Find research datasets worth reusing

opencc-zeroMay 2023View details →

Data from: Social group composition modulates the role of last male sperm precedence in post-copulatory sexual selection

In many species, the order in which males mate with a female explains much of the variation in paternity arising from post-copulatory sexual selection. Research in Drosophila suggests that mating order may account for the majority of the variance in male reproductive success. However, the effects of mating order on paternity bias might not be static but could potentially vary with social or environmental factors. To test this idea, we used an existing dataset, collated from an experiment we previously published (Morimoto et al. 2016), with the addition of unpublished data from the same experiment. These previous experiments manipulated larval density in Drosophila melanogaster which generated variation in male and female body size, assembled groups of individuals of different sizes, and measured the mating success and paternity share of focal males. The data presented here provide information on each focal male's mating order and the frequency in which focal males remated with the same females ('repetitive matings'). We combined this information with our previously reported focal male reproductive success to partition variance in paternity into male mating order and repetitive matings across groups that differed in the body size composition of males and females. We found, as expected, that male mating order explained a considerable portion of the variance in male paternity. However, we also found that the impact of male mating order on male paternity was influenced by the body size composition of groups. Specifically, males that tended to mate last had a greater paternity advantage, and displayed lower variance, in groups containing a heterogenous mixture of male body sizes than in groups with a single male body size. Repetitive mating only had a minor contribution to the variance in male paternity share across all experiments. Overall, our findings contribute to the growing body of research showing that post-copulatory sexual selection is subject to socio-ecological influences.

opencc-by-4.0May 2023View details →

Oxygen availability and body mass modulate ectotherm responses to ocean warming

Data and analysis scripts for the following publication: Duncan et al. In press. Oxygen availability and body mass regulate ectotherm responses to ocean warming. Nature communications   Analysis_script.R is the R script to carry out the main analysis in the manuscript. data.csv is the physiology data to carry out the main analysis in the manuscript.   current_bottom_oxy_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. current_bottom_salt_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. current_bottom_temp_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_oxy_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_salt_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript. future_bottom_temp_monthly.Rda is an environmental layer used to carry out the distribution modelling in the manuscript.   raw respirometry data.zip is the raw respirometry data collected during the experiments for the manuscript. raw_meta_data.xlsx is the meta data related to the respirometry data collected during the experiments. raw_resp_data_script.R is the R script to quantify physiological metrics from experimental data.

opencc-by-4.0Dec 2022View details →

Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery

Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)

opencc-zeroJun 2023View details →

Research data for: Replicative Acinetobacter baumannii strains interfere with phagosomal maturation by modulating the vacuolar pH

Bacterial pneumonia is a common infection of the lower respiratory tract that can afflict patients of all ages. Multidrug-resistant strains of Acinetobacter baumannii are increasingly responsible for causing nosocomial pneumonias, thus posing an urgent threat. Alveolar macrophages play a critical role in overcoming respiratory infections caused by this pathogen. Recently, we and others have shown that new clinical isolates of A. baumannii, but not the common lab strain ATCC 19606 (19606), can persist and replicate in macrophages within spacious vacuoles that we called Acinetobacter Containing Vacuoles (ACV). In this work, we demonstrate that the modern A. baumannii clinical isolate 398, but not the lab strain 19606, can infect alveolar macrophages and produce ACVs in vivo in a murine pneumonia model. Both strains initially interact with the alveolar macrophage endocytic pathway, as indicated by EEA1 and LAMP1 markers; however, the fate of these strains diverges at a later stage. While 19606 is eliminated in an autophagy pathway, 398 replicates in ACVs and are not degraded. We show that 398 reverts the natural acidification of the phagosome by secreting large amounts of ammonia, a by-product of amino acid catabolism. We propose that this ability to survive within macrophages may be critical for the persistence of clinical A. baumannii isolates in the lung during a respiratory infection.

opencc-zeroJun 2023View details →

Data from: Bromodomain-containing protein 4 regulates innate inflammation via modulation of alternative splicing (images and qPCR data)

