Find research datasets worth reusing

opencc-by-4.0Sep 2023View details →

Supplementary material for "A database for the comparison of measured datasets of human voice directivity"

[1] C. Pörschmann. “A database for the comparison of measured datasets of human voice directivity," in Proceedings of the Forum Acusticum, Torino, Italy, 2023.   This study presents a database that allows direct comparison and visualization of datasets from 19 different studies. The data is collected from tables, plots, and datasets from the supplemental material of the respective studies. Some studies present directivity patterns averaged over a whole sentence, while others report phoneme-dependent data. Furthermore, these datasets vary in their sampling grids, with many measured in the horizontal plane and just a few measured spherically. Most datasets included in this work present frequency-band averaged values, for example, in one-third octave bands, while a few newer studies provide the raw data in the form of transfer functions. Furthermore, the supplementary material contains voice directivity datasets determined over a complete sentence determined for a phonetically balanced German sentence (measured twice for 13 subjects).   The .pdf file contains <ul> <li>information on the database that allows comparing the results of 19 publications on voice directivities</li> <li>general information on the voice directivity files in the SOFA format</li> <li>information on the indices and names of the SOFA-files</li> <li>additional plots</li> </ul>   The Database.zip <ul> <li>Excel-file containing datasets from the publications given in frequency-bands</li> <li>SOFA-Files (sampled on sparse grid) of all own datasets from previous studies</li> <li>Matlab scripts for importing, upsampling and  visualizing all voice directivity datasets considered in the database</li> </ul>   The VoiceDirectivitySentence.zip files contain voice directivities patterns averaged over one phonetically balanced sentence in the SOFA format <ul> <li>sampled on the sparse measuring grid</li> <li>upsampled to a dense grid</li> </ul>

Data from: Direct and indirect effects of urbanization, pesticides, and wild insect pollinators on mango yield

<ol> <li>Expanding cities increasingly encroach fertile farmlands, questioning the viability of maintaining agriculture within and around them. Yet, our knowledge on how urbanization influences pollinator communities and the provision of pollination services to crops is limited, especially for the urbanization hotspots of the Global South. </li> <li>Mango (Mangifera indica) is one of the most important fruit crops in tropical countries. To analyze the dependency of mango on its main insect pollinators, and the direct and indirect effects of urbanization and insecticides on pollinator abundance and mango yield, we conducted a pollinator exclusion experiment and sampled flower visitors on 16 mango farms spread across rural-urban landscapes in Bengaluru, a South Indian megacity. </li> <li>We found that allowing flowers access to ants and flying visitors (bees, hoverflies, non-syrphid flies), dramatically increased mango yield by 350%, highlighting the importance of wild insects for mango pollination. We detected a trend between wild bee abundance and the final fruit set, with an increase of 20% when the number of bees increased from 25 to 125. </li> <li>Urbanization did not directly affect pollinator abundance or mango yield. However, the amount of insecticide applications had strong negative effects on wild bee abundance at low and intermediate levels of urbanization, while it had no effect in highly urbanized areas, presumably because of higher availability of flowering resources. Moreover, the amount of insecticides decreased the weight of harvested mango fruits by almost 30%. This may indicate trade-offs between conventional pest control and enhanced crop yields through pollination by wild insects in rural areas. </li> <li> Synthesis and applications. Our results indicate that mango production can be maintained at a profitable level in urbanized landscapes with insect pollinators more than tripling final yield. However, increasing use of insecticides, besides raising farmers' expenses, can have negative effects on wild insect pollinators and mango yield, especially in rural areas. To safeguard crucial pollination services, it is therefore critical to conserve and promote wild insect pollinators by minimizing the negative effects of insecticide applications in these areas. </li> </ol>

opencc-by-4.0Jun 2023View details →

Raw Taxi Data for the d+Au direct photon analysis

Raw Taxi Data for the d+Au direct photon analysis. This files are primarily intended for building software images.

