Positive trigonometric polynomials for strong stability of difference equations

We follow a polynomial approach to analyse strong stability of linear difference equations with rationally independent delays. Upon application of the Hermite stability criterion on the discrete-time homogeneous characteristic polynomial, assessing strong stability amounts to deciding positive definiteness of a multivariate trigonometric polynomial matrix. This latter problem is addressed with a converging hierarchy of linear matrix inequalities (LMIs). Numerical experiments indicate that certificates of strong stability can be obtained at a reasonable computational cost for state dimension and number of delays not exceeding 4 or 5

Investigating the Correlation Between Quality Factor of Metallic Cavities and Electromagnetic Radiation

This research investigates the correlation in reduction of quality factor of a reverberant cavity and that cavity�s ability to radiate. A reverberant cavity was chosen because it provides an idealized model of many commercial electronic devices since they are usually housed in metal casings. Phase 1 of this research investigates multiple methods for optimizing the reduction in Q through the use of RF absorbing material. Phase 2 of this research develops an experimental approach to obtaining the electromagnetic emissions from a metallic cavity using a nested reverberation chamber approach.This research uses a time domain method for determining the Q factor of a small metallic cavity. This research has shown that increasing the surface area of an absorber has a much more significant impact on reducing the Q of a cavity than increasing the volume of the absorbers. This research has also shown that it is more efficient to use several smaller absorbers spaced apart rather than larger single pieces. Another finding from this research is that the same Q levels can be reached with less material by utilizing absorber designs that increase surface area while reducing volume. This research also addresses an erroneous assumption of the time domain Q factor measurements that states that pulse width must be shorter than the wall scattering time in order to not adversely affect the measurements. It has been found that this requirement is unnecessary. By measuring the change in Q of a cavity and the change in emissions from a cavity, a correlation has been found showing that Q reductions from loading directly result in emission reductions, but the amount of reduction of emissions per reduction in Q is frequency dependent. This could mean that the results may vary from one test cavity to the next.Electrical Engineerin

Genome-wide prediction, display and refinement of binding sites with information theory-based models

BACKGROUND: We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. RESULTS: Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths. CONCLUSIONS: Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXRα, AHR and NF-κB p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. Comparisons of genome scans with the original and refined PXR/RXRα information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites

“I’ve Devoted My Entire Life to My Daughter—and She Knows It”: Exploration of Identity Development Among Now-Adult Navajo Native American Adolescent Mothers

n 1992 (n = 21) and 1995 (n = 8), the principal investigator collected data from 29 reservation-residing Navajo Native American teenage mothers. A primary goal of the 1992 and 1995 investigations (Time 1) was to examine the identity status of the young women in relation to commitment to the maternal role using Marcia’s (1980) framework. Results revealed that an approximately equal number of participants could be classified as achieved, moratorium, foreclosed, and diffused (see Dalla, 2000). In 2007 (Time 2), the principal investigator returned to collect follow-up data at the Navajo Reservation, where she interviewed 21 (72%) of the original 29 women. Using a qualitative research strategy, the primary goal of this investigation was to examine developmental trajectories of participants’ identity status in relation to four significant life domains (i.e., maternity, intimate relationships, work/ occupation, and culture). The frequencies of the identity achievement status were higher at Time 2 than at Time 1, and this identity status was also more stable than the other statuses. Findings supported the expectation that presence in the identity achievement status would be positively associated with well-being, whereas the identity diffusion status has a negative association with such functioning. The authors discuss suggestions for continued research and application of findings

Research Article

Mixed modeling and sample size calculations for identifying housekeeping gene

MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects

Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at nucleotide resolution along single DNA strands. Probing with cytosine DNA methyltransferases followed by bisulfite sequencing (MAPit) is an effective technique for mapping protein–DNA interactions. Here, MAPit methylation footprinting with M.CviPI, a GC methyltransferase we previously cloned and characterized, was used to probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells. Because M.CviPI-probed samples contain both CG and GC methylation, we developed a versatile, visually-intuitive program, called MethylViewer, for evaluating the bisulfite sequencing results. Uniquely, MethylViewer can simultaneously query cytosine methylation status in bisulfite-converted sequences at as many as four different user-defined motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data can also be exported for statistical analysis and as publication-quality images. Analysis of hMLH1 MAPit data with MethylViewer showed that endogenous CG methylation and accessible GC sites were both mapped on single molecules at high resolution. Disruption of positioned nucleosomes on single molecules of the PHO5 promoter was detected in budding yeast using M.CviPII, increasing the number of enzymes available for probing protein–DNA interactions. MethylViewer provides an integrated solution for primer design and rapid, accurate and detailed analysis of bisulfite sequencing or MAPit datasets from virtually any biological or biochemical system

Support surfaces for pressure ulcer prevention.

