Find research datasets worth reusing

opencc-by-4.0Nov 2019View details →

Supplementary Data for "Tuning the Redox Activity of Metal–Organic Frameworks for Enhanced, Selective O2 Binding: Design Rules and Ambient Temperature O2 Chemisorption in a Cobalt–Triazolate Framework"

Supplementary dataset to support "Tuning the Redox Activity of Metal–Organic Frameworks for Enhanced, Selective O2 Binding: Design Rules and Ambient Temperature O2 Chemisorption in a Cobalt–Triazolate Framework"

opencc-zeroJun 2020View details →

Data from: Low-dimensional spatio-temporal dynamics underlie cortex-wide neural activity

Cognition arises from the dynamic flow of neural activity through the brain. To capture these dynamics, we used mesoscale calcium imaging to record neural activity across the dorsal cortex of awake mice. We found that the large majority of variance in cortex-wide activity (~75%) could be explained by a limited set of ~14 'motifs' of neural activity. Each motif captured a unique spatio-temporal pattern of neural activity across the cortex. These motifs generalized across animals and were seen in multiple behavioral environments. Motif expression differed across behavioral states and specific motifs were engaged by sensory processing, suggesting the motifs reflect core cortical computations. Together, our results show that cortex-wide neural activity is highly dynamic, but that these dynamics are restricted to a low-dimensional set of motifs, potentially allowing for efficient control of behavior.

opencc-by-4.0May 2020View details →

Data supplement for "Thin-Film Modeling of Resting and Moving Active Droplets"

This dataset contains the data and source files for figures 4-10, 12, and 14-20 in the following publication:  S. Trinschek, F. Stegemerten, K. John and U. Thiele "Thin-Film Modeling of Resting and Moving Active Droplets" published in 2020 in Physical Review E. Please follow the instructions given in 'Readme.txt'.

opencc-zeroJun 2020View details →

Data from: Different genetic basis for ADH activity and plasticity in a novel alcohol environment for Drosophila melanogaster

Phenotypic plasticity is known to enhance population persistence (Wang and Althoff, 2019), facilitate adaptive evolution (Levis et al., 2018), and initiate novel phenotypes in novel environments (Levis and Pfennig, 2016). How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0% and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects and that the Adh locus is not environmentally sensitive to dietary alcohol.

Data from: Vestigial auriculomotor activity indicates the direction of auditory attention in humans

Unlike dogs and cats, people do not point their ears as they focus attention on novel, salient, or task-relevant stimuli. Our species may nevertheless have retained a vestigial pinna-orienting system that has persisted as a "neural fossil" within in the brain for about 25 million years. Consistent with this hypothesis, we demonstrate that the direction of auditory attention is reflected in sustained electrical activity of muscles within the vestigial auriculomotor system. Surface electromyograms (EMGs) were taken from muscles that either move the pinna or alter its shape. To assess reflexive, stimulus-driven attention we presented novel sounds from speakers at four different lateral locations while the participants silently read a boring text in front of them. To test voluntary, goal-directed attention we instructed participants to listen to a short story coming from one of these speakers, while ignoring a competing story from the corresponding speaker on the opposite side. In both experiments, EMG recordings showed larger activity at the ear on the side of the attended stimulus, but with slightly different patterns. Upward movement (perking) differed according to the lateral focus of attention only during voluntary orienting; rearward folding of the pinna's upper-lateral edge exhibited such differences only during reflexive orienting. The existence of a pinna-orienting system in humans, one that is experimentally accessible, offers opportunities for basic as well as applied science.

Data from: Leptin increases sympathetic nerve activity via induction of its own receptor in the paraventricular nucleus

Whether leptin acts in the paraventricular nucleus (PVN) to increase sympathetic nerve activity (SNA) is unclear, since PVN leptin receptors (LepR) are sparse. We show in rats that PVN leptin slowly increases SNA to muscle and brown adipose tissue, because it induces the expression of its own receptor and synergizes with local glutamatergic neurons. PVN LepR are not expressed in astroglia and rarely in microglia; instead, glutamatergic neurons express LepR, some of which project to a key presympathetic hub, the rostral ventrolateral medulla (RVLM). In PVN slices from mice expressing GCaMP6, leptin excites glutamatergic neurons. LepR are expressed mainly in thyrotropin-releasing hormone (TRH) neurons, some of which project to the RVLM. Injections of TRH into the RVLM and dorsomedial hypothalamus increase SNA, highlighting these nuclei as likely targets. We suggest that this neuropathway becomes important in obesity, in which elevated leptin maintains the hypothalamic pituitary thyroid axis, despite leptin resistance.

