Missing channels in two-colour microarray experiments: combining single-channel and two-channel data.

BACKGROUND: There are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments. Resulting analyses therefore often choose between the unacceptable inclusion of poor quality data or the unpalatable exclusion of some (possibly a lot of) good quality data along with the bad. Two such approaches would be a single channel analysis using some of the data from all of the arrays, and an analysis of all of the data, but only from unaffected arrays. In this paper we examine a 'combined' approach to the analysis of such affected experiments that uses all of the unaffected data. RESULTS: A simulation experiment shows that while a single channel analysis performs relatively well when the majority of arrays are affected, and excluding affected arrays performs relatively well when few arrays are affected (as would be expected in both cases), the combined approach out-performs both. There are benefits to actively estimating the key-parameter of the approach, but whether these compensate for the increased computational cost and complexity over just setting that parameter to take a fixed value is not clear. Inclusion of ozone-affected data results in poor performance, with a clear spatial effect in the damage being apparent. CONCLUSION: There is no need to exclude unaffected data in order to remove those which are damaged. The combined approach discussed here is shown to out-perform more usual approaches, although it seems that if the damage is limited to very few arrays, or extends to very nearly all, then the benefits will be limited. In other circumstances though, large improvements in performance can be achieved by adopting such an approach.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

In situ Fluoride Response of Caries Lesions with Different Mineral Distributions at Baseline

The present in situ study investigated the fluoride response of caries lesions with similar mineral loss but two distinct mineral distributions (low- and high-‘R’, calculated as the ratio of mineral loss to lesion depth). Sixteen subjects wore eight gauze-covered enamel specimens with preformed lesions placed buccally on their mandibular partial dentures for periods up to 4 weeks. The participants brushed twice daily for 1 min with an 1,100 ppm F (as NaF) dentifrice. After 3 and 4 weeks, specimens were retrieved and analyzed microradiographically (TMR) and by quantitative light fluorescence (QLF). TMR results revealed that low- and high-R lesions showed opposite behaviors – low-R lesions further demineralized, whereas high-R lesions exhibited some remineralization. In comparison, lesion depth increased in low-R, but remained unchanged in high-R lesions; R decreased in both, but more in high-R lesions; mineral density at the lesion surface remained unchanged in low-R, but increased in high-R lesions. Differences in mineral loss between lesion types increased further between 3 and 4 weeks. QLF did not mirror TMR results as low-R lesions were found to remineralize, whereas high-R lesions remained unchanged. It is likely that low-R lesions differ from high-R lesions chemically and microstructurally; therefore rendering low-R lesion more susceptible to further dissolution. During lesion formation, low-R in contrast to high-R lesions may not lose all of the solubility-determining impurities such as magnesium and carbonate, which can reprecipitate again in different mineral phases within the lesion. In conclusion, mineral distribution at baseline directly impacts in situ lesion response to fluoride

Effect of toothbrushing duration and dentifrice quantity on enamel remineralisation: An in situ randomized clinical trial

Objectives The influence of toothbrushing duration and dentifrice quantity on fluoride efficacy against dental caries is poorly understood. This study investigated effects of these two oral hygiene factors on enamel remineralisation (measured as surface microhardness recovery [SMHR]), enamel fluoride uptake (EFU), and net acid resistance (NAR) post-remineralisation in a randomized clinical study using an in situ caries model. Methods Subjects (n = 63) wore their partial dentures holding partially demineralised human enamel specimens and brushed twice-daily for two weeks, following each of five regimens: brushing for 120 or 45 s with 1.5 g of 1150 ppm F (as NaF) dentifrice; for 120 or 45 s with 0.5 g of this dentifrice; and for 120 s with 1.5 g of 250 ppm F (NaF) dentifrice. Results Comparing brushing for 120 s against brushing for 45 s, SMHR and EFU increased by 20.0% and 26.9% respectively when 1.5 g dentifrice was used; and by 22.8% and 19.9% respectively when 0.5 g dentifrice was used. Comparing brushing with 1.5 g against brushing with 0.5 g dentifrice, SMHR and EFU increased by 35.3% and 51.3% respectively when brushing for 120 s, and by 38.4% and 43.0% respectively when brushing for 45 s. Increasing brushing duration and dentifrice quantity also increased the NAR value. The effects of these two oral hygiene factors on SMHR, EFU, and NAR were statistically significant (p < 0.05 in all cases). Conclusion Brushing duration and dentifrice quantity have the potential to influence the anti-caries effectiveness of fluoride dentifrices. Study NCT01563172 on ClinicalTrials.gov. Clinical significance The effect of two key oral hygiene regimen factors – toothbrushing duration and dentifrice quantity – on fluoride’s anticaries effectiveness is unclear. This 2-week home-use in situ remineralisation clinical study showed both these factors can influence fluoride bioactivity, and so can potentially affect fluoride’s ability to protect against caries

Quantifying the pattern of microbial cell dispersion, density and clustering on surfaces of differing chemistries and topographies using multifractal analysis

