Find research datasets worth reusing

Population-level variation in parasite resistance due to differences in immune initiation and rate of response

Closely related populations often differ in resistance to a given parasite, as measured by infection success or failure. Yet, the immunological mechanisms of these evolved differences are rarely specified. Does resistance evolve via changes to the host's ability to recognize that an infection exists, actuate an effective immune response, or attenuate that response? We tested whether each of these phases of the host response contributed to threespine sticklebacks' recently evolved resistance to their tapeworm Schistocephalus solidus. While marine stickleback and some susceptible lake fish permit fast-growing tapeworms, other lake populations are resistant and suppress tapeworm growth via a fibrosis response. We subjected lab-raised fish from three populations (susceptible marine 'ancestors', a susceptible lake population, a resistant lake population), to a novel immune challenge using an injection of: 1) a saline control, 2) alum, a generalized pro-inflammatory adjuvant that causes fibrosis, 3) a tapeworm protein extract, or 4) a combination of alum and tapeworm protein). With enough time, all three populations generated a robust fibrosis response to the alum treatments. Yet, only the resistant population exhibited a fibrosis response to the tapeworm protein alone. Thus, these populations differed in their ability to respond to the tapeworm protein but shared an intact fibrosis pathway. The resistant population also initiated fibrosis faster in response to alum, and was able to attenuate fibrosis, unlike the susceptible populations' slow but longer-lasting response to alum. As fibrosis has pathological side-effects that reduce fecundity, the faster recovery by the resistant population may reflect an adaptation to mitigate the costs of immunity. Broadly, our results confirm that parasite detection and immune initiation, activation speed, and immune attenuation simultaneously contribute to the evolution of parasite resistance and adaptations to infection in natural populations.

Tree dynamic response and survival in a category-5 tropical cyclone: The case of super typhoon Trami

In the future with climate change, we expect more forest and tree damage due to the increasing strength and changing trajectories of tropical cyclones (TCs). However, to date, we have limited information to estimate likely damage levels, and nobody has ever measured exactly how forest trees behave mechanically during a TC. In 2018, a category-5 TC destroyed trees in our ongoing research plots, in which we were measuring tree movement and wind speed in two different tree spacing plots. We found damaged trees in only the wider spaced plot. Here, we present how trees dynamically respond to strong winds during a TC. Sustained strong winds obviously trigger the damage to trees and forests but inter-tree spacing is also a key factor because the level of support from neighboring trees modifies the effective "stiffness" against the wind both at the single tree and whole forest stand level.

Phantom ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects"

Phantom ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects". Code to process and reconstruct the data is available here: <a href="https://github.com/usc-mrel/lowfield_maxgirf">https://github.com/usc-mrel/lowfield_maxgirf</a>

GWAS on salt stress responses in root system architecture parameters of wild tomato (S. pimpinellifolium)

The population of +/2 200 accessions of wild tomato was screened with the protocol described <a href="https://www.protocols.io/view/studying-root-system-architecture-changes-in-tomat-2mqgc5w">here</a> with the only exception that the plants were transferred 4 days after germination (rather than 3 - described in the protocol). The images were analyzed using the <a href="https://smartroot.github.io/">SmartRoot</a> for days 0, 1, 2, 3, and 4 after transfer to treatment plates (0 or 100 mM NaCl, 1/4 MS, 0.5% sucrose, 0.1% MES, 1% Dashin agar). The data analysis was performed as described <a href="https://rpubs.com/mjulkowska/BIGpimp_RSA_salt">here</a>, while the pareto front calculations were done according to Chandrasekhar & Julkowska paper (<a href="https://www.biorxiv.org/content/10.1101/2021.08.12.456185v1">preprint here</a>). The GWAS was performed using the ASReml script similar to <a href="https://onlinelibrary.wiley.com/doi/10.1111/tpj.15310">Awlia et al. (2021)</a>.

Self-adjuvanting Nanovaccines Boost Lung-resident CD4+ T Cell Immune Responses in BCG-primed mice

The "readcount_genename.xls" file and "fpkm_genename.xls" file contain gene expression data for genes (gene list is detailed in "gene.xls") in the panel. All data were obtained from bone marrow derived dendritic cells from WT C57BL/6 mice treated with KFE8 nanofibers or mock. All RNA sequencing and subsequent processing was performed by Novogene Corporation. The remaining .xls files contain the differential expression analysis for KFE8 nanofiber treatment at four hours compared with mock (NF4vsC4) or KFE8 nanofiber treatment at sixteen hours compared with mock (NF16vsC16). The "pathway analysis Rcode.R" file contains the code used to generate Reactome pathway analysis for both time points.  The "NF16 volc Rcode.R" file contains the code used to generate a volcano plot for the 16 hour time point.

Public Release of Dataset and Code for Accurate and intelligent determination of mechanical response of nodular piles in offshore ground

This is the public release of this repository which contains code and data to accompany the paper: Chen, X.X., Zhan, C.S., Lu, S.L. (2021). Accurate and intelligent determination of mechanical response of nodular piles in offshore ground. PLoS ONE. This file includes the original data of axial force and shaft resistance of piles  in 'dataset.xlsx' and 'data.txt'.  The code in 'LSTM_model.m' requires software of Octave or Matlab.

