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COVID-19 case-fatality–derived age-adjusted risk of death
<p><strong>This is a version of the plot without split into gender-adjusted risks. For the newer version with gender-adjusted curves, please visit </strong><a href="https://zenodo.org/record/3829175">https://zenodo.org/record/3829175</a><br> doi:10.5281/zenodo.3787931</p> <p>This is a plot of the risk of death in COVID-19, which was adjusted by the age and derived from the case fatality data kindly collected by the team of data scientists and data engineers participating in the Kaggle project Data Science for COVID-19 in South Korea (DS4C), which is hosted at https://www.kaggle.com/kimjihoo/coronavirusdataset.</p> <p>The model for the plot was created with the release 2.1 of the Python & C library initially published on April 3, 2020 on GitHub at https://github.com/yuryatin/covid19_age_adjusted_mortality.</p> <p>Please, visit https://github.com/yuryatin/covid19_age_adjusted_mortality for more detailed description of the model and the source code.</p>
2D numerical modelling: the case study of the Arno River at Greve junction
<p>files description:</p> <p>- "nuova mesh_barra.2dm" is the input mesh file for BASEMENT;</p> <p>- "veg. surveys.docx" shows the data collected during the vegetation surveys activities.</p>
SPEC RG Technical Report: A Review of Serverless Use Cases and their Characteristics - Dataset
<p><strong><em>PrettyDataset.xlsx</em></strong></p> <p>Our data set of 89 serverless use cases and their mapping to 24 characteristics. In form of an Excel file to simplify manual inspection. Columns represent characteristics, rows represent use cases.</p> <p><em><strong>Dataset.csv</strong></em></p> <p>Raw version of our data set of 89 serverless use cases and their mapping to 24 characteristics as a CSV file for automated analysis. Columns represent characteristics, rows represent use cases.</p> <p><em><strong>Initial Characterizations.csv</strong></em></p> <p>Reviewer characterizations prior to the discussion and consolidation phase. Required for the calculation of the fleiss kappa score.</p> <p><em><strong>CalculateKappa.py</strong></em></p> <p>Python script for the calculation of the fleiss kappa score shown in the technical report. Requires Python 3.6.</p> <p><em><strong>GenerateFigures.py</strong></em></p> <p>Python script for the generation of all figures shown in the technical report. Requires Python 3.6.</p>
Data from: Patterns of intraspecific variation through ontogeny–a case study of the Cretaceous nautilid Eutrephoceras dekayi and modern Nautilus pompilius
<p>The magnitude and ontogenetic patterns of intraspecific variation can provide important insights into the evolution and development of organisms. Understanding the intraspecific variation of organisms is a key to correctly pursuing studies in major fields of palaeontology. However, intraspecific variation has been largely overlooked in ectocochleate cephalopods, particularly nautilids. Furthermore, little is known regarding the evolutionary pattern. Here, we present morphological data for the Cretaceous nautilid <i>Eutrephoceras dekayi</i> (Morton, 1834) and the modern nautilid <i>Nautilus</i> <i>pompilius </i>Linnaeus, 1758<i> </i>through ontogeny. The data are used to describe the change of conch morphology and to elucidate the evolutionary patterns of intraspecific variation. We discovered the presence of morphological changes at hatching and maturity, which is shared in every conch parameter in <i>E. dekayi</i> and <i>N. pompilius</i>. We also found that intraspecific variation is high in early ontogeny in both taxa, followed by various patterns in later ontogeny. The high variation in early ontogeny may imply their flexibility of changing the timing of growth events, which may have played an important role in nautilid evolutioin. We assume that the decrease in variation in later ontogeny may indicate developmental constraints. Lastly, we compared the similarity/dissimilarity of ontogenetic patterns of variation between taxa. Results reveal that the similarity/dissimilarity of the ontogenetic pattern differs between <i>E. dekayi</i> and <i>N. pompilius</i>. We conclude that this shift in the ontogenetic pattern of variation may be rooted in changes in the developmental program of nautilids through time. We propose that studying ontogenetic patterns of intraspecific variation can provide new insights into the evolution and development of organisms. </p>
plan4res - public dataset for case study 1 part MIM-1: time series used for multi-modal investment pathway modelling