Data from: Human disturbance and the activity patterns and temporal overlap of tapirs and jaguars in reserves of NW Belize.

Human disturbance from tourism and other non-consumptive activities in protected areas may be stressful to wildlife. Animals may move away in space or time to avoid human interaction. For species of particular conservation concern, such as Baird's tapirs (Tapirus bairdii) and jaguars (Panthera onca), a better understanding of how they respond to different levels and types of disturbance is needed in order to manage human visitation to parks in ways that minimize negative outcomes for wildlife. We describe the overlap of activity patterns of tapirs, jaguars, and humans at logged and unlogged sites and at places with low versus high human visitation using camera survey data from protected areas of northwest Belize, 2013-2016. Tapirs were nocturnal in all study sites, with >80 percent of all tapir detections occurring between 1900 h and 0500 h. Their activity patterns were not different in unlogged versus logged sites and did not change with increased human traffic. Jaguars were cathemeral across sites, but had more nocturnal activity at the site with the most human impact. Activity pattern overlap between tapirs and jaguars did not differ significantly between logged and unlogged sites, nor between areas with low and high human activity. Human traffic increased from 2013-2016 at most of the study locations. In conclusion, this camera trap dataset suggests that non-consumptive human disturbance does not alter the activity patterns of tapirs and jaguars in protected areas lacking hunting pressure.

Data from: Assessment of tumor treatment response using active contrast encoding (ACE)-MRI: comparison with conventional DCE-MRI

Purpose: To investigate the validity of contrast kinetic parameter estimates from Active Contrast Encoding (ACE)-MRI against those from conventional Dynamic Contrast-Enhanced (DCE)-MRI for evaluation of tumor treatment response in mouse tumor models. Methods: The ACE-MRI method that incorporates measurement of T1 and B1 into the enhancement curve washout region, was implemented on a 7T MRI scanner to measure tracer kinetic model parameters of 4T1 and GL261 tumors with treatment using bevacizumab and 5FU. A portion of the same ACE-MRI data was used for conventional DCE-MRI data analysis with a separately measured pre-contrast T1 map. Tracer kinetic model parameters, such as Ktrans (permeability area surface product) and ve (extracellular space volume fraction), estimated from ACE-MRI were compared with those from DCE-MRI, in terms of correlation and Bland-Altman analyses. Results: A three-fold increase of the median Ktrans by treatment was observed in the flank 4T1 tumors by both ACE-MRI and DCE-MRI. In contrast, the brain tumors did not show a significant change by the treatment in either ACE-MRI or DCE-MRI. Ktrans and ve values of the tumors from ACE-MRI were strongly correlated with those from DCE-MRI methods with correlation coefficients of 0.92 and 0.78, respectively, for the median values of 17 tumors. The Bland-Altman plot analysis showed a mean difference of -0.01 /min for Ktrans with the 95% limits of agreement of -0.12 /min to 0.09 /min, and -0.05 with -0.37 to 0.26 for ve. Conclusion: The tracer kinetic model parameters estimated from ACE-MRI and their changes by treatment closely matched those of DCE-MRI, which suggests that ACE-MRI can be used in place of conventional DCE-MRI for tumor progression monitoring and treatment response evaluation with a reduced scan time.

opencc-zeroDec 2018View details →

Data from: Young but not defenseless: antifungal activity during embryonic development of a social insect

