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MarTREC Project Datasets for Effect of Permeability Variation of Expansive Yazoo Clay at the Maritime and Multimodal Transportation Infrastructure in Mississippi
<p>The existence of Yazoo clay soil in Mississippi frequently causes distress to the pavement and cause deformation at the slopes in highways and levees, which are a critical component in Maritime and multimodal transportation infrastructure. Each year, fixing the pavement requires a significant maintenance budget of MDOT. Also, the infiltration of the rainwater in the highway and levee slopes leads to landslides, which require millions of maintenance dollars each year. Due to the shrinkage and swelling behavior of the Yazoo clay, the hydraulic conductivity varies over the different seasons and has higher vertical permeability during the dry season. With high vertical permeability, the rainwater can easily percolate in the pavement subgrade and slopes, which accelerates the failure. The current study investigates the change in unsaturated vertical and horizontal permeability and its effect on the maritime and multimodal infrastructures, especially on the pavement and slopes of highway embankment and levees. The attached datasets include the laboratory test and finite element modeling findings.</p>
Data for "Age effect on tree structure and biomass allocation in Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies [L.] Karst.)"
<p>VAPU dataset for tree biomass was collected from southern Finland in 1988-1990 by the Finnish Forest Research Institute (Metla, now Natural Resources Institute Finland, Luke) (VAPU data set).</p> <p>Those sample trees (162 Scots pine and 163 Norway spruce) are originated from the whole VAPU data set. The sheet 'Pine' and 'Spruce' data have been matched between 'sample branch measurements' and the 'biomass' information (by cluster X, Y, and plot, tree number).</p> <p>Biomass estimation for foliage and branches has been described here: https://doi.org/10.1016/j.ecolmodel.2004.04.024 and https://doi.org/10.1093/treephys/25.7.803<br> </p>
Data from: An effective method for ecosystem-scale manipulation of bird abundance and species richness
Manipulation experiments are a cornerstone of ecological research, but can be logistically challenging to execute – particularly when they are intended to isolate the ecological role of large, vagile species, like birds. Despite indirect evidence that birds are influential in many ecosystems, large-scale, multi-year bird manipulation experiments are rare. When these studies are conducted, they are typically realized with caged or netted exclosures, an approach that can be expensive, risky for wildlife, and difficult to maintain. In cases where caged exclosures are not appropriate, alternate approaches are needed to allow rigorous empirical studies on the ecological role of birds. Here, we present and validate a method for experimentally increasing the abundance and richness of birds at the scale of entire aquatic ecosystems. Unlike bird exclusion, this approach is experimentally tractable, appealing to land managers, and possible to deploy over large spatial scales. We tested the efficacy of our approach for increasing bird abundance and species richness at 16 central California ponds. Based on bird visitation data obtained by summer camera trapping, our approach significantly increased bird species richness and abundance at manipulated ponds compared to control ponds. Attractant treatments mitigated the negative effects of a major drought on bird species richness, and generated a near-doubling of bird abundance in the presence of attractants. Treatments had no effect on most mammal species, with the exception of ground squirrels, which increased in abundance in the presence of attractants. These results suggest that attractants are effective in increasing bird abundance and richness. We encourage researchers to consider this approach for experimentally isolating the ecological role of birds in aquatic and open terrestrial ecosystems, especially in cases where cost or logistical constraints preclude the use of caged or netted exclosures.
Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs
<p>While the importance of maternal effects has long been appreciated, a growing body of evidence now points to the paternal environment having an important influence on offspring phenotype. Indeed, research on rodent models suggests that paternal stress leaves an imprint on the behaviour and physiology of offspring via non-genetic information carried in the spermatozoa, however fish have been understudied with regard to these sperm-mediated effects. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors (conspecific-derived alarm cue, chasing, and bright light) before mating and assessing the behavioural and endocrine responses of their offspring, including their behavioural response to conspecific-derived alarm cue. We found that after males are exposed to stress, their larval offspring show weakened responses to stressors. Small RNA sequencing subsequently revealed that the levels of several small noncoding RNAs, including microRNAs, PIWI-interacting RNAs, and tRNA-derived small RNAs, were altered in the spermatozoa of stressed fathers, suggesting that stress-induced alterations to the spermatozoal RNA landscape may contribute to shaping offspring phenotype. The work demonstrates that paternal stress should not be overlooked as a source of phenotypic variation and that spermatozoal small RNAs may be important intergenerational messengers in fish.</p>
Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics
1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. 2. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of 1) the number of taxa included in the regional phylogeny; 2) random vs. targeted sampling of species to assemble the regional species pool; 3) including only species from specific clades rather than broad sampling; 4) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and 5) using phylograms compared to chronograms. 3. We found that including more taxa in a study increases the likelihood of observing significantly non-random phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. 4. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.
Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove
<p>Mangrove forests are ecosystems that constitute a large portion of the world's coastline and span tidal zones below, between, and above the waterline, while the ecosystem as a whole is defined by the health of these tidal microhabitats. However, we are only beginning to understand tidal zone microbial biodiversity and the role of these microbiomes in nutrient cycling. While extensive research has characterized microbiomes in pristine versus anthropogenically impacted mangroves these have, largely, overlooked differences in tidal microhabitats (sublittoral, intertidal, and supralittoral). Unfortunately, the small number of studies that have sought to characterize mangrove tidal zones have occurred in impacted biomes, making interpretation of the results difficult. Here, we characterized prokaryotic populations and their involvement in nutrient cycling across the tidal zones of a pristine mangrove within a Brazilian Environmental Protection Area of the Atlantic Forest. We hypothesized that the tidal zones in pristine mangroves are distinct microhabitats, which we defined as distinct regions that present spatial variations in the water regime and other environmental factors, and as such, these are composed of different prokaryotic communities with distinct functional profiles. Samples were collected in triplicate from zones below, between, and above the tidal waterline. Using 16S rRNA gene amplicon sequencing, we found distinct prokaryotic communities with significantly diverse nutrient cycling functions, as well as specific taxa with varying contribution to functional abundances between zones. Where previous research from anthropogenically impacted mangroves found the intertidal zone to have high prokaryotic diversity and functionally enriched in nitrogen cycling, we find that the intertidal zone from pristine mangroves have the lowest diversity and no functional enrichment, relative to the other tidal zones. The main bacterial phyla in all samples were Firmicutes, Proteobacteria and Chloroflexi while the main archaeal phyla were Crenarchaeota and Thaumarchaeota. Our results differ slightly from other studies where Proteobacteria is the main phyla in mangrove sediments and Firmicutes make up for only a small percentage of the communities. Salinity and organic matter were the most relevant environmental factors influencing these communities. Bacillaceae was the most abundant family at each tidal zone and showed potential to drive a large proportion of the cycling of carbon, nitrogen, phosphorus and sulfur. Our findings suggest that some aspects of mangrove tidal zonation may be compromised by human activity, especially in the intertidal zone.</p>
Datasets for The Effect of COVID-19 on AGU Journal Authors by Gender and Geographical Location
<p>These files provide anonymized source data and tabular data on gender, age, and country of corresponding authors (submitting author) of American Geophysical Union (AGU) journals from January 2018 through June 2020. These datasets supplement an iposter presented at Japan Geosciences Union- American Geophysical Union joint 2020 meeting and supplement the corresponding preprint submission to ESSOAR.</p>
Computed results for Bayesian genome scale modelling temperature effect on yeast metabolism
<p>This repository contains the computed results for reproducing the figures in the manuscript "Li G., et al. Bayesian genome scale modelling identifies thermal determinants of yeast metabolism". The scripts can be found in Github (<a href="https://github.com/Gangl2016/BayesianGEM">https://github.com/Gangl2016/BayesianGEM</a>)</p>
Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees
<p>Data and results of the paper "Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees".</p> <p>- data_table_species.csv: contains life-history and geographical range descriptors, terminal branch length and genomic estimated values for each substitution category, for each species in the dataset. Contains results obtained with both the complete data set and the subsampled dataset with 88 species.</p> <p>- data_table_genes.csv: contains values of substitution count that are sums of the values obtained for every species in the alignment. Also contains the results of HyPhy RELAX analyses for each alignment.</p> <p>- data_table_genes_species.csv: contains estimated values for each substitution category for each species in each alignment. Contains results obtained with both the complete data set and the subsampled dataset with 88 species.</p> <p> </p>
Investigating the Effect of Positional Variation on Mid-Lactation Mammary Gland Transcriptomics in Mice Fed Either a Low-Fat or High-Fat Diet
<p>Investigating the Effect of Positional Variation on Mid-Lactation Mammary Gland Transcriptomics in Mice Fed Either a Low-Fat or High-Fat Diet.</p>
Effects of COVID-19 lockdown on heart rate variability