The effects of surface topography on bacterial distribution across a surface are of extreme importance when designing novel, hygienic or antimicrobial surface coatings. The majority of methods that are deployed to describe the pattern of cell dispersion, density and clustering across surfaces are currently qualitative. This paper presents a novel application of multifractal analysis to quantitatively measure these factors using medically relevant microorganisms (Staphylococcus aureus or Staphylococcus epidermidis). Surfaces (medical grade 316 stainless steel) and coatings (Ti–ZrN, Ti–ZrN/6.0%Ag, Ti–ZrN/15.6%Ag, TiZrN/24.7%Ag) were used in microbiological retention assays. Results demonstrated that S. aureus displayed a more heterogeneous cell dispersion (∆αAS < 1) whilst the dispersion of S. epidermidis was more symmetric and homogeneous (∆αAS ≥ 1). Further, although the surface topography and chemistry had an effect on cell dispersion, density and clustering, the type of bonding that occurred at the surface interface was also important. Both types of cells were influenced by both surface topographical and chemical effects; however, S. aureus was influenced marginally more by surface chemistry whilst S. epidermidis cells was influenced marginally more by surface topography. Thus, this effect was bacterially species specific. The results demonstrate that multifractal analysis is a method that can be used to quantitatively analyse the cell dispersion, density and clustering of retained microorganisms on surfaces. Using quantitative descriptors has the potential to aid the understanding the effect of surface properties on the production of hygienic and antimicrobial coatings

Identification of a Phosphorylation Site for Calcium/Calmodulindependent Protein Kinase II in the NR2B Subunit of the N-Methyl-D-aspartate Receptor

The N-methyl-D-aspartate (NMDA) subtype of excitatory glutamate receptors plays critical roles in embryonic and adult synaptic plasticity in the central nervous system. The receptor is a heteromultimer of core subunits, NR1, and one or more regulatory subunits, NR2A-D. Protein phosphorylation can regulate NMDA receptor function (Lieberman, D. N., and Mody, I. (1994) Nature 369, 235-239; Wang, Y. T., and Salter, M. W. (1994) Nature 369, 233-235; Wang, L.-Y., Orser, B. A., Brautigan, D. L., and MacDonald, J. F. (1994) Nature 369, 230-232). Here we identify a major phosphorylation site on subunit NR2B that is phosphorylated by Ca2+/calmodulin-dependent protein kinase II (CaM kinase II), an abundant protein kinase located at postsynaptic sites in glutamatergic synapses. For the initial identification of the site, we constructed a recombinant fusion protein containing 334 amino acids of the C terminus of the NR2B subunit and phosphorylated it with CaM kinase II in vitro. By peptide mapping, automated sequencing, and mass spectrometry, we identified the major site of phosphorylation on the fusion protein as Ser-383, corresponding to Ser-1303 of full-length NR2B. The Km for phosphorylation of this site in the fusion protein was ~50 nM, much lower than that of other known substrates for CaM kinase II, suggesting that the receptor is a high affinity substrate. We show that serine 1303 in the full-length NR2B and/or the cognate site in NR2A is a major site of phosphorylation of the receptor both in the postsynaptic density fraction and in living hippocampal neurons

Advanced Colloids Experiment (Temperature Controlled) - ACE-T6

Increment 53 - 54 Science Symposium presentation of Advanced Colloids Experiment (ACE-T6) to RPO. The purpose of this event is for Principal Investigators to present their science objectives, testing approach, and measurement methods to agency scientists, managers, and other investigators

Prevalence of Salmonella serotypes on pig carcasses from high- and low-risk herds slaughtered in three abattoirs

The aim of this study was to compare the prevalence of Salmonella serotypes at two different sites on pig carcasses from herds classified as high-risk or low-risk and to elucidate the relationship between carcass contamination levels and serological status. Caecal samples and carcass surface swabs were cultured for Salmonella from a total of 210 pigs from low risk herds (\u3c 19 % of pigs in herd Salmonella seropositive) and 209 pigs from high risk herds (\u3e 32% of pigs in herd Salmonella seropositive) in three abattoirs

Prevalence of infection with Salmonella in Irish pig farms

The objectives of this project were to determine the frequency of infection with Salmonella serotypes in Irish pig farms and to identity the point in the production cycle at which infection is acquired. Salmonellae were isolated from pens in 30 of 59 farrow-to-finish farms sampled. Herds classified as low risk were as likely to be positive as high-risk herds. The prevalence of infection was 2.3% in lactating sows, 5.1% in dry sows, 4.6% in gilts, 5.9% in fatteners, 4.8% in second stage weaners and 8.0% in first stage weaners. Prevalence of infection in lactating sows was lower than in other groups sampled (P≥0.005 and was less in second stage than in first stage weaners (P≥0.005). The predominant serotypes isolated were Typhimurium and Derby. Results show that infection was revalent in all production stages. Classification of herds based on serological results of fatteners may not reflect the prevalence of infection in other production stages

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

Knowledge of mutation processes is central to understanding virtually all evolutionary phenomena and the underlying nature of genetic disorders and cancers. However, the limitations of standard molecular mutation detection methods have historically precluded a genome-wide understanding of mutation rates and spectra in the nuclear genomes of multicellular organisms. We applied two high-throughput DNA sequencing technologies to identify and characterize hundreds of spontaneously arising base-substitution mutations in 10 Caenorhabditis elegans mutation-accumulation (MA)-line nuclear genomes. C. elegans mutation rate estimates were similar to previous calculations based on smaller numbers of mutations. Mutations were distributed uniformly within and among chromosomes and were not associated with recombination rate variation in the MA lines, suggesting that intragenomic variation in genetic hitchhiking and/or background selection are primarily responsible for the chromosomal distribution patterns of polymorphic nucleotides in C. elegans natural populations. A strong mutational bias from G/C to A/T nucleotides was detected in the MA lines, implicating oxidative DNA damage as a major endogenous mutagenic force in C. elegans. The observed mutational bias also suggests that the C. elegans nuclear genome cannot be at equilibrium because of mutation alone. Transversions dominate the spectrum of spontaneous mutations observed here, whereas transitions dominate patterns of allegedly neutral polymorphism in natural populations of C. elegans and many other animal species; this observation challenges the assumption that natural patterns of molecular variation in noncoding regions of the nuclear genome accurately reflect underlying mutation processes