Find research datasets worth reusing

Data Set used in "Full backward and forward dependencies through regional hypothetical extraction method"

This set of data was obtained from EUREGIO database, developed by the Tinbergen Institute, which is a set of global IO tables with regional and sectoral disaggregation. The EUREGIO database collects the productive structure and commercial relations of the WIOD in the period 2000-2010. The table is broken down into 249 administrative regions at the NUTS2 level, from 24 EU countries, 16 non-EU countries, and a block that brings together countries from the rest of the world, making a total of 266 regions. The statistical information is organised in 11 IO tables, one for each year. The data base that we provid in this repository is used in our study with the aim to determine the key regions of the Spanish economy. In order to address this objective, IO tables of smaller dimensions are built, through an aggregation and disaggregation procedure. First, the 14 industries are grouped, then the 4 sectors of final demand and, lastly, the 4 components of value added. Below, the 266 EUREGIO regions are grouped into 21 regions. Of these, 19 regions correspond to Spain <a href="#_ftn1">[1]</a>, one region includes the rest of the NUTS2 in the EU and another region covers the rest of the world. <a href="#_ftnref1">[1]</a> The 17 Spanish regions and the two autonomous cities of Ceuta and Melilla.

Monthly-Mean Model Output for Paper Titled "Do Nudging Tendencies Depend on the Nudging Timescale Chosen in Atmospheric Models?"

These tarballs contains monthly-mean model output, which was primarily what was presented in the AGU JAMES paper titled "Do nudging tendencies depend on the nudging timescale chosen in atmospheric models?". Also included are the scripts used to set up these simulations, allowing reproducibility of the portion of the paper that used 3-hourly output. The 3-hourly output was not included, as it totaled ~7TB.

opencc-zeroMay 2022View details →

A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation

B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.

Exploring Hierarchy and Dependency of Rules for Consistency Checking Between Code and Model (Evaluation Data)

This repository contains the data related to the protocol and results of the evaluation conducted on the HiDeoCR approach.

Data Availability - DRAFT - 'Process-based similarity' revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements

Datasets and R code related to confidential manuscript submission entitled "‘Process-based similarity’ revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements". Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency. Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency.

opencc-zeroMay 2022View details →

A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene

Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and S. latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian Sparse Linear Mixed Models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles were often derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally-dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.

opencc-zeroMay 2022View details →

Data condition dependence in biosynthesized chemical defenses of an aposematic and mimetic Heliconius butterfly

Aposematic animals advertise their toxicity or unpalatability with bright warning coloration. However, acquiring and maintaining chemical defenses can be energetically costly, and consequent associations with other important traits could shape chemical defense evolution. Here, we have tested whether chemical defenses are involved in energetic trade-offs with other traits, or whether the levels of chemical defenses are condition dependent, by studying associations between biosynthesized cyanogenic toxicity and a suite of key life-history and fitness traits in a Heliconius butterfly under a controlled laboratory setting. Heliconius butterflies are well known for the diversity of their warning color patterns and widespread mimicry, and can both sequester the cyanogenic glucosides of their Passiflora host plants and biosynthesize these toxins de novo. We find energetically costly life-history traits to be either unassociated or to show a general positive association with biosynthesized cyanogenic toxicity. More toxic individuals developed faster, had higher mass as adults, and a tendency for increased lifespan and fecundity. These results thus indicate that toxicity level of adult butterflies may be dependent on individual condition, influenced by genetic background or earlier conditions, with maternal effects as one strong candidate mechanism. Additionally, toxicity was higher in older individuals, consistent with previous studies indicating accumulation of toxins with age. As toxicity level at death was independent of lifespan, cyanogenic glucoside compounds may have been recycled to release resources relevant for longevity in these long-living butterflies. Understanding the origins and maintenance of variation in defenses is necessary in building a more complete picture of factors shaping the evolution of aposematic and mimetic systems.

opencc-zeroDec 2021View details →

Migraine monoclonal antibodies against CGRP change brain activity depending on ligand or receptor target – an fMRI study

