Likelihood-based estimation of microsatellite mutation rates

Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.

Ventilation rates in schools and pupil’s performance using computerized assessment tests

Research shows that poor indoor air quality (IAQ) in school buildings can cause a reduction in the students’ performance assessed by short-term computer-based tests; whereas good air quality in classrooms can enhance children's concentration and also teachers’ productivity. Investigation of air quality in classrooms helps us to characterise pollutant levels and implement corrective measures. Outdoor pollution, ventilation equipment, furnishings, and human activities affect IAQ. In school classrooms, the occupancy density is high (1.8–2.4 m2/person) compared to offices (10 m2/person). Ventilation systems expend energy and there is a trend to save energy by reducing ventilation rates. We need to establish the minimum acceptable level of fresh air required for the health of the occupants. This paper describes a project, which will aim to investigate the effect of IAQ and ventilation rates on pupils’ performance and health using psychological tests. The aim is to recommend suitable ventilation rates for classrooms and examine the suitability of the air quality guidelines for classrooms. The air quality, ventilation rates and pupils’ performance in classrooms will be evaluated in parallel measurements. In addition, Visual Analogue Scales will be used to assess subjective perception of the classroom environment and SBS symptoms. Pupil performance will be measured with Computerised Assessment Tests (CAT), and Pen and Paper Performance Tasks while physical parameters of the classroom environment will be recorded using an advanced data logging system. A total number of 20 primary schools in the Reading area are expected to participate in the present investigation, and the pupils participating in this study will be within the age group of 9–11 years. On completion of the project, based on the overall data recommendations for suitable ventilation rates for schools will be formulated.

Ventilation rates in schools

Research shows that poor indoor air quality in school buildings can cause a reduction in the students' performance assessed by short term computer based tests; whereas good air quality in classrooms can enhance children's concentration and also teachers' productivity. Investigation of air quality in classrooms helps us to characterise pollutant levels and implement corrective measures. Outdoor pollution, ventilation equipment, furnishings, and human activities affect indoor air quality. In school classrooms the occupancy density is high (1.8 to 2.4 m(2)/person) compared to offices (10 m(2) /person). Ventilation systems expend energy and there is a trend to save energy by reducing ventilation rates. We need to establish the minimum acceptable level of fresh air required for the health of the occupants. This paper describes a project which will aim to investigate the effect of indoor air quality and ventilation rates on pupils' performance and health using psychological tests. The aim is to recommend suitable ventilation rates for classrooms and examine the suitability of the air quality guidelines for classrooms.

Protocol for the PINCER trial: a cluster randomised trial comparing the effectiveness of a pharmacist-led IT-based intervention with simple feedback in reducing rates of clinically important errors in medicines management in general practices

Background: Medication errors are an important cause of morbidity and mortality in primary care. The aims of this study are to determine the effectiveness, cost effectiveness and acceptability of a pharmacist-led information-technology-based complex intervention compared with simple feedback in reducing proportions of patients at risk from potentially hazardous prescribing and medicines management in general (family) practice. Methods: Research subject group: "At-risk" patients registered with computerised general practices in two geographical regions in England. Design: Parallel group pragmatic cluster randomised trial. Interventions: Practices will be randomised to either: (i) Computer-generated feedback; or (ii) Pharmacist-led intervention comprising of computer-generated feedback, educational outreach and dedicated support. Primary outcome measures: The proportion of patients in each practice at six and 12 months post intervention: - with a computer-recorded history of peptic ulcer being prescribed non-selective non-steroidal anti-inflammatory drugs - with a computer-recorded diagnosis of asthma being prescribed beta-blockers - aged 75 years and older receiving long-term prescriptions for angiotensin converting enzyme inhibitors or loop diuretics without a recorded assessment of renal function and electrolytes in the preceding 15 months. Secondary outcome measures; These relate to a number of other examples of potentially hazardous prescribing and medicines management. Economic analysis: An economic evaluation will be done of the cost per error avoided, from the perspective of the UK National Health Service (NHS), comparing the pharmacist-led intervention with simple feedback. Qualitative analysis: A qualitative study will be conducted to explore the views and experiences of health care professionals and NHS managers concerning the interventions, and investigate possible reasons why the interventions prove effective, or conversely prove ineffective. Sample size: 34 practices in each of the two treatment arms would provide at least 80% power (two-tailed alpha of 0.05) to demonstrate a 50% reduction in error rates for each of the three primary outcome measures in the pharmacist-led intervention arm compared with a 11% reduction in the simple feedback arm. Discussion: At the time of submission of this article, 72 general practices have been recruited (36 in each arm of the trial) and the interventions have been delivered. Analysis has not yet been undertaken.

