Development of seismic design methodologies for rigid wall-flexible diaphragm structures

Evidence indicates that the dynamic behavior of Rigid Wall – Flexible Diaphragm (RWFD) structures is dominated by the diaphragm’s response instead of the walls’ response, and this is a significant departure from the underlying assumptions of the widely used equivalent lateral force method in current building codes. RWFD buildings are common in North America and other parts of the world, and incorporate rigid in-plane concrete or masonry walls and flexible in-plane wood or steel roof diaphragms. With the use of a numerical computer modeling framework developed specifically for this type of building, this study sets out to investigate the seismic response of a variety of building archetypes with the intent to develop a simpler, more rational approach to the engineering design of RWFD buildings. A representative list of building archetypes is developed accounting for a variety of common parameters found in North America involving the building size, shape, diaphragm material, and diaphragm connections. Archetype designs are developed under ASCE/SEI 7-10 and this study’s proposed approach to develop design methodologies uses the FEMA P-695 methodology to evaluate building performance. In addition, two separate seismic force levels were utilized during the assessment representing both moderate and high seismic exposures to evaluate the impact of these parameters

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro

BACKGROUND: Pseudomonas syringae pv tomato DC3000 (DC3000) is a Gram-negative model plant pathogen that is found in a wide variety of environments. To survive in these diverse conditions it must sense and respond to various environmental cues. One micronutrient required for most forms of life is iron. Bioavailable iron has been shown to be an important global regulator for many bacteria where it not only regulates a wide variety of genes involved in general cell physiology but also virulence determinants. In this study we used microarrays to study differential gene regulation in DC3000 in response to changes in levels of cell-associated iron. RESULTS: DC3000 cultures were grown under highly controlled conditions and analyzed after the addition of iron citrate or sodium citrate to the media. In the cultures supplemented with iron, we found that cell-associated iron increased rapidly while culture densities were not significantly different over 4 hours when compared to cultures with sodium citrate added. Microarray analysis of samples taken from before and after the addition of either sodium citrate or iron citrate identified 386 differentially regulated genes with high statistical confidence. Differentially regulated genes were clustered based on expression patterns observed between comparison of samples taken at different time points and with different supplements. This analysis grouped genes associated with the same regulatory motifs and/or had similar putative or known function. CONCLUSION: This study shows iron is rapidly taken up from the medium by iron-depleted DC3000 cultures and that bioavailable iron is a global cue for the expression of iron transport, storage, and known virulence factors in DC3000. Furthermore approximately 34% of the differentially regulated genes are associated with one of four regulatory motifs for Fur, PvdS, HrpL, or RpoD

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs

BACKGROUND: Identification of specific genes and gene expression patterns important for bacterial survival, transmission and pathogenesis is critically needed to enable development of more effective pathogen control strategies. The stationary phase stress response transcriptome, including many σ(B)-dependent genes, was defined for the human bacterial pathogen Listeria monocytogenes using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic ΔsigB mutant, which does not express the alternative σ factor σ(B), a major regulator of genes contributing to stress response, including stresses encountered upon entry into stationary phase. RESULTS: Overall, 83% of all L. monocytogenes genes were transcribed in stationary phase cells; 42% of currently annotated L. monocytogenes genes showed medium to high transcript levels under these conditions. A total of 96 genes had significantly higher transcript levels in 10403S than in ΔsigB, indicating σ(B)-dependent transcription of these genes. RNA-Seq analyses indicate that a total of 67 noncoding RNA molecules (ncRNAs) are transcribed in stationary phase L. monocytogenes, including 7 previously unrecognized putative ncRNAs. Application of a dynamically trained Hidden Markov Model, in combination with RNA-Seq data, identified 65 putative σ(B )promoters upstream of 82 of the 96 σ(B)-dependent genes and upstream of the one σ(B)-dependent ncRNA. The RNA-Seq data also enabled annotation of putative operons as well as visualization of 5'- and 3'-UTR regions. CONCLUSIONS: The results from these studies provide powerful evidence that RNA-Seq data combined with appropriate bioinformatics tools allow quantitative characterization of prokaryotic transcriptomes, thus providing exciting new strategies for exploring transcriptional regulatory networks in bacteria. See minireivew http://jbiol.com/content/8/12/107

A practice-oriented model for pushover analysis of a class of timber-framed masonry buildings

Timber-Framed (TF) masonry is a structural system characterized by high complexity and diversity. Limited experimental and analytical research has been carried out so far to explore their earthquake response, partly due to the complexity of the problem and partly due to the scarcity of TF buildings across the world. Here, a new practice-oriented non-linear (NL) macro-model is presented for TF masonry structures, based on the familiar diagonal strut approach with NL axial hinges in the struts. The constitutive law for the hinges (axial force vs. axial deformation) is derived on the basis of an extensive parametric analysis of the main factors affecting the response of TF masonry panels subjected to horizontal loading. The parameters studied are related to the geometric features of the panel and the strength of wood as well as the connections of the timber elements. The parametric analysis is performed using a micro-model based on Hill-type plasticity and it is shown that in the studied X-braced walls the masonry infills do not make a significant contribution to the lateral load resistance. Empirical expressions are proposed for the yield and maximum displacement and shear of a horizontally loaded TF panel. The model is verified against available experimental data, and is found to capture well the envelopes of the experimental loops. The model is readily applicable to NL static analysis (pushover) analysis for the assessment of the lateral load capacity of TF masonry buildings, as the number of input parameters for deriving the constitutive law has been limited to only five

