Find research datasets worth reusing

opencc-by-4.0Mar 2022View details →

Supplementary Table S3 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S3. Repository data for the global analysis produced for cv Giza 178.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 178 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 178 up regulated genes.    D, GOEA results for Giza 178 down regulated genes.

opencc-zeroMar 2022View details →

Data from: Woody plant secondary chemicals increase in response to abundant deer and arrival of invasive plants in suburban forests

Plants in suburban forests of eastern North America face the dual stressors of high white-tailed deer density and invasion by nonindigenous plants. The combination of chronic deer herbivory and strong competition from invasive plants could alter a plant's stress- and defense-related secondary chemistry, especially for long-lived juvenile trees in the understory, but this has not been studied. We measured foliar total antioxidants, phenolics, and flavonoids in juveniles of two native trees, Fraxinus pennsylvanica (green ash) and Fagus grandifolia (American beech), growing in six forests in the suburban landscape of central New Jersey, USA. The trees grew in experimental plots that had been subject for 2.5 years to factorial treatments of deer access/exclosure X addition/no addition of the nonindigenous invasive grass Microstegium vimineum (Japanese stiltgrass). As other hypothesized drivers of plant secondary chemistry, we also measured non-stiltgrass herb layer cover, light levels, and water availability. Univariate mixed model analysis of the deer and stiltgrass effects and multivariate structural equation modeling (SEM) of all variables showed that both greater stiltgrass cover and greater deer pressure induced antioxidants, phenolics, and flavonoids, with some variation between species. Deer were generally the stronger factor, and stiltgrass effects were most apparent at high stiltgrass density. SEM also revealed that soil dryness directly increased the chemicals; deer had additional positive, but indirect, effects via influence on the soil; in beech PAR positively affected flavonoids; and herb layer cover had no effect. Juvenile trees' chemical defense/stress responses to deer and invasive plants can be protective, but also could have a physiological cost, with negative consequences for recruitment to the canopy. Ecological implications for species and their communities will depend on costs and benefits of stress/defense chemistry in the specific environmental context, particularly with respect to invasive plant competitiveness, extent of invasion, local deer density, and deer browse preferences.

opencc-zeroMar 2022View details →

Predicted alteration of vertebrate communities in response to climate-induced elevational shifts

Aim Climate change is driving species to migrate to novel areas as current environments become unsuitable. As a result, species distributions have shifted uphill in montane ecosystems globally, leading to projections of severe impacts on upland specialist species. Heterogenous dispersal rate among shifting species could result in complex changes to community assemblages. For example, interspecific differences in dispersal ability could lead to the disruption, or creation, of species interactions and processes within communities, likely amplifying the impact of climate change on ecosystems. Here, we provide a comprehensive assessment of the impacts of climate change on communities and ecosystems by developing a novel spatially explicit approach focussing on changes in local populations. Location The Australian Wet Tropics. Method We used a spatially explicit approach to simulate the elevational shift of 7,613 community assemblages (defined at the patch level) along the elevational gradient, using empirical information about the distribution of 202 vertebrate species. We analysed changes in community structures and species co-occurrence derived from the elevational shift as a proxy for potential changes in species interactions. Results Our results showed a consistent pattern of increasing temporal β-dissimilarity between community assemblages along the elevational gradient resulting from local species extinctions. The local extinction rate was especially remarkable at high elevations, suggesting potential mass local extinctions of upland species unable to shift to the isolated mountaintops. Furthermore, the increasing local extinction rate with elevation resulted in a marked decline in species co-occurrence towards mountaintops. Main conclusions Our study highlights the escalating impact of climate change on community assemblages in response to climate-induced elevational shifts in species' ranges, providing a classic example of the "escalator to extinction". Future predictions of the impacts of climate change on ecosystems will benefit from improvements in understanding species interactions and species potential to adapt to a changing environment.

opencc-by-4.0Mar 2022View details →

Role of Alkylhydroperoxidase Rv2159c in the Oxidative Stress Response and Virulence of Mycobacterium tuberculosis

