Find research datasets worth reusing

opennotspecifiedJul 2021View details →

Figure 3. Keratodellitha anubis. Holotype NIGP174739 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process

Figure 3. Keratodellitha anubis. Holotype NIGP174739 (male). A, habitus in right lateral view. B, head in right lateral view. C, head in frontal view. Scale bars: 0.5 mm.

opennotspecifiedJul 2021View details →

F i g u r e 1. K e r a t o d e l l i t h a b a s i l i s c i. H o l o t y p e NIGP174738 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process

F i g u r e 1. K e r a t o d e l l i t h a b a s i l i s c i. H o l o t y p e NIGP174738 (female). A, habitus in right lateral view. B, habitus in left lateral view. Scale bars: 0.5 mm.

opennotspecifiedJul 2021View details →

Figure 8 in Including fossils in phylogeny: a glimpse into the evolution of the superfamily Evanioidea (Hymenoptera: Apocrita) under tip-dating and the fossilized birth-death process

Figure 8. Bayesian time-calibrated tree of Evanioidea. This tree was recovered from a Mkv+G, fossilized birth–death (FBD) model, with uniform distribution and samplestrat = fossiltip, combining extant and extinct species. Bars at each node represent the 95% highest posterior density in dating estimates. Dotted squares represent crown lineages. Abbreviations: L, Lower; Mid, Middle; Oligo, Oligocene; Paleo, Palaeocene; PP, Pliocene + Pleistocene.

opencc-zeroApr 2022View details →

Spatially discrete disturbance processes enhance grassland floral resources

Grasslands provide essential floral resources for both managed and wild pollinators. However, grassland flowers in remaining native landscapes are threatened due to nonnative plant invasions and alterations to historic disturbance regimes such as fire and grazing. The potential for managed disturbance to promote grassland floral resources remains unclear. Fire and grazing historically occurred interactively, but uniform application of each may be a detriment to floral resources and the pollinators depending on them. Though fire can increase resources available to plants and stimulate flowering, it initially destroys floral resources and may delay flower availability. Similarly, grazing removes competitors of flowering plants, but destroys flower heads. To address this knowledge gap, we investigated the impacts patch-burn grazing with one and two seasons of fire per year versus season-long grazing with no fire on floral resources in mixed-grass prairie. In patch-burn treatments, part of each pasture is burned each year, which focuses grazing activity due to the high quality regrowth. We aimed to use fire to remove litter around flowering plants while also sheltering established flower heads from grazing pressure by directing cattle away from regenerating forbs in unburned portions of the landscape. Over two summers, we performed weekly flower surveys in season-long grazing and patch-burn grazing pastures. We analyzed total seasonal floral resources, maximum floral abundance, and seasonal species richness between treatments. Over two years, we surveyed 1,238,241 ramets of 160 species, focusing on 36 common species for individual analysis. We found broad positive associations between patch-burn grazing and total seasonal flower abundance, maximum flower abundance, and species richness compared to traditional management. In most cases, patch-burn grazing with dormant and growing season fires produced higher floral abundance, total seasonal floral resources, and species richness than patch-burning with dormant season fires alone, suggesting benefits of increased levels of pyrodiversity. Synthesis and applications: Under increasing pressure to manage for declining pollinators, rangeland managers must consider strategies to enhance floral resources within the context of livestock production goals. The spatiotemporal interaction of cattle grazing and fire shows promise for promoting floral resource abundance and diversity.

opencc-by-4.0Apr 2022View details →

Processed data for "SpotClean adjusts for spot swapping in spatial transcriptomics data"

This repo contains processed data to reproduce results in the paper "SpotClean adjusts for spot swapping in spatial transcriptomics data".

opencc-by-4.0Feb 2022View details →

Granule ripples in the Kumtagh Desert, China: morphological and sedimentary characteristics, and development processes

