Find research datasets worth reusing

opencc-by-4.0Feb 2020View details →

Data Supporting GoodVibes: automated thermochemistry for heterogeneous computational chemistry data

These files are provided in support of the use case in a recent manuscript showing the use of the Python package <a href="https://github.com/bobbypaton/GoodVibes">GoodVibes</a>. This data set contains Gaussian optimization and frequency calculations on 25 molecules, along with 25 corresponding ORCA single point energy calculations, a YAML file to dictate and format the reaction pathway, and example outputs of the tabulated thermochemistry and a PNG of the potential energy surface graph output. To generate these output files, the command: <pre><code class="language-bash">python -m goodvibes *.log --spc DLPNO --pes PhPy.yaml --graph PhPy.yaml -t 353.15 --imag --invertifreq -5 --media ethanol -c 1 </code></pre> was run in the directory containing the calculation output (.log and .out) files.

opencc-by-4.0Feb 2020View details →

Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction

We include samples of various data types used in the work "Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction" More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/pathway2vec">hallamlab/pathway2vec</a>

opencc-by-4.0Apr 2020View details →

Full results of numerical experiments described in research paper "A conservative index heuristic for routing problems with multiple heterogeneous service facilities"

These files include the complete results of the numerical experiments described in our research paper, "A conservative index heuristic for routing problems with multiple heterogeneous service facilities".

opencc-zeroMay 2020View details →

Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments

Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

opencc-by-4.0Jun 2020View details →

Data of A recurrent neural network-accelerated multi-scale model for elasto-plastic heterogeneous materials subjected to random cyclic and non-proportional loading paths

<pre>Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data) title = "A recurrent neural network-accelerated multi-scale model for elasto-plastic heterogeneous materials subjected to random cyclic and non-proportional loading paths", journal = "Computer Methods in Applied Mechanics and Engineering", pages = " 113234", year = "2020", issn = "0045-7825", doi = "https://doi.org/10.1016/j.cma.2020.113234", author = "Wu, Ling and Nguyen, Van Dung and Kilingar, Nanda Gopala and Noels, Ludovic"</pre>

opencc-by-4.0Jul 2020View details →

Single-cell Transcriptomic Analysis Identifies Extensive Heterogeneity in the Cellular Composition of Mouse Achilles Tendons

Tendon is a dense connective tissue that stores and transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, yet little is known about the diversity of cell types that populate tendon. To address this, we determined the heterogeneity of cell populations within mouse Achilles tendons using single-cell RNA sequencing. In assembling a transcriptomic atlas of Achilles tendons, we identified 11 distinct types of cells, including 3 previously undescribed populations of tendon fibroblasts. This table contains differential gene expression for specific genes identified in distinct populations of cells within tendon tissue.

opencc-zeroJul 2020View details →

Data for: Synthesis and assessment of schwertmannite/few-layer graphene composite for the degradation of sulfamethazine in heterogeneous Fenton-like reaction

Schwertmannite, an iron oxyhydrosulfate mineral, can catalyze Fenton-like reaction to degrade organic contaminants, but the reduction of Fe(III) to Fe(II) on the surface of schwertmannite is a limiting step for the Fenton-like process. In the present study, the schwertmannite/few-layer graphene composite (sch-FLG) was synthesized to promote the catalytic activity of schwertmannite in Fenton-like reaction. It was found that schwertmannite can be successfully carried by FLG in sch-FLG composite, mainly via the chemical bond of Fe-O-C on the surface of sch-FLG. The sch-FLG exhibited a much higher catalytic activity than schwertmannite or FLG for the degradation of SMT in the heterogeneous Fenton-like reaction, which resulted from that the few-layer graphene can pass electrons efficiently. The degradation efficiency of SMT was around 100% under the reaction conditions of H2O2 200-500 mg L-1, sch-FLG dosage 1-2 g L-1, temperature 28-38 °C, and initial solution pH 1-9. During the repeated uses of sch-FLG in Fenton-like reaction, it maintained a certain catalytic activity for the degradation of SMT and the mineral structure was not changed. In addition, SMT may be finally mineralized in Fenton-like reaction catalyzed by sch-FLG, and the possible degradation pathways were proposed. Therefore, the sch-FLG is an excellent catalyst for SMT degradation in heterogeneous Fenton-like reaction.

opencc-zeroJun 2020View details →

Data from: Multiple scales of spatial heterogeneity control soil respiration responses to precipitation across a dryland rainfall gradient

