Search

In this article I give a brief overview of some of the challenges in creating accessible documents for STEM education, as well as why and how GNU TeXmacs can be used to address some of these.

We propose a stochastic model reduction strategy for deterministic and stochastic slow-fast systems with a moderate time scale separation. The stochastic model reduction strategy improves the appro...

We use large deviation theory to study persistent extreme events of temperature, like heat waves or cold spells. We consider the mid-latitudes of a simplified yet Earth-like general circulation model of the atmosphere and numerically estimate large deviation rate functions of near-surface temperature averages over different spatial scales. We find that, in order to represent persistent extreme events based on large deviation theory, one has to look at temporal averages of spatially averaged observables. The spatial averaging scale is crucial, and has to correspond with the scale of the event of interest. Accordingly, the computed rate functions indicate substantially different statistical properties of temperature averages over intermediate spatial scales (larger, but still of the order of the typical scale), as compared to the ones related to any other scale. Thus, heat waves (or cold spells) can be interpreted as large deviations of temperature averaged over intermediate spatial scales. Furthermore, we find universal characteristics of rate functions, based on the equivalence of temporal, spatial, and spatio-temporal rate functions if we perform a re-normalisation by the integrated auto-correlation.

In this paper, we examine the deviations from Gaussianity for two types of a random variable converging to a normal distribution, namely, sums of random variables generated by a deterministic discrete time map and a linearly damped variable driven by a deterministic map. We demonstrate how Edgeworth expansions provide a universal description of the deviations from the limiting normal distribution. We derive explicit expressions for these asymptotic expansions and provide numerical evidence of their accuracy.

We derive Edgeworth expansions that describe corrections to the Gaussian limiting behaviour of slow-fast systems. The Edgeworth expansion is achieved using a semi-group formalism for the transfer operator, where a Duhamel-Dyson series is used to asymptotically determine the corrections at any desired order of the time scale parameter $\varepsilon$. The corrections involve integrals over higher-order auto-correlation functions. We develop a diagrammatic representation of the series to control the combinatorial wealth of the asymptotic expansion in $\varepsilon$ and provide explicit expressions for the first two orders. At a formal level, the expressions derived are valid in the case when the fast dynamics is stochastic as well as when the fast dynamics is entirely deterministic. We corroborate our analytical results with numerical simulations and show that our method provides an improvement on the classical homogenization limit which is restricted to the limit of infinite time scale separation., Comment: accepted for publication in Proceedings of the Royal Society A

We study temporally persistent and spatially extended extreme events of temperature anomalies, i.e. heat waves and cold spells, using large deviation theory. To this end, we consider a simplified yet Earth-like general circulation model of the atmosphere and numerically estimate large deviation rate functions of near-surface temperature in the mid-latitudes. We find that, after a re-normalisation based on the integrated auto-correlation, the rate function one obtains at a given latitude by looking, locally in space, at long time averages agrees with what is obtained, instead, by looking, locally in time, at large spatial averages along the latitude. This is a result of scale symmetry in the spatial-temporal turbulence and of the fact that advection is primarily zonal. This agreement hints at the universality of large deviations of the temperature field. Furthermore, we discover that the obtained rate function is able to describe spatially extended and temporally persistent heat waves or cold spells, if we consider temporal averages of spatial averages over intermediate spatial scales. Finally, we find out that large deviations are relatively more likely to occur when looking at these spatial averages performed over intermediate scales, thus pointing to the existence of weather patterns associated to the low-frequency variability of the atmosphere. Extreme value theory is used to benchmark our results., Comment: 33 pages, 9 figures

Studying extreme events and how they evolve in a changing climate is one of the most important current scientific challenges. Starting from complex climate models, a key difficulty is to be able to run long enough simulations in order to observe those extremely rare events. In physics, chemistry, and biology, rare event algorithms have recently been developed to compute probabilities of events that cannot be observed in direct numerical simulations. Here we propose such an algorithm, specifically designed for extreme heat or cold waves, based on statistical physics approaches. This gives an improvement of more than two orders of magnitude in the sampling efficiency. We describe the dynamics of events that would not be observed otherwise. We show that European extreme heat waves are related to a global teleconnection pattern involving North America and Asia. This tool opens a full range of studies, so far impossible, aimed at assessing quantitatively climate change impacts., Proceedings of the National Academy of Sciences (2017)

The climate is a forced and dissipative nonlinear system featuring non-trivial dynamics of a vast range of spatial and temporal scales. The understanding of the climate's structural and multiscale properties is crucial for the provision of a unifying picture of its dynamics and for the implementation of accurate and efficient numerical models. We present some recent developments at the intersection between climate science, mathematics, and physics, which may prove fruitful in the direction of constructing a more comprehensive account of climate dynamics. We describe the Nambu formulation of fluid dynamics, and the potential of such a theory for constructing sophisticated numerical models of geophysical fluids. Then, we focus on the statistical mechanics of quasi-equilibrium flows in a rotating environment, which seems crucial for constructing a robust theory of geophysical turbulence. We then discuss ideas and methods suited for approaching directly the non-equilibrium nature of the climate system. First, we describe some recent findings on the thermodynamics of climate and characterize its energy and entropy budgets, and discuss related methods for intercomparing climate models and for studying tipping points. These ideas can also create a common ground between geophysics and astrophysics by suggesting general tools for studying exoplanetary atmospheres. We conclude by focusing on non-equilibrium statistical mechanics, which allows for a unified framing of problems as different as the climate response to forcings, the effect of altering the boundary conditions or the coupling between geophysical flows, and the derivation of parametrizations for numerical models., Comment: 44 pages, 22 figures. Major revision with respect to previous version. A glossary of terms is included at the end

We discuss applications of a recently developed method for model reduction based on linear response theory of weakly coupled dynamical systems. We apply the weak coupling method to simple stochastic differential equations with slow and fast degrees of freedom. The weak coupling model reduction method results in general in a non-Markovian system, we therefore discuss the Markovianization of the system to allow for straightforward numerical integration. We compare the applied method to the equations obtained through homogenization in the limit of large time scale separation between slow and fast degrees of freedom. We numerically compare the ensemble spread from a fixed initial condition, correlation functions and exit times from a domain. The weak coupling method gives more accurate results in all test cases, albeit with a higher numerical cost.