1. Observation of composition and morphology First, we selected typical granule ripples of different sizes and development stages at each observation site, and sampled the surface particles (to a depth of 1 cm) on the ridges of 85 granule ripples by scraping the surface with a steel ruler. The sample weight averaged 428 g (with values ranging between 249 and 697 g). We determined the grain-size distribution using a set of 15 standard sieves with a mesh size ranging from 0.0565 mm to 20 mm. We used the parameters proposed by Folk and Ward (1957) to calculate the grain size characteristics: the cumulative grain size of the 20 percentile (P20), and the average grain diameter, sorting coefficient, skewness, and kurtosis. Here, P20 represents the particle size corresponding to the cumulative distribution rate of 20% in the cumulative particle-size distribution diagram. Second, we defined ripple morphological characteristics (the wavelength, ripple height, ripple index, and symmetry coefficient) for 142 granule ripples by measuring their wavelength, ripple height, and ridge position. The ripple index (Z) equaled the ratio of the wavelength to the ripple height. The symmetry coefficient equaled the ratio of the horizontal windward slope length to the horizontal leeward slope length. Wavelength represents the horizontal distance between two crests, and the ripple height is the perpendicular height from the trough to the crest. We also excavated vertical profiles of five typical granule ripples with different sizes, and measured the stratification thickness for one ripple with a wavelength of 5 m, for a vertical profile whose depth was 60 cm. Based on the different grain size characteristics, we identified five strata and therefore obtained five sediment samples with different depths, and analyzed the vertical distribution of particle sizes in the sediment. We installed HOBO U30 field anemometers (Onset Computers, Bourne, MA, USA) at a height of 2 m and installed an eight-direction sand trap in the two areas in January 2011 to obtain the wind speed, wind direction, and the single-width sediment transport for a full year. The sensor type of wind speed and direction was S-WSET-A. The collection frequency for the wind speed and direction was 10 minutes, and the resolution of the wind speed and direction were 0.38 m/s and 1.4°, respectively. It is worth mentioning that Onset anemometers have a 5-degree window where they cannot measure wind direction, between 355 and 0 degrees. Unlike sand ripples, granule ripples are not particularly sensitive to wind direction, and these wind direction data only provide a regional main direction for the research, so a 5-degree window has little impact. The collection frequency of the sediment transport rate was 1 month, and the resolution was 10 g. The width and height of each collecting port of the sand trap were 2 cm and 1.2 m, respectively. 2. Wind tunnel experiment to detect the gravel threshold velocity We performed a wind tunnel simulation experiment to test the impact threshold velocity of the gravels. We used the high-speed wind tunnel at the High Speed Railway Construction Technology National Engineering Laboratory of Central South University in Changsha, Hunan Province in the validation test. We used surface sediments from granule ripples collected at our study area, and screened these sediments through 12 sieves with a mesh size ranging from 1.6 to 31.5 mm. We used the sieved material to create 10 different test surfaces with an average particle size ranging from 1.8 to 25.8 mm, which we subsequently bombarded with saltating particles from an upwind source. The upwind supply rate for the impacting particles was 1.2 kg/min, and their particle size ranged from 0.8 to 1.0 mm, with an average size of 0.9 mm, in all tests. The impacting particles were also obtained from the surface sediments of the granule ripples and were obtained by screening. The gravel bed surface was 80 cm long (parallel to the long axis of the wind tunnel), 40 cm wide, and 3 cm deep with its upper surface level with the wind tunnel floor. To increase the roughness of the surface, we glued a layer of coarse sand with a mean particle size of 0.9 mm that was 4.2 m long by 40 cm wide to the floor of the wind tunnel immediately upwind of the gravel bed. We observed the particles with a high-speed camera in the wind tunnel to determine the type of motion (vibration, roll, obvious roll, saltation, obvious saltation). The wind velocities were measured using a pitot tube at 10 heights (6, 7.5, 13, 21, 41, 83, 123, 161, 220, and 242 mm above the gravel bed). 3. Measurement of the granule ripple migration rate We chose a 25-m2 area at the yardang site, and monitored the migration rate of some smaller typical granule ripples from 11 October 2011 to 15 October 2012 using six marking pins, at an east–west spacing of 5 m between pins. The average wavelength of these granule ripples was 1.6 m and the average height was 0.09 m. The mean grain size in the ridge was 2.08 mm, and the maximum grain size was 6.5 mm. We also chose 11 larger granule ripples  (5 to 9 m in wavelength, 30 to 50 cm in height, granule size in the ridge of 6 to 10 mm) that were continuously distributed at the yardang site, and measured their migration rate over an 8-year period from 2011 to 2019 by using marking pins. Based on the migration rate, we applied the equation developed by Jerolmack et al. (2006) to calculate the sediment creep flux (qc) at the ridge of the granule ripples: qc = (1-p) ρcH / 2 where p is the porosity of the ripple sediment (30%), ρ is the particle density (2650 kg m-3), c is the ripple migration rate (m/year), and H is the ripple height (m).

opencc-by-4.0May 2021View details →

Audio-Visual Analytics Process

Conceptual process of an audio-visual analytics environment: Data is transformed to images and sound for the human analyst who interactively steers the analysis. Created using the <a href="https://thenounproject.com/icon/engineer-1362184/">"engineer" icon by Pawinee E. from the Noun Project</a> under <a href="https://creativecommons.org/licenses/by/2.0/">CC BY</a>.