Direct and indirect estimates of dispersal support strong juvenile philopatry and male-biased dispersal in a freshwater turtle species (Emys orbicularis)

Dispersal has major impacts on population dynamics, population genetics and evolution and is also critical for population management and conservation. Dispersal is frequently sex- and age-specific, but current knowledge is strongly taxonomically biased toward birds and mammals. Here, we provide estimates of dispersal in a threatened freshwater turtle species, the European pond turtle Emys orbicularis. Based on 15 years of Capture-Mark-Recapture (CMR) monitoring and DNA samples from 194 individuals, we quantified both demographic and genetic dispersal between three sites separated by 1.5 to 3.5 km. We also investigated the effect of age and sex on dispersal. Overall, direct (CMR) and indirect (genetic) approaches provided consistent results showing that the studied sites are well connected with a flow of about one to three dozen migrants per generation. Dispersal was both age- and sex-biased in this species, with frequent dispersal of adult males and a strong philopatry of juveniles (of both sexes) and adult females. The strong philopatry of juveniles contrasts with the recurrent higher dispersal rate in young birds and mammals and shows the relevance of investigating dispersal in various taxonomic groups. Our results also provide useful information for the conservation of European pond turtle populations.

Data from: Transcriptome analysis reveals the mechanism underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae

Teleost fish exhibit remarkable sexual plasticity and display divergent developmental systems including hermaphroditism. One of the more fascinating model systems of sexual plasticity is socially controlled sex change, which is often observed in coral reef fish. The Okinawa rubble goby, Trimma okinawae, is a bi-directional sex change fish that can rapidly change its sex in both directions depending on social circumstances. Although behavioral and neuro-endocrinal sex change occurs within an hour and is believed to trigger gonadal changes, the underlying mechanisms remain poorly understood. In this study, we conducted a de novo transcriptome analysis of the T. okinawae brain and identified genes that were differentially expressed between the sexes and genes that were immediately controlled by social stimulation causing a sex change. We found that a larger number of genes are regulated during the male-to-female transition compared with a change from female to male. Several genes showed concordant expression shifts regardless of the sex change direction. Furthermore, some were associated with histone modification in nerve cells and regulated in the same direction. Overall, we identified genes that regulate the rapid behavioral and neuroendocrinal control of sex change and provide insight into the mechanism of sexual plasticity in teleost fish.

Data from: Direct and indirect effects of a fishing ban on lacustrine fish community do not result in a full recovery

<ol> <li>Protected areas are increasingly being promoted as an important means of protecting freshwater biological diversity and ecological processes. A robust assessment of ecological changes in protected areas is fundamental to optimize conservation policies and adaptive management. China's efforts to establish aquatic reserves have attracted worldwide attention, especially the "10-year fishing ban" implemented in the Yangtze River basin.</li> <li>We focused on Liangzi Lake, a freshwater protected area in the Yangtze River basin, to understand the effect of a fishing ban occurring after a short period of overfishing. In this aim, the time series of fish community taxonomic and functional structure encompassing the overfishing period and a post-ban period have been analyzed. Fish community metrics with direct, indirect, and no responses to fishing bans were identified.</li> <li>The results indicate that in the early period of the fishing ban, the trophic level and body size structure of the fish community were in the way of recovery. However, species that prefer benthic habitats did not recover after fishing-induced habitat degradation. Functional traits were more sensitive than taxonomic indices and revealed subtle community changes, such as the recovery of some ecological functions, despite a non-recovering species richness.</li> <li> Synthesis and applications. This study provides a rare case of a freshwater protected area in which the effects of conservation measures are studied with a temporal survey. The effectiveness of the functional trait approach in the application of protected area assessment was demonstrated by revealing the recovery of trophic level and body size structure of fish communities after the implementation of the fishing ban and the inadequacy of habitat restoration efforts. We suggest that in freshwater protected areas, insistence on a fishing ban is necessary but not sufficient for full biodiversity recovery, and other measures are needed, such as habitat restoration and species-focused stocking.</li> </ol>

Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR

Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of Sabella spallanzanii and Bugula neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing in-situ nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and rapid management response to biosecurity threats.

opencc-zeroDec 2022View details →

Data for: Direct and indirect effects of food, fear and management on crop damage by ungulates

