world scenarios. While leveraging deep pre-trained features has been identified as a promising avenue for OOD detection research, our experiments show that state-of-the-art pre-trained models tested on our proposed datasets suffer a significant drop in performance. To address this issue, we propose a post-processing stage for adapting pre-trained features under these distribution shifts before calculating the OOD scores, which significantly enhances the performance of state-of-the-art pre-trained models on our benchmarks.</p>
CIFAR-100-R dataset
<p>Towards Realistic Out-of-Distribution Detection: A Novel Evaluation Framework for Improving Generalization in OOD Detection:</p> <p>This paper presents a novel evaluation framework for Out-of-Distribution (OOD) detection that aims to assess the performance of machine learning models in more realistic settings. We observed that the real-world requirements for testing OOD detection methods are not satisfied by the current testing protocols. They usually encourage methods to have a strong bias towards a low level of diversity in normal data. To address this limitation, we propose new OOD test datasets (CIFAR-10-R, CIFAR-100-R, and ImageNet-30-R) that can allow researchers to benchmark OOD detection performance under realistic distribution shifts. Additionally, we introduce a Generalizability Score (GS) to measure the generalization ability of a model during OOD detection. Our experiments demonstrate that improving the performance on existing benchmark datasets does not necessarily improve the usability of OOD detection models in real-world scenarios. While leveraging deep pre-trained features has been identified as a promising avenue for OOD detection research, our experiments show that state-of-the-art pre-trained models tested on our proposed datasets suffer a significant drop in performance. To address this issue, we propose a post-processing stage for adapting pre-trained features under these distribution shifts before calculating the OOD scores, which significantly enhances the performance of state-of-the-art pre-trained models on our benchmarks.</p>
Supplementary material 9 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Processed TaXon tables of each primer pair (subtracted negative controls and filtered for fish and lamprey taxa OTUs)
Supplementary material 1 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Pairwise comparison of the log-transformed reads of the non-normalized mock community (MC1) compared to the DNA concentration (ng/ul) of each species
Supplementary material 3 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Sampled specimens and their respective species assignment collected for the fish mock community, extraction date, collection site, and concentration after DNA extraction
Supplementary material 4 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
List of all species reported from Germany, their occurrence status, and their presence in the mock community (data from fishbase.org)
Supplementary material 2 from: Macher T-H, Schütz R, Yildiz A, Beermann AJ, Leese F (2023) Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: e103856. https://doi.org/10.3897/mbmg.7.103856
Pairwise comparison of the log-transformed reads of the non-normalized mock community (MC1) compared to log-transformed reads of the normalized mock community (MC2) of each species
FIGURE 11. The A.E. Brant & R in Critical review of "Monograph of Ceratozamia (Zamiaceae, Cycadales): an endangered genus" published in PhytoKeys 208: 1-102 (2022)
FIGURE 11. The A.E. Brant & R. Zúniga 2830 (EAP!) specimen that was designated the holotype of Ceratozamia hondurensis J.L.Haynes, Whitelock, Schutzman & R.S.Adams in the protologue (Haynes et al. 2008) (photos by Mark Bonta; used with permission). This specimen is now apparently lost (R. Fabiola Diaz pers. comm.), and a lectotype was designated in the monograph (Martínez-Dominguez et al. 2022a).