Termites live in environments heavily colonized by diverse microbial communities, including pathogens. Eggs laid within the nest likely experience similar pathogenic pressures as their older nestmates. Consequently, they may have also been under selective pressures to be immune-competent. Through in vitro experiments, we tested the ontogeny, location and strength of embryos' antifungal activity against the fungus Metarhizium brunneum. Extraembryonic washes and intraembryonic components were incubated with fungal conidia, which was then scored for viability. Fungistatic activity was location- and stage-dependent. Extraembryonic washes had relatively weak antifungal activity. Conversely, intraembryonic contents were highly antifungal, exhibiting increased potency through development. Boiling both embryonic washes and intraembryonic contents rescued conidia viability, indicating the antifungal agent(s) is (are) likely proteinaceous. Embryonic protein profiles shifted from putative vitellogenins in young embryos to multiple proteins in subsequent stages, suggesting that the increase in fungistatic activity may be due to the expression of endogenous proteins during embryogenesis. This study is the first to address embryonic antifungal activity in a hemimetabolous eusocial taxon. Our results support the hypothesis that microbes have been significant agents of selection, fostering the evolution of antifungal properties even in the most immature and supposed, most vulnerable stage of development.

opencc-zeroJun 2020View details →

Data from: Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus

The disease chytridiomycosis caused by the fungus Bd has devastated amphibian populations worldwide. Functional genomic contributions to host susceptibility remain enigmatic and vary between species and populations. We conducted experimental Bd infections in Rana yavapaiensis, a species with intraspecific variation in chytridiomycosis susceptibility, to assess the skin and spleen transcriptomic response to infection over time. We predicted that increased immune gene expression would be associated with a positive disease outcome, but we instead found that surviving frogs had significantly reduced immune gene expression compared to susceptible frogs and to uninfected controls. MHC class II gene expression was also significantly higher in susceptible frogs compared to surviving frogs. Furthermore, susceptible frogs expressed a significantly larger number of distinct class II alleles, demonstrating a negative correlation between class II expression, functional diversity, and survival. Expression of the MHC class II locus previously associated with Bd disease outcomes was a significant predictor of Bd infection intensity at early infection stages but not at late infection stages, suggesting initial MHC-linked immune processes are important for ultimate disease outcomes. We infer through disease association and phylogenetic analysis that certain MHC variants are linked to the immune expression that was negatively associated with survival, and we hypothesize that frogs that did not express these alleles could better survive infections. Our study finds that MHC expression at early and late infection stages predicts Bd infection intensity, and suggests that generating a sustained immune response against Bd may be counterproductive for surviving chytridiomycosis in this partially susceptible species.

opencc-by-4.0May 2020View details →

Data for 'Robust Enhancement of Tropical Convective Activity by the 2019 Antarctic Sudden Stratospheric Warming'

These data were used for making plots in the manuscript entitled 'Robust Enhancement of Tropical Convective Activity by the 2019 Antarctic Sudden Stratospheric Warming'. DOI: 10.1029/2020GL088743. Data format is NetCDF.

Data from: Body temperature, heart rate, and activity patterns of two boreal homeotherms in winter: homeostasis, allostasis, and ecological coexistence

<ol> <li>Organisms survive environmental variation by combining homeostatic regulation of critical states with allostatic variation of other traits, and species differences in these responses can contribute to coexistence in temporally-variable environments.</li> <li>In this paper, we simultaneously record variation in three functional traits – body temperature (Tb), heart rate, and activity - in relation to three forms of environmental variation – air temperature (Ta), photoperiod, and experimentally-manipulated resource levels – in free-ranging snowshoe hares and North American red squirrels to characterize distinctions in homeotherm responses to the extreme conditions of northern boreal winters.</li> <li>Hares and squirrels differed in the level and precision of Tb regulation, but also in the allostatic pathways necessary to maintain thermal homeostasis. Hares demonstrated a stronger metabolic pathway (through heart rate variation reflective of the thermogenesis), while squirrels demonstrated a stronger behavioral pathway (through activity variation that minimizes cold exposure).</li> <li>As intermediate-sized, winter-active homeotherms, hares and squirrels share many functional attributes, yet, through the integrated monitoring of multiple functional traits in response to shared environmental variation, our study reveals many pairwise species differences in homeostatic and allostatic traits, that both define and are defined by the natural history, functional niches, and coexistence of sympatric species.</li> </ol>