Mycobacterium tuberculosis, which causes tuberculosis, is one of the leading infectious agents worldwide with a high rate of mortality. Following aerosol inhalation, M. tuberculosis primarily infects the alveolar macrophages, which results in a host immune response that gradually activates various antimicrobial mechanisms, including the production of reactive oxygen species (ROS), within the phagocytes to neutralize the bacteria. OxyR is the master regulator of oxidative stress response in several bacterial species. However, due to the absence of a functional oxyR locus in M. tuberculosis, the peroxidase stress is controlled by alkylhydroperoxidases. M. tuberculosis expresses alkylhydroperoxide reductase to counteract the toxic effects of ROS. In the current study, we report the functional characterization of an ortholgue of alkylhydroperoxidase family member, Rv2159c, a conserved protein with putative peroxidase activity, during stress response and virulence of M. tuberculosis. We generated a gene knockout mutant of M. tuberculosis Rv2159c (MtbΔ2159) by specialized transduction. The MtbΔ2159 was sensitive to oxidative stress and exposure to toxic transition metals. In a human monocyte (THP-1) cell infection model, MtbΔ2159 showed reduced intracellular survival and increased expression of pro-inflammatory molecules, includingIL-1β, IP-10 and MIP-1α, compared to the wild type M. tuberculosis and Rv2159c-complemented MtbΔ2159 strains. Similarly, in a guinea pig model of pulmonary infection, MtbΔ2159 displayed growth attenuation in the lungs, compared to the wild type M. tuberculosis and Rv2159c-complemented MtbΔ2159 strains. Our study suggests that Rv2159c has a significant role in maintaining the cellular homeostasis during stress and virulence of M. tuberculosis.

opencc-by-4.0Mar 2022View details →

Images and data accompanying article: Remarkable response of hollow thermoplastic microspheres-elastomer matrix composites in uniaxial tension.

Images and data accompanying article: Remarkable response of hollow thermoplastic microspheres-elastomer matrix composites in uniaxial tension.* By Michel Coret, Erwan Verron & Pierre Rublon (<a href="http://hal.archives-ouvertes.fr/hal-03480982">https://hal.archives-ouvertes.fr/hal-03480982</a>) Abstract of the article  In the last few years, the mechanical response of hollow thermoplastic micro-spheres-elastomer matrix composites has been investigated. The large majority of the studies focuses on their compressive properties and particularly on the stress-strain response. In the present paper, large strain uniaxial tension experiments are conducted on thermoplastic microspheres filled polyurethane elastomer. Six volume fractions of microspheres are considered. Thanks to a two-camera setup and digital image correlation measurements, the volumetric response of the materials is extensively analyzed. As a major result, the remarkable volumetric behaviour is highlighted: the hydrostatic pressure vs. volume change curves admit several extrema that may be read as the macroscopic signature of the complex microstructural phenomena involved during deformation. Moreover, it is shown that the size of the volumetric loading-unloading hysteresis loop is directly related to the volume fraction of microspheres in the materials. Experimental test methodology is described within the article. The objective of the deposit is to share data. Description of the deposit Objectives: The objective of this deposit is to share all the data needed to retrieve the results presented in the article (<a href="http://hal.archives-ouvertes.fr/hal-03480982">https://hal.archives-ouvertes.fr/hal-03480982</a>). This deposit do not explain any experimental methodology, that can be found in the article. Data overview: <ol> <li>The images taken during the tests (raw data)</li> <li>Force and displacement measured by the tensile machine (raw data).</li> <li>Surface strain field on face and lateral sides of the tensile specimen (obtain by Digital Image Correlation)</li> <li>Averaged and filtered</li> </ol> Data description: 1. Image directories: "YY/MM/DD_poro_xx_spec_nn" <ul> <li>  YY/MM/DD: date of the test</li> <li>  xx: specimen porosity (can be one of these values [0, 05, 10, 15, 20, 25] in %)</li> <li>  nn: Specimen number</li> </ul>    In each directory you will find: <ul> <li>  YY/MM/DD_poro_xx_spec_nn-aaaaa_0.tif (face side *aaaaa* image)</li> <li>  YY/MM/DD_poro_xx_spec_nn-bbbbb_1.tif (lateral side *bbbbb* image</li> <li>  YY/MM/DD_poro_xx_spec_nn.csv (Synchronized analogic data with images) <ul> <li>Column A: Image n°</li> <li>Columns B & C: Image file name</li> <li>Columns D & E: Timestamp</li> <li>Columns F & G: Analog data (Volts)</li> <li>Column H: Position of the jack (millimeter)</li> <li>Column I: Measured force (N)</li> </ul> </li> </ul> 2. Scalar data directory: Data_csv/ <ul> <li>DIC: strain average results from digital image correlation on face side (axis xy) and lateral side (axis yz) <ul> <li>Column A: Image n°</li> <li>Column B, C, D (Hencky strains): exx, eyy & exy</li> <li>Column E, F (Hencky eigen strains): e1 & e2</li> </ul> </li> </ul>      <ul> <li>Machine: displacement and force from tensile machine for each image <ul> <li>Column A: Image n°</li> <li>Columns B & C: Image file name</li> <li>Columns D & E: Timestamp</li> <li>Columns F & G: Analog data (Volts)</li> <li>Column H: Position of the jack (millimeter)</li> <li>Column I: Measured force (N)</li> </ul> </li> </ul>      <ul> <li>Post: Average + smoothed data for each porosities <ul> <li>Column A: Longitudinal stretch $\lambda$</li> <li>Column B: Nominal stress P</li> <li>Column C: Lateral stretch ratio  $\lambda_w=\lambda_t$  </li> </ul> </li> </ul>

