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253 results for “functional organization”
Accompanied data files used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis"
<p>lists of source file used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis" by Jing Yang, Amanda McGovern, Paul Martin, Kate Duffus, Xiangyu Ge, Peyman Zarrineh, Andrew P Morris, Antony Adamson, Peter Fraser, Magnus Rattray & Stephen Eyre. The paper has been accepted by Nature Communications.</p>
Table S1. The influence of extremely low frequency magnetic field (ELF-MF) on different aspects of the organism function
<p><strong>Table S1.</strong> <strong>The influence of extremely low frequency magnetic field (ELF-MF) on different aspects of the organism function</strong> (papers are listed according to year of publication).</p> <p>In order to prepare the table the bibliography research in PubMed was performed using the following keywords in varied combinations:: “electromagnetic field”, “stress”, “corticosterone“, “noradrenaline”, “HPA axis”, “oxidative stress”, “cellular damage”, “BDNF”, “HSP70”, “neurotransmitters”, “cytokines”, “plasticity”, “viability”, “recovery”; “behavior”. We also used Boolean operator “and” to receive the most relevant search results. All articles written in English were manually screened, and the appropriate were identified. The articles published from 2010 to 2020 were taken into consideration. The papers concerning the effects of extremely low frequency magnetic field on a wide spectrum of molecular, neuronal, hormonal and behavioural stress responses were considered and only information related to ELF-MF effects are included in the Table.</p>
Data from: Organic matter and nutrient inputs from large wildlife influence ecosystem function in the Mara River, Africa
Animals can be important vectors for the movement of resources across ecosystem boundaries. Animals add resources to ecosystems primarily through egestion, excretion and carcasses, and the stoichiometry and bioavailability of these inputs likely interacts with characteristics of the recipient ecosystem to determine their effects on ecosystem function. We studied the influence of hippopotamus excretion/egestion and wildebeest carcasses, and their interactions with discharge, in the Mara River, Kenya. We measured nutrient dissolution and decomposition rates of wildlife inputs, the influence of inputs on nutrient concentrations and nutrient limitation in the river and the influence of inputs on biofilm growth and function in both experimental streams and along a gradient of inputs in the river. We found that hippopotamus excretion/egestion increase ammonium and coarse particulate organic matter in the river, and wildebeest carcasses increase ammonium, soluble reactive phosphorus, and total phosphorus. Concentrations of dissolved carbon and nutrients in the water column increased along a gradient of wildlife inputs and during low discharge, although concentrations of particulate carbon decreased during low discharge due to deposition on the river bottom. Autotrophs were nitrogen-limited, and heterotrophs were carbon-limited and nitrogen- and phosphorus- co-limited, upstream of animal inputs, but there was no nutrient limitation downstream of inputs. In experimental streams, hippo and wildebeest inputs together increased biofilm GPP and R. These results differed in the river, where low concentrations of hippo inputs increased gross primary production (GPP) and respiration (R) of biofilms, but high concentrations of hippo inputs in conjunction with wildebeest inputs decreased GPP. Our research shows that inputs from large wildlife alleviate nutrient limitation and stimulate ecosystem metabolism in the Mara River, and that the extent to which these inputs subsidize the ecosystem is mediated by the quantity and quality of inputs and discharge of the river ecosystem. Thus, animal inputs provide an important ecological subsidy to this river, and animal inputs were likely important in many other rivers prior to the widespread extirpation of large wildlife.