Fail-safe optimization of viscous dampers for seismic retrofitting

This paper presents a new optimization approach for designing minimum-cost fail-safe distributions of fluid viscous dampers for seismic retrofitting. Failure is modeled as either complete damage of the dampers or partial degradation of the dampers' properties. In general, this leads to optimization problems with large number of constraints. Thus, the use of a working-set optimization algorithm is proposed. The main idea is to solve a sequence of relaxed optimization sub-problems with a small sub-set of all constraints. The algorithm terminates once a solution of a sub-problem is found that satisfies all the constraints of the problem. The retrofitting cost is minimized with constraints on the inter-story drifts at the peripheries of frame structures. The structures considered are subjected to a realistic ensemble of ground motions, and their response is evaluated with time-history analyses. The transient optimization problem is efficiently solved with a gradient-based sequential linear programming algorithm. The gradients of the response functions are calculated with a consistent adjoint sensitivity analysis procedure. Promising results attained for 3-D irregular frames are presented and discussed. The numerical results highlight the fact that the optimized layout and size of the dampers can change significantly even for moderate levels of damage

Ambient fabrication of flexible and large-area organic light-emitting devices using slot-die coating

The grand vision of manufacturing large-area emissive devices with low-cost roll-to-roll coating methods, akin to how newspapers are produced, appeared with the emergence of the organic light-emitting diode about 20 years ago. Today, small organic light-emitting diode displays are commercially available in smartphones, but the promise of a continuous ambient fabrication has unfortunately not materialized yet, as organic light-emitting diodes invariably depend on the use of one or more time- and energy-consuming process steps under vacuum. Here we report an all-solution-based fabrication of an alternative emissive device, a light-emitting electrochemical cell, using a slot-die roll-coating apparatus. The fabricated flexible sheets exhibit bidirectional and uniform light emission, and feature a fault-tolerant >1-μm-thick active material that is doped in situ during operation. It is notable that the initial preparation of inks, the subsequent coating of the constituent layers and the final device operation all could be executed under ambient air

Genome-Wide Identification of Transcriptional Start Sites in the Plant Pathogen Pseudomonas syringae pv. tomato str. DC3000

RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5′-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5′-ends obtained by this method were consistent with results obtained using global RNA-Seq and 5′RACE. As expected, many 5′-ends were positioned a short distance upstream of annotated genes. We also captured 5′-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 5′-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broad foundation for future investigations of regulation at the genomic and single gene levels

The mbo Operon Is Specific and Essential for Biosynthesis of Mangotoxin in Pseudomonas syringae

Mangotoxin is an antimetabolite toxin produced by certain Pseudomonas syringae pv. syringae strains. This toxin is an oligopeptide that inhibits ornithine N-acetyl transferase, a key enzyme in the biosynthesis of ornithine and arginine. Previous studies have reported the involvement of the putative nonribosomal peptide synthetase MgoA in virulence and mangotoxin production. In this study, we analyse a new chromosomal region of P. syringae pv. syringae UMAF0158, which contains six coding sequences arranged as an operon (mbo operon). The mbo operon was detected in only mangotoxin-producing strains, and it was shown to be essential for the biosynthesis of this toxin. Mutants in each of the six ORFs of the mbo operon were partially or completely impaired in the production of the toxin. In addition, Pseudomonas spp. mangotoxin non-producer strains transformed with the mbo operon gained the ability to produce mangotoxin, indicating that this operon contains all the genetic information necessary for mangotoxin biosynthesis. The generation of a single transcript for the mbo operon was confirmed and supported by the allocation of a unique promoter and Rho-independent terminator. The phylogenetic analysis of the P. syringae strains harbouring the mbo operon revealed that these strains clustered together

The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing

In this study, we evaluated how gene expression differs in mature Pseudomonas aeruginosa biofilms as opposed to planktonic cells by the use of RNA sequencing technology that gives rise to both quantitative and qualitative information on the transcriptome. Although a large proportion of genes were consistently regulated in both the stationary phase and biofilm cultures as opposed to the late exponential growth phase cultures, the global biofilm gene expression pattern was clearly distinct indicating that biofilms are not just surface attached cells in stationary phase. A large amount of the genes found to be biofilm specific were involved in adaptation to microaerophilic growth conditions, repression of type three secretion and production of extracellular matrix components. Additionally, we found many small RNAs to be differentially regulated most of them similarly in stationary phase cultures and biofilms. A qualitative analysis of the RNA-seq data revealed more than 3000 putative transcriptional start sites (TSS). By the use of rapid amplification of cDNA ends (5′-RACE) we confirmed the presence of three different TSS associated with the pqsABCDE operon, two in the promoter of pqsA and one upstream of the second gene, pqsB. Taken together, this study reports the first transcriptome study on P. aeruginosa that employs RNA sequencing technology and provides insights into the quantitative and qualitative transcriptome including the expression of small RNAs in P. aeruginosa biofilms