The input files and processed output data for the OSSEs using particle filter for the forecast of cloud and precipitation

DART_input.tar.gz contains the input files for the DART system for the control run, Exp-1 ~ Exp-5. WRF&WRS_namelist.tar.gz contains the input namelist files for the WPS and WRF model for the nature run, the control run, and Exp-1 ~ Exp-5. cloud_data.tar.gz contains the procssed output data for the WRF/DART system corresponding to the nature run, the control run, and Exp-1 ~ Exp-5. Untarring the file will generate several subdirectories named after the UTC time. For example, 202008200200 denotes the results for at 02:00 UTC, 20 August, 2020. Because the data for all times are quite large (~10G), we only uploaded the data at 02:00 UTC, 20 August, 2020, 10:30 UTC, 20 August, 2020, 19:00 UTC, 20 August, 2020, 03:30 UTC, 21 August, 2020, and 12:00 UTC, 21 August, 2020. Each subdirectory contains preassim_mean.nc and postassim_mean.nc, which mean the posterior and prior estimate of atmosphere state variables and other processed variables. Either preassim_mean.nc or postassim_mean.nc contains the cloud water path (CWP, unit:kgm-2), cloud water content (CWC, which is the sum of the mixing ratio of six cloud hydrometeors, unit: kgkg-1), RE_CLOUD(unit:um), RE_ICE(unit:um), QVAPOR(unit:kgkg-1), T(the perturbation of potential temperature, unit:K). rain_rate.tar.gz contains the procssed output data for the rain rate corresponding to the nature run, the control run, and Exp-4 ~ Exp-5.

Scale-dependent species-area relationship: niche-based versus stochastic processes in a typical subtropical forest

Determining the patterns and drivers of the small-scale species-area relationship (SAR) is crucial for improving our understanding of community assembly and biodiversity patterns. Niche-based and stochastic processes are two principal categories of mechanisms potentially driving SARs. However, their relative importance has rarely been quantified rigorously owing to scale-dependence and the simplified niche volumes often used. In a fully mapped, 24-ha plot of a typical subtropical forest, we built the SARs and well-defined niche-hyper-volumes of a broad range of environmental variables at scales of 10 - 70 m (cell sizes). We then simulated passive sampling and partitioned the variances of the SAR slopes to disentangle the two contrasting mechanisms. We found that the small-scale SAR best followed a power-law relationship, consistent with large-scale SARs. The SAR slope declined with increasing scale; it was lower than expected under passive sampling at scales below 30 m and higher at larger scales. Environmental niches explained more (39%-64%) of the slope at larger scales, exceeding 50% at scales > 30 m, and these niches always captured the majority of the structured slopes. Environmental position (environmental mean values) effects were steady in absolute strength across scales and explained most (98%-68%) of the niche effect, but this proportion decreased with increasing scale. The effect of environmental heterogeneity increased with spatial scales, starting to rise at the 30 m scale after controlling for environmental position. Excluding soil properties from analyses strongly reduced these niche effects, highlighting the importance of soils for structuring the small-scale SAR. There was also substantial stochasticity in the SAR slopes, which was only partially explained by passive sampling. Synthesis: Our results show that the small-scale SAR in the studied subtropical forest follows a power-law, exhibits a scale shift in slope at 30 m, and is strongly shaped by niche effects that are dominated by environmental position relative to heterogeneity. However, soil heterogeneity controls the increase of niche effect and shift in the SAR slope with increasing spatial scales. Hence, edaphic factors can be responsible for scale-dependence in small-scale SARs, thereby linking small-scale and large-scale SARs.

LTEE-TnSeq-processed-data

This repository contains processed data from transposon sequencing (TnSeq) and whole genome sequencing (WGS) of the ancestral strains and evolved clones at 50K from the Lenski Long-Term Evolution Experiment (LTEE). It comprises TnSeq mutant trajectory counts, and output files from WGS analysis using breseq and samtools.