Background: Monoclonal antibodies (mAbs) against calcitonin gene-related peptides (CGRP) are novel treatments for migraine prevention. Based on a previous functional imaging study which investigated the CGRP receptor mAb (erenumab), we hypothesized that (i) the CGRP ligand mAb galcanezumab would alter central trigeminal pain processing; (ii) responders to galcanezumab treatment would show specific hypothalamic modulation in contrast to non-responders; and (iii) the ligand and the receptor antibody differ in brain responses. Methods: Using an established trigeminal nociceptive functional magnetic imaging paradigm, 26 migraine patients were subsequently scanned twice: before and 2–3 weeks after administration of galcanezumab. Results: We found that galcanezumab decreases hypothalamic activation in all patients and that the reduction was stronger in responders than in non-responders. Contrasting erenumab and galcanezumab showed that both antibodies activate a distinct network. We also found that pre-treatment activity of the spinal trigeminal nucleus (STN) and coupling between the STN and the hypothalamus covariates with the response to galcanezumab. Conclusions: These data suggest that despite relative impermeability of the blood-brain barrier for CGRP mAb, mAb treatment induces certain and highly specific brain effects which may be part of the mechanism of their efficacy in migraine treatment. Funding: This work was supported by the German Ministry of Education and Research (BMBF) of ERA-Net Neuron under the project code BIOMIGA (01EW2002 to AM) and by the German Research Foundation (SFB936-178316478-A5 to AM). The funding sources did not influence study conduction in any way. Clinical trial number: The basic science study was preregistered in the Open Science Framework (https://osf.io/m2rc6).

Dataset of "Modelling the Frequency-Dependent Effective Excess Charge Density in Partially Saturated Porous Media"

This dataset supports the research study 'Modelling the Frequency-Dependent Effective Excess Charge Density in Partially Saturated Porous Media' by S. G. Solazzi, L. D Thanh, K. Hu, and D. Jougnot. We provide with a commented MATLAB code (Freq_Sat_SP.m) for estimating the frequency-dependent (i) effective excess charge density, (ii) the electrokinetic coupling coefficient, and (iii) the effective dynamic permeability for partially saturated porous media. The code allows to consider fractal,  lognormal, and double lognormal pore size distributions.

The force response of muscles to activation and length perturbations depends on length history

Recent studies have demonstrated that muscle force is not determined solely by activation under dynamic conditions, and that length history has an important role in determining dynamic muscle force. Yet, the mechanisms for how muscle force is produced under dynamic conditions remain unclear. To explore how muscle force production is determined under dynamic conditions, we investigated the effects of muscle stiffness, activation, and length perturbations on muscle force. First, submaximal isometric contraction was established for whole soleus muscles. Next, the muscles were actively shortened at three velocities. During active shortening, we measured muscle stiffness at L0 and the force response to time-varying activation and length perturbations. We found that muscle stiffness increased with activation but decreased as shortening velocity increased. The slope of the relationship between maximum force and activation amplitude differed significantly among shortening velocities. Also, the intercept and slope of the relationship between length perturbation amplitude and maximum force decreased with shortening velocities. As shortening velocities were related with muscle stiffness, the results suggest that length history determines muscle stiffness and the history-dependent muscle stiffness influences the contribution of activation to muscle force and the contribution of length perturbations to muscle force. A three-parameter viscoelastic model that included a linear spring and linear damper in parallel with tunable history-dependent spring stiffness proportional to measured muscle stiffness predicted history-dependent muscle force with high accuracy. The results and simulations support the hypothesis that muscle force under dynamic conditions can be accurately predicted as the force response of a history-dependent viscoelastic material to length perturbations.

Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression

Supplementary dataset for manuscript "Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression"

Data from: Estimating survival and adoption rates of dependent juveniles

1. Population growth and fitness are typically most sensitive to adult survival in long-lived species, but variation in recruitment often explains most of the variation in fitness, as past selection has canalized adult survival. Estimating juvenile survival until age of independence has proven challenging, because marking individuals in this age class may directly affect survival. For Greater Sage-grouse, uniquely marking juveniles in the first days of life likely results in adverse effects to survival, detection of juveniles is not perfect, and females adopt juveniles from other parents. These challenges are encountered by researchers studying avian and mammalian species with similar life histories, yet, methods do not exist that explicitly estimate all these components of the recruitment process. 2. We propose a novel data collection method and demographic model to simultaneously estimate rates of detection, survival, and adoption of juvenile individuals. Using multiple cameras to film the beginning of juvenile activity on specific days, we obtained counts of juveniles associated with marked females. Increases of juveniles to broods provided information that enabled us to estimate rates of adoption that can be applied at the population level. Losses from broods informed apparent survival. These losses could be attributed to death, or they could be chicks that were adopted by other females. 3. We found evidence that apparent survival of juveniles was influenced by localized weather patterns when chicks were young. Similarly, we found that young chicks were more susceptible to the adverse effect of attending females being flushed by an observer. Both of these patterns diminished quickly as chicks aged. We provide the first-ever estimates of interval-specific adoption rates. 4. Our results suggest that researchers should be cautious when designing studies to estimate juvenile survival. More importantly, they provide insight into adoption, a behavior that has been known to exist for decades.

