Data assimilation for state and parameter estimation: application to morphodynamic modelling

Data assimilation is predominantly used for state estimation; combining observational data with model predictions to produce an updated model state that most accurately approximates the true system state whilst keeping the model parameters fixed. This updated model state is then used to initiate the next model forecast. Even with perfect initial data, inaccurate model parameters will lead to the growth of prediction errors. To generate reliable forecasts we need good estimates of both the current system state and the model parameters. This paper presents research into data assimilation methods for morphodynamic model state and parameter estimation. First, we focus on state estimation and describe implementation of a three dimensional variational(3D-Var) data assimilation scheme in a simple 2D morphodynamic model of Morecambe Bay, UK. The assimilation of observations of bathymetry derived from SAR satellite imagery and a ship-borne survey is shown to significantly improve the predictive capability of the model over a 2 year run. Here, the model parameters are set by manual calibration; this is laborious and is found to produce different parameter values depending on the type and coverage of the validation dataset. The second part of this paper considers the problem of model parameter estimation in more detail. We explain how, by employing the technique of state augmentation, it is possible to use data assimilation to estimate uncertain model parameters concurrently with the model state. This approach removes inefficiencies associated with manual calibration and enables more effective use of observational data. We outline the development of a novel hybrid sequential 3D-Var data assimilation algorithm for joint state-parameter estimation and demonstrate its efficacy using an idealised 1D sediment transport model. The results of this study are extremely positive and suggest that there is great potential for the use of data assimilation-based state-parameter estimation in coastal morphodynamic modelling.

Role of NleH, a Type III Secreted Effector from Attaching and Effacing Pathogens, in Colonization of the Bovine, Ovine, and Murine Gut

The human pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7 colonizes human and animal gut via formation of attaching and effacing lesions. EHEC strains use a type III secretion system to translocate a battery of effector proteins into the mammalian host cell, which subvert diverse signal transduction pathways implicated in actin dynamics, phagocytosis, and innate immunity. The genomes of sequenced EHEC O157: H7 strains contain two copies of the effector protein gene nleH, which share 49% sequence similarity with the gene for the Shigella effector OspG, recently implicated in inhibition of migration of the transcriptional regulator NF-kappa B to the nucleus. In this study we investigated the role of NleH during EHEC O157: H7 infection of calves and lambs. We found that while EHEC Delta nleH colonized the bovine gut more efficiently than the wild-type strain, in lambs the wild-type strain exhibited a competitive advantage over the mutant during mixed infection. Using the mouse pathogen Citrobacter rodentium, which shares many virulence factors with EHEC O157: H7, including NleH, we observed that the wild-type strain exhibited a competitive advantage over the mutant during mixed infection. We found no measurable differences in T-cell infiltration or hyperplasia in colons of mice inoculated with the wild-type or the nleH mutant strain. Using NF-kappa B reporter mice carrying a transgene containing a luciferase reporter driven by three NF-kappa B response elements, we found that NleH causes an increase in NF-kappa B activity in the colonic mucosa. Consistent with this, we found that the nleH mutant triggered a significantly lower tumor necrosis factor alpha response than the wild-type strain.

Ensemble forecasts of a flood-producing storm: comparison of the influence of model-state perturbations and parameter modifications

High-resolution ensemble simulations (Δx = 1 km) are performed with the Met Office Unified Model for the Boscastle (Cornwall, UK) flash-flooding event of 16 August 2004. Forecast uncertainties arising from imperfections in the forecast model are analysed by comparing the simulation results produced by two types of perturbation strategy. Motivated by the meteorology of the event, one type of perturbation alters relevant physics choices or parameter settings in the model's parametrization schemes. The other type of perturbation is designed to account for representativity error in the boundary-layer parametrization. It makes direct changes to the model state and provides a lower bound against which to judge the spread produced by other uncertainties. The Boscastle has genuine skill at scales of approximately 60 km and an ensemble spread which can be estimated to within ∼ 10% with only eight members. Differences between the model-state perturbation and physics modification strategies are discussed, the former being more important for triggering and the latter for subsequent cell development, including the average internal structure of convective cells. Despite such differences, the spread in rainfall evaluated at skilful scales is shown to be only weakly sensitive to the perturbation strategy. This suggests that relatively simple strategies for treating model uncertainty may be sufficient for practical, convective-scale ensemble forecasting.

