A Stochastic Covariance Shrinkage Approach to Particle Rejuvenation in the Ensemble Transform Particle Filter

Rejuvenation in particle filters is necessary to prevent the collapse of the weights when the number of particles is insufficient to sample the high probability regions of the state space. Rejuvenation is often implemented in a heuristic manner by the addition of stochastic samples that widen the support of the ensemble. This work aims at improving canonical rejuvenation methodology by the introduction of additional prior information obtained from climatological samples; the dynamical particles used for importance sampling are augmented with samples obtained from stochastic covariance shrinkage. The ensemble transport particle filter, and its second order variant, are extended with the proposed rejuvenation approach. Numerical experiments show that modified filters significantly improve the analyses for low dynamical ensemble sizes.

Focusing on mRNA Granules and Stalled Polysomes Amidst Diverse Mechanisms Underlying mRNA Transport, mRNA Storage, and Local Translation

In neurons, mRNAs are transported to distal sites to allow for localized protein synthesis. There are many diverse mechanisms underlying this transport. For example, an individual mRNA can be transported in an RNA transport particle that is tailored to the individual mRNA and its associated binding proteins. In contrast, some mRNAs are transported in liquid-liquid phase separated structures called neuronal RNA granules that are made up of multiple stalled polysomes, allowing for rapid initiation-independent production of proteins required for synaptic plasticity. Moreover, neurons have additional types of liquid-liquid phase–separated structures containing mRNA, such as stress granules and P bodies. This chapter discusses the relationships between all of these structures, what proteins distinguish them, and the possible roles they play in the complex control of mRNA translation at distal sites that allow neurons to use protein synthesis to refine their local proteome in many different ways.

Vertical transport of sediment-associated metals and cyanobacteria by ebullition in a stratified lake

Bubbles adsorb and transport particulate matter in a variety of natural and engineered settings, including industrial, freshwater, and marine systems. While methane-containing bubbles emitted from anoxic sediments are found widely in freshwater ecosystems, relatively little attention has been paid to the possibility that these bubbles transport particle-associated chemical or biological material from sediments to surface waters of freshwater lakes. We triggered ebullition and quantified transport of particulate material from sediments to the surface by bubbles in Upper Mystic Lake, MA, and in a 15 m tall experimental column. Particle transport was positively correlated with the volume of gas bubbles released from the sediment, and particles transported by bubbles appear to originate almost entirely in the sediment, rather than being scavenged from the water column. Concentrations of arsenic, chromium, lead, and cyanobacterial cells in bubble-transported particulate material were similar to those of bulk sediment, and particles were transported from depths exceeding 15 m, implying the potential for daily average fluxes as large as 0.18 µg arsenic m−2 and 2×104 cyanobacteria cells m−2 in the strongly stratified Upper Mystic Lake. Bubble-facilitated arsenic transport currently appears to be a modest component of total arsenic cycling in this lake. Although more work is needed to reduce uncertainty in budget estimates, bubble-facilitated cyanobacterial transport has the potential to contribute substantially to the cyanobacteria cell recruitment to the surface of this lake and may thus be of particular importance in large, deep, stratified lakes.

Vertical transport of sediment-associated metals and cyanobacteria by ebullition in a stratified lake

Bubbles adsorb and transport particulate matter both in industrial and marine systems. While methane-containing bubbles emitted from anoxic sediments are found extensively in aquatic ecosystems, relatively little attention has been paid to the possibility that such bubbles transport particle-associated chemical or biological material from sediments to surface waters of freshwater lakes. We quantified transport of particulate material from sediments to the surface by bubbles in Upper Mystic Lake, MA and in a 15 m tall experimental column. Vertical particle transport was positively correlated with the volume of gas bubbles released from the sediment. Particles transported by bubbles originated almost entirely in the sediment, rather than being scavenged from the water column. Concentrations of arsenic, chromium, lead, and cyanobacterial cells in bubble-transported particulate material were similar to those of bulk sediment, and particles were transported from depths exceeding 15 m, resulting in daily fluxes as large as 0.005 µmol of arsenic m−2 and 4 × 104 cyanobacterial cells m−2 in the strongly stratified Upper Mystic Lake. While bubble-facilitated arsenic transport currently appears to be a modest component of total arsenic cycling in this lake, bubble-facilitated cyanobacterial transport could comprise as much as 17 % of recruitment in this lake and may thus be of particular importance in large, deep, stratified lakes.

Preservation of organic carbon during active fluvial transport and particle abrasion

Oxidation of particulate organic carbon (POC) during fluvial transit releases CO2 to the atmosphere and can influence global climate. Field data show large POC oxidation fluxes in lowland rivers; however, it is unclear if POC losses occur predominantly during in-river transport, where POC is in continual motion within an aerated environment, or during transient storage in floodplains, which may be anoxic. Determination of the locus of POC oxidation in lowland rivers is needed to develop process-based models to predict POC losses, constrain carbon budgets, and unravel links between climate and erosion. However, sediment exchange between rivers and floodplains makes differentiating POC oxidation during in-river transport from oxidation during floodplain storage difficult. Here, we isolated in-river POC oxidation using flume experiments transporting petrogenic and biospheric POC without floodplain storage. Our experiments showed solid phase POC losses of 0%–10% over ∼103 km of fluvial transport, compared to ∼7% to >50% losses observed in rivers over similar distances. The production of dissolved organic carbon (DOC) and dissolved rhenium (a proxy for petrogenic POC oxidation) was consistent with small POC losses, and replicate experiments in static water tanks gave similar results. Our results show that fluvial sediment transport, particle abrasion, and turbulent mixing have a minimal role on POC oxidation, and they suggest that POC losses may accrue primarily in floodplain storage.

A reduced-complexity model for sediment transport and step-pool morphology

A new particle-based reduced-complexity model, CAST, to simulate sediment transport and channel morphology in steep streams is presented. CAST contains phenomenological parameterizations, deterministic or stochastic, of sediment supply, bed load transport, particle entrainment and deposition in a cellular-automaton space with uniform grain size. The model can reproduce a realistic bed morphology and typical fluctuations in transport rates observed in steep channels. Particle hop distances, from entrainment to deposition, are well-fitted by exponential distributions, in agreement with field data. The effect of stochasticity both in the entrainment and in the input rate is shown. A stochastic parameterization of the entrainment is essential to create and maintain a realistic channel morphology, while sediment transport in CAST shreds the input signal and its stochastic variability. A jamming routine has been added to CAST to simulate the grain-grain and grain-bed interactions that lead to particle jamming and step formation in a step-pool stream. The results show that jamming is effective in generating steps in unsteady conditions. Steps are created during high- flow periods and they survive during low flows only in sediment- starved conditions, in agreement with the jammed-state hypothesis of Church and Zimmermann (2007). Reduced-complexity models such as CAST can give new insight into the dynamics of complex phenomena (such as sediment transport and bedform stability) and be useful to test research hypotheses, being an effective complement to fully physically-based models.