openother-ncApr 2022View details →

TAU Spatial Room Impulse Response Database (TAU-SRIR DB)

DESCRIPTION The TAU Spatial Room Impulse Response Database (TAU-SRIR DB) database contains spatial room impulse responses (SRIRs) captured in various spaces of Tampere University (TAU), Finland, for a fixed receiver position and multiple source positions per room, along with separate recordings of spatial ambient noise captured at the same recording point. The dataset is intended for emulation of spatial multichannel recordings for evaluation and/or training of multichannel processing algorithms in realistic reverberant conditions and over multiple rooms. The major distinct properties of the database compared to other databases of room impulse responses are: <ul> <li>Capturing in a high resolution multichannel format (32 channels) from which multiple more limited application-specific formats can be derived (e.g. tetrahedral array, circular array, first-order Ambisonics, higher-order Ambisonics, binaural).</li> <li>Extraction of densely spaced SRIRs along measurement trajectories, allowing emulation of moving source scenarios.</li> <li>Multiple source distances, azimuths, and elevations from the receiver per room, allowing emulation of complex configurations for multi-source methods.</li> <li>Multiple rooms, allowing evaluation of methods at various acoustic conditions, and training of methods with the aim of generalization on different rooms.</li> </ul> The RIRs were collected by staff of TAU between 12/2017 - 06/2018, and between 11/2019 - 1/2020. The data collection received funding from the European Research Council, grant agreement 637422 <a href="https://cordis.europa.eu/project/id/637422">EVERYSOUND</a>. NOTE: This database is a work-in-progress. We intend to publish additional rooms, additional formats, and potentially higher-fidelity versions of the captured responses in the near future, as new versions of the database in this repository.   REPORT AND REFERENCE A compact description of the dataset, recording setup, recording procedure, and extraction can be found in: Politis., Archontis, Adavanne, Sharath, & Virtanen, Tuomas (2020). A Dataset of Reverberant Spatial Sound Scenes with Moving Sources for Sound Event Localization and Detection. In Proceedings of the Detection and Classification of Acoustic Scenes and Events 2020 Workshop (DCASE2020), Tokyo, Japan. available <a href="https://dcase.community/documents/workshop2020/proceedings/DCASE2020Workshop_Politis_88.pdf">here</a>. A more detailed report specifically focusing on the dataset collection and properties will follow.   AIM The dataset can be used for generating multichannel or monophonic mixtures for testing or training of methods under realistic reverberation conditions, related to e.g. multichannel speech enhancement, acoustic scene analysis, and machine listening, among others. It is especially suitable for the follow application scenarios: <ul> <li>monophonic and multichannal reverberant single- or multi-source speech in multi-room reverberant conditions</li> <li>monophonic and multichannel polyphonic sound events in multi-room reverberant conditions </li> <li>single-source and multi-source localization in multi-room reverberant conditions, in static or dynamic scenarios</li> <li>single-source and multi-source tracking in multi-room reverberant conditions, in static or dynamic scenarios</li> <li>sound event localization and detection in multi-room reverberant conditions, in static or dynamic scenarios</li> </ul>   SPECIFICATIONS The SRIRs were captured using an [Eigenmike](https://mhacoustics.com/products) spherical microphone array. A [Genelec G Three loudspeaker](https://www.genelec.com/g-three) was used to playback a maximum length sequence (MLS) around the Eigenmike. The SRIRs were obtained in the STFT domain using a least-squares regression between the known measurement signal (MLS) and far-field recording independently at each frequency. In this version of the dataset the SRIRs and ambient noise are downsampled to 24kHz for compactness. The currently published SRIR set was recorded at nine different indoor locations inside the Tampere University campus at Hervanta, Finland. Additionally, 30 minutes of ambient noise recordings were collected at the same locations with the IR recording setup unchanged. SRIR directions and distances differ with the room. Possible azimuths span the whole range of $\phi\in[-180,180)$, while the elevations span approximately a range between $\theta\in[-45,45]$ degrees. The currently shared measured spaces are as follows: <ol> <li>Large open space in underground bomb shelter, with plastic-coated floor and rock walls. Ventilation noise. Circular source trajectory.</li> <li>Large open gym space. Ambience of people using weights and gym equipment in adjacent rooms. Circular source trajectory.</li> <li>Small classroom (PB132) with group work tables and carpet flooring. Ventilation noise. Circular source trajectory.</li> <li>Meeting room (PC226) with hard floor and partially glass walls. Ventilation noise. Circular source trajectory.</li> <li>Lecture hall (SA203) with inclined floor and rows of desks. Ventilation noise. Linear source trajectory.</li> <li>Small classroom (SC203) with group work tables and carpet flooring. Ventilation noise. Linear source trajectory.</li> <li>Large classroom (SE203) with hard floor and rows of desks. Ventilation noise. Linear source trajectory.</li> <li>Lecture hall (TB103) with inclined floor and rows of desks. Ventilation noise. Linear source trajectory.</li> <li>Meeting room (TC352) with hard floor and partially glass walls. Ventilation noise. Circular source trajectory.