Using a sensitive statistical test we determine whether or not one can detect the breakdown of linear response given observations of deterministic dynamical systems. A goodness-of-fit statistics is developed for a linear statistical model of the observations, based on results on central limit theorems for deterministic dynamical systems, and used to detect linear response breakdown. We apply the method to discrete maps which do not obey linear response and show that the successful detection of breakdown depends on the length of the time series, the magnitude of the perturbation and on the choice of the observable. We find that in order to reliably reject the assumption of linear response for typical observables sufficiently large data sets are needed. Even for simple systems such as the logistic map, one needs of the order of $10^6$ observations to reliably detect the breakdown, if less observations are available one may be falsely led to conclude that linear response theory is valid. The amount of data required is larger the smaller the applied perturbation. For judiciously chosen observables the necessary amount of data can be drastically reduced, but requires detailed {\em{a priori}} knowledge about the invariant measure which is typically not available for complex dynamical systems. Furthermore we explore the use of the fluctuation-dissipation theorem (FDT) in cases with limited data length or coarse-graining of observations. The FDT, if applied naively to a system without linear response, is shown to be very sensitive to the details of the sampling method, resulting in erroneous predictions of the response., Comment: Published in Physica D (2016)

In this paper we address the use of rare event computation techniques to estimate small over-threshold probabilities of observables in determin-istic dynamical systems. We demonstrate that the genealogical particle analysis algorithms can be successfully applied to a toy model of atmospheric dynamics, the Lorenz '96 model. We furthermore use the Ornstein-Uhlenbeck system to illustrate a number of implementation issues. We also show how a time-dependent objective function based on the fluctuation path to a high threshold can greatly improve the performance of the estimator compared to a fixed-in-time objective function.

Objective To assess the effect of a prospective screening strategy for the early diagnosis of celiac disease (CD) in children with Down syndrome (DS). Study design Blood samples were taken from 155 children with DS. Buccal swabs were also taken from 9 of these children for determination of human leukocyte antigen (HLA)-DQ2 or HLA-DQ8 positivity. Independently, immunoglobulin A anti-endomysium-(EMA) and anti-tissue transglutaminase antibodies (TGA) were tested. An intestinal biopsy was performed to confirm the diagnosis of CD. Results Sixty-three children (40.6%) had test results that were positive for HLA-DQ2 or HLA-DQ8. Results of HLA DQ-typing of DNA isolated from blood and buccal swabs were identical. Eight of the children in whom test results were positive for HLA-DQ2/8 also had positive test results for EMA and TGA. CD was confirmed in 7 of these children with an intestinal biopsy, and in 1 child, CD was suggested with improvement on a gluten-free diet. Conclusions We found a prevalence of CD in children with DS of 5.2% (10 times higher than the general Dutch population). We recommend HLA-DQ2/8 typing from buccal swabs in the first year of life and initiating serologic screening of children with DS in whom test results are positive for HLA-DQ2 or DQ8 at age 3 years. Early knowledge of negative HLA-DQ2/8 status can reassure most parents that their children do not have a CD risk.

Hydroxyacid dehydrogenases of lactic acid bacteria, which catalyze the stereospecific reduction of branched-chain 2-keto acids to 2-hydroxyacids, are of interest in a variety of fields, including cheese flavor formation via amino acid catabolism. In this study, we used both targeted and random mutagenesis to identify the genes responsible for the reduction of 2-keto acids derived from amino acids in Lactococcus lactis . The gene panE , whose inactivation suppressed hydroxyisocaproate dehydrogenase activity, was cloned and overexpressed in Escherichia coli , and the recombinant His-tagged fusion protein was purified and characterized. The gene annotated panE was the sole gene responsible for the reduction of the 2-keto acids derived from leucine, isoleucine, and valine, while ldh , encoding l -lactate dehydrogenase, was responsible for the reduction of the 2-keto acids derived from phenylalanine and methionine. The kinetic parameters of the His-tagged PanE showed the highest catalytic efficiencies with 2-ketoisocaproate, 2-ketomethylvalerate, 2-ketoisovalerate, and benzoylformate ( V max / K m ratios of 6,640, 4,180, 3,300, and 2,050 U/mg/mM, respectively), with NADH as the exclusive coenzyme. For the reverse reaction, the enzyme accepted d -2-hydroxyacids but not l -2-hydroxyacids. Although PanE showed the highest degrees of identity to putative NADP-dependent 2-ketopantoate reductases (KPRs), it did not exhibit KPR activity. Sequence homology analysis revealed that, together with the d -mandelate dehydrogenase of Enterococcus faecium and probably other putative KPRs, PanE belongs to a new family of d -2-hydroxyacid dehydrogenases which is unrelated to the well-described d -2-hydroxyisocaproate dehydrogenase family. Its probable physiological role is to regenerate the NAD + necessary to catabolize branched-chain amino acids, leading to the production of ATP and aroma compounds.

The food-borne pathogen Listeria monocytogenes has the ability to survive extreme environmental conditions due to an extensive interacting network of stress responses. It is able to grow and survive at relatively high temperatures in comparison with other non-sporulating food-borne pathogens. To investigate the heat-shock response of L. monocytogenes, whole-genome expression profiles of cells that were grown at 37 degrees C and exposed to 48 degrees C were examined using DNA microarrays. Transcription levels were measured over a 40 min period after exposure of the culture to 48 degrees C and compared with those of unexposed cultures at 37 degrees C. After 3 min, 25 % of all genes were differentially expressed, while after 40 min only 2 % of all genes showed differential expression, indicative of the transient nature of the heat-shock response. The global transcriptional response was validated by analysing the expression of a set of 13 genes by quantitative PCR. Genes previously identified as part of the class I and class III heat-shock response and the class II stress response showed induction at one or more of the time points investigated. This is believed to be the first study to report that several heat-shock-induced genes are part of the SOS response in L. monocytogenes. Furthermore, numerous differentially expressed genes that have roles in the cell division machinery or cell wall synthesis were down-regulated. This expression pattern is in line with the observation that heat shock results in cell elongation and prevention of cell division.

