On the hydrophobicity of peptides:comparing empirical predictions of peptide log P values

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis's LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r(2) values, with ALogP being the most effective (r( 2) = 0.822) and MLogP the least (r(2) = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides - ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides - PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides - QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides - LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.

Encouraging student to reflect on their employment experience

The purpose behind this case study is to share with a wider audience of placement officers, tutors and those who are involved in the management of placement students or employment of graduates, the approach taken to encourage reflective learning in undergraduate placement students at Aston Business School. Reflective learning forms an important foundation of the placement year at Aston Business School, where a professional placement is a mandatory element of the four year degree, for all Home/EU students (optional for International students) who are taking a Single Honours degree (i.e. a fully business programme). The placement year is not compulsory for those students taking a Combined Honours degree (i.e. a degree where two unrelated subjects are studied), although approximately 50% of those students taking an Aston Business School subject opt to take a placement year. Students spend their year out undertaking a ‘proper’ job within a company or public sector organisation. They are normally paid a reasonable salary for their work (in 2004/5 the average advertised salary was £13,700 per annum). The placement year is assessed, carrying credits which amount to a contribution of 10% towards the students’ final degree. The assessment methods used require the students to submit an academic essay relating theory to practice, a factual report about the company which can be of use to future students, and a log book, the latter being the reflective piece of work. Encouragement to reflect on the placement year has always been an important feature of Aston Business School’s approach to learning. More recently, however, feedback from employers indicated that, although our students have excellent employability skills, “they do not think about them” (Aston Business School Advisory Panel, 2001). We, therefore, began some activities which would encourage students to go beyond the mere acquisition of skills and knowledge. This work became the basis of a programme of introductions to reflective learning, mentoring and awareness of different learning styles written up in Higson and Jones (2002). The idea was to get students used to the idea of reflection on their experiences well before they entered the placement year.

Effect of lutein and antioxidant dietary supplementation on contrast sensitivity in age-related macular disease:A randomized controlled trial

Objective: The aim of the study is to determine the effect of lutein combined with vitamin and mineral supplementation on contrast sensitivity in people with age-related macular disease (ARMD). Design: A prospective, 9-month, double-masked randomized controlled trial. Setting: Aston University, Birmingham, UK and a UK optometric clinical practice. Subjects: Age-related maculopathy (ARM) and atrophic age-related macular degeneration (AMD) participants were randomized (using a random number generator) to either placebo (n = 10) or active (n=15) groups. Three of the placebo group and two of the active group dropped out. Interventions: The active group supplemented daily with 6 mg lutein combined with vitamins and minerals. The outcome measure was contrast sensitivity (CS) measured using the Pelli-Robson chart, for which the study had 80% power at the 5% significance level to detect a change of 0.3log units. Results: The CS score increased by 0.07 ± 0.07 and decreased by 0.02 ± 0.18 log units for the placebo and active groups, respectively. The difference between these values is not statistically significant (z = 0.903, P = 0.376). Conclusion: The results suggest that 6 mg of lutein supplementation in combination with other antioxidants is not beneficial for this group. Further work is required to establish optimum dosage levels.

Size distribution curves of senile plaques in patients with Alzheimer’s disease: do plaques grow according to the log-normal model?

The size frequency distributions of diffuse, primitive and cored senile plaques (SP) were studied in single sections of the temporal lobe from 10 patients with Alzheimer’s disease (AD). The size distribution curves were unimodal and positively skewed. The size distribution curve of the diffuse plaques was shifted towards larger plaques while those of the neuritic and cored plaques were shifted towards smaller plaques. The neuritic/diffuse plaque ratio was maximal in the 11 – 30 micron size class and the cored/ diffuse plaque ratio in the 21 – 30 micron size class. The size distribution curves of the three types of plaque deviated significantly from a log-normal distribution. Distributions expressed on a logarithmic scale were ‘leptokurtic’, i.e. with excess of observations near the mean. These results suggest that SP in AD grow to within a more restricted size range than predicted from a log-normal model. In addition, there appear to be differences in the patterns of growth of diffuse, primitive and cored plaques. If neuritic and cored plaques develop from earlier diffuse plaques, then smaller diffuse plaques are more likely to be converted to mature plaques.