</li> </ol> The measurement trajectories were organised in groups, with each group being specified by a circular or linear trace at the floor at a certain distance from the z-axis of the microphone. For circular trajectories two ranges were measured, a close and a far one, except room TC352, where the same range was measured twice, but with different furniture configuration and open or closed doors. For linear trajectories also two ranges were measured, close and far, but with linear paths at either side of the array, resulting in 4 unique trajectory groups, with the exception of room SA203 where 3 ranges were measured resulting on 6 trajectory groups. Linear trajectory groups are always parallel to each other, in the same room. Each trajectory group had multiple measurement trajectories, following the same floor path, but with the source at different heights.  The SRIRs are extracted from the noise recordings of the slowly moving source across those trajectories, at an angular spacing of approximately every 1 degree from the microphone. Instead of extracting SRIRs at equally spaced points along the path (e.g. every 20cm), this extraction scheme was found more practical for synthesis purposes, making emulation of moving sources at an approximately constant angular speed easier. More details on the trajectory geometries can be found in the README file and the measinfo.mat file.   RECORDING FORMATS As with the DCASE2019-2021 datasets, currently the database is provided in two formats, first-order Ambisonics, and a tetrahedral microphone array - both derived from the Eigenmike 32-channel recordings. For more details on the format specifications, check the README.  We intend to add additional formats of the database, of both higher resolution (e.g. higher-order Ambisonics), or lower resolution (e.g. binaural).   REFERENCE DOAs For each extracted RIR across a measurement trajectory there is a direction-of-arrival (DOA) associated with it, which can be used as the reference direction for sound source spatialized using this RIR, for training or evaluation purposes. The DOAs were determined acoustically from the extracted RIRs, by windowing the direct sound part and applying a broadband version of the MUSIC localization algorithm on the windowed multichannel signal. The DOAs are provided as Cartesian components [x, y, z] of unit length vectors.   SCENE GENERATOR A set of routines is shared, here termed scene generator, that can spatialize a bank of sound samples using the SRIRs and noise recordings of this library, to emulate scenes for the two target formats. The code is similar to the one used to generate the <a href="https://doi.org/10.5281/zenodo.5476980">TAU-NIGENS Spatial Sound Events 2021</a> dataset, and has been ported to Python from the original version written in Matlab. The generator can be found [**here**](https://github.com/danielkrause/DCASE2022-data-generator), along with more details on its use.  The generator at the moment is set to work with the <a href="https://zenodo.org/record/2535878">NIGENS</a> sound event sample database, and the <a href="https://zenodo.org/record/4060432">FSD50K</a> sound event database, but additional sample banks can be added with small modifications. The dataset together with the generator has been used by the authors in the following public challenges: - <a href="https://dcase.community/challenge2019/task-sound-event-localization-and-detection">DCASE 2019 Challenge Task 3</a>, to generate the TAU Spatial Sound Events 2019 dataset (<a href="https://doi.org/10.5281/zenodo.2599196">development</a>/<a href="https://doi.org/10.5281/zenodo.3377088">evaluation</a>) - <a href="https://dcase.community/challenge2020/task-sound-event-localization-and-detection">DCASE 2020 Challenge Task 3</a>, to generate the <a href="https://doi.org/10.5281/zenodo.4064792">TAU-NIGENS Spatial Sound Events 2020</a> dataset - <a href="https://dcase.community/challenge2021/task-sound-event-localization-and-detection">DCASE2021 Challenge Task 3</a>, to generate the <a href="https://doi.org/10.5281/zenodo.5476980">TAU-NIGENS Spatial Sound Events 2021</a> dataset - <a href="https://dcase.community/challenge2022/task-sound-event-localization-and-detection">DCASE2022 Challenge Task 3</a>, to generate additional <a href="https://doi.org/10.5281/zenodo.6406873">SELD synthetic mixtures for training the task baseline</a> NOTE: The current version of the generator is work-in-progress, with some code being quite "rough". If something does not work as intended or it is not clear what certain parts do, please contact us.   DATASET STRUCTURE The dataset contains a folder of the SRIRs (TAU-SRIR_DB), with all the SRIRs per room in a single MAT file. The file rirdata.mat contains some general information such as sample rate, format specifications, and most importantly the DOAs of every extracted SRIR. The file measinfo.mat contains measurement and recording information in each room. Finally, the dataset contains a folder of spatial ambient noise recordings (TAU-SNoise_DB), with one subfolder per room having two audio recordings fo the spatial ambience, one for each format, FOA or MIC. For more information on how to SRIRs and DOAs are organized, check the README.   DOWNLOAD The files TAU-SRIR_DB.z01, ..., TAU-SRIR_DB.zip contain the SRIRs and measurement info files. The files TAU-SNoise_DB.z01, ..., TAU-SNoise_DB.zip contain the ambient noise recordings. Download the zip files and use your preferred compression tool to unzip these split zip files. To extract a split zip archive (named as zip, z01, z02, ...), you could use, for example, the following syntax in Linux or OSX terminal: Combine the split archive to a single archive: <pre><code>zip -s 0 split.zip --out single.zip</code></pre> Extract the single archive using unzip: <pre><code>unzip single.zip</code></pre>   LICENSE The database is published under a custom **open non-commercial with attribution** license. It can be found in the `LICENSE.txt` file that accompanies the data.