Data from: Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally-managed fields
<p>The structure and function of fungal communities in the coffee rhizosphere is shaped by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities in markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic or transitional management in two regions of Costa Rica. We amplified the ITS2 region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, more leaf litter, and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium than conventionally-managed fields, although differences between organic and conventionally-managed fields in shade, calcium and magnesium depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally-managed fields were also correlated with shade, soil acidity, nitrate, and copper. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse and plant pathogens were more abundant in organic than in conventionally-managed fields, while saprotroph-plant pathogens were more abundant in conventionally-managed fields. These differences reflected environmental differences and depended on region.</p> <p><b>IMPORTANCE</b></p> <p>Rhizosphere fungi play key roles in ecosystems, as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management shape rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but also maintains a greater richness of saprotrophic, plant pathogenic and mycoparasitic fungi that has implications for efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.</p>
Reactivity, fate and functional roles of dissolved organic matter in anoxic inland waters
<p class="Textkrper1">The transit of organic matter (OM) through the aquatic compartment of its global cycle has been intensively studied, traditionally with a focus on the processing and degradation of its dissolved fraction (DOM). Because this is so intimately related to oxidation, the notion tenaciously persists that where dioxygen (O<sub>2</sub>) is absent, DOM turnover is markedly slowed. In this Opinion Piece, we outline how diverse processes shape, transform and degrade DOM also in anoxic aquatic environments, and we focus here on inland waters as a particular case study. A suite of biogeochemical DOM functions that have received comparatively little attention may only be expressed in anoxic conditions, and may result in enhanced biogeochemical roles of these deoxygenated habitats on a network scale.</p>
Ecoregional patterns of protist communities in mineral and organic soils: assembly processes, functional traits and diversity of testate amoebae in Northern Eurasia
<p>TA_Traits.csv file includes trait data for testate amoebae. TA_Abundance.csv file includes environmental variables (soil type and region) and relative abundance data of testate amoebae.</p>
Supporting data: Functional plasticity of the swim bladder as an acoustic organ for communication in a vocal fish
<div> <p>In this study, we show that the swim bladder of male plainfin midshipman fish (<em>Porichthys notatus</em>) exhibits reproductive state-dependent changes in morphology and function for sound production and reception. We quantified swim bladder morphometrics and utilized psuedolandmarking to identify differences in nonreproductive and reproductive male swim bladders. We utilized auditory evoked potential recordings, to measure the auditory sensitivity of saccular hair cells in response to sound pressure levels ranging from 97 - 154 dB re: 1 µPa to determine how the swim bladder contributes to midshipman auditory sensitivity. Finally, we used finite element modeling to explore the frequency response of nonreproductive and reproductive male swim bladders.</p> </div>
Organic compounds drive growth in phytoplankton taxa from different functional groups
<p>Phytoplankton are usually considered autotrophs, but an increasing number of studies shows that many taxa are able to also utilise organic carbon. Acquiring nutrients and energy from different sources might enable an efficient uptake of required substances and provide a strategy to deal with a varying resource availability, especially in highly dynamic ecosystems such as estuaries. In our study we investigated the effects of 31 organic carbon sources on the growth (proxied by differences in cell counts after 24 h exposure) of 17 phytoplankton strains from the Elbe estuary spanning four functional groups. All of our strains were able to make use of at least 1 and up to 26 organic compounds for growth. Pico-sized green algae such as <em>Mychonastes</em>, as well as the nano-sized green alga <em>Monoraphidium </em>in particular were positively affected by a high variety of substances. Reduced light availability, typically appearing in turbid estuaries and similar habitats, resulted in an overall poorer ability to utilise organic substances for growth, indicating that organic carbon acquisition was not primarily a strategy to deal with darkness. Our results give further evidence for mixotrophy being an ubiquitous ability of phytoplankton and highlight the importance to consider this trophic strategy in research.</p>