Gender equality and hiring process in oil mining companies: A case of Lokichar in Turkana, Kenya

This paper centers on the findings of a study done by the authors of this paper in 2019 titled Change in Gender Roles as a Factor in Gender Participation and Empowerment in the Oil Mining Industry: A Case of Lokichar, Kenya. One of the objectives; determining whether the oil mining companies promotes gender equity in Lokichar is explored. The null hypothesis testing on whether there is no relationship between equal hiring and equal opportunity for men and women to work in mining activities is discussed. The data was collected from a sample of three hundred (300) respondents selected through systematic random and purposive sampling methods. The studies target group was the active labour force aged between 15 to 64 years. Those who retired from work were also targeted. Two levels of analysis were adopted: Univariate and Bivariate. Chi-square was used to test the hypotheses. Major finding indicates that there is a relationship between equal hiring and equal opportunity for men and women to work in mining activities. The paper recommends that issues like compensation, decision making, royalty sharing, power relations are well spelt in policies like the Mining Bill (2014) to ensure gender mainstreaming and no ambiguity in interpretation.

Impact of Cloud Process in the Mixing State and Microphysical Properties of Soot Particles: Implications in Light Absorption Enhancement

The data of paper of "Impact of Cloud Process in the Mixing State and Microphysical Properties of Soot Particles: Implications in Light Absorption Enhancement".

Altitudinal dispersal process drives community assembly of montane small mammals

Montane small mammals are subjected to strong forces of dispersal limitation and habitat filtering that mainly operate on their community structures along the altitudinal direction. However, so far little is known about the relative contributions of dispersal and niche processes to their community assembly. By applying the newly-proposed PER-SIMPER/DNCI (dispersal–niche continuum index) framework to small mammal occurrence data collected from 21 extensive altitudinal gradients, we quantitatively assess the relative importance of dispersal and niche processes on mammalian community assembly in a large mountainous region of southwest China. We compared the pairwise DNCI values among assemblages from low, middle, and high altitudinal zones and overall DNCI values between glires and insectivores that differ in dispersal abilities to test three explicit (altitudinal connectivity, environmental difference, and dispersal ability) hypotheses. The overall DNCI values for all small mammal species combined (-12.7 ± 0.4, 90 species), glires (-12.8 ± 0.5, 56 species) and insectivores (-13.5 ± 1.4, 34 species) values were all negative, while insectivores showed a lower value than glires. For both all species combined and glires, we found a lower pairwise DNCI value between the low and high altitudinal zones than that between the other two pairs of altitudinal zones. Our study indicated that altitudinal dispersal process dominates the taxonomic composition of small mammal assemblages in this region. Importantly, the results reinforced the idea that community structures of less vagile taxa are more subjected to dispersal limitation, yet another idea that assemblages from further altitudinal areas are more differentiated by dispersal process was only supported in glires and all species combined. Community biologists should therefore pay attention to recent climate-induced upward range shifts by montane species, which may dramatically alter their community structures in different altitudinal zones through dynamics of immigration and mountaintop extinction.

opencc-by-4.0Nov 2021View details →

Underlying data / Hydrothermal carbonization as an alternative sanitation technology: process optimization and development of low-cost reactor

Experimental data of a research publication "Hydrothermal carbonization as an alternative sanitation technology: process optimization and development of low-cost reactor" is provided. Background: The provision of safe sanitation services is essential for human well-being and environmental integrity, but it is often lacking in less developed communities with insufficient financial and technical resources. Hydrothermal carbonization (HTC) has been suggested as an alternative sanitation technology, producing value-added products from faecal waste. We evaluated the HTC technology for raw human waste treatment in terms of resource recovery. In addition, we constructed and tested a low-cost HTC reactor for its technical feasibility. Methods: Raw human faeces were hydrothermally treated in a mild severity range (≤ 200 °C and ≤ 1 hr). The total energy recovery was analysed from the energy input, higher heating value (HHV) of hydrochar and biomethane potential of process water. The nutrient contents were recovered through struvite precipitation employing process water and acid leachate from hydrochar ash. A bench-scale low-cost reactor (BLR) was developed using widely available materials and tested for human faeces treatment. Results: The hydrochar had HHVs (23.2 - 25.2 MJ / kg) comparable to bituminous coal. The calorific value of hydrochar accounted for more than 90 % of the total energy recovery. Around 78 % of phosphorus in feedstock was retained in hydrochar ash, while 15 % was in process water. 72 % of the initial phosphorus can be recovered as struvite when deficient Mg and NH4 are supplemented. The experiments with BLR showed stable operation for faecal waste treatment with an energy efficiency comparable to a commercial reactor system. Conclusions:  This research presents a proof of concept for the hydrothermal treatment of faecal waste as an alternative sanitation technology, by providing a quantitative evaluation of the resource recovery of energy and nutrients. The experiments with the BLR demonstrate the technical feasibility of the low-cost reactor and support its further development on a larger scale to reach practical implementation