Bromodomain-containing Protein 4 (BRD4) is a transcriptional regulator which coordinates gene expression programs controlling cancer biology, inflammation, and fibrosis. In the context of virus-infection, BRD4-specific inhibitors (BRD4i) block the release of pro-inflammatory cytokines and prevent downstream epithelial plasticity<a>. </a>Although the chromatin modifying functions of BRD4 in inducible gene expression have been extensively investigated, its roles in post-transcriptional regulation are not well understood. Given BRD4's interaction with the transcriptional elongation complex and spliceosome, we hypothesize that BRD4 is a functional regulator of mRNA processing. To address this question, we combine data-independent analysis - parallel accumulation-serial fragmentation (diaPASEF) with RNA-sequencing to achieve deep and integrated coverage of the proteomic and transcriptomic landscapes of human small airway epithelial cells exposed to viral challenge and treated with BRD4i. The transcript-level data was further interrogated for alternative splicing analysis, and the resulting datasets were correlated to identify pathways subject to post-transcriptional regulation. We discover that BRD4 regulates alternative splicing of key genes, including Interferon-related Developmental Regulator 1 (IFRD1) and X-Box Binding Protein 1 (XBP1), related to the innate immune response and the unfolded protein response. These findings extend the transcriptional elongation-facilitating actions of BRD4 in control of post-transcriptional RNA processing in innate signaling.

opencc-by-4.0Jun 2023View details →

Output and data used in publication "Glacial isostatic adjustment modulates lateral migration rate and morphology of the Red River (North Dakota, USA, and Manitoba Canada)" in GRL

Here we provide the output sea level used to calculate change in slope along studied rivers as well as locations of meanders and cutoffs. Please see the read.me file and publication for details.

opencc-by-4.0Jun 2023View details →

Dynamic nuclear polarization by two-pulse phase modulation - Data

Experimental data associated Redrouthu et al. Dynamic nuclear polarization by two-pulse phase modulation, The Journal of Chemical Physics, doi: 10.1063/5.0153053.

opencc-by-4.0Jun 2023View details →

Hindbrain modules differentially transform activity of single collicular neurons to coordinate movements

Seemingly simple behaviors such as swatting a mosquito or glancing at a signpost involve the precise coordination of multiple body parts. Neural control of coordinated movements is widely thought to entail transforming a desired overall displacement into displacements for each body part. Here we reveal a different logic implemented in the mouse gaze system. Stimulating superior colliculus (SC) elicits head movements with stereotyped displacements but eye movements with stereotyped endpoints. This is achieved by individual SC neurons whose branched axons innervate modules in medulla and pons that drive head movements with stereotyped displacements and eye movements with stereotyped endpoints, respectively. Thus, single neurons specify a mixture of endpoints and displacements for different body parts, not overall displacement, with displacements for different body parts computed at distinct anatomical stages. Our study establishes an approach for unraveling motor hierarchies and identifies a logic for coordinating movements and the resulting pose.

opencc-by-4.0Jul 2023View details →

Data for 'Rethinking variability in bedrock rivers: sensitivity of hillslope sediment supply to precipitation events modulates bedrock incision during floods'