Listeria monocytogenes is a gram-positive intracellular pathogen responsible for opportunistic infections in humans and animals. Here we identified and characterized the dtpT gene (lmo0555) of L. monocytogenes EGD-e, encoding the di- and tripeptide transporter, and assessed its role in growth under various environmental conditions as well as in the virulence of L. monocytogenes . Uptake of the dipeptide Pro-[ 14 C]Ala was mediated by the DtpT transporter and was abrogated in a Δ dtpT isogenic deletion mutant. The DtpT transporter was shown to be required for growth when the essential amino acids leucine and valine were supplied as peptides. The protective effect of glycine- and proline-containing peptides during growth in defined medium containing 3% NaCl was noted only in L. monocytogenes EGD-e, not in the Δ dtpT mutant strain, indicating that the DtpT transporter is involved in salt stress protection. Infection studies showed that DtpT contributes to pathogenesis in a mouse infection model but has no role in bacterial growth following infection of J774 macrophages. These studies reveal that DptT may contribute to the virulence of L. monocytogenes .

Listeria monocytogenes is a ubiquitous food-borne pathogen found widely distributed in nature as well as an undesirable contaminant in a variety of fresh and processed foods. This ubiquity can be at least partly explained by the ability of the organism to grow at high osmolarity and reduced temperatures, a consequence of its ability to accumulate osmo- and cryoprotective compounds termed osmolytes. Single and multiple deletions of the known osmolyte transporters BetL, Gbu, and OpuC significantly reduce growth at low temperatures. During growth in brain heart infusion broth at 7°C, Gbu and OpuC had a more pronounced role in cryoprotection than did BetL. However, upon the addition of betaine to defined medium, the hierarchy of transporter importance shifted to Gbu > BetL > OpuC. Upon the addition of carnitine, only OpuC appeared to play a role in cryoprotection. Measurements of the accumulated osmolytes showed that betaine is preferred over carnitine, while in the absence of a functional Gbu, carnitine was accumulated to higher levels than betaine was at 7°C. Transcriptional analysis of the genes encoding BetL, Gbu, and OpuC revealed that each transporter is induced to different degrees upon cold shock of L. monocytogenes LO28. Additionally, despite being transcriptionally up-regulated upon cold shock, a putative fourth osmolyte transporter, OpuB (identified by bioinformatic analysis and encoded by lmo1421 and lmo1422 ), showed no significant contribution to listerial chill tolerance. Growth of the quadruple mutant LO28ΔBCGB (Δ betL Δ opuC Δ gbu Δ opuB ) was comparable to the that of the triple mutant LO28ΔBCGsoe (Δ betL Δ opuC Δ gbu ) at low temperatures. Here, we conclude that betaine and carnitine transport upon low-temperature exposure is mediated via three osmolyte transporters, BetL, Gbu, and OpuC.

A spontaneous high hydrostatic pressure (HHP)-tolerant mutant of Listeria monocytogenes ScottA, named AK01, was isolated previously. This mutant was immotile and showed increased resistance to heat, acid and H2O2 compared with the wild type (wt) (Karatzas, K.A.G. and Bennik, M.H.J. 2002 Appl Environ Microbiol 68: 3183-3189). In this study, we conclusively linked the increased HHP and stress tolerance of strain AK01 to a single codon deletion in ctsR (class three stress gene repressor) in a region encoding a highly conserved glycine repeat. CtsR negatively regulates the expression of the clp genes, including clpP, clpE and the clpC operon (encompassing ctsR itself), which belong to the class III heat shock genes. Allelic replacement of the ctsR gene in the wt background with the mutant ctsR gene, designated ctsRDeltaGly, rendered mutants with phenotypes and protein expression profiles identical to those of strain AK01. The expression levels of CtsR, ClpC and ClpP proteins were significantly higher in ctsRDeltaGly mutants than in the wt strain, indicative of the CtsRDeltaGly protein being inactive. Further evidence that the CtsRDeltaGly protein lacks its repressor function came from the finding that the Clp proteins in the mutant were not further induced upon heat shock, and that HHP tolerance of a ctsR deletion strain was as high as that of a ctsRDeltaGly mutant. The high HHP tolerance possibly results from the increased expression of the clp genes in the absence of (active) CtsR repressor. Importantly, the strains expressing CtsRDeltaGly show significantly attenuated virulence compared with the wt strain; however, no indication of disregulation of PrfA in the mutant strains was found. Our data highlight an important regulatory role of the glycine-rich region of CtsR in stress resistance and virulence.

The heat-adaptive response of the psychrotrophic spoilage bacterium Bacillus weihenstephanensis DSM11827 is described. It is demonstrated that vegetative cells of B. weihenstephanensis adapts to heat exposure at 47 degrees C by prior exposure to heat at the nonlethal temperature of 38 degrees C. For this adaptive response, protein synthesis is required and maximum adaptation was noted after 15 min to 2 h prior exposure at 38 degrees C. By using two-dimensional gel electrophoresis (2D-E), an overview of the heat-shock proteins (HSPs) of B. weihenstephanensis was obtained and it was shown that the production of 15 proteins increased upon exposure to 38 degrees C. In more detail, the use of specific antibodies revealed induction of the HSPs DnaK, DnaJ, GroEL, ClpC, ClpP and ClpX of B. weihenstephanensis. In addition, also pre-exposure to other stresses than heat, such as exposure to a high salt concentration, low pH, a high ethanol concentration or low temperature, resulted in development of increased heat tolerance of B. weihenstephanensis, and during these conditions, an increased production of some HSPs was noted. This phenomenon of cross-protection might be of substantial importance in relation to the design of safe minimal processing regimes.

