Contributions to the Minimum Linear Arrangement Problem

The Minimum Linear Arrangement problem (MinLA) consists in finding an ordering of the nodes of a weighted graph, such that the sum of the weighted edge lengths is minimized. We report on the usefulness of a new model within a branch-and-cut-and-price algorithm for solving MinLA problems to optimality. The key idea is to introduce binary variables d_{ijk}, that are equal to 1 if nodes i and j have distance k in the permutation. We present formulations for complete and for sparse graphs and explain the realization of a branch-and-cut-and-price algorithm. Furthermore, its different settings are discussed and evaluated. To the study of the theoretical aspects concerning the MinLA, we contribute a characterization of a relaxation of the corresponding polyeder

Evaluation of a Health Education Intervention for Rural Preschool and Kindergarten Children in the Southeastern United States: A Cluster Randomized Trial

This research employed a matched-pairs randomized field experiment design to evaluate a classroom-based health education intervention for pre-Kindergarten and Kindergarten children in a rural region of the southeastern United States. Schools were matched on demographic characteristics, then one school from each pair was randomly assigned to the treatment group and one to the delayed treatment group. The intervention included a field trip experience and an integrated curriculum designed to increase knowledge about nutrition, physical activity, and sleep. Staff conducted individual assessments of changes in knowledge with a random sample of children from each classroom (252 children from treatment classrooms; 251 children from delayed treatment classrooms). We used a multilevel linear regression with maximum likelihood estimation to incorporate the effects of clustering at the classroom and school level while examining the effects of the intervention on individual assessment change scores. During the intervention period, an estimated 3,196 children (treatment: 1,348 students in 68 classrooms in 10 schools; delayed treatment: 1,848 students in 86 classrooms in 10 schools) participated in the intervention. Children in the treatment group had significantly larger assessment change scores than children in the delayed treatment group. Findings suggest significant beneficial effects of the intervention on health knowledge

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms

BACKGROUND: Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be extracted in a reasonable way and funneled into manageable and functionally meaningful patterns. Genes may be reasonably combined using knowledge about their interaction behaviour. On a proteomic level, biochemical research has elucidated an increasingly complete image of the metabolic architecture, especially for less complex organisms like the well studied bacterium Escherichia coli. RESULTS: We sought to discover central components of the metabolic network, regulated by the expression of associated genes under changing conditions. We mapped gene expression data from E. coli under aerobic and anaerobic conditions onto the enzymatic reaction nodes of its metabolic network. An adjacency matrix of the metabolites was created from this graph. A consecutive ones clustering method was used to obtain network clusters in the matrix. The wavelet method was applied on the adjacency matrices of these clusters to collect features for the classifier. With a feature extraction method the most discriminating features were selected. We yielded network sub-graphs from these top ranking features representing formate fermentation, in good agreement with the anaerobic response of hetero-fermentative bacteria. Furthermore, we found a switch in the starting point for NAD biosynthesis, and an adaptation of the l-aspartate metabolism, in accordance with its higher abundance under anaerobic conditions. CONCLUSION: We developed and tested a novel method, based on a combination of rationally chosen machine learning methods, to analyse gene expression data on the basis of interaction data, using a metabolic network of enzymes. As a case study, we applied our method to E. coli under oxygen deprived conditions and extracted physiologically relevant patterns that represent an adaptation of the cells to changing environmental conditions. In general, our concept may be transferred to network analyses on biological interaction data, when data for two comparable states of the associated nodes are made available

An optically actuated surface scanning probe

We demonstrate the use of an extended, optically trapped probe that is capable of imaging surface topography with nanometre precision, whilst applying ultra-low, femto-Newton sized forces. This degree of precision and sensitivity is acquired through three distinct strategies. First, the probe itself is shaped in such a way as to soften the trap along the sensing axis and stiffen it in transverse directions. Next, these characteristics are enhanced by selectively position clamping independent motions of the probe. Finally, force clamping is used to refine the surface contact response. Detailed analyses are presented for each of these mechanisms. To test our sensor, we scan it laterally over a calibration sample consisting of a series of graduated steps, and demonstrate a height resolution of ∼ 11 nm. Using equipartition theory, we estimate that an average force of only ∼ 140 fN is exerted on the sample during the scan, making this technique ideal for the investigation of delicate biological samples

Policosanol Contents and Composition of Grain Sorghum Kernels and Dried Distillers Grains