Data and R code for "Negative effects of wind on plant hydraulics at the global scale"
<p>To minimize ontogenetic and methodological variation, we only included trait data that met the following criteria: (a) plants were grown in natural ecosystems, excluding greenhouse and common garden experiments; (b) measurements were made on adult plants and not on seedlings; (c) hydraulic traits were measured on terminal stem or branch segments in the sapwood at the crown; and (d) trait data were calculated as the mean value for each species at the same site when data were from multiple sources.</p> <p>Climate data were obtained either from the original reports or from WorldClim version 2 (http://worldclim.org/version2) if the original data were not available. The following variables were extracted from WorldClim: mean annual wind speed, mean annual precipitation, mean annual temperature, precipitation seasonality, temperature seasonality, precipitation of driest month, and minimum temperature of coldest month. The VPD data was extracted from the TerraClimate dataset (http://www.climatologylab.org/terraclimate.html). Annual PET (potential evapotranspiration) data were extracted from the CGIAR-CSI consortium (http://www.cgiar-csi.org/data). The moisture index (MI) is the ratio of precipitation to PET.</p> <p>Simple linear regression was used to examine the relationships between two variables, utilizing the 'lm' function in R software. Partial regression analysis was conducted using the R package VISREG to investigate the relationships between wind speed and plant hydraulics while controlling for other variables. This analysis helped to illustrate the independent effect of wind on plant hydraulics. The Random Forest machine-learning algorithm (implemented using the R package randomForest) was utilized to assess the relative importance of environmental variables for each plant hydraulic trait. The Mean Decrease in Gini was calculated as the average of a variable's total decrease in node impurity, taking into account the proportion of samples that reach that node in each individual decision tree in the random forest. This provides a measure of a variable's importance in estimating the value of the target variable across all of the trees in the forest. A higher Mean Decrease in Gini value indicates greater importance of the variable. Multiple regression analyses were performed to develop predictive equations for plant hydraulic traits using environmental variables. To test for hydraulic traits-wind speed slope directions and differences among species groups in different climatic regions, we used standardized major axis (SMA) analyses. The R package SMATR was employed for these analyses. We considered <em>p </em>< 0.05 as the threshold for statistical significance in all models.</p>
FIGURE 6. Principal component analysis of the nine call measurements for various species selections. A: all small Anthus species except A. cervinus; B: two types of calls of A. r. rubescens and A. [r.] japonicus. C: only common-type calls of A. r. rubescens and A. [r.] japonicus; D: A. petrosus and different A. spinoletta subspecies; E: A. petrosus and A. s. spinoletta. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE 6. Principal component analysis of the nine call measurements for various species selections. A: all small Anthus species except A. cervinus; B: two types of calls of A. r. rubescens and A. [r.] japonicus. C: only common-type calls of A. r. rubescens and A. [r.] japonicus; D: A. petrosus and different A. spinoletta subspecies; E: A. petrosus and A. s. spinoletta.
FIGURE5. Sonograms of various calls from Anthus [rubescens] japonicus: A) M-shaped calls (xeno-canto.org: XC267502); B) and C) common calls (xeno-canto.org: XC437043 & The Sound Approach: 02.050. MR. 01938.02) and A. r. rubescens: D and E common calls (xeno-canto.org: XC598639, XC599314). in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE5. Sonograms of various calls from Anthus [rubescens] japonicus: A) M-shaped calls (xeno-canto.org: XC267502); B) and C) common calls (xeno-canto.org: XC437043 & The Sound Approach: 02.050. MR. 01938.02) and A. r. rubescens: D and E common calls (xeno-canto.org: XC598639, XC599314).
Bayesian phylodynamic and phylogeographic analyses of invasive, hypervirulent Streptococcus agalactiae sequence type 283 dataset and R code
<p>Supplementary dataset S1, R code, and subsampled trees</p>
Supplementary material 2 from: van den Broek R, Álvarez Fidalgo P, Smit J (2023) A new species of the genus Conosiphon Becker, 1923 and the first records of this genus for Europe (Diptera, Asilidae). ZooKeys 1181: 59-79. https://doi.org/10.3897/zookeys.1181.105663
Full details of the specimens of Conosiphon ianus Álvarez Fidalgo & van den Broek, sp. nov. used for DNA barcoding
Supplementary material 1 from: van den Broek R, Álvarez Fidalgo P, Smit J (2023) A new species of the genus Conosiphon Becker, 1923 and the first records of this genus for Europe (Diptera, Asilidae). ZooKeys 1181: 59-79. https://doi.org/10.3897/zookeys.1181.105663
Data compilation of live specimens of Conosiphon ianus Álvarez Fidalgo & van den Broek, sp. nov.
F I G U R E 1 in The nutritional importance of invertebrates to female Cebus capucinus imitator in a highly seasonal tropical dry forest
F I G U R E 1 The (a) monthly fruit energy density versus the monthly percentage of energy intake from invertebrates for all female capuchins studied and (b) group-level linear regression results between ripe fruit energy density and the percentage of energy intake from invertebrates (log transformed) for our three capuchin study groups. One outlier month (> 2 SD from the mean) was removed from the intergroup analysis
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.