To monitor the ability of the food-borne opportunistic pathogen Bacillus cereus to survive during minimal processing of food products, we determined its heat-adaptive response. During pre-exposure to 42°C, B. cereus ATCC 14579 adapts to heat exposure at the lethal temperature of 50°C (maximum protection occurs after 15 min to 1 h of pre-exposure to 42°C). For this heat-adaptive response, de novo protein synthesis is required. By using two-dimensional gel electrophoresis, we observed 31 heat-induced proteins, and we determined the N-terminal sequences of a subset of these proteins. This revealed induction of stress proteins (CspB, CspE, and SodA), proteins involved in sporulation (SpoVG and AldA), metabolic enzymes (FolD and Dra), identified heat-induced proteins in related organisms (DnaK, GroEL, ClpP, RsbV, HSP16.4, YflT, PpiB, and TrxA), and other proteins (MreB, YloH, and YbbT). The upregulation of several stress proteins was confirmed by using antibodies specific for well-characterized heat shock proteins (HSPs) of B. subtilis . These observations indicate that heat adaptation of B. cereus involves proteins that function in a variety of cellular processes. Notably, a 30-min pre-exposure to 4% ethanol, pH 5, or 2.5% NaCl also results in increased thermotolerance. Also, for these adaptation processes, protein synthesis is required, and indeed, some HSPs are induced under these conditions. Collectively, these data show that during mild processing, cross-protection from heating occurs in pathogenic B. cereus , which may result in increased survival in foods.

The success of Listeria monocytogenes as a food-borne pathogen owes much to its ability to survive a variety of stresses, both in the external environment prior to ingestion and subsequently within the animal host. Growth at high salt concentrations and low temperatures is attributed mainly to the accumulation of organic solutes such as glycine betaine and carnitine. We utilized a novel system for generating chromosomal mutations (based on a lactococcal pWVO1-derived Ori + RepA − vector, pORI19) to identify a listerial OpuC homologue. Mutating the operon in two strains of L. monocytogenes revealed significant strain variation in the observed activity of OpuC. Radiolabeled osmolyte uptake studies, together with growth experiments in defined media, linked OpuC to carnitine and glycine betaine uptake in Listeria . We also investigated the role of OpuC in contributing to the growth and survival of Listeria in an animal (murine) model of infection. Altering OpuC resulted in a significant reduction in the ability of Listeria to colonize the upper small intestine and cause subsequent systemic infection following peroral inoculation.

There is a considerable interest in the cold adaptation of food-related bacteria, including starter cultures for industrial food fermentations, food spoilage bacteria and food-borne pathogens. Mechanisms that permit low-temperature growth involve cellular modifications for maintaining membrane fluidity, the uptake or synthesis of compatible solutes, the maintenance of the structural integrity of macromolecules and macromolecule assemblies, such as ribosomes and other components that affect gene expression. A specific cold response that is shared by nearly all food-related bacteria is the induction of the synthesis so-called cold-shock proteins (CSPs), which are small (7 kDa) proteins that are involved in mRNA folding, protein synthesis and/or freeze protection. In addition, CSPs are able to bind RNA and it is believed that these proteins act as RNA chaperones, thereby reducing the increased secondary folding of RNA at low temperatures. In this review established and novel aspects concerning the structure, function and control of these CSPs are discussed. A model for bacterial cold adaptation, with a central role for ribosomal functioning, and possible mechanisms for low-temperature sensing are discussed.

Low-temperature adaptation and cryoprotection were studied in the thermophilic lactic acid bacterium Streptococcus thermophilus CNRZ302. S. thermophilus actively adapts to freezing during a pretreatment at 20°C, resulting in an approximately 1,000-fold increased survival after four freeze-thaw cycles compared to mid-exponential-phase cells grown at an optimal temperature of 42°C. No adaptation is observed when cells are exposed to a temperature (10°C) below the minimal growth temperature of the strain (just below 15°C). By two-dimensional gel electrophoresis several 7-kDa cold-induced proteins were identified, which are the major induced proteins after a shift to 20°C. These cold shock proteins were maximally expressed at 20°C, while the induction level was low after cold shock to 10°C. To confirm the presence of csp genes in S. thermophilus , a PCR strategy was used which yielded products of different sizes. Sequence analysis revealed csp -like sequences that were up to 95% identical to those of csp genes of S. thermophilus ST1-1, Streptococcus dysgalactiae , Streptococcus pyogenes , and Lactococcus lactis . Northern blot analysis revealed a seven- to ninefold induction of csp mRNA after a temperature shift to 20°C, showing that this thermophilic bacterium indeed contains at least one cold-inducible csp gene and that its regulation takes place at the transcriptional level.

Exogenously provided carnitine (beta-hydroxy-L-tau-N-trimethyl aminobutyrate) was found to stimulate aerobic growth of enterohaemorrhagic Escherichia coli O157:H7 in a medium of inhibitory osmotic strength. Its osmoprotective ability is comparable with that of betaine. As carnitine is an important compound in mammalian tissues, it is suggested that it might play a role in the growth of the pathogen on low water activity (aw) meat products. Using specific uptake mutants of E. coli K-12, it was established that, under osmotic stress, carnitine accumulates in the cytoplasm following import through the ProP and ProU transport systems. Betaine and carnitine also protect E. coli cells while growing anaerobically at inhibitory osmolarity. Under these conditions, an E. coli K-12 strain with lesions in both proP and proU accumulates low levels of L-carnitine but fails to accumulate betaine when these compounds are supplied in the external medium. This is probably a result of uptake of L-carnitine by the secondary transporter CaiT. The caiT gene forms part of the caiTABCDE operon which encodes the carnitine pathway, and is transcribed during anaerobic growth in the presence of carnitine. However, further experiments revealed that the carnitine pathway, including CaiT, does not play a significant role in osmoregulation of E. coli during anaerobiosis. Together, the results indicate that ProP and ProU are the sole transport systems involved in carnitine influx, both in aerobically and anaerobically osmotically stressed E. coli cells.