Morphological integration, canalization, and plasticity in response to emergence time in Abutilon theophrasti

The relationships between trait plasticity and canalization, and between phenotypic integration and plasticity, have been under debate, largely because direct evidence is still scarce for their associations, especially in response to environments. To investigate the relationships between canalization, integration and phenotypic plasticity in response to emergence time, we conducted a field experiment with an annual herbaceous species of Abutilon theophrasti, by subjecting plants to four treatments of emergence time (spring, late spring, summer and late summer), to measure a number of morphological traits and analyze correlations of plasticity with canalization and integration in these traits, at two stages of plant growth. Results showed plants with delayed emergence had higher phenotypic integration and more positive correlations between integration and plasticity, but less negative correlations between decreased canalization and plasticity, compared to those emerged in spring. Results suggested significant environmental changes that induce plastic responses, rather than environmental stress, can result in greater phenotypic integration in plants. Negative correlations between decreased canalization and plasticity occurred more frequently in plants emerging in spring and the least frequently in those emerging in summer, suggesting their relationship depends on specific environmental conditions and the degree of plasticity. Both increased phenotypic integration and decreased canalization might merely be the outcome of plastic responses, rather than mechanisms constraining or facilitating plasticity.

Memory array locations, delay times, and participant response

Deliberative decisions based on an accumulation of evidence over time depend on working-memory, and working memory has limitations, but how these limitations affect deliberative decision-making is not understood. We used human psychophysics to assess the impact of working-memory limitations on the fidelity of a continuous decision variable. Participants decided the average location of multiple visual targets. This computed, continuous decision variable degraded with time and capacity in a manner that depended critically on the strategy used to form the decision variable. This dependence reflected whether the decision variable was computed either: 1) immediately upon observing the evidence, and thus stored as a single value in memory; or 2) at the time of the report, and thus stored as multiple values in memory. These results provide important constraints on how the brain computes and maintains temporally dynamic decision variables. The following data is the responses and trial information collected from each subject in each condition: Simultaneous Perceived, Simultaneous Computed, Sequential Perceived, and Sequential Computed.