<p>Public data set which is used within the plan4res project for performing case study 1 "Multi-modal European energy concept for achiving COP21" - Multi-modal Investment modelling (MIM) Part 1: Time series for the reference year 2015</p> <p>The related documentation is included in plan4res' deliverable D4.5 chapter 3.2 (see 10.5281/zenodo.3785010) </p> <p>The data set includes the following data:</p> <p>a) characteristic annual load profiles for large industrial heat demand for chemical, iron & steel, food & beverage and pulp & paper industries for the reference year 2015</p> <p>HOTMAPS__TD_OUT_D_CHEM__20200608T160653__20200422T120000Z__v01.csv <br> HOTMAPS__TD_OUT_D_FOOD__20200608T160724__20200422T120000Z__v01.csv <br> HOTMAPS__TD_OUT_D_IRON__20200608T160705__20200422T120000Z__v01.csv HOTMAPS__TD_OUT_D_PAPER__20200608T160715__20200422T120000Z__v01.csv </p> <p>b) characteristic demand profiles for road-side car passenger transport and availability of cars for charging while (home) parking for the reference year 2015 </p> <p>SIEMENS__TD_OUT_D_RoadCar__20200608T160627__20200401T120000Z__v01.csv SIEMENS__TD_CAP_CarPark__20200608T160637__20200401T120000Z__v01.csv </p> <p>c) load profiles for exogeneous demand of electricity for the reference year 2015. The exogenous demand includes all electricity consumptions not explicitly modeled within MIM modeling.</p> <p>HRE4__TD_OUT_ElectricityExo__20200608T160732__20200401T120000Z__v01.csv </p> <p>c) regionally resolved demand profiles for (individual) space heating and space cooling for the reference year 2015</p> <p>HRE4__TRD_CAP_Cool_2015__20200608T160051__20200401T120000Z__v01.csv <br> HRE4__TRD_CAP_HeatInd_2015__20200608T155849__20200401T120000Z__v01.csv</p> <p>d) regionally resolved generation profiles of electricity from photovoltaic, wind onshore, wind offshore, hydro run-of-river, and for heat generation from solar thermal for the reference year 2015</p> <p>NINJA__TRD_CAP_PV_2015__20200608T160440__20191104T120000Z__v01.csv <br> NINJA__TRD_CAP_WindOFF_2015__20200608T155422__20191104T120000Z__v01.csv <br> NINJA__TRD_CAP_WindON_2015__20200608T155251__20191104T120000Z__v01.csv HRE4__TRD_CAP_HydroRoR_2015__20200608T155550__20200401T120000Z__v01.csv <br> HRE4__TRD_CAP_SolarThermal_2015__20200608T155718__20200401T120000Z__v01.csv </p> <p>e) regionally resolved generation profile of electricity from wind offshore transformed in a way to represent potential capacity factors in future as stated by doi:10.2760/041705. Data based on reference year 2015</p> <p>SIEMENS__TRD_CAP_WindOFF_2040__20200608T155127__20200401T120000Z__v01.csv </p> <p>x) A list of geographical description of the zone hierarchy data used in MIM for the EU33 region set.:</p> <p>SIEMENS__ZoneHierarchy_MIM_EU33__20181231T120000Z___20200131T1200000Z__v001.csv </p> <p>Further info:</p> <p>Time series are based on historical data for the reference year 2015. </p> <p>Values are normalized over one reference year in a way that either the maximum = 1 (CAP) or the integral = 1 (OUT).</p> <p>All values are listed in arbitrary units. </p> <p>All country names are according to ISO 3166-1 alpha-2.</p>
ARTICONF Use Case Focus Group -2 Dataset
<p>This dataset corresponds to focus group discussion for ARTICONF use cases. The members participating in this discussion are from various sectors and industries.</p>
Supplementary videos for "Active flow network generates molecular transport by packets: case of the endoplasmic reticulum"
<p>Videos showing simulated motion on the active flow network for different switching timescales. In particular, compare <span class="math-tex">\(\tau_{\text{switch}} = 3 \text{ s}\)</span> to <span class="math-tex">\(\tau_{\text{switch}} = 30 \text{ ms}\)</span>. The red bubbles are proportional to the number of particles present in a node. Initially, all particles are placed in a central source node.</p>
Data from: Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes
<p>While theory predicts that dispersal is a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical studies are needed to quantify its role. In many studies, dispersal reduction appears to promote diversification, although some analyses of migratory species suggest otherwise. Here we test for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a molecular phylogeny for the group, comprising >95% of extant lineages, and applied State-dependent Speciation Extinction models to estimate speciation, extinction, and diversification rates. In contrast to some previous studies, we revealed higher diversification rates in non-migratory lineages. The reduced gene flow experienced by non-migratory galaxiids appears to have increased diversification under conditions of allopatry or local adaptation. Migratory galaxiid lineages, by contrast, are genetically homogeneous within landmasses, but may also be rarely able to colonise other landmasses in the temperate Southern Hemisphere. The life history state exhibiting higher diversification likely reflects the spatial context of the study system relative to species dispersal abilities, by means of the intermediate dispersal model; the accurate quantification of dispersal abilities will aid in our understanding of these likely interactions.</p>