SUMMARY: A family of genes encoding cold-shock proteins, named cspA, cspB, cspC, cspD and cspE, was cloned and sequenced from Lactococcus lactis MG1363. The genes cspA and cspB and the genes cspC and cspD are located in tandem repeats, an organization of csp genes that has never been encountered before. The five genes encode small (7.1-706 kDa) proteins with high mutual sequence identities (up to 85 O/O) and high identities (about 45-65 %) with the major cold- shock proteins from Escherichia coli (CspA) and Bacillus subtilis (CspB)., Northern-blot analysis revealed single transcripts of about 300 nucleotides for each csp gene and showed that cspA, cspB, cspC and cspD mRNA levels were strongly increased upon cold shock to 10 "C (about lo-, 40-, 10- and 30-fold compared to 30 "C, respectively), whereas the cspE mRNA level was not increased. The expression of the cold-induced csp genes was highest in the. 6-8 h lag phase after cold shock. A differential expression in time, in which cspA and cspC were maximally expressed at 2 h and cspB and cspD at 4 h after cold shock, was observed. The -35 and -10 regions of the five promoters were identified and transcriptional start sites were mapped in each case by primer extension at different temperatures which confirmed that regulation takes place at the transcriptional level. Significant differences were observed between the 5′-untranslated leader regions of the four cold-induced csp genes and the corresponding region of the non-cold-induced cspE gene.

Meteorologisches Institut, KlimaCampus, Universita¨t Hamburg, Hamburg, Germany(Dated: April 23, 2013)An investigation of the distribution of finite time trajectory divergence is performed on an Atmo-spheric Global Circulation Model. The distribution of the largest local Lyapunov exponent showsa significant probability for negative values over time spans up to 10 days. This effect is presentfor resolutions up to wave numbers l = 42 (≈250km). The probability for a negative local largestLyapunov exponent decreases over time, similarly to the predictions of the Fluctuation Theoremfor entropy production. The model used is hydrostatic with variable numbers of vertical levels anddifferent horizontal resolutions.

In this paper we consider the problem of deriving approximate autonomous dynamics for a number of variables of a dynamical system, which are weakly coupled to the remaining variables. In a previous paper we have used the Ruelle response theory on such a weakly coupled system to construct a surrogate dynamics, such that the expectation value of any observable agrees, up to second order in the coupling strength, to its expectation evaluated on the full dynamics. We show here that such surrogate dynamics agree up to second order to an expansion of the Mori-Zwanzig projected dynamics. This implies that the parametrizations of unresolved processes suited for prediction and for the representation of long term statistical properties are closely related, if one takes into account, in addition to the widely adopted stochastic forcing, the often neglected memory effects., 14 pages, 1 figure

We consider two weakly coupled systems and adopt a perturbative approach based on the Ruelle response theory to study their interaction. We propose a systematic way of parameterizing the effect of the coupling as a function of only the variables of a system of interest. Our focus is on describing the impacts of the coupling on the long term statistics rather than on the finite-time behavior. By direct calculation, we find that, at first order, the coupling can be surrogated by adding a deterministic perturbation to the autonomous dynamics of the system of interest. At second order, there are additionally two separate and very different contributions. One is a term taking into account the second-order contributions of the fluctuations in the coupling, which can be parameterized as a stochastic forcing with given spectral properties. The other one is a memory term, coupling the system of interest to its previous history, through the correlations of the second system. If these correlations are known, this effect can be implemented as a perturbation with memory on the single system. In order to treat this case, we present an extension to Ruelle's response theory able to deal with integral operators. We discuss our results in the context of other methods previously proposed for disentangling the dynamics of two coupled systems. We emphasize that our results do not rely on assuming a time scale separation, and, if such a separation exists, can be used equally well to study the statistics of the slow variables and that of the fast variables. By recursively applying the technique proposed here, we can treat the general case of multi-level systems.

We reconsider the theory of the linear response of non-equilibrium steady states to perturbations. We first show that by using a general functional decomposition for space-time dependent forcings, we can define elementary susceptibilities that allow to construct the response of the system to general perturbations. Starting from the definition of SRB measure, we then study the consequence of taking different sampling schemes for analysing the response of the system. We show that only a specific choice of the time horizon for evaluating the response of the system to a general time-dependent perturbation allows to obtain the formula first presented by Ruelle. We also discuss the special case of periodic perturbations, showing that when they are taken into consideration the sampling can be fine-tuned to make the definition of the correct time horizon immaterial. Finally, we discuss the implications of our results in terms of strategies for analyzing the outputs of numerical experiments by providing a critical review of a formula proposed by Reick., 21 pages, 1 figures

A premature neonate, presenting with vomiting, abdominal distention and rectal blood loss, was found to have pneumatosis intestinalis on plain abdominal X-ray. These findings are indicative of necrotizing enterocolitis.

The classical product state capacity of a noisy quantum channel with memory is investigated. A forgetful noise-memory channel is constructed by Markov switching between two depolarizing channels which introduces non-Markovian noise correlations between successive channel uses. The computation of the capacity is reduced to an entropy computation for a function of a Markov process. A reformulation in terms of algebraic measures then enables its calculation. The effects of the hidden-Markovian memory on the capacity are explored. An increase in noise-correlations is found to increase the capacity.

The recent elucidation of many of the biochemical pathways involved in flavour formation in fermented food products has given an impetus to the food and ingredients industry to reshape their strain development programs. In this paper we highlight some of the latest developments and illustrate the prospects for starter culture development by exploitation of the diversity in flavour forming capacity among natural isolates.