Foraging on crops by wild ungulates may create human-wildlife conflicts through reducing crop production. Ungulates interact with and within complex socio-ecological systems, making the reduction of crop damage a challenging task. Aside from ungulate densities, crop damage is influenced by different drivers affecting ungulate foraging behavior: food availability and food quality in the landscape (i.e. the foodscape) as well as fear from hunting and scaring actions (i.e. the landscape of fear) may together affect the degree of damage via both direct and indirect effects. A better understanding of the individual effects of these potential drivers behind crop damage is needed, as is an appreciation of whether the effects are dependent on ungulate density. We investigated this by applying path analysis to test indirect and direct links between ungulate density, foodscape, landscape of fear and, human management goals on crop damage of oats and grass, respectively. Our results suggest that crop type is the major driver behind crop damage, with more damage to oats than to leys, implying that human decisions (i.e changing crop type) influence the level of crop damage. We found that management goals and actions influenced the foodscape and the landscape of fear, by affecting the amount of forage produced in the agricultural landscape and the amount of scaring actions. Additionally, we found that supplementary feeding influenced the local ungulate densities in the area. Our results highlight the importance of including human actions on multiple levels when assessing drivers behind damage by ungulates in managed landscapes. We suggest that more studies using path analysis on multiple scales are needed in order to tackle complex issues such as crop damage and other human-wildlife conflicts.

opencc-zeroAug 2023View details →

Directional and stabilizing selection shaped morphological, reproductive, and physiological traits of the invader Solidago canadensis

Trait evolution in invasive plant species is important because it can impact demographic parameters key to invasion success. Invasive plant species often show phenotypic clines along geographic and climatic gradients. However, the relative contributions of natural selection and neutral evolutionary processes to phenotypic trait variation among populations of invasive plants remains unclear. A common method to assess whether a trait has been shaped by natural selection or neutral evolutionary processes is to compare the geographical pattern for the trait of interest to the divergence in neutral genetic loci (i.e., QST-FST comparisons). A redundancy analysis (RDA) can facilitate identification of putative agents of natural selection on the trait. Here, we employed both a QST-FST comparisons approach and RDA to infer whether natural selection shaped traits of invasive populations of S. canadensis in China and identify the potential environmental drivers of natural selection. We addressed two questions: (1) Does natural selection drive phenotypic trait variation among S. canadensis populations? (2) Do climatic, latitudinal, longitudinal, and altitudinal gradients drive patterns of genetic variation among S. canadensis populations? We found significant directional selection for several morphological and reproductive traits (i.e., QST >FST) and stabilizing selection for physiological traits (i.e., QST < FST). The RDA showed that stem biomass of S. canadensis was strongly positively correlated with longitude, while leaf width ratio and specific leaf area were significantly positively correlated with mean diurnal range. Stem biomass had a strong negative correlation with annual precipitation. Moreover, height of S. canadensis individuals was strongly positively correlated with altitude and precipitation of the wettest quarter. Precipitation seasonality that was associated with longitudinal shift in China likely selected for larger stem biomass in S. canadensis. Overall, these results suggest that longitudinal and altitudinal clines in climate exerted strong selection pressures that shaped phenotypic traits of S. canadensis.

opencc-zeroAug 2023View details →

Site-directed placement of three-dimensional DNA origami

The combination of lithographic methods with 2D DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micron scale. Here we extend this concept to the third dimension by mounting 3D DNA origami onto nano-patterned substrates, followed by silicification to provide mechanical and chemical stability. We created fully addressable, three-dimensional nanopatterns of hybrid DNA-silica structures with heights up to 50 nm and feature size in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to 3D-position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and 3D-patterned surfaces and integrated devices designed on the molecular level while reaching macroscopic dimensions.

opencc-by-4.0Jun 2023View details →

Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples

This dataset comprises: 1. The design of RNA oligonucleotide baits for Agilent Technologies’ SureSelect target enrichment - 54756 RNA oligonucleotide "baits" (120 bp each) designed to perform whole-genome capture and sequencing of Francisella tularensis directly from clinical samples (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. RNA oligonucleotide “baits” were designed to span the Francisella tularensis chromosome and plasmid, accounting for the genetic variability among publicly available genome sequences. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 54756 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. 2. Genome assemblies of 17 Francisella tularensis samples generated in the context of validation and application of SureSelect target enrichment for Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples   File “Ft_assembly_metadata.xlsx” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers. The archive “Ft_assemblies.zip” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. More details can be found in the following publication: (available soon)

opencc-by-4.0Dec 2022View details →

Supplementary Information for "In-situ Plasma Studies using a Direct Current Microplasma in a Scanning Electron Microscope"