<p><strong>Introduction: </strong>Strict lockdown rules were imposed to the French population from 17 March to 11 May 2020, which may result in limited possibilities of physical activity, modified psychological and health states. This report is focused on HRV parameters kinetics before, during and after this lockdown period.</p> <p><strong>Methods:</strong> 95 participants were included in this study (27 women, 68 men, 37 ± 11 years, 176 ± 8 cm, 71 ± 12 kg), who underwent regular orthostatic tests (a 5-minute supine followed by a 5-minute standing recording of heart rate (HR)) on a regular basis before (BSL), during (CFN) and after (RCV) the lockdown. HR, power in low- and high-frequency bands (LF, HF, respectively) and root mean square of the successive differences (RMSSD) were computed for each orthostatic test, and for each position. Subjective well-being was assessed on a 0-10 visual analogic scale (VAS). The participants were split in two groups, those who reported an improved well-being (WB+, increase >2 in VAS score) and those who did not (WB-) during CFN.</p> <p><strong>Results:</strong> Out of the 95 participants, 19 were classified WB+ and 76 WB-. There was an increase in HR and a decrease in RMSSD when measured supine in CFN and RCV, compared to BSL in WB-, whilst opposite results were found in WB+ (i.e. decrease in HR and increase in RMSSD in CFN and RCV; increase in LF and HF in RCV). When pooling data of the three phases, there was a moderate significant correlation between VAS and HR, RMSSD, HF, respectively, in the supine position; the higher the VAS score (i.e., subjective well-being), the higher the RMSSD and HF and the lower the HR. In standing position, HRV parameters were not modified during CFN.</p> <p><strong>Conclusion:</strong> Our results suggest that the strict COVID-19 lockdown likely had opposite effects on French population as 20% of participants improved parasympathetic activation (RMSSD, HF) and rated positively this period, whilst 80% showed altered responses and deteriorated well-being. The changes in HRV parameters during and after the lockdown period were in line with subjective well-being responses. The observed recordings may reflect a large variety of responses (anxiety, anticipatory stress, change on physical activity…) beyond the scope of the present study. However, these results confirmed the usefulness of HRV as a non-invasive means for monitoring well-being and health in the general population.</p>
Variations in tree growth provide limited evidence of species mixture effects in Interior West U.S.A. mixed-conifer forests
<p>1. In mixed stands, species complementarity (e.g., facilitation and competition reduction) may enhance forest tree productivity. Although positive mixture effects have been identified in forests worldwide, the majority of studies have focused on two-species interactions in managed systems with high functional diversity. We extended this line of research to examine mixture effects on tree productivity across landscape-scale compositional and environmental gradients in the low functional diversity, fire-suppressed, mixed-conifer forests of the U.S. Interior West.</p> <p>2. We investigated mixture effects on the productivity of <i>Pinus ponderosa</i>, <i>Pseudotsuga menziesii</i>, and <i>Abies concolor</i>. Using region-wide forest inventory data, we created individual-tree generalized linear mixed models and examined the growth of these species across community gradients. We compared the relative influences of stand structure, age, competition, and environmental stress on mixture effects using multi-model inference. We analyzed growth of neighboring tree species to infer whether a mixture effect in a single species translated to the stand-level.</p> <p>3. We found support for a positive mixture effect in <i>P. menziesii</i>, although our results were equivocal in light of a weaker but still plausible alternative model. Growth of <i>P. menziesii</i> neighboring species in mixed stands declined or held constant depending on aridity, suggesting that a positive mixture effect in <i>P. menziesii</i> does not necessarily extend to the stand level. We found no evidence for mixture effects in <i>P. ponderosa</i>, <i>A. concolor</i> or their neighboring species.</p> <p>4. Complementarity appears to have a limited influence on tree growth in the mixed-conifer systems of the U.S. Interior West, reflecting limited functional diversity. Historical changes in stand structure following fire exclusion, particularly high stand densities, may limit the potential for positive species mixture effects. The limited species pool of Interior West forests increases the risk that, without careful management, what functional diversity exists could be lost to compositional changes resulting from stand dynamics or disturbance.</p>
Agile Accelerator Program: From Industry-Academia Collaboration to Effective Agile Training
<p>The agile accelerator program takes place in a Brazilian technology park, as a collaboration between a university and a world-renowned technology company, specialized in agile development and consulting. This partnership has 8-year long with the main goal of preparing undergraduate students to work in high-performance agile teams. This partnership created a culturally rich environment for student learning while influencing other companies to follow the same initiative within this technology park. We conducted a Case Study aiming to characterize this partnership (explaining how it works) and the resulting program, understanding the benefits to the program students. Our results point out the importance of the kind of partnership that provides an immersive learning environment to students, where students can learn empirically, with real projects and real stakeholders and how important it was for the program's former students to enter the job market. This successful enhanced students' training program on agile software development through the blending of culture between institutions can be of inspiration to those interested in aiming to bridge the gap between academia and industry.</p>