Monitoring DNA hybridization with Organic Electrochemical Transistors functionalized with Polydopamine
<p>Dataset of the paper "Monitoring DNA hybridization with Organic Electrochemical Transistors functionalized with Polydopamine" published in<em> Macromolecular Materials and Engineering</em>, DOI:10.1002/mame.202100880</p> <p>The data in the excel file are organized as follows:</p> <p>In <strong>Transfer_fc-target</strong> tab is reported the mean of the I<sub>DS </sub>vs V<sub>GS</sub> curves for each of the datasets, for every concentration of fc-target.</p> <p>In <strong>Transfer_pc-target</strong> tab is reported the mean of I<sub>DS </sub>vs V<sub>GS</sub> curves for each of the datasets, for every concentration of pc-target.</p> <p>In <strong>Transfer_nc-target</strong> tab is reported the mean of the I<sub>DS </sub>vs V<sub>GS</sub> curves for 0 and 100 nM nc-target.</p> <p>In the <strong>CV</strong> tab, we show the potential vs Ag/AgCl and the current of the Cyclic Voltammetry of every gate functionalization step, shown in figure 1c of the manuscript.</p>
Phytoplankton assemblage shifts with dissolved organic matter properties: a functional perspective for sentinel lakes
<p>1. Climate change is altering both dissolved organic matter (DOM) properties and phytoplankton dynamics in lakes. High-altitude lakes are good sentinels of global change. However, their value as sentinels depends on how well we understand their functioning. This study analyzed physical, chemical, and biological data during three pre-defined periods running from complete ice-cover right to the end of the ice-free season, in a high-altitude oligotrophic lake. A functional approach was used to assess how relationships between DOM and the planktonic community vary over time.</p> <p>2. Phytoplankton functional change was found to occur with shifts in dissolved organic matter. During the ice-influenced period, from February to the end of the thaw, the phytoplankton community was dominated by small autotrophs and mixotrophic flagellates and DOM from sediment and terrestrial origin dominated the DOM pool of the lake. Phytoplankton diversity and richness increased during the post-snowmelt overturn period, when terrestrial DOM dominated the DOM pool. Finally, large siliceous autotrophs, competitive under low nitrogen concentrations and high temperature, dominated almost exclusively during the late summer period. Increased phytoplankton biomass meant that phytoplankton-derived DOM was dominant during the late summer period.</p> <p>3. These phenological changes in the phytoplankton community resulted in functional shifts at the base of the food web. Based on the relationships between the variables in the study, it can be deduced that the nature of the relationship between phytoplankton and bacteria progressively shifted from strong top-down control exerted by phytoplankton over bacteria toward predominantly bottom-up control at the end of the ice-free season.</p> <p>4. Synthesis. Using a field survey starting from complete ice-cover and lasting right to the end of the ice-free season in a sentinel lake, we show seasonal shifts in the link between dissolved organic matter properties and plankton community traits. Differences in environmental conditions and DOM origin explained variation in phytoplankton community structure and function, pointing to seasonal shifts in microbial food web interactions. Our research suggests that, under climate change, the balance between mixotrophy and autotrophy and the control exerted by phytoplankton over bacterioplankton will change in oligotrophic high-altitude lakes with large, vegetated catchments. </p>
DEM data for Functional morphology of the Ediacaran organism Tribrachidium heraldicum
<p>This is the dataset for DEM particles from CFD-DEM simulations for tribrachidium.</p>
Continuous Non-Functional Requirements: Practices, Opportunities, and Trade-offs for Small, Agile Organizations
<p>This data represents two artifacts from our research in evaluating how small, agile organizations manage non-functional requirements in conjunction with continuous practices. It includes our base interview questions and the resulting codebook.</p> <p>This page includes supplementary materials associated with our paper entitled "Continuous Non-Functional Requirements: Practices, Opportunities, and Trade-offs for Small, Agile Organizations".</p>
Supplementary Data for "Identifying Promising Metal−Organic Frameworks for Heterogeneous Catalysis via High-Throughput Periodic Density Functional Theory"
<p>Supplementary data to accompany:</p> <p>A.S. Rosen, J.M. Notestein, R.Q. Snurr. "Identifying Promising Metal-Organic Frameworks for Heterogeneous Catalysis via High-Throughput Periodic Density Functional Theory", J. Comput. Chem (2019). DOI: 10.1002/jcc.25787</p>