Radioimmunoassay of insulin and glucagon with studies on the obese hyperglycaemic syndrome in mice

Sensitive and precise radioimmunoassays for insulin and glucagon have been established. Although it was possible to employ similar precepts to the development of both hormone assays, the establishment of a reliable glucagon radioimmunoassay was complicated by the poor immunogenicity and instability of the peptide. Thus, unlike insulin antisera which were prepared by monthly injection of guinea pigs with crystalline insulin emulsified in adjuvant, the successful production of glucagon antisera was accomplished by immunisation of rabbits and guinea pigs with glucagon covalently linked to bovine plasma albumin. The conventional chloramine-T iodination with purification by gel chromatography was only suitable for the production of labelled insulin. Quality tracer for use in the glucagon radioimmunoassay was prepared by trace iodination, with subsequent purification of monoiodinated glucagon by anion exchange chromatography. Separation of free and antibody bound moieties by coated charcoal was applicable to both hormone assays, and a computerised data processing system, relying on logit-log transformation, was used to analyse all assay results. The assays were employed to evaluate the regulation of endocrine pancreatic function and the role of insulin and glucagon in the pathogenesis of the obese hyperglycaemic syndrome in mice. In the homozygous (ob/ob) condition, mice of the Birmingham strain were characterised by numerous abnormalities of glucose homeostasis, several of which were detected in heterozygous (ob/+) mice. Obese mice exhibited pancreatic alpha cell dysfunction and hyperglucagonaemia. Investigation of this defect revealed a marked insensitivity of an insulin dependent glucose sensing mechanism that inhibited glucagon secretion. Although circulating glucagon was of minor importance in the maintenance of hyperinsulinaemia, lack of suppression of alpha cell function by glucose and insulin contributed significantly to both the insulin insensitivity and the hyperglycaemia of obese mice.

Ecological studies on high-rate biological filters with special reference to microbial biosynthesis and nitrification

Pilot scale studies of high rate filtration were initiated to assess its potential as either a primary 'roughing' filter to alleviate the seasonal overloading of low rate filters on Hereford sewage treatment works - caused by wastes from cider production - or as a two stage high rate process to provide complete sewage treatment. Four mineral and four plastic primary filter media and two plastic secondary filter media were studied. The hydraulic loading applied to the primary plastic media (11.2 m3 /m3 .d) was twice that applied to the mineral media. The plastic media removed an average around 66 percent and the mineral media around 73 percent of the BOD applied when the 90 percentile BOD concentration was 563 mg/1. At a hydraulic loading of 4 m3 /m3 .d the secondary filters removed most of the POD from partially settled primary filter effluents, with one secondary effluent satisfying a 25 mg/1 BOD and 30 mg/1 SS standard. No significant degree of nitrification was achieved. Fungi dominated the biological film of the primary filters, with invertebrate grazers having little influence on film levels. Ponding did not arise, and modular media supported lower film levels than random-fill types. Secondary filter film levels were low, being dominated by bacteria. The biological loading applied to the filters was related to sludge dewaterability, with the most readily conditionable sludges produced by filters supporting heavy film. Sludges produced by random-fill media could be dewatered as readily as those produced by low rate filters treating the same sewage. Laboratory scale studies showed a relationship between log effluent BOD and nitrification achieved by biological filters. This relationship and the relationship between BOD load applied and removed observed in all filter media could he used to optimise operating conditions required in biological filters to achieve given effluent BOD and ammoniacal nitrogen standards.