Processed Data 1 : Spatial multi-omic map of human myocardial infarction

We provide here the processed snRNA-seq, snATAC-seq, and visium data for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022

Data from: Parallel processing in speech perception with local and global representations of linguistic context

Speech processing is highly incremental. It is widely accepted that human listeners continuously use the linguistic context to anticipate upcoming concepts, words, and phonemes. However, previous evidence supports two seemingly contradictory models of how a predictive context is integrated with the bottom-up sensory input: Classic psycholinguistic paradigms suggest a two-stage process, in which acoustic input initially leads to local, context-independent representations, which are then quickly integrated with contextual constraints. This contrasts with the view that the brain constructs a single coherent, unified interpretation of the input, which fully integrates available information across representational hierarchies, and thus uses contextual constraints to modulate even the earliest sensory representations. To distinguish these hypotheses, we tested magnetoencephalography responses to continuous narrative speech for signatures of local and unified predictive models. Results provide evidence that listeners employ both types of models in parallel. Two local context models uniquely predict some part of early neural responses, one based on sublexical phoneme sequences, and one based on the phonemes in the current word alone; at the same time, even early responses to phonemes also reflect a unified model that incorporates sentence-level constraints to predict upcoming phonemes. Neural source localization places the anatomical origins of the different predictive models in nonidentical parts of the superior temporal lobes bilaterally, with the right hemisphere showing a relative preference for more local models. These results suggest that speech processing recruits both local and unified predictive models in parallel, reconciling previous disparate findings. Parallel models might make the perceptual system more robust, facilitate processing of unexpected inputs, and serve a function in language acquisition.

Processed data and scripts for visualization of Kotsuki et al. (2022; GMDD)

Processed data and scripts for visualization of Kotsuki et al. (2022; GMDD)

opennotspecifiedJul 2016View details →

Distribution. SW Brazil, known only from two sites, the type locality in Rondonia and Juruena (Mato Grosso State)Descriptive notes Head-body ¢.230 mm, tail ¢.80 mm. No specific data are available for body weight. Rondon's Tuco-tuco is medium-sized. Dorsal hairs are pale at bases and sepia at tips. Head and venterare slightly rufous, and tail is uniform brown. Skull is robust and depressed. Inter-maxillaries are also robust, with lateral protruding expansion; maxillaries are narrow; and mandible is strong and wide. Supraorbital process protrudes, and traverse occipital-temporal crest is straight. Bullae are inflated. in Ctenomyidae

Distribution. SW Brazil, known only from two sites, the type locality in Rondonia and Juruena (Mato Grosso State)Descriptive notes Head-body ¢.230 mm, tail ¢.80 mm. No specific data are available for body weight. Rondon's Tuco-tuco is medium-sized. Dorsal hairs are pale at bases and sepia at tips. Head and venterare slightly rufous, and tail is uniform brown. Skull is robust and depressed. Inter-maxillaries are also robust, with lateral protruding expansion; maxillaries are narrow; and mandible is strong and wide. Supraorbital process protrudes, and traverse occipital-temporal crest is straight. Bullae are inflated.

Photoluminescence processes in τ-phase Dy3+/Tb3+-codoped Ba1.3Ca0.7SiO4 phosphors for solid-state lighting

The τ-phase-Ba1.3Ca0.7SiO4 phosphors co-doped with 3 mol% Dy3+ and ~1-5 mol% Tb3+ trivalent rare-earth ions were prepared by the gel-combustion method. The structure-property relation of the samples was examined by X-ray diffraction, scanning electron microscopy, and spectrophotometer. Here, the effect of Tb3+'s concentration on the spectroscopic properties of Dy3+/Tb3+ co-doped Ba1.3Ca0.7SiO4 phosphors was explored by using the photoluminescence excitation, emission, and decay curves. Importantly, the photonic energy transfer from (Dy3+: 4F9/2 + Tb3+: 7F6) to (Dy3+: 6H15/2 + Tb3+:5D4) was observed, in which the Dy3+ ions acts as a light-emitting donor whereas the Tb3+ ions as a light-absorbing acceptor, resulting in an enhanced emission from the co-doped Ba1.3Ca0.7SiO4: Dy3+/Tb3+ phosphors. Finally, the chromaticity coordinates were determined from the measured emission spectra, locating at the green and white light regions. This observation indicates that the characteristic emission color could be tuned from white to green by varying Tb3+ concentrations under ultraviolet light.