Data and code from: Opposite, but insufficient, phenological responses to climate in two circumpolar seabirds: relative roles of phenotypic plasticity and selection

The magnitude of climate change has been greatest in the Arctic, accelerating climate-induced shifts in phenology, but wildlife responses vary. Variation may be due to the relative importance of phenotypic plasticity or phenotypic selection. Here, we examine and contrast the environmental drivers of plasticity in breeding phenology of two circumpolar seabirds at their receding summer range limit using unique datasets of marked individuals covering 25 and 30 years. Based on prior knowledge of the local ecosystems, we predicted that climate would generate opposing patterns of plasticity in the two populations. Laying phenology of kittiwakes in the Gulf of Alaska was associated with a large-scale climate oscillation (Pacific Decadal Oscillation) while the Arctic-breeding murres adjusted laying to sea-ice conditions. Kittiwakes laid earlier after experiencing colder climate about two years prior and laying dates did not advance over the study, but murres laid earlier when warmer climate led to earlier spring sea-ice break-up, and murre laying dates advanced by one week since 1990. Selection favoured earlier laying in both species. Both populations adjusted breeding phenology to environmental variation, but we anticipate opposing effects on phenology with continued climate change. Ice-constrained species can likely adapt to some extent because plasticity can provide the necessary shift to this physical barrier, although individuals were only able to adjust by ~one week while ice conditions advanced by over a month. In more temperate regions, where phenology is driven by bottom-up effects, plasticity and selection counteract one another leading to limited adaptability. We provide insights into the likely adjustments by Arctic marine animals to an increasingly warmer and ice-less summer.

Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity

Global change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to diversity loss and how this affects their responses to global change. Here, we performed a common garden experiment testing whether plant responses to global change are influenced by their selection history and the conditioning history of soil at different plant diversity levels. Using seeds of four grass species and soil samples from a 14-year-old biodiversity experiment, we grew the offspring of the plants either in their own soil or in soil of a different community, and exposed them either to drought, increased nitrogen input, or a combination of both. Under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, soil history, and to a lesser extent plant history, had species-specific effects on trait expression. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which in turn affects plant eco-evolutionary pathways. How this change affects species' response to global change and whether this can cause a feedback loop should be investigated in more detail in future studies.

opencc-by-4.0Apr 2022View details →

ARISE-SAI-1.5: Assessing Responses and Impacts of Solar climate intervention on the Earth system with Stratospheric Aerosol Injection, with cooling to 1.5C

Assessing Responses and Impacts of Solar climate intervention on the Earth system with Stratospheric Aerosol Injection (ARISE-SAI) is a set of simulations carried out with the Community Earth System Model, version 2 with the Whole Atmosphere Community Climate Model, version 6 (CESM2(WACCM6)) that aims at simulating a plausible deployment of solar climate intervention of stratospheric aerosol injection to enable community assessment of responses of the Earth system. This first set of simulations introduce stratospheric aerosol injection at ~ 21 km in simulated year 2035, called ARISE-SAI-1.5, utilize the middle-of-the-road SSP2-4.5 emission scenario,, and keep global mean surface air temperature near 1.5°C above the pre-industrial value. Sulfur dioxide injections in the ARISE-SAI-1.5 simulations are placed at four injection locations (15°S, 15°N, 30°S, 30°N) into one grid box at 180° longitude, and midpoint altitude of 21.6 km. The injection amount at each latitude is specified annually by a “controller” algorithm. This strategy ensures that the global mean surface temperature (T0), north-south temperature gradient (T1), and equator-to-pole temperature gradient (T2) remain close to ~ 1.5°C above the pre-industrial value throughout the simulation.   The files contained here contain output of surface temperature (TREFHT), total precipitation (PRECT), SO4, and controller log files with amounts of SO2 injection.

opencc-by-4.0Aug 2021View details →

Predicting cancer prognosis and drug response from the tumor microbiome

Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA-seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression data, can predict cancer prognosis and drug response to some extent – microbial abundances are significantly less predictive of prognosis than gene expression, although remarkably, similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.