Political economy of state-building: power after peace

The purpose of this volume is to examine and evaluate the impact of international state-building interventions on the political economy of post-conflict countries over the last 20 years. It analyses how international interventions have shaped political and economic dynamics and structures – both formal and informal – and what kind of state, and what kind of state-society relations have been created as a result, through three different lenses: first, through the approaches taken by different international actors like the UN, the International Financial Institutions, or the European Union, to state-building; second, through detailed analysis of key state-building policies; and third, through a wide range of country case studies. Amongst the recurring themes that are highlighted by the book’s focus on the political economy of state-building, and that help to explain why international state-building interventions have tended to fall short of the visions of interveners and local populations alike are evidence of important continuities between war-time and “post-conflict” economies and authority structures, which are often consolidated as a consequence of international involvement; tensions arising from what are often the competing interests and values held by different interveners and local actors; and, finally, the continuing salience of economic and political violence in state-building processes and war-to-peace transitions. The book aims to offer a more nuanced understanding of the complex impact of state-building practices on post-conflict societies, and of the political economy of post-conflict state-building.

Mutation of toxB and a truncated version of the efa-1 gene in Escherichia coli O157 : H7 influences the expression and secretion of locus of enterocyte effacement-encoded proteins but not intestinal colonization in calves or sheep

Enterohemorrhagic Escherichia coli (EHEC) strains comprise a broad group of bacteria, some of which cause attaching and effacing (AE) lesions and enteritis in humans and animals. Non-O157:H7 EHEC strains contain the gene efa-1 (referred to in previous publications as efa1), which influences adherence to cultured epithelial cells. An almost identical gene in enteropathogenic E. coli (lifA) mediates the inhibition of lymphocyte proliferation and proinflammatory cytokine synthesis. We have shown previously that significantly lower numbers of EHEC 05 and 0111 efa-1 mutants are shed in feces following experimental infection in calves and that these mutants exhibit reduced adherence to intestinal epithelia compared with isogenic wild-type strains. E. coli O157:H7 strains lack efa-1 but encode a homolog on the pO157 plasmid (toxB/l7095) and contain a truncated version of the efa-1 gene (efa-1'/z4332 in O island 122 of the EDL933 chromosome). Here we report that E. coli O157:H7 toxB and efa-1' single and double mutants exhibit reduced adherence to cultured epithelial cells and show reduced expression and secretion of proteins encoded by the locus of enterocyte effacement (LEE), which plays a key role in the host-cell interactions of EHEC. The activity of LEE1, LEE4, and LEE5 promoters was not significantly altered in E. coli O157:H7 strains harboring toxB or efa-1' mutations, indicating that the effect on the expression of LEE-encoded secreted proteins occurs at a posttranscriptional level. Despite affecting type III secretion, mutation of toxB and efa-1' did not significantly affect the course of fecal shedding of E. coli O157:H7 following experimental inoculation of 10- to 14-day-old calves or 6-week-old sheep. Mutation of tir caused a significant reduction in fecal shedding of E. coli O157:H7 in calves, indicating that the formation of AE lesions is important for colonization of the bovine intestine.

Colonization of 8-week-old conventionally reared goats by Escherichia coli O157:H7 after oral inoculation

Enterohaemorrhagic Escherichia coli O157 : H7 infections of man have been associated with consumption of unpasteurized goat's milk and direct contact with kid goats on petting farms, yet little is known about colonization of goats with this organism. To assess the contribution of flagella and intimin of E coli O157 : H7 in colonization of the goat, 8-week-old conventionally reared goats were inoculated orally in separate experiments with 1 X 10(10) c.f.u. of a non-verotoxigenic strain of E coli O157: H7 (strain NCTC 12900 Nal(r)), an aflagellate derivative (DMB1) and an intimin-deficient derivative (DMB2). At 24 In after inoculation, the three E coli O157 : H7 strains were shed at approximately 5 X 1 04 c.f.u. (g faeces)(-1) from all animals. Significantly fewer intimin-deficient bacteria were shed only on days 2 (P = 0(.)003) and 4 (P = 0(.)014), whereas from day 7 to 29 there were no differences. Tissues from three animals inoculated with wild-type E coli O157 : H7 strain NCTC 12900 Nalr were sampled at 24,48 and 96 In after inoculation and the organism was cultured from the large intestine of all three animals and from the duodenum and ileum of the animal examined at 96 h. Tissues were examined histologically but attaching-effacing (AE) lesions were not observed at any intestinal site of the animals examined at 24 or 48 In. However, the animal examined at 96 h, which had uniquely shed approximately 1 x 10(7) E coli O157: H7 (g faeces)(-1) for the preceding 3 days, showed a heavy, diffuse infection with cryptosporidia. and abundant, multifocal AE lesions in the distal colon, rectum and at the recto-anal junction. These AE lesions were confirmed by immunohistochemistry to be associated with E coli O157: H7.