opencc-zeroAug 2020View details →

Data from: Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment

Microplastics are recognized as an emerging contaminant worldwide. Although microplastics have been shown to strongly affect organisms in aquatic environments, less is known about whether and how microplastics can affect different taxa within a soil community, and it is unclear whether these effects can cascade through soil food webs. By conducting a microplastic manipulation experiment, i.e. adding low-density polyethylene fragments in the field, we found that microplastic addition significantly affected the composition and abundance of microarthropod and nematode communities. Contrary to soil fauna, we found only small effects of microplastics on the biomass and structure of soil microbial communities. Nevertheless, structural equation modeling revealed that the effects of microplastics strongly cascade through the soil food webs, leading to the modification of microbial functioning with further potential consequences on soil carbon and nutrient cycling. Our results highlight that taking into account the effects of microplastics at different trophic levels is important to elucidate the mechanisms underlying the ecological impacts of microplastic pollution on soil functioning.

opencc-zeroAug 2020View details →

Data from: Attention-related modulation of caudate neurons depends on superior colliculus activity

Recent work has implicated the basal ganglia in visual perception and attention, in addition to their traditional role in motor control. The basal ganglia, especially the caudate nucleus "head" (CDh) of the striatum, receive indirect anatomical connections from the superior colliculus (SC), a midbrain structure that is known to play a crucial role in the control of visual attention. To test the possible functional relationship between these subcortical structures, we recorded CDh neuronal activity before and during unilateral SC inactivation in a spatial attention task. SC inactivation significantly altered the attention-related modulation of CDh neurons and strongly impaired the classification of task epochs based on CDh activity. Only inactivation of the same-side of SC as recorded CDh neurons, not the opposite-side, had these effects. These results demonstrate a novel interaction between SC activity and attention-related visual processing in the basal ganglia.

opencc-by-4.0May 2020View details →

New understanding of the spatiotemporal lightning activity over the Tibetan Plateau based on WWLLN data

The submitted data are associated with the figures in the paper titled "New understanding of the spatiotemporal lightning activity over the Tibetan Plateau based on WWLLN data". The following is the abstract of this paper.   The spatiotemporal distribution of the lightning activity over the Tibetan Plateau (TP) has been previously studied based on data from the Lightning Imaging Sensor (LIS) aboard the polar-orbit Tropical Rainfall Measuring Mission satellite. In this study, using lightning data from the World Wide Lightning Location Network (WWLLN), we reinvestigated the lightning activity over the TP and found that the geographic and seasonal lightning distributions suggested by the WWLLN are somewhat different from those obtained from the LIS. In particular, 1) while the LIS indicates strong lightning activity over the northeastern TP, the WWLLN indicates relatively weak lightning activity over the region; 2) the WWLLN indicates the existence of a center with relatively frequent lightning activity over the south-by-west TP, which is not indicated by the LIS; furthermore, 3) the WWLLN indicates the most frequent lightning in August and September, while the LIS suggests July and June. The black body temperature data from the Fengyun-2E geostationary satellite (as a proxy of deep convection), thunderstorm day data, and local cloud-to-ground lightning data strongly support the lightning spatiotemporal distribution patterns suggested by the WWLLN. The difference between the WWLLN and LIS data is attributed to their very different sample numbers and observation methods, and the situation that lightning tends to occur in the lower part of TP thunderstorms. Owing to the time-continuous nature, the WWLLN data were also used to obtain the ten-day distributions of lightning in space and time and the diurnal variation of lightning. This study may further elucidate our knowledge of the lightning activity over the TP.

opencc-zeroSep 2020View details →

Energy consumption and greenhouse gas emissions data of activated carbon production using different biomass

This dataset includes the energy consumption and Greenhouse Gas emissions data of activated carbon production using 73 different types of woody biomass. Understanding the environmental implications of activated carbon (AC) produced from diverse biomass feedstocks is critical for biomass screening and process optimization for sustainability. Many studies have developed Life Cycle Assessment (LCA) for biomass-derived AC. However, most of them either focused on individual biomass species with differing process conditions or compared multiple biomass feedstocks without investigating the impacts of feedstocks and process variations. Developing LCA for AC from diverse biomass is time-consuming and challenging due to the lack of process data (e.g., energy and mass balance). This study addresses these knowledge gaps by developing a modeling framework that integrates artificial neural network (ANN), a machine learning approach, and kinetic-based process simulation. The integrated framework is able to generate Life Cycle Inventory data of AC produced from 73 different types of woody biomass with 250 characterization data samples. The results show large variations in energy consumption and GHG emissions across different biomass species (43.4–277 MJ/kg AC and 3.96–22.0 kg CO2-eq/kg AC). The sensitivity analysis indicates that biomass composition (e.g., hydrogen and oxygen content) and process operational conditions (e.g., activation temperature) have large impacts on energy consumption and GHG emissions associated with AC production.