Aims – Soil respiration (Rs) is a major pathway for releasing fixed carbon back to the atmosphere. However, controls over Rs are poorly understood in arid and hyper-arid systems where microbial activity is frequently constrained by moisture. We addressed key uncertainties in Rs: 1) How do short-term rainfall pulses affect Rs at sites that differ in long-term precipitation inputs?, 2) how do Rs responses to short and long-term rainfall differ across soil surfaces?, and 3) how are Rs responses affected by local-scale attributes? Methods – We measured Rs responses to rainfall pulses over a 48 h period. Working across a climate gradient, we compared Rs responses on two contrasting soil surfaces which both had two vegetation/soil morphology patch types that differed in organic matter inputs and accumulation. Results – Rates of Rs were low, but highly responsive to rainfall pulses. Stimulation of Rs by rainfall was generally greater in areas with higher annual rainfall. However, patterns for Rs responses to rainfall differed greatly on the two soil surfaces and among patch types. Conclusions – The strong role of patch type and soil surface in controlling Rs points to the need to carefully consider small-scale spatial and temporal variation when interpreting dryland biogeochemical fluxes.

opencc-zeroMar 2021View details →

Plant intraspecific functional trait variation is related to within-habitat heterogeneity and genetic diversity in Trifolium montanum L.

Intraspecific trait variation (ITV), based on available genetic diversity, is one of the major means plant populations can respond to environmental variability. The study of functional trait variation and diversity has become popular in ecological research, e.g. as a proxy for plant performance influencing fitness. Up to now, it is unclear which aspects of intraspecific functional trait variation (iFDCV) can be attributed to the environment or genetics under natural conditions. Here, we examined 260 individuals from 13 locations of the rare (semi-)dry calcareous grassland species Trifolium montanum L. in terms of iFDCV, within-habitat heterogeneity, and genetic diversity. The iFDCV was assessed by measuring functional traits (releasing height, biomass, leaf area, specific leaf area, leaf dry matter content, Fv/Fm, performance index, stomatal pore surface, and stomatal pore area index). Abiotic within-habitat heterogeneity was derived from altitude, slope exposure, slope, leaf area index, soil depth, and further soil factors. Based on microsatellites, we calculated expected heterozygosity (He) because it best-explained, among other indices, iFDCV. We performed multiple linear regression models quantifying relationships among iFDCV, abiotic within-habitat heterogeneity and genetic diversity, and also between separate functional traits and abiotic within-habitat heterogeneity or genetic diversity. We found that abiotic within-habitat heterogeneity influenced iFDCV twice as strong compared to genetic diversity. Both aspects together explained 77% of variation in iFDCV (Radj² = 0.77, F2, 10 = 21.66, p < 0.001). The majority of functional traits (releasing height, biomass, specific leaf area, leaf dry matter content, Fv/Fm and performance index) were related to abiotic habitat conditions indicating responses to environmental heterogeneity. In contrast, morphology-related functional traits (releasing height, biomass and leaf area) were only related to genetics. Our results suggest that both within-habitat heterogeneity and genetic diversity affect iFDCV, and are thus crucial to consider when aiming to understand or predict changes of plant species performance under changing environmental conditions.

Enhanced Heterogenous Hydration of SO2 Through Immobilization of Pyridinic-N on Carbon Materials

Carbon materials doped with nitrogen has long been utilized for SO2 removal from flue gases for the benefits of environment. The role of water is generally regarded as hydration of SO3 which is formed through the oxidization of SO2. However, the hydrolysis of SO2, especially on the surface of N doped carbon materials, was almost ignored. In this study, the hydrolysis of SO2 was investigated in detail on the pyridinic nitrogen (PyN) doped graphene (GP) surfaces. It is found that, compared to the homogenous hydrolysis of SO2 assisted with NH3 in gas phase, the heterogeneous hydrolysis is much more thermodynamically and kinetically favorable. Specifically, when a single H2O molecule is involved, the energy barrier for SO2 hydrolysis is as low as 0.15 eV, with 0.59 eV released, indicating the hydrolysis of SO2 can occur at rather low water concentration and temperature. Thermodynamic integration molecular dynamics results show the feasibility of the hydrogenated substrate recovery and the immobilized N acting as a catalytic site for SO2 hydrolysis. Our findings show that the heterogeneous hydrolysis of SO2 should be universal and potentially uncover the puzzling reaction mechanism for SO2 catalytic oxidation at low temperature by N doped carbon materials.

opencc-by-4.0Aug 2020View details →

Polygenic modelling of treatment effect heterogeneity

Xu, ZM, Burgess, S. Polygenic modelling of treatment effect heterogeneity. Genetic Epidemiology. 2020; 1– 12. <a href="https://doi.org/10.1002/gepi.22347">https://doi.org/10.1002/gepi.22347</a> File contains:  1. Summary statistics of genome-wide interaction study (between moderating variants and HMGCR pharmacomimetic score) 2. Random forest of interaction tree (RFIT) objects.  See README for detail