Influence of colostrum deprivation and concurrent Cryptosporidium parvum infection on the colonization and persistence of Escherichia coli O157:H7 in young lambs

Escherichia coli O157: H7 and Cryptosporidium parvum infections of man have been associated with direct contact with small ruminants. Colostrum protects neonates against gastrointestinal pathogens, and orphan lambs, which are common on petting farms, may be deprived of this protection. In a recent study, it was demonstrated that high shedding of E coli O157 : H7 by an 8-week-old goat kid was associated with coincidental C. parvum infection. Furthermore, both pathogens were co-located in the distal gastrointestinal tract. It was hypothesized that colostrum deprivation and pre-infection with C. parvum predisposed young ruminants to colonization and increased shedding of E coli O157: H7. To test this, 21 lambs 5 weeks of age were divided into four groups as follows: (A) colostrum-deprived and inoculated with E coli O157: H7, (B) colostrum-deprived and inoculated with C. parvum and then E coli O157: H7, (C) conventionally reared and inoculated with E coli O157: H7, (D) conventionally reared and inoculated with C. parvum and then E coli O15 7: H7. C. parvum was detected between 8 and 12 days post-inoculation in most of the infected lambs. At 24 h post-inoculation with E coli O157: H7, all lambs were shedding between 5 x 10(4) and 5 x 10(7) c.f.u. E coli O157: H7 per gram of faeces. E coli O157: H7 was shed in higher numbers in the groups pre-inoculated with C. parvum, whether conventionally reared or colostrum-deprived. Interestingly, for the colostrum-deprived lambs on day 3, a significant difference in shedding of E coli O157: H7 was observed (P= 0-038), with the lambs inoculated with E coli alone yielding higher counts than those pre-inoculated with C. parvum. From day 15 onwards, shedding of E coli O157: H7 was highest from the colostrum-deprived C. parvum-infected lambs, then (in descending order of shedding) the colostrum-deprived lambs, the conventionally reared lambs infected with C. parvum, and the conventionally reared animals. In total, four animals were euthanized, two at 24 h and two at 96 h post inoculation with E coli 0 157: H7 (two conventionally reared and two colostrum-deprived). All animals euthanized were from groups pre-inoculated with C. parvum prior to challenge with E coli O157 : H7. On examination of tissues, in three of the four animals examined, multifocal attaching and effacing lesions were observed in the caecum, colon, rectum and at the recto-anal junction, and were confirmed by immunolhistochemistry to be associated with E coli O157: H7.

Role of intimin-Tir interactions and the Tir-cytoskeleton coupling protein in the colonization of calves and lambs by Escherichia coli O157:H7

Intimin facilitates intestinal colonization by enterohemorrhagic Escherichia coli O157:H7; however, the importance of intimin binding to its translocated receptor (Tir) as opposed to cellular coreceptors is unknown. The intimin-Tir interaction is needed for optimal actin assembly under adherent bacteria in vitro, a process which requires the Tir-cytoskeleton coupling protein (TccP/EspF(U)) in E. coli O157:H7. Here we report that E. coli O157:H7 tir mutants are at least as attenuated as isogenic eae mutants in calves and lambs, implying that the role of intimin in the colonization of reservoir hosts can be explained largely by its binding to Tir. Mutation of tccP uncoupled actin assembly from the intimin-Tir-mediated adherence of E. coli O157:H7 in vitro but did not impair intestinal colonization in calves and lambs, implying that pedestal formation may not be necessary for persistence. However, an E. coli O157:H7 tccP mutant induced typical attaching and effacing lesions in a bovine ligated ileal loop model of infection, suggesting that TccP-independent mechanisms of actin assembly may operate in vivo.

Colonization, persistence, and tissue tropism of Escherichia coli O26 in conventionally reared weaned lambs

Escherichia coli O26 is recognized as an emerging pathogen associated with disease in both ruminants and humans. Compared to those of E. coli O157:117, the shedding pattern and location of E. coli O26 in the gastrointestinal tract (GIT) of ruminants are poorly understood. In the studies reported here, an stx-negative E. coli O26 strain of ovine origin was inoculated orally into 6-week-old lambs and the shedding pattern of the O26 strain was monitored by serial bacteriological examination of feces. The location of colonization in the GIT was examined at necropsy at two time points. The numbers of O26 organisms excreted in feces declined from approximately 10(7) to 10(4) CFU per gram of feces by day 7 and continued at this level for a further 3 weeks. Beyond day 30, excretion was from few animals, intermittent, and just above the detection limit. By day 38, all fecal samples were negative, but at necropsy, O26 organisms were recovered from the upper GIT, specifically the ileum. However, no attaching-effacing (AE) lesions were observed. To identify the location of E. coli O26 within the GIT early after inoculation, two lambs were examined postmortem, 4 days postinoculation. High numbers of O26 organisms were recovered from all GIT sites examined, and similar to 10(9) CFU were recovered from 1 gram of ileal tissue from one animal. Despite high numbers of O26 organisms, AE lesions were identified on the mucosa of the ascending colon of only one animal. These data indicate that E. coli O26 readily colonizes 6-week-old lambs, but the sparseness of AE lesions suggests that O26 is well adapted to this host, and mechanisms other than those dependent upon intimin may play a role in persistence.