BACKGROUND: Pressure ulcers (also known as bedsores, pressure sores, decubitus ulcers) are areas of localised damage to the skin and underlying tissue due to pressure, shear or friction. They are common in the elderly and immobile and costly in financial and human terms. Pressure-relieving beds, mattresses and seat cushions are widely used as aids to prevention in both institutional and non-institutional settings. OBJECTIVES: This systematic review seeks to answer the following questions: to what extent do pressure-relieving cushions, beds, mattress overlays and mattress replacements reduce the incidence of pressure ulcers compared with standard support surfaces? how effective are different pressure-relieving surfaces in preventing pressure ulcers, compared to one another? SEARCH STRATEGY: The Specialised Trials Register of the Cochrane Wounds Group (compiled from regular searches of many electronic databases including MEDLINE, CINAHL and EMBASE plus handsearching of specialist journals and conference proceedings) was searched up to January 2004, Issue 3, 2004 of the Cochrane Central Register of Controlled Trials was also searched. The reference sections of included studies were searched for further trials. SELECTION CRITERIA: Randomised controlled trials (RCTs), published or unpublished, which assessed the effectiveness of beds, mattresses, mattress overlays, and seating cushions for the prevention of pressure ulcers, in any patient group, in any setting. RCTs were eligible for inclusion if they reported an objective, clinical outcome measure such as incidence and severity of new of pressure ulcers developed. Studies which only reported proxy outcome measures such as interface pressure were excluded. DATA COLLECTION AND ANALYSIS: Trial data were extracted by one researcher and checked by a second. The results from each study are presented as relative risk for dichotomous variables. Where deemed appropriate, similar studies were pooled in a meta analysis. MAIN RESULTS: 41 RCTs were included in the review. Foam alternatives to the standard hospital foam mattress can reduce the incidence of pressure ulcers in people at risk. The relative merits of alternating and constant low pressure devices, and of the different alternating pressure devices for pressure ulcer prevention are unclear.Pressure-relieving overlays on the operating table have been shown to reduce postoperative pressure ulcer incidence, although one study indicated that an overlay resulted in adverse skin changes. One trial indicated that Australian standard medical sheepskins prevented pressure ulcers. There is insufficient evidence to draw conclusions on the value of seat cushions, limb protectors and various constant low pressure devices as pressure ulcer prevention strategies.A study of Accident & Emergency trolley overlays did not identify a reduction in pressure ulcer incidence. There are tentative indications that foot waffle heel elevators, a particular low air loss hydrotherapy mattress and an operating theatre overlay are harmful. REVIEWERS' CONCLUSIONS: In people at high risk of pressure ulcer development, consideration should be given to the use of higher specification foam mattresses rather than standard hospital foam mattresses. The relative merits of higher-tech constant low pressure and alternating pressure for prevention are unclear. Organisations might consider the use of pressure relief for high risk patients in the operating theatre, as this is associated with a reduction in post-operative incidence of pressure ulcers. Seat cushions and overlays designed for use in Accident & Emergency settings have not been adequately evaluated

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Background: Estrogen receptors alpha (ERa) and beta (ERb) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERb being able to modulate the effects of ERa on gene transcription and cell proliferation. ERb is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERb in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results: Expression of full-length ERb in hormone-responsive, ERa-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERb and 6024 ERa binding sites in estrogen-stimulated cells, comprising sites occupied by either ERb, ERa or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERb+ vs ERb- cells, 424 showed one or more ERb site within 10 kb. These putative primary ERb target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERb binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions: Results indicate that the vast majority of the genomic targets of ERb can bind also ERa, suggesting that the overall action of ERb on the genome of hormone-responsive BC cells depends mainly on the relative concentration of both ERs in the cell