The aim of this work was to investigate the behavior of thermophilic esterase EST2 fromAlicyclobacillus acidocaldariusin milk and cheese models. The pure enzyme was used to compare the EST2 hydrolytic activity to the activity of endogenous esterase EstA fromLactococcus lactis. The results indicate that EST2 exhibits 30-fold-higher esterase activity than EstA. As EstA has thioesterase activity, EST2 was assayed for this activity under the optimal conditions determined for EstA (namely, 30°C and pH 7.5). Although it is a thermophilic enzyme, EST2 exhibited eightfold-higher thioesterase activity than EstA withS-methyl thiobutanoate. The abilities of EST2 and EstA to synthesize short-chain fatty acid esters were compared. Two methods were developed to do this. In the first method a spectrophotometric assay was used to monitor the synthesis of esters by the pure enzymes usingp-nitrophenol as the alcohol substrate. The synthetic activities were also evaluated under conditions that mimicked those present in milk and/or cheese. The second method involved evaluation of the synthetic abilities of the enzymes when they were directly added to a model cheese matrix. Substantial ester synthesis by EST2 was observed under both conditions. Finally, esterase and thioesterase activities were evaluated in milk using the purified EST2 enzyme and in the model cheese matrix using a strain ofL. lactisNZ9000 harboring the EST2 gene and thus overproducing EST2. Both the esterase and thioesterase activities measured in milk and in the cheese matrix were much greater than the activities of the controls.

Bacillus cereus is a spore-forming gram-positive rod that is increasingly being recognized as a food-borne pathogen. It may cause illness through the production of a range of virulence factors. The most important virulence factors are a heat-stable emetic toxin, which causes vomiting, and several enterotoxins that cause diarrhea (14, 23). The symptoms of food-borne disease caused by B. cereus are generally mild and self-limiting, but in rare instances they can also be life-threatening, as was shown in 1998 when a food-poisoning outbreak in France, which was attributable to B. cereus, caused the deaths of three persons. The B. cereus strain that caused this outbreak produced a novel cytotoxin, CytK, which caused necrotic enteritis (30). B. cereus can also be the causative agent of other diseases, such as periodontitis, fulminant endophthalmitis, and meningitis in immunocompromised patients (2, 11, 12). Because of the ubiquitous presence of B. cereus in the environment, it can easily contaminate food production or processing systems (23). B. cereus has the potential for multiple adaptive response pathways (20). These pathways may contribute to survival of the cells during food processing and storage and thus may contribute to the importance of B. cereus as a food-borne pathogen. Vegetative cells of B. cereus also play an important role in the pathogenesis of food-borne illness, because they produce the diarrheal enterotoxins in the host small intestine (31). In this situation, B. cereus has to deal with the stresses that it experiences in the gastrointestinal tract. Indeed, for some food-borne pathogens, the ability to mount a stress response is a prerequisite for virulence in the gastrointestinal tract (10). Taxonomically, B. cereus is closely related to Bacillus thuringiensis and Bacillus anthracis. Together with Bacillus weihenstephanensis and Bacillus mycoides, these organisms form the B. cereus group. The members of this group are genotypically so similar that it has been proposed that the members of the B. cereus group should be considered members of the same species (17). However, the phenotypic differences among B. cereus, B. anthracis, and B. thuringiensis are substantial. While B. cereus causes generally mild cases of food-borne illness, B. anthracis is the etiological agent of the often lethal disease anthrax (22). B. thuringiensis, on the other hand, is generally considered a beneficial microorganism; it produces insecticidal toxins and is widely used as a biological control agent to counter insect pests in agriculture (41). Whole-genome sequencing of B. cereus ATCC 14579 (20) and B. anthracis Ames (39) and suppressive subtraction hybridization (38) have revealed some distinct genomic differences that distinguish B. cereus and B. thuringiensis from B. anthracis, but these differences do not seem to explain the phenotypic disparities in the B. cereus group mentioned above. The functional properties that differentiate these organisms are thought to be mostly caused by genes carried on plasmids or, possibly, by altered gene expression among strains (39). Previously, a number of stress-induced proteins of B. cereus were identified by two-dimensional gel electrophoresis. These proteins included RsbV, the antagonist of the anti-sigma factor of σB, which was found to be upregulated during heat shock (33). This strongly suggested that a σB response is triggered during heat shock and potentially also under other stress conditions. σB has been studied extensively in several gram-positive bacteria. This protein is a secondary subunit of RNA polymerase that is known to play an important role in regulating gene expression when there are major changes in the environment. The model organism for study of σB is Bacillus subtilis (see reference 36 for a recent review). sigB null mutants of B. subtilis have decreased resistance to heat, acid, ethanol, salt, and oxidative stress (35). Similar effects have also been described for sigB null mutants of the human pathogens Listeria monocytogenes and Staphylococcus aureus (1, 5, 7, 8). The regulatory network leading to expression of σB in B. subtilis has been extensively studied for a number of years. Two differentially regulated pathways lead to activation of σB in B. subtilis. The first pathway is induced under environmental stress conditions (like ethanol exposure and osmotic shock), and the second pathway is induced by a decrease in the level of intracellular ATP (36, 48). The regulatory network leading to σB activation and repression functions by a so-called partner switching mechanism. In this system, interactions between the anti-sigma factor of σB (RsbW) and the anti-sigma factor antagonist (RsbV) and more regulators further upstream in the regulatory cascade are controlled by serine phosphorylation and dephosphorylation. This leads to the formation or dissociation of protein-protein complexes, which can finally lead to the release of σB from an RsbW-σB complex (35). More than 200 general stress response genes are under the control of σB in B. subtilis, and these genes encode proteins with a wide variety of cellular functions (19, 34, 37). In B. anthracis the alternative sigma factor σB was shown to be a minor virulence factor and to be activated during the stationary growth phase and after a heat shock (9). In this paper, we describe the sigB operon of B. cereus ATCC 14579 and a predicted novel regulator of σB activity (RsbY), which is located directly downstream of the sigB operon. σB was activated under several stress conditions, particularly during heat shock but also during other stresses, such as osmotic upshock and ethanol exposure. No correlation between intracellular ATP levels and σB activation was found, indicating that σB activation is not triggered by energy depletion. We mapped two σB-dependent promoters in the σB operon, which revealed the transcriptional organization of the σB operon in B. cereus. Finally, a sigB null mutant exhibited impaired survival at 50°C after preadaptation to 42°C compared to the survival of the parent strain. This indicates that σB plays a role in the adaptive response of B. cereus during heat stress.