Effects of protected areas on welfare of local households: the case of Maasai Mara National Reserve in Kenya
<ol> <li>Protected areas are vital for biodiversity conservation although some have been criticized for not providing adequate socio-economic benefits to local people. However, empirical studies on socio-economic impacts of protected areas that control for confounding factors are rare.</li> <li>Here, we assessed the potential impacts of Maasai Mara National Reserve in South-Western Kenya on welfare (indicated by levels of income, consumption, and assets) of, and poverty incidence among 423 randomly selected local households. We used descriptive statistics to summarize demographic and socio-economic statuses of the households. Then, we estimated effects of the protected area on welfare of the households using ordinary least - squares regression model and entropy balancing.</li> <li>The protected area did not have any significant effect on welfare of, and poverty levels among the households. Households that lived within a 5 km radius of the protected area boundary incurred significantly higher crop destruction and livestock depredation losses than households that lived 5 - 25 km from the boundary. Nevertheless, majority of the households held positive views about the protected area due to direct and indirect benefits that they had already gained or expected to gain from it in the future.</li> <li>These results suggest that interventions are needed to reduce losses caused by wildlife in the protected area and improve its social and economic benefits to the local households.</li> </ol>
Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)
<p>Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic dataset, including <span>14,208 loci (>2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. </span>Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid datasets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting (ILS). We use this phylogeny to establish a new<span> higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order.</span> We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved ~79.5 million years ago (Ma) in the late Cretaceous, but that most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma)<span>. </span>Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when datasets are large and yield high support for phylogenetic relationships.</p>
CoP vs. CoM stabilization strategies: the tightrope balancing case
<p>This study proposes a generalization of the ankle and hip postural strategies to be applied to the large class of skills that share the same basic challenge of defeating the destabilizing effect of gravity on the basis of the same neuromotor control organization, adapted and specialized to variable number of degrees of freedom, different body parts, different muscles, and different sensory feedback channels. In all the cases we can identify two crucial elements (the CoP - Center of Pressure and the CoM - Center of Mass) and the central point of the paper is that most balancing skills can be framed in the CoP-CoM interplay and can be modeled as a combination/alternation of two basic stabilization strategies: the standard well investigated COPS (or CoP strategy, the default option), where the CoM is the controlled variable and the CoP is the control variable, and the less investigated COMS (or CoM strategy), where CoP and CoM must exchange their role because the range of motion of the CoP is strongly constrained by environmental conditions.</p> <p>The paper focuses on the tightrope balancing skill where sway control in the sagittal plane is modeled in terms of the COPS while the more challenging sway in the coronal plane is modeled in terms of the COMS, with the support of a suitable balance pole. Both stabilization strategies are implemented as state-space intermittent, delayed feedback controllers, independent of each other. Extensive simulations support the degree of plausibility, generality, and robustness of the proposed approach.</p>
Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees
<p>It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes.</p>
Very high rate GPS observables at San Pedro Martir, Mexico (SPIG) continously operating station: dataset for the case study. Part 4.