Three-dimensional soil organic carbon density by logarithmic function and coefficient scaling in Yangtze River Delta, China
<h3>Three-dimensional soil organic carbon density (SOCD) dataset with 90-m resolution generated by Lin, S., Zhu, Q., Yin, B., Yang, G., Liao, K., Lai, X., Guo, C., 2025. Generating three-dimensional soil organic carbon density dataset by soil depth function and correction methods in Yangtze River Delta, China. Environmental Modelling & Software, <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.envsoft.2025.106582" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.envsoft.2025.106582.</span></span></a></h3> <h3>Here, based on the best performance, the three-dimensional SOCD generated by LF corrected with coefficient scaling method were provided. The accurate SOCD maps with the spatial resolution of 90-m at any specific depth interval can be generated by our method. This dataset includes:</h3> <ul> <li>Spatial distribution map of parameter 1 (p1) of LF (LF_p1.tif)</li> <li>Spatial distribution map of parameter 2 (p2) of LF (LF_p2.tif)</li> <li>The calculation code and fitted functions of scaling coefficient a, k of LF (fitted_fx_scalingcoff.m)</li> <li>Readme.docx</li> </ul> <p>Note: the unit of SOCD is kg m-2; the spatial distribution maps provided by this dataset does not mask any water bodies.</p> <p><strong>How to use our dataset? Please refer to our article and Readme.docx for more details.</strong></p> <p> </p> <p> </p>
Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function
<p>Dataset for Ono et al., 2024.<br>Contains all source data from the Tarchini laboratory, including illustrative images and raw data for quantification, as well as the data file containing statistical analysis. It also contains the data file produced by the Cullen laboratory reporting behavioral data. </p>
Supporting data for 'Rapid quantification of methane in water with parts-per-billion sensitivity using a metal-organic framework-functionalized quartz crystal resonator'
<p>Supporting data for the preprint 'Rapid quantification of methane in water with parts-per-billion sensitivity using a metal-organic framework-functionalized quartz crystal resonator' published at ChemRxiv (doi://10.26434/chemrxiv-2024-x62zz)</p> <p> </p>
Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"
<p>Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"</p>
Input Data for "Protein Function Prediction for newly sequenced organisms"
<p>The input sequence files in FASTA format and the detailed list of all organisms excluded when testing each specific bacterium.</p>
Data from: Climatic water availability mainly drives context-dependency of tree functional diversity effects on soil organic carbon storage in European forests
<p>The interplay of forest stand and environmental factors shape soil organic C (SOC) storage in forest ecosystems but little is known about their relative impacts in different soil layers. Moreover, how environmental factors modulate the impact of stand factors, particularly species mixing, on SOC storage, is largely unexplored. In this study conducted in 21 forest triplets (two-species mixed stand and respective monocultures nearby) distributed in Europe, we tested the hypothesis that stand factors (functional identity and diversity) have stronger effects on topsoil (FF+0-10 cm) C storage than environmental factors (climatic water availability, clay+silt content, oxalate-extractable Al - Al<sub>ox</sub>) but that the opposite occurs in the subsoil (10-40 cm). We also tested the hypothesis that functional diversity improves SOC storage under high climatic water availability, clay+silt contents, Al<sub>ox</sub>. We characterized functional identity as the proportion of broadleaved species (beech and/or oak), and functional diversity as the product of broadleaved and conifer (pine) proportions. The results show that functional identity was the main driver of topsoil C storage while climatic water availability had the largest control on subsoil C storage. Contrary to expectations, functional diversity decreased topsoil C storage under increasing climatic water availability but the opposite was observed in the subsoil. Functional diversity effects on topsoil C increased with increasing clay+silt content, while its effects on subsoil C was negative at increasing Al<sub>ox</sub> content. This suggests that functional diversity effect on SOC storage along environmental gradients depends on the specific environmental factor and the soil depth under consideration.</p>
Dataset: Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla
<p>First release upon acceptance of the paper. </p>
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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)
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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.