This is the repository for model code, sample data, and plotting scripts for the OTTER model for Python. The file OTTERPy.py contains the actual model code The file OTTERPlottingFuncs.py contains a few scripts for plotting model results. The four sample data files in the repository are results from two long (1.5million model year) runs at different rock uplift rates which took several days to run on the IU Bloomington Quartz supercomputing cluster. This data should be viewed and plotted using the OTTERPlottingFuncs.py script. See that code for information on how to select which model to plot.   <pre><code>Glossary of variables - this is pretty close to exhaustive, there are a probably a couple of throwaway variables not listed here. a: Sternberg's law multiplier Ah: drainage area from Hack's Law (m^2) beta: fraction of sediment transported as bedload from 0 to 1 D: grain size at each node (m) dA: change in drainage area from node to node (m^2) depth_thresh: sediment depth at which bedrock erosion can occur Do: initial grain size Do: grain size at headwaters (m) dQs: change in sediment supply from node to node dt: time step (years) dx: space step (m) dz_b: bedrock erosion at each node dz_s: change in sed depth dz_b_t: bedrock erosion saved through time dz_b_store: bedrock erosion stored dz_s_store: sed depth change stored eQ: exponent for scaling Qw from Ah eroded_sedsup: sediment created by bedrock erosion eW: exponent for scaling W from Qw F: fractional bedrock exposure g: gravitational acceleration (M/s^2) H: water depth Hc: Hack's Law constant He: Hack's law Exponent initial_sedsup: Sediment supply in first 10k yr (equal to uplift) kf: bedrock erodibility kQ: constant for scaling Qw from Ah kv: parameter controlling discharge variability - Crave & Davy, 2001. Lower kv is more variable kw: lateral bedrock erosion constant kWid: constant for scaling W from Qw last_z: elevation at channel mouth lmbda: sediment porosity n: manning's roughness coefficient onlyonce: changes from 0 to 1 to make sure the uplift pulse only happens one time onoff: turns sediment on and off entirely onoffsedvar: turns stochastic sediment on and off Qs: sediment supply along the length of the river Qs_down: downstream sediment flux at each node Qt: sediment transport capacity Qw: water discharge Qwo: initial water discharge QwScale: array of scalar multipliers for Qw, from the chosen distribution R: effective density of submerged sediment rho_w: density of water (kg/m^3) rho_s: density of sediment (kg/m^3) savesteps: at what time should we save outputs? sed_depth: depth of seidment at each node (m) SedStore: storing snapshots of sediment thickness through time slope: river gradient (negative usually) SlopeStore: storing snapshots of channel slope through time tarray: array of model time tau_b: basal shear stress tau_c: critical shields criterion for initiation of sediment motion time: model duration (years) topo: channel elevation (bedrock + sediment) upinc: size up uplift pulse, as a multiplier of initial uplift rate upinctime: when should the pulse happen? (years) uplift: uplift field across the entire domain uprate: initial uplift rate, if using constant uplift across domain W: channel width WidthStore: storing snapshots of channel width through time Wo: initial channel width yr2sec: number of seconds in a year z: bedrock channel elevation ZStore: storing snapshots of bedrock elevation through time</code></pre>

opencc-zeroJul 2023View details →

Data from: Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover

Human activities, directly and indirectly, impact ecological engineering activities of subterranean rodents. As engineering activities of burrowing rodents are affected by, and reciprocally affect vegetation cover via feeding, burrowing and mound building, human influence such as settlements and livestock grazing, could have cascading effects on biodiversity and ecosystem processes such as bioturbation. However, there is limited understanding of the relationship between human activities and burrowing rodents. The aim of this study was therefore to understand how human activities influence the ecological engineering activity of the giant root-rat (Tachyoryctes macrocephalus), a subterranean rodent species endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We collected data on human impact, burrowing activity and vegetation during February and March of 2021. Using path analysis, we tested (1) direct effects of human settlement on the patterns of livestock grazing intensity, (2) direct and indirect impacts of humans and livestock grazing intensity on the root-rat burrow density, and (3) whether human settlement and livestock grazing influence the effects of giant root-rat burrow density on vegetation and vice versa. We found lower levels of livestock grazing intensity further from human settlement than in its proximity. We also found a significantly increased giant root-rat burrow density with increasing livestock grazing intensity. Seasonal settlement and livestock grazing intensity had an indirect negative and positive effect on giant root-rat burrow density, respectively, both via vegetation cover. Analysing the reciprocal effects of giant root-rat on vegetation, we found a significantly decreased vegetation cover with increasing density of giant root-rat burrows, and indirectly with increasing livestock grazing intensity via giant root-rat burrow density. Our results demonstrate that giant root-rats play a synanthropic engineering role that affects vegetation structure and ecosystem processes.

