Bioinformatics: A challenge for statisticians

Bioinformatics is a subject that requires the skills of biologists, computer scientists, mathematicians and staisticians. This paper introduces the reader to one small aspect of the subject: the study of microarrays. It describes some of the complexities of the enormous amounts of data that are available and shows how simple statistical techniques can be used to highlight deficiencies in that data

Off-critical Casimir effect in Ising slabs with antisymmetric boundary conditions in <i>d</i>=3

The universal scaling function W+−(y) of the Casimir force (y is a temperature-dependent variable) away from the critical point for thermodynamic systems in the Ising universality class confined between two parallel plates with antisymmetric boundary conditions [denoted (ab)=(+−)] has been analyzed using the extended de Gennes–Fisher local-functional method. Results on the universal function W+−(y) are presented in spatial dimension d=3 applying the extended sine parametric model for temperatures T>TR, where T>TR is the critical temperature of the roughening transition. The asymptotic behavior of W+−(y) for large values of the scaling variable y, y→±∞, is analyzed in general dimension d for T≫Tc, where Tc is the bulk critical temperature, and in d≥3 for T≪TR

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene&#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Motif effects in Affymetrix GeneChips seriously affect probe intensities

An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. © 2012 The Author(s)

THM and HAA formation from NOM in raw and treated surface waters

The disinfection by-product (DBP) formation potential (FP) of natural organic matter (NOM) in surface water sources has been studied with reference to the key water quality determinants (WQDs) of UV absorption (UV254), colour, and dissolved organic carbon (DOC) concentration. The data set used encompassed raw and treated water sampled over a 30-month period from 30 water treatment works (WTWs) across Scotland, all employing conventional clarification. Both trihalomethane (THM) and haloacetic acid (HAA) FPs were considered. In addition to the standard bulk WQDs, the DOC content was fractionated and analysed for the hydrophobic (HPO) and hydrophilic (HPI) fractions. Results were quantified in terms of the yield (dDBPFP/dWQD) and the linear regression coefficient R2 of the yield trend. The NOM in the raw waters was found to comprise 30–84% (average 66%) of the more reactive HPO material, with this proportion falling to 18–63% (average 50%) in the treated water. Results suggested UV254 to be as good an indicator of DBPFP as DOC or HPO for the raw waters, with R2 values ranging from 0.79 to 0.82 for THMs and from 0.71 to 0.73 for HAAs for these three determinants. For treated waters the corresponding values were significantly lower at 0.52–0.67 and 0.46–0.47 respectively, reflecting the lower HPO concentration and thus UV254 absorption and commensurately reduced precision due to the limit of detection of the analytical instrument. It is concluded that fractionation offers little benefit in attempting to discern or predict chlorinated carbonaceous DBP yield for the waters across the geographical region studied. UV254 offered an adequate estimate of DBPFP based on a mean yield of ∼2600 and ∼2800 μg per cm−1 absorbance for THMFP for the raw and treated waters respectively and ∼3800 and2900 μg cm−1 for HAAFP, albeit with reduced precision for the treated waters

Developing an On-Line Interactive Health Psychology Module.

On-line teaching material in health psychology was developed which ensured a range of students could access appropriate material for their course and level of study. This material has been developed around the concept of smaller 'content chunks' which can be combined into whole units of learning (topics), and ultimately, a module. On the basis of the underlying philosophy that the medium is part of the message, we considered interactivity to be a key element in engaging the student with the material. Consequently, the key aim of this development was to stimulate and engage students, promoting better involvement with the academic material, and hence better learning. It was hoped that this was achieved through the development of material including linked programmes and supporting material, small Java Scripts and basic email, forms and HTML additions. This material is outlined as are some of the interactive activities introduced, and the preliminary student and tutor experience described

Investigation of advanced navigation and guidance system concepts for all-weather rotorcraft operations

Results are presented of a survey conducted of active helicopter operators to determine the extent to which they wish to operate in IMC conditions, the visibility limits under which they would operate, the revenue benefits to be gained, and the percent of aircraft cost they would pay for such increased capability. Candidate systems were examined for capability to meet the requirements of a mission model constructed to represent the modes of flight normally encountered in low visibility conditions. Recommendations are made for development of high resolution radar, simulation of the control display system for steep approaches, and for development of an obstacle sensing system for detecting wires. A cost feasibility analysis is included