Multi-stakeholder Validation of Entrustable Professional Activities in Family Medicine - Survey Responses

Survey Responses from the 2021 Multi-Stakeholder Validation of Entrustable Professional Activities in Family Medicine medical education research project.

opencc-by-4.0Nov 2021View details →

Dataset for publication: Test Bench and Frequency Response of a Magnetic Antenna used in GIS PD Measurements

Data set belonging to the <a href="https://ieeexplore.ieee.org/xpl/conhome/9611374/proceeding">2021 IEEE Electrical Insulation Conference (EIC)</a> paper with DOI: <a href="https://doi.org/10.1109/EIC49891.2021.9612372">10.1109/EIC49891.2021.9612372</a> The authors preprint is available from Zendodo with DOI: <a href="https://doi.org/10.5281/zenodo.5815710">10.5281/zenodo.5815710</a>.  Mier Escurra, Christian; Mor, Armando Rodrigo Test Bench and Frequency Response of a Magnetic Antenna used in GIS PD Measurements

Extirpated prairie species demonstrate more variable phenological responses to warming than extant congeners

Premise of the study. Shifting phenology in response to climate is one mechanism that can promote population persistence and geographic spread; therefore, species with limited ability to phenologically track changing environmental conditions may be more susceptible to population declines. Alternatively, apparently, nonresponding species may demonstrate divergent responses to multiple environmental conditions experienced across seasons. Methods. Capitalizing on herbarium records from across the Midwestern United States and detailed botanical surveys documenting local extinctions over the past century, we investigate whether extirpated and extant taxa differ in their phenological responses to temperature and precipitation experienced during winter and spring (during flowering and the growing season prior to flowering) or in their magnitude of flowering time shift over the past century. Key results. Although warmer temperatures across seasons advanced flowering, extirpated and extant species differed in the magnitude of their phenological responses to winter and spring warming. Extirpated species demonstrated inconsistent phenological responses to warmer spring temperatures. Meanwhile, extant species consistently advanced flowering in response to warmer spring temperatures. In contrast, extirpated species advanced flowering more than extant species in response to warmer winter temperatures. Greater spring precipitation tended to delay flowering for both extirpated and extant taxa. Finally, both extirpated and extant taxa delayed flowering over time. Conclusions. This study highlights the importance of understanding phenological responses to seasonal warming and indicates that extirpated species may demonstrate more variable phenological responses to temperature than extant congeners, a finding consistent with the hypothesis that appropriate phenological responses may reduce species' likelihood of extinction.

opencc-zeroDec 2021View details →

Adaptive potential of Coffea canephora from Uganda in response to climate change

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programs. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defense pathways in coffee. Seventy-one SNPs were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, like the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex-situ conservation strategies are discussed.

Data and code from: Traits and phylogenies modulate the environmental responses of wood-inhabiting fungal communities across spatial scales

Identifying the spatial scales at which community assembly processes operate is fundamental for gaining a mechanistic understanding of the drivers shaping ecological communities. In this study, we examined whether and how traits and phylogenetic relationships structure fungal community assembly across spatial scales. We applied joint species distribution modelling to a European-scale dataset on 215 wood-inhabiting fungal species, which includes data on traits, phylogeny and environmental variables measured at the local (log-level) and regional (site-level) scales. At the local scale, wood-inhabiting fungal communities were mostly structured by deadwood decay stage, and the trait and phylogenetic patterns along this environmental gradient suggested the lack of diversifying selection. At regional scales, fungal communities and their trait distributions were influenced by climatic and connectivity-related variables. The fungal climatic niches were not phylogenetically structured, suggesting that diversifying selection or stabilizing selection for climatic niches has played a strong role in wood-inhabiting communities. In contrast, we found a strong phylogenetic signal in the responses to connectivity-related variables, revealing phylogenetic homogenization in small and isolated forests. Altogether, our results show that species-level traits and phylogenies modulate the responses of wood-inhabiting fungi to environmental processes acting at different scales. This result suggests that the evolutionary histories of fungal traits diverge along different environmental axes.

Data for: Specificity of California mouse pup vocalizations in response to olfactory stimuli

To investigate flexibility in vocal signaling by rodent pups, we examined whether olfactory stimuli influence characteristics of pup calls and how these calls may be affected by sex and litter size in California mice (Peromyscus californicus). Pups were isolated and recorded during a 3-minute baseline period followed by a 5-minute exposure to bedding containing scent from their home cage, scent from the home cage of an unfamiliar family, coyote urine, or no scent (control). Latency to call, call rate, and call characteristics (duration, frequency, and amplitude) were compared between the baseline and scent-exposure periods and among olfactory conditions. Compared to the control condition, pups from 2-pup litters called more quietly when exposed to odor from a predator, while pups from 3-pup litters called more loudly. Additionally, pups showed non-significant tendencies to reduce call rates in response to odors from their home cage and to increase call rates when exposed to predator urine. Lastly, males produced higher-frequency calls and more ultrasonic vocalizations than females. These results indicate that pup calling behavior in this species can be influenced by acute olfactory stimuli as well as litter size and sex. The flexibility of pup calling in response to these three variables potentially increases the communication value of pup calls and help shape the parents' responses.