opencc-by-4.0Jul 2023View details →

The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile main figures

Raw microscopy data associated with the publication "The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile" in elife journal. Main figures

opencc-zeroJul 2023View details →

The plant toxin 4-methylsulfinylbutyl isothiocyanate decreases herbivore performance and modulate cellular and humoral immunity

Insect herbivores frequently encounter plant defense molecules, but the physiological and ecological consequences for their immune systems are not fully understood. The majority of studies attempting to relate levels of plant defensive chemistry to herbivore immune responses have used natural population or species-level variation in plant defensive chemistry. Yet, this potentially confounds the effects of plant defense chemistry with other potential traits that may affect the expression of herbivore immunity such as development time and nutritional quality. We have used an artificial diet containing known quantities of a plant toxin (4-methylsulfinylbutyl isothiocyanate; 4MSOB-ITC or ITC), an isothiocyanate present in many plants in the genus Brassica, to explicitly explore the effects of a plant toxin on the cellular and humoral immune responses of the generalist herbivore Trichoplusia ni (Lepidoptera: Noctuidae) that frequently feeds on glucosinolate-containing plants. Caterpillars feeding on diets with high concentrations of ITC experienced reduced survivorship and growth rates. High concentrations of ITC suppressed the appearance of several types of hemocytes and melanization activity, which are critical defenses against parasitic Hymenoptera and microbial pathogens. In terms of T. ni humoral immunity, only the antimicrobial peptide (AMP) genes lebocin and gallerimycin were significantly upregulated in caterpillars fed on diets containing high levels of 4MSOB-ITC relative to caterpillars that were provided with ITC-free diet. Surprisingly, challenging caterpillars with a non-pathogenic strain of Escherichia coli resulted in the upregulation of the AMP gene cecropin. Feeding on high concentrations of plant toxins hindered caterpillar development and decreased cellular immunity but conferred mixed effects on humoral immunity. Our findings provide novel insights into the effects of herbivore diet composition on insect performance demonstrating the role of specific plant defense toxins that shape herbivore immunity and trophic interactions.

opencc-by-4.0Dec 2022View details →

Antimicrobial peptides modulate lung injury by altering the intestinal microbiota

This repository contains the OTU tables for "Antimicrobial peptides modulate pulmonary inflammation by altering the intestinal microbiota" by Abdelgawad and Nicola et al., an analysis of the role of antimicrobial peptide in the gut-lung axis during hyperoxia-induced lung injury. This work was supported by the National Heart, Lung, and Blood Institute of the U.S. National Institutes of Health, K NIH: K08 HL151907 (KW), K08 HL141652 (CL), K08 DK120871 (AO); the Kaul Pediatric Research Institute at Children’s of Alabama (KW), and the Microbiome Center at UAB (KW). The funding agencies had no role in the design, conduct, and analysis of the study or in the decision to submit the manuscript for publication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. All data in this repository is the intellectual property of the authors and may be utilized for academic publication only with prior written permission.

