The importance of neuronal morphology in brain function has been recognized for over a century. The broad applicability of “digital reconstructions” of neuron morphology across neuroscience ...subdisciplines has stimulated the rapid development of numerous synergistic tools for data acquisition, anatomical analysis, three-dimensional rendering, electrophysiological simulation, growth models, and data sharing. Here we discuss the processes of histological labeling, microscopic imaging, and semiautomated tracing. Moreover, we provide an annotated compilation of currently available resources in this rich research “ecosystem” as a central reference for experimental and computational neuroscience.
Neuronal morphology and brain function are intertwined. In this Primer, Parekh and Ascoli discuss reconstruction of neuronal morphology. They cover the processes of labeling, imaging, and tracing of neurons and provide an annotated compilation of currently available resources for digital reconstruction.
Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, ...recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.
Understanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons.
A Critical Comparison Among Pansharpening Algorithms Vivone, Gemine; Alparone, Luciano; Chanussot, Jocelyn ...
IEEE transactions on geoscience and remote sensing,
05/2015, Letnik:
53, Številka:
5
Journal Article
Recenzirano
Pansharpening aims at fusing a multispectral and a panchromatic image, featuring the result of the processing with the spectral resolution of the former and the spatial resolution of the latter. In ...the last decades, many algorithms addressing this task have been presented in the literature. However, the lack of universally recognized evaluation criteria, available image data sets for benchmarking, and standardized implementations of the algorithms makes a thorough evaluation and comparison of the different pansharpening techniques difficult to achieve. In this paper, the authors attempt to fill this gap by providing a critical description and extensive comparisons of some of the main state-of-the-art pansharpening methods. In greater details, several pansharpening algorithms belonging to the component substitution or multiresolution analysis families are considered. Such techniques are evaluated through the two main protocols for the assessment of pansharpening results, i.e., based on the full- and reduced-resolution validations. Five data sets acquired by different satellites allow for a detailed comparison of the algorithms, characterization of their performances with respect to the different instruments, and consistency of the two validation procedures. In addition, the implementation of all the pansharpening techniques considered in this paper and the framework used for running the simulations, comprising the two validation procedures and the main assessment indexes, are collected in a MATLAB toolbox that is made available to the community.
Neurons and glia have distinct yet interactive functions but are both characterized by branching morphology. Dendritic trees have been digitally traced for over 40 years in many animal species, ...anatomical regions, and neuron types. Recently, long‐range axons also are being reconstructed throughout the brain of many organisms from invertebrates to primates. In contrast, less attention has been paid until lately to glial morphology. Thus, although glia and neurons are similarly abundant in the nervous systems of humans and most animal models, glia have traditionally been much less represented than neurons in morphological reconstruction repositories such as NeuroMorpho.Org. This is rapidly changing with the advent of high‐throughput glia tracing. NeuroMorpho.Org introduced glial cells in 2017 and today they constitute nearly a third of the database content. It took NeuroMorpho.Org 10 years to collect the first 40,000 neurons and now that amount of data can be produced in a single publication. This not only demonstrates the spectacular technological progress in data production, but also demands a corresponding advancement in informatics processing. At the same time, these publicly available data also open new opportunities for quantitative analysis and computational modeling to identify universal or cell‐type‐specific design principles in the cellular architecture of nervous systems. As a first application, we demonstrated that supervised machine learning of tree geometry classifies neurons and glia with practically perfect accuracy. Furthermore, we discovered a new morphometric biomarker capable of robustly separating these cell classes across multiple species, brain regions, and experimental preparations, with only sparse sampling of branch measurements.
Diversity of digitally reconstructed glia (astrocytes, oligodendrocytes, microglia, and other types) freely available for download and reuse at NeuroMorpho.Org in terms of experimental provenance, animal species, anatomical region, cell type, tracing platform, and more.
Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the ...boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network.
It is now widely accepted that boreal rivers and streams are regionally significant sources of carbon dioxide (CO₂), yet their role as methane (CH₄) emitters, as well as the sensitivity of these ...greenhouse gas (GHG) emissions to climate change, are still largely undefined. In this study, we explore the large‐scale patterns of fluvial CO₂ and CH₄ partial pressure (pCO₂, pCH₄) and gas exchange (k) relative to a set of key, climate‐sensitive river variables across 46 streams and rivers in two distinct boreal landscapes of Northern Québec. We use the resulting models to determine the direction and magnitude of C‐gas emissions from these boreal fluvial networks under scenarios of climate change. River pCO₂ and pCH₄ were positively correlated, although the latter was two orders of magnitude more variable. We provide evidence that in‐stream metabolism strongly influences the dynamics of surface water pCO₂ and pCH₄, but whereas pCO₂ is not influenced by temperature in the surveyed streams and rivers, pCH₄ appears to be strongly temperature‐dependent. The major predictors of ambient gas concentrations and exchange were water temperature, velocity, and DOC, and the resulting models indicate that total GHG emissions (C‐CO₂ equivalent) from the entire network may increase between by 13 to 68% under plausible scenarios of climate change over the next 50 years. These predicted increases in fluvial GHG emissions are mostly driven by a steep increase in the contribution of CH₄ (from 36 to over 50% of total CO₂‐equivalents). The current role of boreal fluvial networks as major landscape sources of C is thus likely to expand, mainly driven by large increases in fluvial CH₄ emissions.