Supplementary information for the article "In-situ Plasma Studies using a Direct Current Microplasma in a Scanning Electron Microscope" containing the videos of in-situ SEM imaging (mp4 files), raw data/images, and Jupyter notebooks (ipynb files) for data treatment and plots. Link to the publication: <a href="https://doi.org/10.1002/admt.202301632" target="_blank" rel="noopener">https://doi.org/10.1002/admt.202301632</a> Link to the preprint: <a href="https://doi.org/10.48550/arXiv.2308.15123" target="_blank" rel="noopener">https://doi.org/10.48550/arXiv.2308.15123</a> Explanation of the data files can be found in the Information.pdf file. The Videos folder contains the in-situ SEM image series mentioned in the paper. If there are any questions/bugs, feel free to contact me at the email given on <a href="https://orcid.org/0000-0002-5898-0713" target="_blank" rel="noopener">ORCID.</a>

opencc-zeroAug 2023View details →

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

opencc-by-4.0Jul 2023View details →

3D kinematics and kinetics of change of direction motions reconstructed from virtual inertial sensor data through optimal control simulation

This is the data belonging to the publication "Estimating 3D kinematics and kinetics from inertial sensor data through musculoskeletal movement simulations". This study investigated the feasibility and accuracy of reconstructing, especially change of direction motions, with a 3D full-body musculoskeletal model by tracking virtual inertial sensor data in optimal control simulations. We used the recordings of 90 trials with optical motion capture to generate marker tracking simulations from which we computed virtual inertial sensor data. Using this data, we compared inertial tracking simulations and marker tracking simulations. Please see the README and the publication for further details.

opencc-zeroSep 2023View details →

A gradual migratory divide determines not only the direction of migration but also migration strategy of a social migrant bird

Migratory divides separate populations of migratory animals, facilitating the evolution of intraspecific differences in migration strategies. Migration strategies are expected to be different for birds using different flyways and environments, but the knowledge regarding the impact of the flyway on individual migration strategies is scarce. By using satellite tracking and neckband resightings, we reveal the existence and structure of a gradual migratory divide between two European flyway populations of greylag geese Anser anser. Birds breeding at the far end of the Gulf of Bothnia in the Baltic Sea coast use the Western Flyway; those breeding in the Gulf of Finland the Central Flyway and those breeding between these extremes scatter to the two flyways. By using Gaussian process modelling, we show that migration strategies differed between the flyways. The birds using Western Flyway migrated earlier in autumn, performed longer annual migration and made a clear stopover during migration, whereas the birds using Central Flyway flew directly to their wintering sites. The gradual migratory divide that also divides migration strategies provides insights to migratory divides in birds with learned migration. Distinct migration strategies in different flyways provide exciting possibilities to further study the factors driving migration strategies.

opencc-zeroSep 2023View details →

Data for: A cell surface-binding antibody atlas nominates a MUC18-directed antibody-drug conjugate for targeting melanoma