Intra- and interspecific variability of specific leaf area mitigate the reduction of community stability in response to warming and nitrogen addition

Global environmental changes are reducing the diversity and affecting the functioning of natural ecosystems as well as their ability to reliably provide ecosystem functions and services to mankind. Many studies have shown that a greater plant diversity can stabilize community productivity against environmental fluctuations. However, most of these studies focused on plant species richness, thus overlooking the potential role of functional traits in stabilizing community productivity against environmental fluctuations. Whether and how functional trait mean and variability influence community stability in response to environmental changes and their relative contributions to community stability are largely unknown. Here, we used a 10-year experiment to investigate the role of species richness, as well as functional mean and intra- and interspecific variability of specific leaf area (SLA) of plants within- and among communities in driving community stability in response to nitrogen (N) addition and warming. We found that both N addition and warming reduced the temporal stability of community productivity by reducing species richness and its contribution to species asynchrony and species stability. In contrast, changes in the mean and variability of SLA in response to N addition and warming mitigated the reduction of community stability. Specifically, N addition reduced variation in SLA both by reducing interspecific differences in SLA within communities and differences in mean values of SLA among communities. Warming increased intraspecific differences in SLA among communities, leading to higher species stability that partly buffered the reduction of community stability. Our study demonstrates the role of trait mean and variability in mitigating the reduction of community stability in response to two pervasive global environmental changes. Gaining a deeper understanding of the processes linking global changes and the stability of our ecosystems requires integrating both trait mean values and trait variability.

Data for: Individual differences in song plasticity in response to social stimuli and singing position

Individual animals can react to the changes in their environment by exhibiting behaviours in an individual-specific way leading to individual differences in phenotypic plasticity. However, the effect of multiple environmental factors on multiple traits is rarely tested. Such a complex approach is necessary to assess the generality of plasticity and to understand how among-individual differences in the ability to adapt to changing environments evolve. This study examined whether individuals adjust different song traits to varying environmental conditions in the collared flycatcher (Ficedula albicollis), a passerine with complex song. We also aimed to reveal among-individual differences in behavioural responses by testing whether individual differences in plasticity were repeatable. The presence of general plasticity across traits and/or contexts was also tested. To assess plasticity, we documented 1) short-scale temporal changes in song traits in different social contexts (after exposition to male stimulus, female stimulus or without stimuli), and 2) changes concerning the height from where the bird sang (singing position), used as a proxy of predation risk and acoustic transmission conditions. We found population-level relationships between singing position and both song length and complexity, as well as social context-dependent temporal changes in song length and maximum frequency. We found among-individual differences in plasticity of song length and maximum frequency along both the temporal and positional gradients. These among-individual differences in plasticity were repeatable. Some of the plastic responses correlated across different song traits and environmental gradients. Overall, our results show that the plasticity of bird song 1) depends on the social context, 2) exists along different environmental gradients and 3) there is evidence for trade-offs between the responses of different traits to different environmental variables. Our results highlight the need to consider individual differences and to investigate multiple traits along multiple environmental axes when studying behavioural plasticity.

Network analysis reveals that acute stress exacerbates gene regulatory responses of the gill to seawater in Atlantic salmon

The transition from freshwater to seawater represents a physiological challenge for Atlantic salmon smolts preparing for downstream migration. Stressors occurring during downstream migration to the ocean impair the ability of smolts to maintain osmotic/ionic homeostasis in seawater. The molecular mechanisms underlying this interaction are not fully understood, especially at the organ level. We combined RNA-Seq with measures of whole-animal homeostasis to examine gene expression dynamics in the gills of smolts associated with impaired seawater tolerance after an aquaculture-related stressor. Smolts were given a 24 h seawater tolerance test before and after exposure to an acute handling/confinement stress. RNA-Seq followed by differential expression and weighted gene correlation network analysis (WGCNA) was used to quantify the transcriptional response of the gill to handling/confinement stress, seawater and their interaction. Exposure to acute stress was associated with a general stress response and impaired osmotic/ionic homeostasis in seawater. We identified gene networks in the gill exhibiting response to acute stress alone, seawater alone, and others exhibiting combined effects of both stress and seawater. Our findings indicate that acute handling/ confinement stress increases the intensity of seawater-related gene expression and suggest that increased investment in mechanisms related to ion transport may be part of a compensatory response to impaired seawater tolerance in smolts.

opencc-by-4.0Apr 2022View details →

Response of Plutella xylostella to the sublethal exposure of fluxametamide under laboratory conditions

Data set generated during the laboratory experiments on toxicity of fluxametamide against diamondback moth Plutella xylostella, and its sublethal effects on life table parameters of this pest. Fluxametamide exhibited an exceptional insecticidal activities against the larval stages of Plutella xylostella. This is a raw data set with the replication for each treatments.