The gene encoding the alternative sigma factor σ B in Listeria monocytogenes is induced upon exposure of cells to several stresses. In this study, we investigated the impact of a sigB null mutation on the survival of L. monocytogenes EGD-e at low pH, during high-hydrostatic-pressure treatment, and during freezing. The survival of Δ sigB mutant exponential-phase cells at pH 2.5 was 10,000-fold lower than the survival of EGD-e wild-type cells. Moreover, the Δ sigB mutant failed to show an acid tolerance response. Upon preexposure for 1 h to pH 4.5, the survival at pH 2.5 was 100,000-fold lower for the Δ sigB mutant than for the wild type. The glutamate decarboxylase (GAD) acid resistance system is important in survival and adaptation of L. monocytogenes in acidic conditions. The σ B dependence of the gad genes ( gadA , gadB , gadC , gadD , and gadE ) was analyzed in silico. Putative σ B -dependent promoter sites were found upstream of the gadCB operon (encoding a glutamate/γ-aminobutyrate antiporter and a glutamate decarboxylase, respectively) and the lmo2434 gene ( gadD , encoding a putative glutamate decarboxylase). Reverse transcriptase PCR revealed that expression of the gadCB operon and expression of gadD are indeed σ B dependent. In addition, a proteomics approach was used to analyze the protein expression profiles upon acid exposure. Although the GAD proteins were not recovered, nine proteins accumulated in the wild type but not in the Δ sigB strain. These proteins included Pfk, GalE, ClpP, and Lmo1580. Exposure to pH 4.5, in order to preload cells with active σ B and consequently with σ B -dependent general stress proteins, also provided considerable protection against high-hydrostatic-pressure treatment and freezing. The combined data argue that the expression of σ B -dependent genes provides L. monocytogenes with nonspecific multiple-stress resistance that may be relevant for survival in the natural environment as well as during food processing.

Listeria monocytogenes is a gram-positive food-borne pathogen that is highly resistant to osmotic stress (NaCl concentrations of up to 10%) and can grow at refrigeration temperatures (31). This characteristic growth and survival under such adverse environmental conditions is attributed mainly to the accumulation of the organic compounds glycine betaine (N,N,N-trimethylglycine) (16, 18) and carnitine (β-hydroxy-γ-N-trimethylaminobutyrate) (3). Accumulated to high internal concentrations without adversely affecting vital cellular processes, these compounds are often referred to as compatible solutes (32). In general, compatible solutes are small, highly soluble molecules which carry no net charge at physiological pH and function to stabilize protein structure and function while also maintaining cell volume at elevated osmolarity (14, 27). As well as glycine betaine and carnitine, other compounds, such as sugars, amino acids, amino acid derivatives, sulfate esters, and small peptides, have been shown to function as effective compatible solutes in bacterial cells (14). For L. monocytogenes cells grown in complex media with 7.5% added NaCl, increases in glycine betaine and carnitine levels were accompanied by elevated concentrations of potassium, glutamate, glycine, alanine, and proline (18). However, while proline at extracellular concentrations of

Listeria monocytogenes is a psychrotrophic food-borne pathogen that is problematic for the food industry because of its ubiquitous distribution in nature and its ability to grow at low temperatures and in the presence of high salt concentrations. Here we demonstrate that the process of adaptation to low temperature after cold shock includes elevated levels of cold shock proteins (CSPs) and that the levels of CSPs are also elevated after treatment with high hydrostatic pressure (HHP). Two-dimensional gel electrophoresis combined with Western blotting performed with anti-CspB of Bacillus subtilis was used to identify four 7-kDa proteins, designated Csp1, Csp2, Csp3, and Csp4. In addition, Southern blotting revealed four chromosomal DNA fragments that reacted with a csp probe, which also indicated that a CSP family is present in L. monocytogenes LO28. After a cold shock in which the temperature was decreased from 37°C to 10°C the levels of Csp1 and Csp3 increased 10- and 3.5-fold, respectively, but the levels of Csp2 and Csp4 were not elevated. Pressurization of L. monocytogenes LO28 cells resulted in 3.5- and 2-fold increases in the levels of Csp1 and Csp2, respectively. Strikingly, the level of survival after pressurization of cold-shocked cells was 100-fold higher than that of cells growing exponentially at 37°C. These findings imply that cold-shocked cells are protected from HHP treatment, which may affect the efficiency of combined preservation techniques.

Members of the group of 7-kDa cold-shock proteins (CSPs) are the proteins with the highest level of induction upon cold shock in the lactic acid bacterium Lactococcus lactis MG1363. By using double-crossover recombination, two L. lactis strains were generated in which genes encoding CSPs are disrupted: L. lactis NZ9000ΔAB lacks the tandemly orientated cspA and cspB genes, and NZ9000ΔABE lacks cspA, cspB , and cspE . Both strains showed no differences in growth at normal and at low temperatures compared to that of the wild-type strain, L. lactis NZ9000. Two-dimensional gel electrophoresis showed that upon disruption of the cspAB genes, the production of remaining CspE at low temperature increased, and upon disruption of cspA, cspB , and cspE , the production of CspD at normal growth temperatures increased. Northern blot analysis showed that control is most likely at the transcriptional level. Furthermore, it was established by a proteomics approach that some (non-7-kDa) cold-induced proteins (CIPs) are not cold induced in the csp -lacking strains, among others the histon-like protein HslA and the signal transduction protein LlrC. This supports earlier observations (J. A. Wouters, M. Mailhes, F. M. Rombouts, W. M. De Vos, O. P. Kuipers, and T. Abee, Appl. Environ. Microbiol. 66:3756–3763, 2000). that the CSPs of L. lactis might be directly involved in the production of some CIPs upon low-temperature exposure. Remarkably, the adaptive response to freezing by prior exposure to 10°C was significantly reduced in strain NZ9000ΔABE but not in strain NZ9000ΔAB compared to results with wild-type strain NZ9000, indicating a notable involvement of CspE in cryoprotection.

