Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium
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Sourjik, Victor (Ed.)
Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm’s depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.Free, publicly-accessible full text available February 1, 2025 -
Free, publicly-accessible full text available September 30, 2024
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Abstract We prove that it is possible to obtain the exact closure of SIR pairwise epidemic equations on a configuration model network if and only if the degree distribution follows a Poisson, binomial, or negative binomial distribution. The proof relies on establishing the equivalence, for these specific degree distributions, between the closed pairwise model and a dynamical survival analysis (DSA) model that was previously shown to be exact. Specifically, we demonstrate that the DSA model is equivalent to the well-known edge-based Volz model. Using this result, we also provide reductions of the closed pairwise and Volz models to a single equation that involves only susceptibles. This equation has a useful statistical interpretation in terms of times to infection. We provide some numerical examples to illustrate our results.
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Abstarct This work presents a theoretical framework for the safety‐critical control of time delay systems. The theory of control barrier functions, that provides formal safety guarantees for delay‐free systems, is extended to systems with state delay. The notion of control barrier functionals is introduced, to attain formal safety guarantees by enforcing the forward invariance of safe sets defined in the infinite dimensional state space. The proposed framework is able to handle multiple delays and distributed delays both in the dynamics and in the safety condition, and provides an affine constraint on the control input that yields provable safety. This constraint can be incorporated into optimization problems to synthesize pointwise optimal and provable safe controllers. The applicability of the proposed method is demonstrated by numerical simulation examples.
Free, publicly-accessible full text available August 1, 2024 -
Free, publicly-accessible full text available July 1, 2024
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Abstract There is a growing need for past weather and climate data to support science and decision-making. This paper describes the compilation and construction of a global multivariable (air temperature, pressure, precipitation sum, number of precipitation days) monthly instrumental climate database that encompasses a substantial body of the known early instrumental time series. The dataset contains series compiled from existing databases that start before 1890 (though continuing to the present) as well as a large amount of newly rescued data. All series underwent a quality control procedure and subdaily series were processed to monthly mean values. An inventory was compiled, and the collection was deduplicated based on coordinates and mutual correlations. The data are provided in a common format accompanied by the inventory. The collection totals 12452 meteorological records in 118 countries. The data can be used for climate reconstructions and analyses. It is the most comprehensive global monthly climate dataset for the preindustrial period so far.
Free, publicly-accessible full text available December 1, 2024 -
Abstract Documentary climate data describe evidence of past climate arising from predominantly written historical documents such as diaries, chronicles, newspapers, or logbooks. Over the past decades, historians and climatologists have generated numerous document-based time series of local and regional climates. However, a global dataset of documentary climate time series has never been compiled, and documentary data are rarely used in large-scale climate reconstructions. Here, we present the first global multi-variable collection of documentary climate records. The dataset DOCU-CLIM comprises 621 time series (both published and hitherto unpublished) providing information on historical variations in temperature, precipitation, and wind regime. The series are evaluated by formulating proxy forward models (i.e., predicting the documentary observations from climate fields) in an overlapping period. Results show strong correlations, particularly for the temperature-sensitive series. Correlations are somewhat lower for precipitation-sensitive series. Overall, we ascribe considerable potential to documentary records as climate data, especially in regions and seasons not well represented by early instrumental data and palaeoclimate proxies.
Free, publicly-accessible full text available December 1, 2024 -
Abstract Networks of weakly coupled oscillators had a profound impact on our understanding of complex systems. Studies on model reconstruction from data have shown prevalent contributions from hypernetworks with triplet and higher interactions among oscillators, in spite that such models were originally defined as oscillator networks with pairwise interactions. Here, we show that hypernetworks can spontaneously emerge even in the presence of pairwise albeit nonlinear coupling given certain triplet frequency resonance conditions. The results are demonstrated in experiments with electrochemical oscillators and in simulations with integrate-and-fire neurons. By developing a comprehensive theory, we uncover the mechanism for emergent hypernetworks by identifying appearing and forbidden frequency resonant conditions. Furthermore, it is shown that microscopic linear (difference) coupling among units results in coupled mean fields, which have sufficient nonlinearity to facilitate hypernetworks. Our findings shed light on the apparent abundance of hypernetworks and provide a constructive way to predict and engineer their emergence.more » « less
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Abstract The perennial ice-covered lakes of the Antarctic McMurdo Dry Valleys harbour oligotrophic microbial communities that are separated geographically from other aquatic systems. Their microbiomes include planktonic microbes as well as lift-off mat communities that emerge from the ice. We used the ShortBRED protein family profiler to quantify the antibiotic resistance genes (ARGs) from metagenomes of lift-off mats emerging from ice and from filtered water samples of Lake Fryxell and Lake Bonney. The overall proportion of ARG hits was similar to that found in temperate-zone rural ponds with moderate human inputs. Specific ARGs showed distinct distributions for the two lakes and for mat vs planktonic sources. Metagenomic taxa distributions showed that mat phototrophs consisted mainly of cyanobacteria or Betaproteobacteria, whereas the water column phototrophs were mainly protists. An enrichment culture of the Betaproteobacterium Rhodoferax antarcticus from a Lake Fryxell mat sample showed an unusual mat-forming phenotype not previously reported for this species. Its genome showed no ARGs associated with Betaproteobacteria but had ARGs consistent with a minor Pseudomonas component. The Antarctic lake mats and water showed specific ARGs distinctive to the mat and water sources, but overall ARG levels were similar to those of temperate water bodies with moderate human inputs.more » « less
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Aqueous Zn/MnO 2 batteries with their environmental sustainability and competitive cost, are becoming a promising, safe alternative for grid-scale electrochemical energy storage. Presented as a promising design principle to deliver a higher theoretical capacity, this work offers fundamental understanding of the dissolution–deposition mechanism of Zn/β-MnO 2 . A multimodal synchrotron characterization approach including three operando X-ray techniques (powder diffraction, absorption spectroscopy, and fluorescence microscopy) is coupled with elementally resolved synchrotron X-ray nano-tomography. Together they provide a direct correlation between structural evolution, reaction chemistry, and 3D morphological changes. Operando synchrotron X-ray diffraction and spectroscopy show a crystalline-to-amorphous phase transition. Quantitative modeling of the operando data by Rietveld refinement for X-ray diffraction and multivariate curve resolution (MCR) for X-ray absorption spectroscopy are used in a complementary fashion to track the structural and chemical transitions of both the long-range (crystalline phases) and short-range (including amorphous phases) ordering upon cycling. Scanning X-ray microscopy and full-field nano-tomography visualizes the morphology of electrodes at different electrochemical states with elemental sensitivity to spatially resolve the formation of the Zn- and Mn-containing phases. Overall, this work critically indicates that for Zn/MnO 2 aqueous batteries, the reaction pathways involving Zn–Mn complex formation upon cycling become independent of the polymorphs of the initial electrode and sheds light on the interplay among structural, chemical, and morphological evolution for electrochemically driven phase transitions.more » « lessFree, publicly-accessible full text available June 14, 2024