<p>Archived data is on a Trimble raw T02 format from a Trimble NetR9 receiver. Complete metadata for the station can be obtained at the TLALOCNet archive at <strong>http://tlalocnet.udg.mx</strong>.</p> <p>This dataset is a high rate (50hz) version of the SPIG continous GPS station observables that is otherwise available as a 15 sec recording on the TLALOCNet archive (<strong>http://tlalocnet.udg.mx</strong>).</p> <p>Any use of this dataset or parts of it must give the proper acknowledgement, including the Zenodo assigned DOI (10.5281/zenodo.4002090) as follows:</p> <p>This material is partly based on GPS data provided by the SSN-Trans-boundary, Land and Atmosphere Long-term Observational and Collaborative Network (TLALOCNet; Cabral-Cano et al., 2018 and Pérez-Campos et al., 2018) jointly operated by Servicio de Geodesia Satelital (SGS) and Servicio Sismológico Nacional (SSN) at the Instituto de Geofísica-Universidad Nacional Autónoma de México in collaboration with UNAVCO, Inc. We gratefully acknowledge all the personnel from SGS, SSN and UNAVCO for station installation, maintenance, data acquisition, permanent IT support and data distribution. TLALOCNet and related GPS operations at SGS are supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT) projects 253760 and 2017-01-5955, by the National Science Foundation grant EAR-1338091 and supplemental support from UNAM-Instituto de Geofísica.<br> <br> <strong>References</strong>.</p> <p>E. Cabral-Cano, X. Pérez-Campos, B. Márquez-Azúa, M. A. Sergeevaa, L. Salazar-Tlaczani, C. DeMets, D. Adams, J. Galetzka, K. Feaux, Y. L. Serra, G. S. Mattioli, and M. Miller, 2018. TLALOCNet: A Continuous GPS-Met Backbone in Mexico for Seismotectonic, and Atmospheric Research. Seismological Research Letters, v. 89, n. 2ª, p. 373-381. https://doi.org/10.1785/0220170190.</p> <p>X. Pérez‐Campos, V.H. Espíndola, J. Pérez, J. A. Estrada C. Cárdenas Monroy, D. Bello, Adriana González‐López, Daniel González Ávila, Moisés Gerardo Contreras Ruiz Esparza, Rafael Maldonado, Yi Tan, Iván Rodríguez Rasilla, Miguel Ángel Vela Rosas, José Luis Cruz, Arturo Cárdenas, Fernando Navarro Estrada, Alejandro Hurtado, Antonio de Jesús Mendoza Carvajal, Edgar Montoya‐Quintanar, Miguel A. Pérez‐Velázquez, 2018. The Mexican National Seismological Service: An Overview. Seismological Research Letters, v. 89, n. 2ª, p.318-323. https://doi.org/10.1785/0220170186.</p>
Very high rate GPS observables at Coeneo, Mexico (UCOE) continously operating station: dataset for the case study. Part 3.
<p>Archived data is on a Trimble raw T02 format from a Trimble NetR9 receiver. Complete metadata for the station can be obtained at the TLALOCNet archive at <strong>http://tlalocnet.udg.mx</strong>.</p> <p>This dataset is a high rate (50hz) version of the UCOE continous GPS station observables that is otherwise available as a 15 sec recording on the TLALOCNet archive (<strong>http://tlalocnet.udg.mx</strong>).</p> <p>Any use of this dataset or parts of it must give the proper acknowledgement, including the Zenodo assigned DOI (10.5281/zenodo.4002072) as follows:</p> <p>This material is partly based on GPS data provided by the Trans-boundary, Land and Atmosphere Long-term Observational and Collaborative Network (TLALOCNet; Cabral-Cano et al., 2018) jointly operated by Servicio de Geodesia Satelital (SGS) at the Instituto de Geofísica-Universidad Nacional Autónoma de México in collaboration with UNAVCO, Inc. We gratefully acknowledge Armando Carrillo-Vargas and all the personnel from SGS and UNAVCO at for station installation, maintenance, data acquisition, permanent IT support and data distribution. TLALOCNet and related GPS operations at SGS are supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT) projects 253760 and 2017-01-5955, by the National Science Foundation grant EAR-1338091 and supplemental support from UNAM-Instituto de Geofísica.<br> <br> <strong>References</strong>.</p> <p>E. Cabral-Cano, X. Pérez-Campos, B. Márquez-Azúa, M. A. Sergeevaa, L. Salazar-Tlaczani, C. DeMets, D. Adams, J. Galetzka, K. Feaux, Y. L. Serra, G. S. Mattioli, and M. Miller, 2018. TLALOCNet: A Continuous GPS-Met Backbone in Mexico for Seismotectonic, and Atmospheric Research. Seismological Research Letters, v. 89, n. 2ª, p. 373-381. https://doi.org/10.1785/0220170190.</p>
Case Studies analysis of prospects for different CSP technology concepts - Input data
<p><strong>Description of the dataset</strong></p> <p>This dataset contains the input data (.inc files) for Balmorel, used for the Case Studies analysis of prospects for different CSP technology concepts conducted within Deliverable 8.1 in the MUSTEC project.</p> <p>For description of the modelled scenarios, results and findings, see: Schöniger, F., Resch, G. (2019):<em> Case Studies analysis of prospects for different CSP technology concepts. </em>Deliverable 8.1 MUSTEC project, TU Wien, Wien.</p> <p>For information on the project see: https://www.mustec.eu/</p> <p><strong>Data format</strong></p> <p>We provide the data in form of the data folders holding the .inc files for the scenarios described in the report above.</p> <p>The original Balmorel source code is available under https://github.com/balmorelcommunity/Balmorel under the ISC license. It was adapted in order to include a new technology generating electricity from heat (GETOH). The inputs for this development were kindly supported by DTU and Ea Energy Analyses with previously done works.</p>