Corporate Governance, Corporate Social Responsibility and Corporate Sustainability: The Moderating Role of Top Management Commitment

<table align="center"> <tbody> <tr> <td> Design/Methodology/Approach: We used the non-probability sampling technique by employing convenience sampling for data collection. By employing a survey questionnaire, data were collected from 397 employees of SMEs in Ghana. The IBM Statistical Package for Social Science (SPSS) version 25.0 and IBM's Analysis of Moments of Structures (AMOS) version 24 software packages were employed as analytical tools in this investigation. </td> </tr> </tbody> </table>

The height-dependent delayed ionospheric response to solar EUV - data comparison - secondary files 141 - 143

Secondary files for doy 141 - 143 For comparison with the observational results a TIE-GCM v2.0 model run in the 2.5 × 2.5 configuration is calculated. In order to converge to stable initial condition the model runs for 30 days prior to the final simulation starting at 28 March 2019. This initial run is configured with default parameters. The final run from 27 April 2019 to 24 May 2019 uses the default configuration of TIE-GCM with the Heelis Electric Convection Field Model (Heelis et al., 1982) as the high-latitude potential model. The input forcing is used from the NASA/GSFC’s OMNI data set

The height-dependent delayed ionospheric response to solar EUV - data comparison - secondary files 135 - 140

Secondary files for doy 135 - 140 For comparison with the observational results a TIE-GCM v2.0 model run in the 2.5 × 2.5 configuration is calculated. In order to converge to stable initial condition the model runs for 30 days prior to the final simulation starting at 28 March 2019. This initial run is configured with default parameters. The final run from 27 April 2019 to 24 May 2019 uses the default configuration of TIE-GCM with the Heelis Electric Convection Field Model (Heelis et al., 1982) as the high-latitude potential model. The input forcing is used from the NASA/GSFC’s OMNI data set

The height-dependent delayed ionospheric response to solar EUV - data comparison - secondary files 129 - 134

Secondary files for doy 129 - 134 For comparison with the observational results a TIE-GCM v2.0 model run in the 2.5 × 2.5 configuration is calculated. In order to converge to stable initial condition the model runs for 30 days prior to the final simulation starting at 28 March 2019. This initial run is configured with default parameters. The final run from 27 April 2019 to 24 May 2019 uses the default configuration of TIE-GCM with the Heelis Electric Convection Field Model (Heelis et al., 1982) as the high-latitude potential model. The input forcing is used from the NASA/GSFC’s OMNI data set

The height-dependent delayed ionospheric response to solar EUV - data comparison - secondary files 117 - 122

Secondary files for doy 117 - 122 For comparison with the observational results a TIE-GCM v2.0 model run in the 2.5 × 2.5 configuration is calculated. In order to converge to stable initial condition the model runs for 30 days prior to the final simulation starting at 28 March 2019. This initial run is configured with default parameters. The final run from 27 April 2019 to 24 May 2019 uses the default configuration of TIE-GCM with the Heelis Electric Convection Field Model (Heelis et al., 1982) as the high-latitude potential model. The input forcing is used from the NASA/GSFC’s OMNI data set

The height-dependent delayed ionospheric response to solar EUV - data comparison

For comparison with the observational results a TIE-GCM v2.0 model run in the 2.5 × 2.5 configuration is calculated. In order to converge to stable initial condition the model runs for 30 days prior to the final simulation starting at 28 March 2019. This initial run is configured with default parameters. The final run from 27 April 2019 to 24 May 2019 uses the default configuration of TIE-GCM with the Heelis Electric Convection Field Model (Heelis et al., 1982) as the high-latitude potential model. The input forcing is used from the NASA/GSFC’s OMNI data set Secondary files: 117 - 122: <a href="https://zenodo.org/record/6004534">https://zenodo.org/record/6004534</a> 123 - 128: <a href="https://zenodo.org/record/6006516">https://zenodo.org/record/6006516</a> 129 - 134: <a href="https://zenodo.org/record/6009777">https://zenodo.org/record/6009777</a> 135 - 140: <a href="https://zenodo.org/record/6014195">https://zenodo.org/record/6014195</a> 141 - 143: <a href="https://zenodo.org/record/6014201">https://zenodo.org/record/6014201</a>

opencc-by-4.0Dec 2021View details →

Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal

Datasets and analysis notebooks for recreating the analysis described in the paper. biom tables of the original datasets used in the meta-analysis are not included due to privacy issues. Instead, we include the biom table containing the NRMD for each study/ASV Updated data and notebooks can also be found at the github page:  <a href="https://github.com/amnona/paper-metaanalysis">https://github.com/amnona/paper-metaanalysis</a> NOTE: files here are provided in a per-directory .zip file in order to preserve internal directory structure.