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325 results for “Mediation analysis”
Do natural enemies mediate conspecific negative distance- and density-dependence of trees? A meta-analysis of exclusion experiments
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Data from: Towards a predictive framework for biocrust mediation of plant performance: a meta-analysis
Understanding the importance of biotic interactions in driving the distribution and abundance of species is a central goal of plant ecology. Early vascular plants likely colonized land occupied by biocrusts — photoautotrophic, surface-dwelling soil communities comprised of cyanobacteria, bryophytes, lichens, and fungi — suggesting biotic interactions between biocrusts and plants may have been at play for some 2,000 million years. Today, biocrusts coexist with plants in dryland ecosystems worldwide, and have been shown to both facilitate or inhibit plant species performance depending on ecological context. Yet, the factors that drive the direction and magnitude of these effects remain largely unknown. We conducted a meta-analysis of plant responses to biocrusts using a global dataset encompassing 1,004 studies from six continents. Our meta-analysis revealed there is no simple positive or negative effect of biocrusts on plants. Rather, plant responses differ by biocrust composition and plant species traits and vary across plant ontogeny. Moss-dominated biocrusts facilitated, while lichen-dominated biocrusts inhibited overall plant performance. Plant responses also varied among plant functional groups: C4 grasses received greater benefits from biocrusts compared to C3 grasses, and plants without N-fixing symbionts responded more positively to biocrusts than plants with N-fixing symbionts. Biocrusts decreased germination but facilitated growth of non-native plant species. Our results suggest that interspecific variation in plant responses to biocrusts, contingent on biocrust type, plant traits, and ontogeny can have strong impacts on plant species performance. These findings have important implications for understanding plant community assembly processes and ecosystem responses to global change.
Data from: Pollinator-mediated gene flow connects green roof populations across the urban matrix: a paternity analysis of the self-compatible forb Penstemon hirsutus
Gene flow between populations can help maintain genetic diversity and prevent inbreeding, which is especially important for small, fragmented habitats. Many plant species rely on pollinators to move pollen between populations. In urban areas, insufficient pollinator services may result in limited gene flow, which can have negative consequences such as genetic drift and inbreeding depression. Furthermore, restored populations that are established with few founders of low genetic diversity may have limited long-term population persistence. Here, we tested the hypotheses that populations of a self-compatible forb established on urban green roofs fromnursery stock are genetically depauperate and that limited gene (pollen) flow between populations will result in increased inbreeding. We compared the neutral genetic diversity of Penstemon hirsutus, using nine microsatellite loci, between three green roof populations established from nursery stock and three natural populations. We also established ten experimental populations on green roofs and measured rates of outcrossing and inbreeding and identified the movement of pollen within and between roofs using a paternity analysis. We found that neutral genetic diversity of populations established from nursery stock was lower than that of natural populations, although the level of inbreeding was also lower on the green roofs. In our experimental populations, we found that the rates of outcrossing and inbreeding varied between the roof populations. Our results suggest that inbreeding may be correlated with cover of co-flowering species but not with any of the other measured site properties. The location of likely pollen donors suggested that on average, 75% of pollen was derived from plants within the population (including self) and 25% came from plants on different roofs. Our results document realized pollen movement within and between green roofs, demonstrating that these habitats provide important connectivity in a fragmented environment.
AgRP neuron cis-regulatory analysis across hunger states reveals that IRF3 mediates leptin's acute effects
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Fire decreases soil enzyme activities and reorganizes microbially-mediated nutrient cycles: a meta-analysis
<p class="MsoNormal"><span>The biogeochemical signature of fire shapes the functioning of many ecosystems. Fire changes nutrient cycles not only by volatilizing plant material, but also by altering organic matter decomposition—a process regulated by soil extracellular enzyme activities (EEAs). However, our understanding of fire effects on EEAs and their feedbacks to nutrient cycles is incomplete. We conducted a meta-analysis with 301 field studies and found that fire significantly decreased EEAs by ~20-40%. Fire decreased EEAs by decreasing soil microbial biomass and organic matter substrates. Soil nitrogen-acquiring EEA decreased alongside decreasing available nitrogen, likely from fire-driven volatilization of nitrogen and decreased microbial activity. Fire decreased soil phosphorus-acquiring EEA but increased available phosphorus, likely from pyro-mineralization of organic phosphorus. These findings suggest that fire suppresses soil microbes and consumes their substrates, thereby slowing microbially-mediated nutrient cycles (especially phosphorus) via decreased EEAs. These changes can become increasingly important as fire regimes in many ecosystems continue to shift in response to global change.</span></p>
Is species richness mediated by functional and genetic divergence? A global analysis in birds
<p class="MsoNormal">Unravelling why species richness varies shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes. Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank. We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that packing is comparatively greater in tropical points relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis. Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness.</p>
Quantitative analysis of electroporation-mediated intracellular delivery via bioorthogonal luminescent reaction
<p>The data of the paper entitled "Quantitative analysis of electroporation-mediated intracellular delivery via bioorthogonal luminescent reaction"</p>
Data for "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis"
<p>This dataset was used to make tables and figures for the study entitled "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis", which was submitted to Global Change Biology in October 2022. It contains a meta-analysis database focusing on the effects of warming on soil C storage, root biomass and soil respiration.</p>