Grain sorghum can be a major source of policosanols, long-chained alcohols, that have beneficial physiological activities. Sorghum dried distillers grains (DDG), a by-product of ethanol production from grain sorghum. contain a large amount of policosanols. Content and composition of policosanols in long-chained lipids extracted from grain sorghum kernels and DDG were determined. Long-chained lipids were extracted using hot hexane or hot ethanol. The major components of the long-chained lipids extracted from grain sorghum kernels. as determined using HPLC were policosanols (37-44%), aldehydes (44-55%), and acids (4-5%). Long-chained lipids from DDG contained 52% policosanols, 23% aldehydes. 6.4% acids. and l7% wax esters/steryl esters. Composition of policosanols in DDG matched the composition in grain sorghum kernels, as determined by gas chromatography. even though the content of policosanols in DDG was greater than the content in grain sorghum kernels. Policosonal composition ranges were 0-1% C22:0, 0-3% C24:0. 6-8% C26:0, l% C27:0. 43-47% C28:0. 1-2% C29:0. 40-43% C30:0. and 1-4% C32:0

Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep

BACKGROUND: The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relatively little research has been performed into sheep genetics, and DNA sequences are available for only a small number of sheep genes. RESULTS: In this work we have sequenced over 47 thousand expressed sequence tags (ESTs) from libraries developed from healing bone in a sheep model of fracture healing. These ESTs were clustered with the previously available 10 thousand sheep ESTs to a total of 19087 contigs with an average length of 603 nucleotides. We used the newly identified sequences to develop RT-PCR assays for 78 sheep genes and measured differential expression during the course of fracture healing between days 7 and 42 postfracture. All genes showed significant shifts at one or more time points. 23 of the genes were differentially expressed between postfracture days 7 and 10, which could reflect an important role for these genes for the initiation of osteogenesis. CONCLUSION: The sequences we have identified in this work are a valuable resource for future studies on musculoskeletal healing and regeneration using sheep and represent an important head-start for genomic sequencing projects for Ovis aries, with partial or complete sequences being made available for over 5,800 previously unsequenced sheep genes

Shape-induced force fields in optical trapping

Advances in optical tweezers, coupled with the proliferation of two-photon polymerization systems, mean that it is now becoming routine to fabricate and trap non-spherical particles. The shaping of both light beams and particles allows fine control over the flow of momentum from the optical to mechanical regimes. However, understanding and predicting the behaviour of such systems is highly complex in comparison with the traditional optically trapped microsphere. In this Article, we present a conceptually new and simple approach based on the nature of the optical force density. We illustrate the method through the design and fabrication of a shaped particle capable of acting as a passive force clamp, and we demonstrate its use as an optically trapped probe for imaging surface topography. Further applications of the design rules highlighted here may lead to new sensors for probing biomolecule mechanics, as well as to the development of optically actuated micromachines

Magnetic-Responsive Carbon Nanotubes Composite Scaffolds for Chondrogenic Tissue Engineering

The demand for engineered scaffolds capable of delivering multiple cues to cells continues to grow as the interplay between cell fate with microenvironmental and external cues is revealed. Emphasis has been given to develop stimuli-responsive scaffolds. These scaffolds are designed to sense an external stimulus triggering a specific response (e.g., change in the microenvironment, release therapeutics, etc.) and then initiate/modulate a desired biofunction. Here, magnetic-responsive carboxylated multi-walled carbon nanotubes (cMWCNTs) are integrated into 3D collagen/polylactic acid (PLA) scaffold via a reproducible filtration-based method. The integrity and biomechanical performance of the collagen/PLA scaffolds are preserved after cMWCNT integration. In vitro safety assessment of cMWCNT/collagen/PLA scaffolds shows neither cytotoxicity effects nor macrophage pro-inflammatory response, supporting further in vitro studies. The cMWCNT/collagen/PLA scaffolds enhance chondrocytes metabolic activity while maintaining high cell viability and extracellular matrix (i.e., type II collagen and aggrecan) production. Comprehensive in vitro study applying static and pulsed magnetic field on seeded scaffolds shows no specific cell response in dependence with the applied field. This result is independent of the presence or absence of cMWCNT into the collagen/PLA scaffolds. Taken together, these findings provide additional evidence of the benefits to exploit the CNTs outstanding properties in the design of stimuli-responsive scaffolds.publishedVersio