The physiological and regulatory effects of overproduction of five cold shock proteins (CSPs) of Lactococcus lactis were studied. CspB, CspD, and CspE could be overproduced at high levels (up to 19% of the total protein), whereas for CspA and CspC limited overproduction (0.3 to 0.5% of the total protein) was obtained. Northern blot analysis revealed low abundance of the cspC transcript, indicating that the stability of cspC mRNA is low. The limited overproduction of CspA is likely to be caused by low stability of CspA since when there was an Arg-Pro mutation at position 58, the level of CspA production increased. Using two-dimensional gel electrophoresis, it was found that upon overproduction of the CSPs several proteins, including a number of cold-induced proteins of L. lactis , were induced. Strikingly, upon overproduction of CspC induction of CspB, putative CspF, and putative CspG was also observed. Overproduction of CspB and overproduction of CspE result in increased survival when L. lactis is frozen (maximum increases, 10- and 5-fold, respectively, after 4 freeze-thaw cycles). It is concluded that in L. lactis CSPs play a regulatory role in the cascade of events that are initiated by cold shock treatment and that they either have a direct protective effect during freezing (e.g., RNA stabilization) or induce other factors involved in the freeze-adaptive response or both.

The behavior of Campylobacter jejuni at environmental temperatures was examined by determining the physiological activities of this human pathogen. The minimal growth temperatures were found to be 32 and 31°C for strains 104 and ATCC 33560, respectively. Both strains exhibited a sudden decrease in growth rate from the maximum to zero within a few degrees not only near the maximal growth temperature but also near the minimal growth temperature. This could be an indication that a temperature-dependent transition in the structure of a key enzyme(s) or regulatory compound(s) determines the minimal growth temperature. Oxygen consumption, catalase activity, ATP generation, and protein synthesis were observed at temperatures as low as 4°C, indicating that vital cellular processes were still functioning. PCR analysis showed that cold shock protein genes, which play a role in low-temperature adaptation in many bacteria, are not present in C. jejuni . The fact that chemotaxis and aerotaxis could be observed at all temperatures shows that the pathogen is able to move to favorable places at environmental temperatures, which may have significant implications for the survival of C. jejuni in the environment.

We study correlations in a bipartite, Fermionic, free state in terms of perturbations induced by one party on the other. In particular, we show that all so conditioned free states can be modelled by an auxiliary Fermionic system and a suitable completely positive map., 17 pages, no figures

Low-temperature adaptation and cryoprotection were studied in the lactic acid bacterium Lactococcus lactis MG1363. An approximately 100-fold increased survival after freezing was observed when cells were shocked to 10 degrees C for 4 h compared to mid-exponential-phase cells grown at 30 degrees C, indicating an active protection against freezing. Using two-dimensional gel electrophoresis a group of 7 kDa cold-induced proteins (CSPs) was identified that corresponds to a previously described family of csp genes of L. lactis MG1363 (Wouters et al., 1998, Microbiology 144, 2885-2893). The 7 kDa CSPs appeared to be the most strongly induced proteins upon cold shock to 10 degrees C. Northern blotting and two-dimensional gel electrophoresis showed that the csp genes were maximally expressed at 10 degrees C, while induction was lower at 20 and 4 degrees C. However, pre-incubation at 20 and 4 degrees C, as well as stationary-phase conditions, also induced cryoprotection (approx. 30-, 130- and 20-fold, respectively, compared to 30 degrees C mid-exponential phase). For all treatments leading to an increased freeze survival (exposure to 4, 10 and 20 degrees C and stationary-phase conditions), increased levels of three proteins (26, 43 and 45 kDa) were observed for which a role in cryoprotection might be suggested. Increased freeze survival coincides with increased CSP expression, except for stationary-phase conditions. However, the level of observed freeze protection does not directly correlate with the csp gene expression levels. In addition, for the first time specific overproduction of a CSP in relation to freeze survival was studied. This revealed that L. lactis cells overproducing CspD at 30 degrees C show a 2-10-fold increased survival after freezing compared to control cells. This indicates that the 7 kDa cold-shock protein CspD may enhance the survival capacity after freezing but that other factors supply additional cryoprotection.

The climate system is a complex, chaotic system with many degrees of freedom and variability on a vast range of temporal and spatial scales. Attaining a deeper level of understanding of its dynamical processes is a scientific challenge of great urgency, especially given the ongoing climate change and the evolving climate crisis. In statistical physics, complex, many-particle systems are studied successfully using the mathematical framework of Large Deviation Theory (LDT). A great potential exists for applying LDT to problems relevant for geophysical fluid dynamics and climate science. In particular, LDT allows for understanding the fundamental properties of persistent deviations of climatic fields from the long-term averages and for associating them to low-frequency, large scale patterns of climatic variability. Additionally, LDT can be used in conjunction with so-called rare events algorithms to explore rarely visited regions of the phase space and thus to study special dynamical configurations of the climate. These applications are of key importance to improve our understanding of high-impact weather and climate events. Furthermore, LDT provides powerful tools for evaluating the probability of noise-induced transitions between competing metastable states of the climate system or of its components. This in turn essential for improving our understanding of the global stability properties of the climate system and of its predictability of the second kind in the sense of Lorenz. The goal of this review is manifold. First, we want to provide an introduction to the derivation of large deviation laws in the context of stochastic processes. We then relate such results to the existing literature showing the current status of applications of LDT in climate science and geophysical fluid dynamics. Finally, we propose some possible lines of future investigations., 72 pages, 17 figures, Riv. Nuovo Cim. (2021)