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
<p>How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, High-Throughput Sequencing (HTS) technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this study, using 13,909 full-length barcodes obtained by Sanger sequencing or the SOAPBarcode metabarcoding method, we showed that competition was the main assembly mechanism for the moth communities studied in temperate forests of China. The two sequencing methods showed highly consistent results with regards to both diversity composition and community assembly mechanism. Significant phylogenetic signals and structure suggested that the focal moth communities were the result of the non-neutral assembly process, which was further confirmed by results of neutral assembly test that accounted for immigration and speciation rates. In conclusion, HTS coupled with a well-curated DNA barcode library can facilitate community assembly inferences, especially for speciose taxonomic groups.</p>
Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)
<p>Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid <i>Diictodon feliceps</i>. Distorted <i>Diictodon </i>crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, 'saddle-shape' deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known 'biological' signals and subjected to uniform shear, deformation was typically the main source of variance but accurate 'biological' information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed <i>Diictodon </i>specimens exhibit significant dispersion around the 'true' position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.</p>
Data from: Avian ecological succession in the Amazon: a long-term case study following experimental deforestation
<p>Approximately 20% of the Brazilian Amazon has now been deforested, and the Amazon is currently experiencing the highest rates of deforestation in a decade, leading to large-scale land-use changes. Roads have consistently been implicated as drivers of ongoing Amazon deforestation and may act as corridors to facilitate species invasions. <span>Long-term data, however, are necessary to determine how ecological succession alters avian communities following deforestation and whether established roads lead to a constant influx of new species. </span> </p> <p>We used data across nearly 40 years from a large-scale deforestation experiment in the central Amazon to examine the avian colonization process in a spatial and temporal framework, considering the role that roads may play in facilitating colonization.</p> <p>Since 1979, 139 species that are not part of the original forest avifauna have been recorded, including more secondary forest species than expected based on the regional species pool. Among the 35 species considered to have colonized and become established, a disproportionate number were secondary forest birds (63%), almost all of which first appeared during the 1980s. These new residents comprise about 13% of the current community of permanent residents.</p> <p><span>Widespread generalists associated with secondary forest colonized quickly following deforestation, with few new species added after the first decade, despite a stable road connection. Few species associated with riverine forest or specialized habitats colonized, despite road connection to their preferred source habitat. </span>Colonizing species remained restricted to anthropogenic habitats and did not infiltrate old-growth forests nor displace forest birds.</p> <p>Deforestation and expansion of road networks into <i>terra firme </i>rainforest will continue to create degraded anthropogenic habitat. Even so, the initial pulse of colonization by non-primary forest bird species was not the beginning of a protracted series of invasions in this study, and the process appears to be reversible by forest succession. </p>
VTR case studies datasets: myoglobin against hemoglobin, RBDs of SARS-CoV-1 vs. SARS-CoV-2, and glucose-tolerant vs. non-tolerant β-glucosidases
<p>Description of the four files:</p> <ol> <li><strong>contacts.xlsx</strong> <ul> <li>List of detected contacts for the three case studies</li> </ul> </li> <li><strong>pymol_files_case_study_1.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 1: comparison between contacts of myoglobin against hemoglobin</li> </ul> </li> <li><strong>pymol_files_case_study_2.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 2: comparison between contacts of RBDs of SARS-CoV-1 vs. SARS-CoV-2 both complexed with the cell receptor ACE2</li> </ul> </li> <li><strong>pymol_files_case_study_3.zip</strong> <ul> <li>Contains files in PDB format of the analyzed structures, and files in PML format used to display visualizations in the PyMOL tool for the case study 3: comparison between contacts of glucose-tolerant vs. non-tolerant β-glucosidases </li> </ul> </li> </ol>
Caterpillars on a phytochemical landscape: the case of alfalfa and the Melissa blue butterfly
<p>Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant-animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to quantify plant metabolites and the performance of caterpillars as affected by both individual compounds and suites of covarying phytochemicals. We find that survival, development time and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti-herbivore action. The plant-insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes.</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.