Evolution in response to climate in the native and introduced ranges of a globally distributed plant

The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (HCN production—an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of Trifolium repens. HCN production is a polymorphic trait controlled by variation at two Mendelian loci (Ac and Li). Using phenotypic assays, we estimated within-population frequencies of HCN production and dominant alleles at both loci (i.e., Ac and Li) from 10,575 plants sampled from 131 populations on 5 continents, and then compared these frequencies to those from historical data collected in the 1950s. There were no clear relationships between changes in the frequency of HCN production, Ac, or Li and changes in temperature between contemporary and historical samples. We did detect evidence of continued evolution to temperature gradients in the introduced range, whereby the slope of contemporary clines for HCN and Ac in relation to winter temperature became steeper than historical clines and more similar to native clines. These results suggest that cyanogenesis clines show no clear changes through time in response to global warming, but introduced populations continue to adapt to their contemporary environments.

Morphological plasticity in response to emergence time and population density in Abutilon theophrasti (Malvaceae)

Increased density and delayed emergence are two major biotic factors in nature that have profound and complex effects on plants. No studies have attempt to compare the responses of plants to the two factors via morphological plasticity, particularly in dynamic patterns. We subjected plants of Abutilon theophrasti to four emergence times and three planting densities and measured and analyzed a number of mass and morphological traits at different growth stages. Across both stages, plants emerged in late spring had the highest total mass, and spring and late-spring plants had higher stem mass allocation than later germinants, but plants with delayed emergence had higher leaf and reproductive mass allocation, more leaves and less lateral roots, but lower stem length, stem and root diameter than early-emerged plants. Plants at high density performed lower in total mass and most other traits, but performed better in stem allocation and length, with shorter petioles and lateral roots, than at lower densities. In competition for resources, plants will prefer stem elongation to leaf/root growth, and even at the cost of reproduction to ensure the survival of the present generations when competition is intense or lethal. By contrast, plants will prefer the investment into leaf and reproductive growth to stem/root growth, for offspring persistence, when shortened lifetime does not threaten the contemporary survival. The contrasting strategies revealed the intelligence of plants in balancing between survival, growth and reproduction, depending on environmental contexts.

opencc-by-4.0May 2022View details →

Chiral monoterpenes reveal forest emission mechanisms and drought responses

This data was obtained during the Biosphere 2 - Water and Life Dynamics measurement campaign between September 2019 and December 2019 inside the Biosphere 2 tropical rainforest, Arizona, USA (DOI: 10.1126/science.abj6789). The Biosphere 2 tropical rainforest was subjected to a 4 month drought and rewetting experiment. This data includes mixing ratios of Isoprene, (-)-alpha-pinene, (+)-alpha-pinene, (-)-beta-pinene, (-)-limonene, (+)-limonene, (-)-camphene, (+)-camphene and gamma-terpinene calculated from data measured with a gas chromatograph - mass spectrometer. This data was sampled to see how the atmospheric concentration of compounds changed due to drought and rewetting. The data also includes the 13C enrichment measurements of chiral monoterpenes and isoprene taken with a gas chromatograph - isotope ratio mass spectrometer and proton reaction mass spectrometer, respectively. The 13C enrichment experiments were conducted on two individual days during the campaign, once during pre-drought and once during the severe drought. This experiment was conducted to see which compounds became enriched in 13C when the atmosphere was exposed to a large amount of 13CO2. Also included are sorbent tube measurements taken from branch cuvettes attached to Piper sp. and Clitoria fairchildiana plants, and also taken from soil chambers. The purpose of these measurements was to see how the emissions or uptakes of compounds from the plants and soil contributed to the total atmospheric concentration. The sorbent tubes were subsequently thermally desorbed into a gas chromatograph time of flight mass spectrometer. Also included is the temperature, photosynthetically active radiation, relative humidity, vapour pressure deficit, soil moisture, and photosynthesis rate data