Lakes are a major component of boreal landscapes, and whereas lake CO₂emissions are recognized as a major component of regional C budgets, there is still much uncertainty associated to lake ...CH₄fluxes. Here, we present a large‐scale study of the magnitude and regulation of boreal lake summer diffusive CH₄fluxes, and their contribution to total lake carbon (C) emissions, based on in situ measurements of concentration and fluxes of CH₄and CO₂in 224 lakes across a wide range of lake type and environmental gradients in Québec. The diffusive CH₄flux was highly variable (mean 11.6 ± 26.4 SD mg m⁻² d⁻¹), and it was positively correlated with temperature and lake nutrient status, and negatively correlated with lake area and colored dissolved organic matter (CDOM). The relationship between CH₄and CO₂concentrations fluxes was weak, suggesting major differences in their respective sources and/or regulation. For example, increasing water temperature leads to higher CH₄flux but does not significantly affect CO₂flux, whereas increasing CDOM concentration leads to higher CO₂flux but lower CH₄flux. CH₄contributed to 8 ± 23% to the total lake C emissions (CH₄ + CO₂), but 18 ± 25% to the total flux in terms of atmospheric warming potential, expressed as CO₂‐equivalents. The incorporation of ebullition and plant‐mediated CH₄fluxes would further increase the importance of lake CH₄. The average Q₁₀of CH₄flux was 3.7, once other covarying factors were accounted for, but this apparent Q₁₀varied with lake morphometry and was higher for shallow lakes. We conclude that global climate change and the resulting shifts in temperature will strongly influence lake CH₄fluxes across the boreal biome, but these climate effects may be altered by regional patterns in lake morphometry, nutrient status, and browning.
During transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on ...downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale.
The very peculiar characteristics of zwitterions, as well as a clearand unambiguous definition, have been overlooked in past literature. However, these compounds are particularly important in view of ...the impact they have had in the recent past and will likely continue to have in the future as components of performing functional organic and hybrid materials. In this Account, we primarily aim to define critically important organic concepts of zwitterions regarding both their design and nomenclature. We will particularly focus on a specific kind of zwitterions we define as π-conjugated zwitterions. These types of zwitterions are systems pertaining to the class ofdonor–acceptor (push–pull) molecules. In the ground state, they are preferentially represented in terms of an electron donor moiety bearing a negative net charge, and electron acceptor one bearing a positive net charge connected by a conjugated bridge. As such, they are possibly the most effective example of push–pull structure, possessing relevant features for applications like nonlinear optics, photovoltaics, imaging, and high capacitance dielectrics. In addition, the interaction between these dipolar compounds and the environment is highly specific and can be exploited in the construction of well-organized nanostructures, both in solution and in the solid state. According to the Gold Book of IUPAC for nomenclature, the distinction between zwitterions and the charged molecule called a betaine is subtle. The betaine is a particular class of zwitterion possessing an onium atom not bearing a hydrogen. The two terms are often considered equivalent, thus generating confusion while retrieving literature. In this Account, we define and describe π-conjugated zwitterions systems that are dipolar in the ground state, admitting resonance limiting structures that are neutral and chargeless. For the purpose of this Account and to the benefit of researchers striving to retrieve materials-related zwitterion literature data, we suggest to use the term π-zwitterions instead of the commonly used plain term “zwitterions”. We show that this definition enables the clear identification of a class of compounds having unique properties distinct from “dipolar conjugated compounds.” We describe the most common donor and acceptor groups in π-zwitterions. In particular, we focus our attention on the special case of the nitrile functionality, which tends to be contiguous to a negative charge. We also address special emphasis to benzenoid components that are substituted by heteroaromatic units in π-zwitterions, because the HOMO–LUMO energetic consequences are specifically involved in these cases. We make reference to the paradigmatic case of π-zwitterions second order nonlinear optical properties. Here, the value of the first hyperpolarizability β versus the alternation in bond length turns out to be a measure of the balance of the chargeless and the dipolar contribution to the description of the zwitterion ground state. We also report literature data, collected both from our group and others, concerning π-zwitterions containing heteroaromatic and/or nitrile groups, those based on the most performing acceptors so far described, and merocyanines. With particular reference to merocyanines, we show how π-zwitterions can play a fundamental role in the fast growing field of organic photovoltaics. Finally, we present π-zwitterions made up of heteroaromatic groups that open new scenarios in heteroaromatic chemistry.
PDF