Data from: ApoE is a correlate of phenotypic heterogeneity in Alzheimer's disease in a national cohort

Objective: To compare the proportion of APOEε4 genotype carriers in aphasic versus amnestic variants of Alzheimer's disease (AD). Method: The proportion of APOEε4 carriers was compared among 3 groups. 1) Forty-two patients with primary progressive aphasia (PPA) and AD pathology (PPA/AD) enrolled in the Northwestern Alzheimer Disease Center Clinical Core. 2) 1,418 patients with autopsy confirmed AD and amnestic dementia of the Alzheimer-type (DAT/AD); 3) 2,608 cognitively normal controls (NC). The latter two groups were compiled from the National Alzheimer Coordinating Center (NACC) database. Logistic regression models analyzed the relationship between groups and APOEε4 carrier status, adjusting for age of onset and sex as needed. Results: Using NC as the reference and adjusting for sex and age, the DAT/AD group was 3.97 times more likely to be APOEε4 carriers. Adjusting for sex and age at symptom onset, the DAT/AD group was 2.46 times as likely to be carriers compared to PPA/AD. There was no significant difference in the proportion of APOEε4 carriers for PPA/AD compared to NC. PPA subtypes included 24 logopenic, 10 agrammatic nonfluent, and eight either mixed (n=5) or too severe (n=3) to subtype. The proportion of carriers and non carriers was similar for logopenic and agrammatic subtypes, both having fewer carriers. Conclusion: The proportion of APOEε4 carriers was elevated in amnestic but not aphasic manifestations of AD. These results suggest that APOEε4 is an anatomically selective risk factor that preferentially increases the vulnerability to AD pathology of memory-related medial temporal areas rather that language-related neocortices.

Phylogeny estimation given sequence length heterogeneity

Abstract Phylogeny estimation is a major step in many biological studies, and has many well known challenges. With the dropping cost of sequencing technologies, biologists now have increasingly large datasets available for use in phylogeny estimation. Here we address the challenge of estimating a tree given large datasets with a combination of full-length sequences and fragmentary sequences, which can arise due to a variety of reasons, including sample collection, sequencing technologies, and analytical pipelines. We compare two basic approaches: (1) computing an alignment on the full dataset and then computing a maximum likelihood tree on the alignment, or (2) constructing an alignment and tree on the full length sequences and then using phylogenetic placement to add the remaining sequences (which will generally be fragmentary) into the tree. We explore these two approaches on a range of simulated datasets, each with 1000 sequences and varying in rates of evolution, and two biological datasets. Our study shows some striking performance differences between methods, especially when there is substantial sequence length heterogeneity and high rates of evolution. We find in particular that using UPP to align sequences and RAxML to compute a tree on the alignment provides the best accuracy, substantially outperforming trees computed using phylogenetic placement methods. We also find that FastTree has poor accuracy on alignments containing fragmentary sequences. Overall, our study provides insights into the literature comparing different methods and pipelines for phylogenetic estimation, and suggests directions for future method development.

Data from: Early-life conditions determine the between-individual heterogeneity in plasticity of calving date in reindeer

1. Phenotypic plasticity has become a key-concept to enhance our ability to understand the adaptive potential of species to track the pace of climate change by allowing a relatively rapid adjustment of life history traits. 2. Recently, population-level trends of an earlier timing of reproduction to climate change have been highlighted in many taxa but only few studies have explicitly taken into consideration between-individual heterogeneity in phenotypic plasticity. 3. Using a long-term data of a semi-domesticated reindeer (Rangifer tarandus) population, we demonstrated that females differed greatly in their mean calving date but only slightly in the magnitude of their plastic response to the amount of precipitation in April. We also showed that despite the absence of a population trend, females individually responded to the amount of precipitation in April by delaying their calving dates. 4. Females' calving date under average climatic conditions was best predicted by their birthdate, their physical condition in March-April-May before their first calving season and by their first calving date. The degree of their phenotypic plasticity was not dependent on any of the females' attributes early in life tested in this study. However, females who delayed their calving dates in response to a higher amount of precipitation in April slightly produced less calves over their reproductive life. 5. These findings confirmed that early life conditions of female reindeer can shape their phenotypic value during reproductive life, supporting the importance of maternal effects in shaping individuals' lifetime reproductive success. Whether females differed in the magnitude of their plastic response to climatic changes has received contrasted responses for various ungulate species. This calls for more research to enhance our understanding of the underlying mechanisms leading to the complexity of plastic responses among populations to cope with current climate change.

opencc-zeroSep 2020View details →

Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)

Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evoutionary history of a species, providing the premise for studying the response of organisms to rapid cimate change. However, for most species how exacty the spatial heterogeneity promotes popuation divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographica and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as wel as genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome‐environment association analyses identified 16 putatively adaptive loci mainly related mainly to biotic and abiotic stress resistance. Our genome wide data provide new insights into the important roe of environmenta heterogeneity in shaping genetic structure, and access the footprints of ocal adaptation in an ancient reictual species, informing future conservation efforts. <div> <div class="gtx-trans-icon"> </div> </div>

opencc-by-nd-4.0Nov 2020View details →

The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics - Dataset

This is the dataset used in the manuscript "The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics" by Raatz et al. The code used to generate the data and figures can be found at https://doi.org/10.5281/zenodo.4461667.

opencc-zeroNov 2020View details →

Ant-hill heterogeneity and grassland management

1. In many grasslands, some ants act as ecological engineers to produce long-lasting soil structures which have a considerable influence on the patterns and dynamics of plant, vertebrate and invertebrate species. They promote species richness and diversity. 2. The yellow meadow ant, Lasius flavus, is the most abundant allogenic ecological engineer in grazed European grasslands, producing vegetated long-lasting mounds. Its ratio of influence to biomass is remarkably high. Grassland restoration projects frequently attempt to re-introduce grasslands on abandoned arable fields. When this ant does not colonise naturally it should be introduced. It probably limits the abundance of grasses in a similar manner to hemi-parasitic plant species. 3. Ant-hills make a distinctive contribution to grassland heterogeneity. Measurements on mounds in a single grassland over 45 years document the dynamics of the same 200+ ant-hills in volume, surface area and basal area. As the mounds aged they increased in size and took over a higher proportion of the grassland surface. Occupied mounds continued to grow, abandoned mounds decreased in volume and some disappeared entirely. 4. Four plant species favoured by the soil heaped by the ants were also monitored. Two woody perennials grew up through heaped soil and two short-lived species colonised its surface. As the mounds became occupied some of these species significantly increased, and when they were abandoned some decreased. 5. In a grassland, the ant-hill population provides a fluctuating subset of plant and animal species which are characteristic of temporary habitats. This seems likely to reduce the rate of local extinctions which might otherwise result from fluctuations in grazing pressure. In conservation settings, ant-hills should be introduced or maintained where possible, and considered in planning grassland maintenance and management.Minhyuk Seo

opencc-zeroDec 2020View details →

A meta-analysis of effects of physiological integration in clonal plants under homogeneous vs. heterogeneous environments

Summary 1. Clonal plants play key roles in maintaining community productivity and stability in many ecosystems. Connected individuals (ramets) of clonal plants can translocate and share e.g. photosynthates, water and nutrients, and such physiological integration may affect performance of clonal plants both<a name="_Hlk51046980"> in heterogeneous and homogeneous environments. </a>However, we still lack a general understanding of whether or how physiological integration in clonal plants differs across homogeneous vs. heterogeneous environments. 2. We compiled data from 198 peer reviewed scientific studies conducted in 19 countries with 108 clonal plant species from 35 families, and carried out a meta-analysis of effects of physiological integration on 16 traits related to plant growth, morphology, physiology or allocation. Our analyses evaluated these relationships in A) heterogeneous environments where at least one resource essential for plant growth (e.g. light, soil water and mineral nutrients) or non-resource factor (e.g. grazing, trampling and burial) is spatially non-uniformly distributed, and B) homogeneous environments where all these factors are spatially uniformly distributed. 3. Physiological integration increased growth of whole clones in both homogeneous and heterogeneous environments due to its highly significant contribution to growth of recipient ramets. Integration did not affect growth of donor ramets in heterogeneous environments, but decreased it in homogeneous environments. 4. Integration affected physiological traits of donor ramets in neither homogeneous nor heterogeneous environments. It did not affect any physiological traits of recipient ramets in homogeneous environments, but increased most of them in heterogeneous environments. For donor ramets, integration increased height by 53% and internode length by 37% in heterogeneous environments, but had no effect in homogeneous environments. For recipient ramets, integration increased height by 73% in homogeneous environments and by 115% in heterogeneous environments, and increased internode length by 35% only under heterogeneous environments. In heterogeneous environments, integration increased biomass allocation to roots of donor ramets under high water/nutrient conditions and decreased it under high light. 5. Physiological integration plays a strong role in clonal plant physiology, morphology, and growth, especially for recipient ramets in heterogeneous environments. Therefore, physiological integration may have contributed to the widespread of clonal plants in nature and their dominance in many ecosystems. It may also play important roles in invasion success of alien clonal plants and in maintaining functions and stability of ecosystems where clonal plants are abundant.