The influence of the chemical nature of dispersed phase on stability in oil-in-water emulsions

Some of the problems arising from the inherent instability of emulsions are discussed. Aspects of emulsion stability are described and particular attention is given to the influence of the chemical nature of the dispersed phase on adsorbed film structure and stability, Emulsion stability has been measured by a photomicrographic technique. Electrophoresis, interfacial tension and droplet rest-time data were also obtained. Emulsions were prepared using a range of oils, including aliphatic and aromatic hydrocarbons, dispersed In a solution of sodium dodecyl sulphate. In some cases a small amount of alkane or alkanol was incorporated into the oil phase. In general the findings agree with the classical view that the stability of oil-in-water emulsions is favoured by a closely packed interfacial film and appreciable electric charge on the droplets. The inclusion of non-ionic alcohol leads to enhanced stability, presumably owing to the formation of a "mixed" interfacial film which is more closely packed and probably more coherent than that of the anionic surfactant alone. In some instances differences in stability cannot he accounted for simply by differences in interfacial adsorption or droplet charge. Alternative explanations are discussed and it is postulated that the coarsening of emulsions may occur not only hy coalescence but also through the migration of oil from small droplets to larger ones by molecular diffusion. The viability of using the coalescence rates of droplets at a plane interface as a guide to emulsion stability has been researched. The construction of a suitable apparatus and the development of a standard testing procedure are described. Coalescence-time distributions may be correlated by equations similar to those presented by other workers, or by an analysis based upon the log-normal function. Stability parameters for a range of oils are discussed in terms of differences in film drainage and the natl1re of the interfacial film. Despite some broad correlations there is generally poor agreement between droplet and emulsion stabilities. It is concluded that hydrodynamic factors largely determine droplet stability in the systems studied. Consequently droplet rest-time measurements do not provide a sensible indication of emulsion stability,

Effects of yellow filters on visual acuity, contrast sensitivity and reading under conditions of forward light scatter

Background Yellow filters are sometimes recommended to people with low vision. Our aim was investigate the effects of three commercial yellow filters on visual acuity and contrast sensitivity (with and without glare) and reading (without glare) under conditions of forward light scatter (FLS). Method Fifty-five healthy subjects were assessed with Corning Photochromic Filters (CPFs) 450, 511 and 527 and a filter producing FLS. The effects on log MAR visual acuity, Pelli–Robson contrast sensitivity with and without glare, and reading (measured with MNRead charts) without glare were determined. Results Statistically significant differences were found between the overall effect of glare and between CPFs for visual acuity and contrast sensitivity. A gradual decline in visual acuity, contrast sensitivity and reading with increasing CPF absorption was noted. Conclusion Effects of CPF450, 511, 527 on visual acuity, contrast sensitivity and reading under conditions of FLS were negative but not clinically significant.

Testing for financial crashes using the Log Periodic Power Law model

Many papers claim that a Log Periodic Power Law (LPPL) model fitted to financial market bubbles that precede large market falls or 'crashes', contains parameters that are confined within certain ranges. Further, it is claimed that the underlying model is based on influence percolation and a martingale condition. This paper examines these claims and their validity for capturing large price falls in the Hang Seng stock market index over the period 1970 to 2008. The fitted LPPLs have parameter values within the ranges specified post hoc by Johansen and Sornette (2001) for only seven of these 11 crashes. Interestingly, the LPPL fit could have predicted the substantial fall in the Hang Seng index during the recent global downturn. Overall, the mechanism posited as underlying the LPPL model does not do so, and the data used to support the fit of the LPPL model to bubbles does so only partially. © 2013.

Statnote 35: are the data log-normal?

In many of the Statnotes described in this series, the statistical tests assume the data are a random sample from a normal distribution These Statnotes include most of the familiar statistical tests such as the ‘t’ test, analysis of variance (ANOVA), and Pearson’s correlation coefficient (‘r’). Nevertheless, many variables exhibit a more or less ‘skewed’ distribution. A skewed distribution is asymmetrical and the mean is displaced either to the left (positive skew) or to the right (negative skew). If the mean of the distribution is low, the degree of variation large, and when values can only be positive, a positively skewed distribution is usually the result. Many distributions have potentially a low mean and high variance including that of the abundance of bacterial species on plants, the latent period of an infectious disease, and the sensitivity of certain fungi to fungicides. These positively skewed distributions are often fitted successfully by a variant of the normal distribution called the log-normal distribution. This statnote describes fitting the log-normal distribution with reference to two scenarios: (1) the frequency distribution of bacterial numbers isolated from cloths in a domestic environment and (2), the sizes of lichenised ‘areolae’ growing on the hypothalus of Rhizocarpon geographicum (L.) DC.