Recent advances in targeted therapy and immunotherapy have substantially improved the treatment of melanoma. However, therapeutic strategies are still needed for unresponsive or treatment-relapsed melanoma patients. To discover antibody-drug conjugate (ADC)-tractable cell surface targets for melanoma, we developed an atlas of melanoma cell surface binding antibodies (pAbs) using a proteome-scale antibody array platform (PETAL). Target identification of pAbs led to development of melanoma cell killing ADCs against LGR6, TRPM1, ASAP1, and MUC18, among others. MUC18 was overexpressed in both tumor cells and tumor-infiltrating blood vessels across major melanoma subtypes, making it a potential dual-compartment and universal melanoma therapeutic target. AMT-253, an MUC18-directed ADC based on topoisomerase I inhibitor exatecan and a self-immolative T moiety, had a higher therapeutic index compared to its microtubule inhibitor-based counterpart and favorable pharmacokinetics and tolerability in monkeys. AMT-253 exhibited MUC18-specific cytotoxicity through DNA damage and apoptosis and a strong bystander killing effect, leading to potent antitumor activities against melanoma cell line and patient-derived xenograft models. Tumor vasculature-targeting by a mouse MUC18-specific antibody-T1000-exatecan conjugate inhibited tumor growth in human melanoma xenografts. Combination therapy of AMT-253 with an anti-angiogenic agent generated higher efficacy than single agent in a mucosal melanoma model. Beyond melanoma, AMT-253 was also efficacious in a wide range of MUC18-expressing solid tumors. Efficient target/antibody discovery in combination with the T moiety-exatecan linker-payload exemplified here may facilitate discovery of new ADC to improve cancer treatment.

opencc-by-4.0Sep 2023View details →

Column size for direct displacement based design of base-isolated RC frame buildings

In this paper, a method of computer-added program-based algorithm is introduced to evaluate the possible floor-wise column size for direct displacement-based design of base-isolated reinforced concrete frame buildings. The design storey drifts are kept low as base isolated buildings are mostly intended to achieve low storey drift fully-operational performance level under spectrum-compatible ground motions. Lead rubber bearing is used as base isolator and designed according to the UBC-97 maximum vertical load method. The frame deformation components considered in the algorithm are column tip displacement due to flexure, average column displacement due to shear, and joint rotation due to flexure and shear. It was observed that the proposed method effectively determines the storey-wise column size for various building plans, heights upto 9-storey and base displacement upto 350mm for target storey drift upto 0.25%.

opencc-by-4.0Sep 2023View details →

20230822-IKEM: Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced.

This archive contains the results of a multi-agent simulation experiment [1] carried out with Lazy lavender [2] environment. Experiment Label: 20230822-IKEM Experiment design: Agents interact by playing games with objects and adapt their ontologies to agree on decision taking. Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced. Experiment setting: Agents learn decision trees (transformed into ontologies); choose the objects (and partners) to interact with; adapt by splitting their leaf nodes Hypotheses: 1) Agents will be able to fulfil their motivation in terms of increased exploration (exploratory motivations) and decreased exploration (non-exploratory motivation). 2) Agents with exploratory motivation will be more complete, but less accurate than the baseline and non-exploration. 3) Curious agents will be more accurate and complete, but converge slower in comparison with creativity. 4) In more complex settings (higher number of agents and properties), exploration leads to more completeness, accuracy, distance and faster convergence than the baseline. 5) Agents with non-exploratory motivation will be less accurate and complete than the baseline. 6) The indirect learning models have a higher accuracy and completeness than the direct models. 7) Agents with socially oriented intrinsic motivation will have less diverse knowledge, but agree more and converge faster than agents with individual intrinsic motivation. 8) Heterogeneously motivated agents will have a higher accuracy and completeness, but lower diversity and converge slower than homogeneously motivated agents. Detailed information can be found in index.html or notebook.ipynb. [1] <a href="\">https://sake.re/20230822-IKEM</a> [2] <a href="\">https://gitlab.inria.fr/moex/lazylav/</a>

opencc-by-4.0Oct 2023View details →

Datasets for "The direct and indirect effects of the environmental factors on global terrestrial gross primary productivity over the past four decades"

The environmental changes can affect gross primary productivity (GPP) by altering not only the biogeochemical characteristics of the photosynthesis system (direct effects) but also the structure of the vegetation canopy (indirect effects). However, comprehensively quantifying the multi-pathway effects of environmental change on GPP is currently challenging. We proposed a framework to analyse the changes in global GPP by combining a nested machine-learning model and a theoretical photosynthesis model. We quantified direct and indirect effects of changes in key environmental factors (atmospheric CO2 concentration, temperature, solar radiation, vapor pressure deficit (VPD), and soil moisture) on global GPP from 1982 to 2020.  The three datasets(RF_LAI, RF_GPP, and RF_GPPlai) are derived from LAI random forest model, GPP random forest model and hierarchical nested model respectively.