An experimental test of the Allee effects range limitation hypothesis
<p>Data and code for a simple N-mixture model in JAGS Merker, S.A and Chandler, R.B. In Press. An experimental test of the Allee effects range limitation hypothesis. Journal of Animal Ecology.</p> <p>JAE-data.gzip contains the data required to run the model including:</p> <ol> <li>scaled and center covariates of detection</li> <li>a 3 dimensional array containing counts of Canada warbler (cardellina canadensis) at 71 point count locations over 4 years</li> <li>A climate PCA derived from PRISM data.</li> </ol> <p>The model itself is described in the .jAG file "Abundance_EN_clim-trt-D.JAG"</p> <p>Merker_Chandler_Appendices is an Rmarkdown file for the appendices of the article</p>
Raw data for "Examining the effects of transcranial direct current stimulation on human episodic memory with machine learning"
<p>This is the raw dataset for "Examining the effects of transcranial direct current stimulation on human episodic memory with machine learning". Each .xlsx file represents an experimental results of a single participant.</p> <p>Directory description:</p> <p>Eng_sham - the results from experiments without stimulation on English sample from Medvedeva, 2019.</p> <p>Eng_vlPFC - the results from experiments with vLPFC stimulation on English sample from Medvedeva, 2019.</p> <p>enc_off_new - the results from experiments with dLPFC offline encoding stimulation on Russian sample.</p> <p>enc_on_new - the results from experiments with dLPFC online encoding stimulation on Russian sample.</p> <p>sham_no stimulation - the results from experiments without stimulation offline encoding stimulation on Russian sample.</p> <p>vlPFC_stimulation - the results from experiments with vLPFC stimulation on Russian sample.</p> <p>Age.xlsx - the ages of the participants</p> <p> </p>
Data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history''
<p><em>Eva Bons, Christine Leemann, Karin J. Metzner, Roland R. Regoes</em></p> <p>This repository contains all the data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history'</p> <p>See the readme after unpacking the .zip for a description of the files</p>
Typology of antipassive coding patterns and frequency effects of antipassives
Basic information about antipassives in languages with at least some ergative patterns
Allopatric divergence of cooperators confers cheating resistance and limits the effects of a defector mutation
<p>Studies of microbial social defectors that 'cheat' on cooperative genotypes generally focus on interactions with their cooperative parents, yet in nature defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting the cheaters' spread and potentially the overall equilibrium frequency of cheaters. The bacterium Myxococcus xanthus undergoes cooperative multicellular development upon starvation, but some developmental defectors can cheat on cooperators, outcompeting them within mixed groups. We show that a defector disrupted at the signaling gene csgA has a narrow cheating range among diverse natural cooperators owing to antagonisms not specifically targeted at defectors. More strikingly, lab-evolved cooperators only slightly differentiated from the defector have allopatrically evolved beyond its cheating range by accumulating fewer than 20 mutations when development was not directly under selection. Cooperators might diversify not only with respect to which defectors cheat on them, but also in the potential for a particular mutation to reduce expression of cooperative trait or generate a cheating phenotype. We tested this by constructing a new csgA mutation in several highly diverged cooperators. The mutation generated very different sporulation phenotypes – from a complete defect to no defect – indicating that genetic background effects can limit the set of genomes for which a given mutation creates a defector and potentiates cheating. Our results suggest that natural populations feature geographic mosaics of cooperators diversified in susceptibility to cheating by any given defector and in the social phenotypes generated by any given mutation in a cooperation gene.</p>
Dataset related to publication "Heating of hip joint implants in MRI: the combined effect of radiofrequency and switched-gradient fields"
<p>The datasets reported in the figures of the article "Heating of hip joint implants in MRI: the combined effect of radiofrequency and switched-gradient fields" by Alessandro Arduino, Umberto Zanovello, Jeff Hand, Luca Zilberti, Rüdiger Brühl, Mario Chiampi and Oriano Bottauscio, accepted for publication to Magnetic Resonance Imaging on Dec. 9th, 2020. A link to the article will be given after its final publication.</p>
Seasonal Effects in Gastrointestinal Parasite Prevalence, Richness and Intensity in Vervet Monkeys Living in a Semi-Arid Environment
<p>Data and R Notebook for Seasonal Effects in Gastrointestinal Parasite Prevalence, Richness and Intensity in Vervet Monkeys Living in a Semi-Arid Environment</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.