Impacts of flowering density on pollen dispersal and gametic diversity are scale dependent

Pollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., co-flowering density) shapes pollination patterns remains understudied. We monitored co-flowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of co-flowering density on these patterns was scale-dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood co-flowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how co-flowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.

MAVEN 40k dependency data

This is the dependency data used in the "Analyzing the Criticality of Apache Maven Packages Through a Temporal Dependency Graph" paper, with the following structure: <pre><code>{"pkgs":[{ "name": "react", "versions": { "1.00": { "timestamp": "06-05-2022T10:00:01", "dependencies": { "name": "^1.0.2" } } } }, ... ]}</code></pre>

Size-dependent intraspecific variation in wood traits has little impact on aboveground carbon estimates in a tropical forest landscape

There is increasing evidence that intraspecific trait variation plays a role in governing rates of ecosystem functioning. While wood traits such as wood specific gravity (WSG) and wood carbon concentration (WCC) are key drivers of forest aboveground carbon (AGC) stocks, the sources of intraspecific variation in these wood traits and the consequences of this variation on AGC are poorly known, especially in the tropics. Here, we investigated intraspecific variation in wood specific gravity (WSG) and wood carbon concentration (WCC) from 556 individual trees belonging to 15 species that well characterize different successional stages of seasonal evergreen forests in Southeast Asia. Specifically, we tested the contribution of individual or species characteristics (tree size, growth rate and regeneration guilds) and local environmental conditions (topographic wetness index and successional stages) to intraspecific variation in WSG and WCC, and assessed the consequences of intraspecific variation in these wood traits on AGC estimates in 14 permanent forest plots established along a successional gradient in Khao Yai National park, Thailand. We found that tree size was the main driver of intraspecific variation in WSG and WCC as tree sizes increased from 10−100 cm in diameter, WSG increased by 7.3%, while WCC increased by 2.4% in heartwood, 1.6% and 2.7% in sapwood without and with volatile carbon included. There was no effect of the topographic wetness and other local environment condition in wood traits led to a slight overestimation of AGC in young secondary forests (+0.09 to +1.29%) and a small underestimation in older forests (-0.86 to -2.87%), but overall AGC estimates (13 of 14 forest plots) remained within error margins (the 95% interval). Our study provides evidence that tree size variation translates into intraspecific variability in wood traits, whereas local environmental conditions related to topography successional stages had no effect on wood trait variability. While size-dependent variation in WSG and WCC have largely been undocumented and thus ignored in forest carbon assessment approaches, we highlight that it has a limited impact on AGC estimates, indicating that it does not invalidate current forest carbon stock estimation approaches.

Benefit of introgression depends on genetic variation in cereal breeding programs

We investigated the benefit from introgression of external lines into a cereal breeding program and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment (G×E) for the latter trait, using genomic data of a historical barley breeding program as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N=10) major and many (N~990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium, and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding program. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programs are advised to carefully consider the level of genetic variation in a trait available in their breeding program before deciding to introgress germplasms.