Structural and magnetic studies of Schiff base complexes of nickel(ii) nitrite: change in crystalline state, ligand rearrangement and a very rare μ-nitrito-1κO:2κN:3κO′ bridging mode

Four new nickel(II) complexes, [Ni2L2(NO2)2]·CH2Cl2·C2H5OH, 2H2O (1), [Ni2L2(DMF)2(m-NO2)]ClO4·DMF (2a), [Ni2L2(DMF)2(m-NO2)]ClO4 (2b) and [Ni3L¢2(m3-NO2)2(CH2Cl2)]n·1.5H2O (3) where HL = 2-[(3-amino-propylimino)-methyl]-phenol, H2L¢ = 2-({3-[(2-hydroxy-benzylidene)-amino]-propylimino}-methyl)-phenol and DMF = N,N-dimethylformamide, have been synthesized starting with the precursor complex [NiL2]·2H2O, nickel(II) perchlorate and sodium nitrite and characterized structurally and magnetically. The structural analyses reveal that in all the complexes, NiII ions possess a distorted octahedral geometry. Complex 1 is a dinuclear di-m2-phenoxo bridged species in which nitrite ion acts as chelating co-ligand. Complexes 2a and 2b also consist of dinuclear entities, but in these two compounds a cis-(m-nitrito-1kO:2kN) bridge is present in addition to the di-m2-phenoxo bridge. The molecular structures of 2a and 2b are equivalent; they differ only in that 2a contains an additional solvated DMF molecule. Complex 3 is formed by ligand rearrangement and is a one-dimensional polymer in which double phenoxo as well as m-nitrito-1kO:2kN bridged trinuclear units are linked through a very rare m3-nitrito-1kO:2kN:3kO¢ bridge. Analysis of variable-temperature magnetic susceptibility data indicates that there is a global weak antiferromagnetic interaction between the nickel(II) ions in four complexes, with exchange parameters J of -5.26, -11.45, -10.66 and -5.99 cm-1 for 1, 2a, 2b and 3, respectively

Resting state cortico-thalamic-striatal connectivity predicts pesponse to dorsomedial prefrontal rTMS in major depressive disorder

Despite its high toll on society, there has been little recent improvement in treatment efficacy for Major Depressive Disorder (MDD). The identification of biological markers of successful treatment response may allow for more personalized and effective treatment. Here we investigate whether resting state functional connectivity predicted response to treatment with rapid transcranial magnetic stimulation (rTMS) to dorsomedial prefrontal cortex (dmPFC). Twenty five individuals with treatment-refractory MDD underwent a 4-week course of dmPFC-rTMS. Before and after treatment, subjects received resting state functional MRI scans and assessments of depressive symptoms using the Hamilton Depresssion Rating Scale (HAMD17). We found that higher baseline cortico-cortical connectivity (dmPFC-subgenual cingulate and subgenual cingulate to dorsolateral PFC) and lower cortico-thalamic, cortico-striatal and cortico-limbic connectivity were associated with better treatment outcomes. We also investigated how changes in connectivity over the course of treatment related to improvements in HAMD17 scores. We found that successful treatment was associated with increased dmPFC-thalamic connectivity and decreased sgACC-caudate connectivity, Our findings provide insight into which individuals might respond to rTMS treatment and the mechanisms through which these treatments work.

Corporate institutions in a weakened welfare state: a Rawlsian perspective

This paper re-examines the import of Rawls’s theory of justice for private sector institutions in the face of the decline of the welfare state. The argument is based on a Rawlsian conception of justice as the establishment of a basic structure of society that guarantees a fair distribution of primary goods. We propose that the decline of the welfare state witnessed in Western countries over the past forty years prompts a reassessment of the boundaries of the basic structure in order to include additional corporate institutions. A discussion centered on the primary good of self-respect, but extensible to power and prerogatives as well as income and wealth, examines how the legislator should intervene in private sector institutions to counterbalance any unfairness that results from the decline of the welfare state.