Recurrent pain symptoms in adolescents with generalized and specific problematic Internet use: Associations analysis, confounding and mediating effects of comorbid psychosocial problems
<p>Problematic Internet use (PIU) in adolescents is a global public health issue especially exacerbated by the restrictions caused by the COVID-19 epidemic. The authors assume a negative impact of PIU not only in relation to adolescents' mental health and social behaviour but also relative to somatic components of their health, particularly concerning the occurrence of pain symptoms – recurrent headache (RH), recurrent abdominal pain (RAP), and recurrent back pain (RBP). The present study aims to identify the associations between different types of PIU (generalized PIU – PIUgen, problematic computer game use – PUgame, and problematic social media use – PUsocial), and pain symptoms (RH, RAP and RBP), and to determine the role of psychosocial factors in the emergence of these associations.</p> <p><strong>Methods: </strong>The<strong> </strong>research represents a one-stage observational study of 4,411 adolescents (53.6% girls; Mage = 14.53±1.52) in an unbiased school sample, held in three large cities of Central Siberia. The frequency and intensity of pain symptoms over the past three months were ascertained by completing a number of questionnaires. The following questionnaires were used to identify PIU and its types: the Chen Internet Addiction Scale (CIAS for PIUgen), the Game Addiction Scale for Adolescents (GASA for PUgame), and The Social Media Disorder Scale (SMDS for PUsocial). The psychological problems were assessed using The Strengths and Difficulties Questionnaire (SDQ). Logistic and linear regression, as well as mediation analysis, were used.</p> <p><strong>Results:</strong> Considering both the frequency and intensity of pain, along with the presence of psychosocial problems as a confounder, a direct association of RH with PUsocial only was revealed (OR = 1.68, CI = 1.33–2.11). Using the same criteria, RAP in this sample was associated with PIUgen and PUsocial (OR = 1.99, CI = 1.51–2.62 and 2.10, CI = 1.62–2.72, respectively). RBP, according to the obtained data, was also associated with PIUgen and PUsocial both in terms of pain frequency (OR = 1.99, CI = 1.53–2.57 and OR = 2.20, CI = 1.44–3.38, respectively) and intensity. PUgame was weakly associated only with RAP and showed no significant association with RH and RBP. The mediation analysis indicated that the revealed positive associations were largely mediated by psychosocial problems comorbid for PIUgen and PUsocial (but not PUgame).</p> <p><strong>Conclusions: </strong>The<strong> </strong>frequently reported association of recurrent pain symptoms with PIU in adolescents is largely mediated by comorbid psychosocial problems. The direct effect of excessive Internet use on somatic pain symptoms in adolescents is mild-to-moderate and depends on the content predominantly consumed.</p>
Cognitive Behavior Therapy for Insomnia: Analysis of Components, Mediators and Moderators
ClinicalTrials.gov study NCT02984670. IPD Sharing: NO. Countries: 1. Publications: 3.
Mediation Analysis in Cardiac Surgery
ClinicalTrials.gov study NCT07092683. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Recurrent pain symptoms in adolescents with generalized and specific problematic Internet use: Associations analysis, confounding and mediating effects of comorbid psychosocial problems
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Data from: Pollinator-mediated gene flow connects green roof populations across the urban matrix: a paternity analysis of the self-compatible forb Penstemon hirsutus
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Nitrogen-fixing plants increase soil nitrogen and neighboring plant biomass, but decrease community diversity: A meta-analysis reveals the mediating role of soil texture
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Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower
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Fire decreases soil enzyme activities and reorganizes microbially-mediated nutrient cycles: a meta-analysis
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Is species richness mediated by functional and genetic divergence? A global analysis in birds
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Data from: Towards a predictive framework for biocrust mediation of plant performance: a meta-analysis
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Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies
<p>Conspecific negative distance- and density-dependence is believed to be one of the most important mechanisms controlling forest community assembly and species diversity globally. SoilPlant pathogens, and insect and mammalian herbivores, are the most common natural enemy types that have been implicated in this phenomenon, but their relative importancegeneral effects at different plant life stages isare still unclear. Here, we conduct a meta-analysis of studies that involved robust manipulative experiments, using fungicides, insecticides, and exclosures, to assess the contributions of different natural enemy types to distance- and density-dependent effects at seed and seedling stages. We found that natural enemies cause stronger distance- and density-dependent mortality caused by natural enemies was most likely at the seedling stage than the seed stage. Fungicide treatments can change significantand was greater at higher mean annual temperatures. Seedling mortality was significantly weakened when fungi were removed. By contrast, negative distance- and density-dependent mortality to non-significance at the seedling stage. Negative conspecific distance- and density-dependence is not a general pattern at the seed stage. High seed mass reduced distance- and density-dependent mortality. Seed studies excluding only large mammals found significant negative conspecific distance-dependent mortality, but exclusion of all mammals resulted in a non-significant mortality.effect of conspecifics. Our study suggests that soilplant pathogens are a major cause of distance- and density-dependent mortality at the seedling stage, althoughwhile the impacts of herbivores on seedlings have been understudied. At the seed stage, large and small mammals respectively weaken and enhance negative conspecific distance-dependent mortality. Future research should identify specific agents of mortality, investigate the interactions among different enemy types, and assess how global change drivers may affect the dynamics of natural enemies and thus influence the strength of conspecific distance- and density-dependence.</p>
Data from: Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions
The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues.
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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.