opencc-by-4.0Dec 2023View details →

FEDORA. Data from teaching module implementations in Finland

<table> <tbody> <tr> <td> The dataset contains data collected in two-round implementations of new experimental teaching-learning course “My city of the future”,  with Finnish secondary school students, that are analysed to capture the main trends in the data regarding the established framework, with specific focus on effects on the course module on students, and the capacity of the module to address higher-level standards of future-oriented science education. Specifically, the dataset includes: (i) answers to questionnaires, (ii)  transcripts of interviews (iii)  materials created by students (in Finnish), (iv) processed versions of aforementioned data such as coded interview transcripts or numeric data on code frequencies, and (v) results from the analysis of this data using thematic, discourse and phenomenographic qualitative methods. An aggregated version of student’s backgrounds (e.g. gender ratios) are also provided. </td> </tr> </tbody> </table>     <a href="https://zenodo.org/communities/futuresthinking?page=1&size=20">FEDORA Project</a> README: README Data Set Title: FEDORA. Data from teaching modules implementations in Finland Data Set Author/s: Antti Laherto, Tapio Rasa, Iina Hyyppä (University of Helsinki) Data Set Contact Person/s: Tapio Rasa (University of Helsinki), ORCID 0000-0003-1315-5207, tapio.rasa@helsinki.fi; Data Set License: this data set is distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Publication Year: 2024 Project Info: FEDORA (Future-oriented Science EDucation to enhance Responsibility and engagement in the society of Acceleration and uncertainty, funded by European Union, Horizon 2020 Programme. Grant Agreement num. 872841, www.fedora-project.eu)   Data set Contents The data set consists of: 1) Interview transcripts from students who participated in an experimental, twice implemented future-oriented science learning module ("My City of the Future") in Finland over 2022-2023; 2) Students' output in future-oriented learning tasks over the module; 3) Questionnaire data on students' future thinking; 4) Students' background data in aggregate, anonymised form (e.g. gender ratio); 5) Processed forms of aforementioned data (such as qualitatively coded datasets).   Data set Documentation See DOI:10.5281/zenodo.8199147 (TBA)

opencc-zeroJul 2023View details →

Microglia modulate TNFα‐mediated synaptic plasticity

The pro-inflammatory cytokine tumor necrosis factor α (TNFα) tunes the capacity of neurons to express synaptic plasticity. It remains, however, unclear how TNFα mediates synaptic positive (=change) and negative (=stability) feedback mechanisms. We assessed effects of TNFα on microglia activation and synaptic transmission onto CA1 pyramidal neurons of mouse organotypic entorhino–hippocampal tissue cultures. TNFα mediated changes in excitatory and inhibitory neurotransmission in a concentration-dependent manner, where low concentration strengthened glutamatergic neurotransmission via synaptic accumulation of GluA1-only-containing AMPA receptors and higher concentration increased inhibition. The latter induced the synaptic accumulation of GluA1-only-containing AMPA receptors as well. However, activated, pro-inflammatory microglia mediated a homeostatic adjustment of excitatory synapses, that is, an initial increase in excitatory synaptic strength at 3 h returned to baseline within 24 h, while inhibitory neurotransmission increased. In microglia-depleted tissue cultures, synaptic strengthening triggered by high levels of TNFα persisted and the impact of TNFα on inhibitory neurotransmission was still observed and dependent on its concentration. These findings underscore the essential role of microglia in TNFα-mediated synaptic plasticity. They suggest that pro-inflammatory microglia mediate synaptic homeostasis, that is, negative feedback mechanisms, which may affect the ability of neurons to express further plasticity, thereby emphasizing the importance of microglia as gatekeepers of synaptic change and stability.

Scripts, inputs and outputs of Module 4 ANOVA test regarding Deliverable D6.3 "Performance and Impact assessment" in the IP4MaaS project

All the materials, inputs, models, and scripts that are used in the performance assessment toolbox (IP4MaaS project, Deliverable D6.3 Performance and Impact Assessment) are available in the attached folder.  The attached folder contains the following: Module 4_Calculation of ANOVA test (the input, formulation, macros, and scripts of ANOVA test per each IP4MaaS demo site). The scripts have been designed for easy adoption in other projects with similar end goals. While the scripts operate on the codified representation of the traveller profiles, functionalities, and service providers, there is no restriction on the type of codification used. The only factor that the scripts assume is the order of the variables introduced for codification. That is the traveller profile variable (wherever applicable), followed by the Functionality variable, followed by the Service Provider variable. As long as the order is maintained, the scripts self-analyze the number of variables representing the traveller profiles, functionalities, and service providers, and perform calculations (USI, Effectiveness) and analysis (Regression and BN), Hence, in a similar framework, the scripts may be used for performing data analysis on a large data set with no restriction on the number of functionalities, service providers or subsets of traveller profiles. Documented Scripts can be found in a downloadable ZIP file here.