SoftwareThatMatters - Analyzing the effect of introducing time as a component in Python dependency graphs

This is a data set produced as a result of the research conducted during my bachelor thesis project "Analyzing the effect of introducing time as a component in Python dependency graphs". This set contains 3 parts: <ul> <li>The raw data that was gathered in order to be processed.</li> <li>The processed data that was used for the construction of the graph.</li> <li>The results that were produced during this research.</li> </ul> More information can be found on the repository of this research project: <a href="https://github.com/AndreiPurcaru/SoftwareThatMatters">SoftwareThatMatters</a>

Data for "Quantum-corrected thickness-dependent thermal conductivity in amorphous silicon predicted by machine learning molecular dynamics simulations"

This is the data set for the preprint <a href="https://arxiv.org/abs/2206.07605">arXiv:2206.07605</a> [cond-mat.mtrl-sci], obtained by the GPUMD code. Here are 6 directories.     1). NEMD     2). NEPpotential     3). PDOS     4). kappa-quenchRate     5). kappa-size     6). kappa-temperature      1). NEMD directory contains calculations of ballistic conductance using NEMD method, where 6 independent cycles are run to average. 2). NEPpotential directory is the trained NEP potential. 3). PDOS directory contains phonon density of states of a-Si samples generated by the quench rate of 10^{11} K/s. 4). kappa-quenchRate directory contains HNEMD calculations of a-Si samples which are prepared using melt-quench temperature protocols with the quench rates covering from 10^{11} to 5x10^{12} K/s. In each case, 3 independent cycles are run. 5). kappa-size directory contains HNEMD calculations based on different supercells. 6 independent cycles are run. 6). kappa-temperature directory contains HNEMD calculations of a-Si samples which are prepared for different targeted temperatures using slow quench rate of 10^{11} K/s.

Turning summer into winter: nutrient dynamics, temperature, density dependence, and invasive species drive bioenergetic processes and growth of a keystone coldwater fish

A combination of global changes such as species invasions, climate change, and nutrient pollution have altered ecosystems, food webs, and the bioenergetic processes that control growth. These changes are especially pronounced in freshwater ecosystems and often lead to rapid variation in fish growth and dependent ecosystems services such as fishery yield. Understanding the mechanisms driving growth responses to environmental change is important for interpreting past dynamics and sustainably managing ecosystems. This study uses integrated bioenergetics and growth modeling to understand how nutrient dynamics, species invasions, and changing temperatures have altered growth of the keystone pelagic whitefish (Coregonus wartmanni) in Lake Constance, Germany from 1925 to 2020. Growth variation was modeled by allowing covariates to alter temperature-dependent consumption, while size-specific metabolism varied only with temperature. Consumption and growth increased strongly to a maximum with phosphorous, and this effect was stronger when intraspecific competition (measured as whitefish biomass) was low. Increasing whitefish biomass reduced growth under mesotrophic conditions, but had no effect under oligotrophic conditions. In contrast, increasing competition with invasive three-spined stickleback (Gasteosteus aculeauts) was predicted to reduce growth even under oligotrophic conditions. The invasion has effectively turned summer into winter for whitefish, with older fish ceasing to grow and younger fish losing up to 10% of their body weight during the normal growing season in subsequent years. Warming is predicted to further reduce whitefish growth due to competition with invasive stickleback, which would further alter zooplankton food availability and reduce already low fishery yields. These results demonstrate the importance of considering biotic interactions and synergistic effects in global change studies, as well as the value of mechanistic-based models for understanding effects. Similar growth responses to ecosystem change are likely within and across ecosystems, and bioenergetic models can help understand effects to support informed ecosystem management.

Frequency-dependent viscosity of salmon ovarian fluid has biophysical implications for sperm-egg interactions

Gamete-level sexual selection of externally fertilising species is usually achieved by modifying sperm behaviour with mechanisms thought to alter the chemical environment in which gametes perform. In fish this can be accomplished through the ovarian fluid, a substance released with the eggs at spawning. While its biochemical effects in relation to sperm energetics have been investigated, the influence of the physical environment in which sperm compete remains poorly explored. Our objective was therefore to gain insights on the physical structure of this fluid and potential impacts on reproduction. Using soft-matter physics approaches of steady-state and oscillatory viscosity measurements, we subjected salmon ovarian fluids to variable shear stresses and frequencies resembling those exerted by sperm swimming through the fluid near eggs. We show that this fluid, which in its relaxed state is a gel-like substance, displays a non-Newtonian viscoelastic and shear-thinning profile, where the viscosity decreases with increasing shear rates. We concurrently find that this fluid obeys the Cox-Merz rule below 7.6 Hz and infringes it above, thus indicating a shear-thickening phase where viscosity increases provided it is probed gently enough. This suggests the presence of a unique frequency-dependant structural network with relevant implications on sperm energetics and fertilisation dynamics.