Developments in linear and integer programming

In this review we describe recent developments in linear and integer (linear) programming. For over 50 years Operational Research practitioners have made use of linear optimisation models to aid decision making and over this period the size of problems that can be solved has increased dramatically, the time required to solve problems has decreased substantially and the flexibility of modelling and solving systems has increased steadily. Large models are no longer confined to large computers, and the flexibility of optimisation systems embedded in other decision support tools has made on-line decision making using linear programming a reality (and using integer programming a possibility). The review focuses on recent developments in algorithms, software and applications and investigates some connections between linear optimisation and other technologies

Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont “Candidatus Erwinia dacicola”. Ca. E. dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genomes and one transcriptome assembly. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interactions with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes involved in urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis

On the generation and propagation of Rossby waves in an ocean with a zonally shoaling mixed layer

This paper presents the theory for freely propagating and forced Rossby waves in a continuously stratified ocean where the bouyancy frequency, N, varies with longitude and depth. In this study zonal variations in N occur because the climatological mixed layer depth, h, varies with longitude.With the assumption that changes in h occur on a length scale which is large compared to a horizontal wavelength the free modes on a β-plane are examined. It is found that realistic mixed layer depth changes can cause amplitude modulations, the largest amplitudes occurring where the mixed layer is shallowest. The requirement that h variations occur slowly is removed by employing a numerical model to study the free modes in a continuously stratified meridional channel. A criterion, based on the ratio of a horizontal length scale associated with the wave packet and the internal Rossby radius, is derived for determining when a free mode may be affected by the zonal variations in the stratification. Using climatological mixed layer depth data at 35N in the Atlantic (taken from Lamb, 1984) the basin modes are numerically determined. The major response is now concentrated where the mixed layer is deepest. This apparent contradiction is explained. A general theory is presented for calculating the forced basin mode response in terms of the free modes. As an example, a wind stress curl is applied as a body force over the mixed layer for a finite duration. After the forcing is removed the percentage that each basin mode contributes to the total solution is calculated. It is found that the dominant response to wind stress curl forcing can be significantly affected by the presence of a variable depth mixed layer. The implication of this study for the interaction between baroclinic Rossby waves and mixed layer dynamics is discussed

Mechanics of failure in FRP strengthened reinforced concrete in shear

Carbon fibre reinforced polymer (CFRP) composite sheets and bars were used to strengthen reinforced concrete across a known plane to resist shear friction. The uncracked push-off specimens were either externally reinforced with CFRP sheets with a reinforcement ratio of 0.8% and 1.6% or internally with CFRP bars as additional shear reinforcement corresponding to 0.8% reinforcement ratio. Two ratios of internal steel reinforcement were considered representing the nominal stirrup reinforcement according to both historic (0.17%) and current design codes (0.26%). The effects of varying anchorage length of the CFRP on the shear friction capacity of the push-off specimens with externally bonded reinforcement (EBR) were studied through various strengthening schemes. Experimental results showed an increase in shear strength ranging from 23 – 84% compared to the unstrengthened control specimens. Tests with various wrapping schemes showed no evidence that additional shear friction capacity can be developed when beyond a sufficient anchorage length. However, specimens with short anchorage length failed prematurely due to the early debonding of the CFRP. The shear friction strength of the initially uncracked push- off specimens was determined using experimental results combining the shear friction contribution of the individual structural components, extending the currently accepted approach for internal steel reinforcement

Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches

Concrete structures using fabric formwork

Using fabric formwork, it is possible to cast architecturally interesting, optimised structures that use up to 40% less concrete than an equivalent strength prismatic section, thereby offering the potential for significant embodied energy savings in new concrete structures. This paper reports on the philosophy of and background to fabric formwork before techniques for the design, optimisation and shape prediction of fabric formed concrete beams are presented. The practicality of construction with non-orthogonal elements is discussed before the results of new structural test data, undertaken at the University of Bath on 4m span 'T' beam elements formed in reusable fabric moulds, are presented. Potential areas of future development for fabric formwork, including the use of woven advanced composite fabrics as permanent participating formwork and the feasibility of uniform strength prestressed beams, are then discussed The practicality of construction with non-orthogonal elements is discussed before the results of new structural test data, undertaken at the University of Bath on 4m span ‘T’ beam elements formed in reusable fabric moulds, are presented. Potential areas of future development for fabric formwork, including the use of woven advanced composite fabrics as permanent participating formwork and the feasibility of uniform strength prestressed beams, are then discussed

Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli

peer-reviewedLactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate) and ATCC27782 (bovine isolate), but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to PWOT. BAN was the recipient of an Embark studentship from the Irish Research Council for Science Engineering and Technology. TD and KN were supported by the Alimentary Pharmabiotic Centre, funded by Science Foundation Ireland

Serviceability of non-prismatic concrete beams: Combined-interaction method

Interest in the shape optimisation of concrete members is increasing alongside the availability of fabric formwork as a relatively simple technique to cast non-prismatic concrete structures. Research has shown that up 40% of concrete can be saved when shape optimised concrete beams are cast in fabric forms. However, optimisation results in members with non-uniform cross-sections and the resulting beam is less stiff than an equivalent strength prismatic beam. Serviceability, rather than strength, may govern the design of such members and therefore understanding the serviceability behaviour (deflection and cracking) of shape optimised concrete members becomes is a critical design consideration. There are many methods which can be used to evaluate serviceability behaviour of reinforced concrete beams, including the full-interaction method, which assumes no slip between the reinforcement and the surrounding concrete, and the partial-interaction method which accounts for slip. The full-interaction method is based on a smeared crack approach and so is unsuited for the prediction of cracking behaviour. The partial-interaction method, on the other hand, assumes that cracks form through bond-stress transfer only. In the case of non-prismatic concrete beams, the cracking capacity varies along the member. Therefore, cracking can occur over extended regions (full and partial bond interaction regions) and so it can be argued that neither of these models is fully suitable for the prediction of deflections and cracking of shape-optimised concrete beams. In this paper, a novel combined-interaction method is, for the first time, presented to predict the serviceability behaviour of non-prismatic concrete beams by simulating both full and partial bond interactions at different cracked and uncracked regions along the length of the member. In order to validate this approach, two non-prismatic simply supported beams were cast and tested. The test results for deflections, crack widths and crack spacings were in good agreement with the predicted results

Neuroimaging in Parkinson's disease dementia: Connecting the dots

Dementia is a common and devastating symptom of Parkinson’s disease but the anatomical substrate remains unclear. Some evidence points towards hippocampal involvement but neuroimaging abnormalities have been reported throughout the brain and are largely inconsistent across studies. Here, we test whether these disparate neuroimaging findings for Parkinson’s disease dementia localize to a common brain network. We used a literature search to identify studies reporting neuroimaging correlates of Parkinson’s dementia (11 studies, 385 patients). We restricted our search to studies of brain atrophy and hypometabolism that compared Parkinson’s patients with dementia to those without cognitive involvement. We used a standard coordinate-based activation likelihood estimation meta-analysis to assess for consistency in the neuroimaging findings. We then used a new approach, coordinate-based network mapping, to test whether neuroimaging findings localized to a common brain network. This approach uses resting-state functional connectivity from a large cohort of normative subjects (n = 1000) to identify the network of regions connected to a reported neuroimaging coordinate. Activation likelihood estimation meta-analysis failed to identify any brain regions consistently associated with Parkinson’s dementia, showing major heterogeneity across studies. In contrast, coordinate-based network mapping found that these heterogeneous neuroimaging findings localized to a specific brain network centred on the hippocampus. Next, we tested whether this network showed symptom specificity and stage specificity by performing two further analyses. We tested symptom specificity by examining studies of Parkinson’s hallucinations (9 studies, 402 patients) that are frequently co-morbid with Parkinson’s dementia. We tested for stage specificity by using studies of mild cognitive impairment in Parkinson’s disease (15 studies, 844 patients). Coordinate-based network mapping revealed that correlates of visual hallucinations fell within a network centred on bilateral lateral geniculate nucleus and correlates of mild cognitive impairment in Parkinson’s disease fell within a network centred on posterior default mode network. In both cases, the identified networks were distinct from the hippocampal network of Parkinson’s dementia. Our results link heterogeneous neuroimaging findings in Parkinson’s dementia to a common network centred on the hippocampus. This finding was symptom and stage-specific, with implications for understanding Parkinson’s dementia and heterogeneity of neuroimaging findings in general

Urban transportation: Perspectives on mobility and choice

A study of urban transportation systems are presented characterized by intensive scrutiny of many ideas, philosophies, and academic perspectives. This report is intended to communicate some dimensions of the urban transportation problem to the general public