Scripts, inputs and outputs of Module 5 USI travellers, TSPs and Effectiveness regarding Deliverable D6.3 "Performance and Impact assessment" in the IP4MaaS project

All the materials, inputs, models, and scripts that are used in the performance assessment toolbox (IP4MaaS project, Deliverable D6.3 Performance and Impact Assessment) are available in the attached folder.  The attached folder contains the following: Module 5_Results and outputs of USI Travellers, USI TSPs, Effectiveness (Travellers & TSPs) and the average of Effectiveness of all functionalities individually across all 6 demo sites (inputs, calculation, formulation, scripts of USI travellers, TSPs and Effectiveness per each IP4MaaS demo site). The scripts have been designed for easy adoption in other projects with similar end goals. While the scripts operate on the codified representation of the traveller profiles, functionalities, and service providers, there is no restriction on the type of codification used. The only factor that the scripts assume is the order of the variables introduced for codification. That is the traveller profile variable (wherever applicable), followed by the Functionality variable, followed by the Service Provider variable. As long as the order is maintained, the scripts self-analyze the number of variables representing the traveller profiles, functionalities, and service providers, and perform calculations (USI, Effectiveness) and analysis (Regression and BN), Hence, in a similar framework, the scripts may be used for performing data analysis on a large data set with no restriction on the number of functionalities, service providers or subsets of traveller profiles. Documented Scripts can be found in a downloadable ZIP file here.

Scripts, inputs and outputs of Module 1 AHP analysis regarding Deliverable D6.3 "Performance and Impact assessment" in the IP4MaaS project

All the materials, inputs, models, and scripts that are used in the performance assessment toolbox (IP4MaaS project, Deliverable D6.3 Performance and Impact Assessment) are available in the attached folder.  The attached folder contains the following: Module 1_AHP and Pairwise comparison matrix calculation_IP4MaaS II (formulations and calculations of pairwise comparison matrix per each IP4MaaS demo site). The scripts have been designed for easy adoption in other projects with similar end goals. While the scripts operate on the codified representation of the traveller profiles, functionalities, and service providers, there is no restriction on the type of codification used. The only factor that the scripts assume is the order of the variables introduced for codification. That is the traveller profile variable (wherever applicable), followed by the Functionality variable, followed by the Service Provider variable. As long as the order is maintained, the scripts self-analyze the number of variables representing the traveller profiles, functionalities, and service providers, and perform calculations (USI, Effectiveness) and analysis (Regression and BN), Hence, in a similar framework, the scripts may be used for performing data analysis on a large data set with no restriction on the number of functionalities, service providers or subsets of traveller profiles. Documented Scripts can be found in a downloadable ZIP file here.

Scripts, inputs and outputs of Module 2 Regression analysis regarding Deliverable D6.3 "Performance and Impact assessment" in the IP4MaaS project

All the materials, inputs, models, and scripts that are used in the performance assessment toolbox (IP4MaaS project, Deliverable D6.3 Performance and Impact Assessment) are available in the attached folder.  The attached folder contains the following: Module 2_Regression analysis (inputs, scripts, and formulations of regression analysis per each IP4MaaS demo site). The scripts have been designed for easy adoption in other projects with similar end goals. While the scripts operate on the codified representation of the traveller profiles, functionalities, and service providers, there is no restriction on the type of codification used. The only factor that the scripts assume is the order of the variables introduced for codification. That is the traveller profile variable (wherever applicable), followed by the Functionality variable, followed by the Service Provider variable. As long as the order is maintained, the scripts self-analyze the number of variables representing the traveller profiles, functionalities, and service providers, and perform calculations (USI, Effectiveness) and analysis (Regression and BN), Hence, in a similar framework, the scripts may be used for performing data analysis on a large data set with no restriction on the number of functionalities, service providers or subsets of traveller profiles. Documented Scripts can be found in a downloadable ZIP file here.