opencc-by-4.0Sep 2020View details →

Data collection for Tsuji et al., 2020, Microbial ecology of phototrophs in Boreal Shield lakes, Chapter 3: Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes (PhD thesis)

This data collection includes supplementary or raw data files related to Chapter 3 of the PhD thesis of Jackson M. Tsuji, "Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes" (in "Microbial ecology of phototrophs in Boreal Shield lakes"). Specifically, the following files are included: <ul> <li>ASV_table_non_rarefied_counts.tsv.gz -- non-rarefied ASV table containing 16S rRNA gene amplicon data presented in this study as raw counts. Beyond the index column and sample columns, two additional columns, "Consensus.Lineage" and "Sequence" are included in the table. These columns include the taxonomic classification of the ASV (according to Silva) and the ASV sequence, respectively.</li> <li>ASV_table_non_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>ASV_table_rarefied_counts.tsv.gz -- same as "ASV_table_non_rarefied_counts.tsv.gz", except that data is rarefied to 12,000 sequences per sample. Five samples were dropped due to having <12,000 sequences.</li> <li>ASV_table_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>MAG_abundances_to_unassembled_reads.tsv.gz -- table like an ASV table showing the relative abundances (expressed as percentages) of metagenome-assembled genomes within metagenomes. Aside from the index column and sample columns, additional columns are included to provide the taxonomic classification of the MAGs (based on the Genome Taxonomy Database) and the CheckM statistics of the MAGs. Relative abundances of MAGs in a metagenome are calculated as the number of mapped reads to the MAGs from the given metagenome divided by the total number of unassembled metagenome reads for that metagenome (times 100%).</li> <li>MAG_abundances_to_assembled_reads.tsv.gz -- same as above, except that relative abundances are divided by the total number of unassembled metagenome reads for that metagenome that mapped to that metagenome's assembled contigs.</li> <li>core_sample_metadata.tsv -- table of core physico-chemical and geographic metadata for the samples in this study (used to build biplots presented in the chapter). Note that "nd" means "no data available", and any measurements below detection limits have been set to 0. A limited number of values were inferred from other sampling time points -- these are noted in the table for TDFe measurements, and in addition, the light attenuation coefficient for Lake 373 in Sept. 2017 was inferred from the Sept. 2016 coefficient due to no light data being available for Sept. 2017 samples.</li> <li>metadata_descriptions.tsv -- descriptions of all metadata columns in the above file.</li> </ul>

opencc-by-4.0Nov 2019View details →

Data used for the paper Andres Parra-Puerto, Kai Ling NG, Kieran Fahy, Angela E Goode, Mary P. Ryan, and Anthony Kucernak Supported Transition Metal Phosphides: Activity Survey for HER, ORR, OER and Corrosion Resistance in Acid and Alkaline Electrolytes ACS Catalysis, 2019 DOI: 10.1021/acscatal.9b03359

This is an updated version of the spreadsheet which corrects the first version which had the wrong datasets provided for figure 2 c and d (ORR)    The data in this spreadsheet was used to produce the figures in the paper Andres Parra-Puerto, Kai Ling NG, Kieran Fahy, Angela E Goode, Mary P. Ryan, and Anthony Kucernak Supported Transition Metal Phosphides: Activity Survey for HER, ORR, OER and Corrosion Resistance in Acid and Alkaline Electrolytes ACS Catalysis, 2019 DOI: 10.1021/acscatal.9b03359Please cite the above reference if you wish to use this data

opencc-by-4.0Sep 2020View details →

data set related to article Actigraph assessment for measuring upper limb activity in unilateral cerebral palsy

<pre>This record contains raw data related to article Actigraph assessment for measuring upper limb activity in unilateral cerebral palsy</pre>