Ventilation rates in schools

Research shows that poor indoor air quality (IAQ) in school buildings can cause a reduction in the students' performance assessed by short-term computer-based tests: whereas good air quality in classrooms can enhance children's concentration and also teachers' productivity. Investigation of air quality in classrooms helps us to characterise pollutant levels and implement corrective measures. Outdoor pollution, ventilation equipment, furnishings, and human activities affect IAQ. In school classrooms, the occupancy density is high (1.8-2.4m(2)/person) compared to offices (10 m(2)/person). Ventilation systems expend energy and there is a trend to save energy by reducing ventilation rates. We need to establish the minimum acceptable level of fresh air required for the health of the occupants. This paper describes a project, which will aim to investigate the effect of IAQ and ventilation rates on pupils' performance and health using psychological tests. The aim is to recommend suitable ventilation rates for classrooms and examine the suitability of the air quality guidelines for classrooms. The air quality, ventilation rates and pupils' performance in classrooms will be evaluated in parallel measurements. In addition, Visual Analogue Scales will be used to assess subjective perception of the classroom environment and SBS symptoms. Pupil performance will be measured with Computerised Assessment Tests (CAT), and Pen and Paper Performance Tasks while physical parameters of the classroom environment will be recorded using an advanced data logging system. A total number of 20 primary schools in the Reading area are expected to participate in the present investigation, and the pupils participating in this study will be within the age group of 9-11 years. On completion of the project, based oil the overall data recommendations for suitable ventilation rates for schools will be formulated. (C) 2006 Elsevier Ltd. All rights reserved.

Temperature and the development rates of thrips: evidence for a constraint on local adaptation?

Typically, the relationship between insect development and temperature is described by two characteristics: the minimum temperature needed for development to occur (T-min) and the number of day degrees required (DDR) for the completion of development. We investigated these characteristics in three English populations of Thrips major and T tabaci [Cawood, Yorkshire (N53degrees49', W1degrees7'); Boxworth, Cambridgeshire (N52degrees15', W0degrees1'); Silwood Park, Berkshire (N51degrees24', W0degrees38')], and two populations of Frankliniella occidentalis (Cawood; Silwood Park). While there were no significant differences among populations in either T-min (mean for T major = 7.0degreesC; T tabaci = 5.9degreesC; F. occidentalis = 6.7degreesC) or DDR (mean for T major = 229.9; T tabaci = 260.8; F occidentalis = 233.4), there were significant differences in the relationship between temperature and body size, suggesting the presence of geographic variation in this trait. Using published data, in addition to those newly collected, we found a negative relationship between T-min. and DDR for F occidentalis and T tabaci, supporting the hypothesis that a trade-off between T-min and DDR may constrain adaptation to local climatic conditions.

Neuromuscular junction morphology, fiber-type proportions, and satellite-cell proliferation rates are altered in MyoD(-/-) mice

Gene compensation by members of the myogenic regulatory factor (MRF) family has been proposed to explain the apparent normal adult phenotype of MyoD(-/-) mice. Nerve and field stimulation were used to investigate contraction properties of muscle from MyoD(-/-) mice, and molecular approaches were used to investigate satellite-cell behavior. We demonstrate that MyoD deletion results in major alterations in the organization of the neuromuscular junction, which have a dramatic influence on the physiological contractile properties of skeletal muscle. Second, we show that the lineage progression of satellite cells (especially initial proliferation) in the absence of MyoD is abnormal and linked to perturbations in the nuclear localization of beta-catenin, a key readout of canonical Wnt signaling. These results show that MyoD has unique functions in both developing and adult skeletal muscle that are not carried out by other members of the MRF family.

Use of the LMS adaptive signal processing technique to improve signal data rates from practical oil well logging equipment

The simulation and development work that has been undertaken to produce a signal equaliser used to improve the data rates from oil well logging instruments is presented. The instruments are lowered into the drill bore hole suspended by a cable which has poor electrical characteristics. The equaliser described in the paper corrects for the distortions that occur from the cable (dispersion and attenuation) with the result that the instrument can send data at 100 K.bits/second down its own suspension cable of 12 Km in length. The use of simulation techniques and tools were invaluable in generating a model for the distortions and proved to be a useful tool when site testing was not available.

Ensemble prediction for nowcasting with a convection-permitting model—I: description of the system and the impact of radar-derived surface precipitation rates

A key strategy to improve the skill of quantitative predictions of precipitation, as well as hazardous weather such as severe thunderstorms and flash floods is to exploit the use of observations of convective activity (e.g. from radar). In this paper, a convection-permitting ensemble prediction system (EPS) aimed at addressing the problems of forecasting localized weather events with relatively short predictability time scale and based on a 1.5 km grid-length version of the Met Office Unified Model is presented. Particular attention is given to the impact of using predicted observations of radar-derived precipitation intensity in the ensemble transform Kalman filter (ETKF) used within the EPS. Our initial results based on the use of a 24-member ensemble of forecasts for two summer case studies show that the convective-scale EPS produces fairly reliable forecasts of temperature, horizontal winds and relative humidity at 1 h lead time, as evident from the inspection of rank histograms. On the other hand, the rank histograms seem also to show that the EPS generates too much spread for forecasts of (i) surface pressure and (ii) surface precipitation intensity. These may indicate that for (i) the value of surface pressure observation error standard deviation used to generate surface pressure rank histograms is too large and for (ii) may be the result of non-Gaussian precipitation observation errors. However, further investigations are needed to better understand these findings. Finally, the inclusion of predicted observations of precipitation from radar in the 24-member EPS considered in this paper does not seem to improve the 1-h lead time forecast skill.

Dissolution rates of earthworm-secreted calcium carbonate

The dissolution of CaCO3 granules secreted by earthworms in soil leaching columns was governed by soil pH and exchange sites available for Ca. Results indicate that granules could last for significant periods of time in soils and that, therefore, granules could be an important source of soil calcite.

Detecting intraday periodicities with application to high frequency exchange rates

Many recent papers have documented periodicities in returns, return volatility, bid–ask spreads and trading volume, in both equity and foreign exchange markets. We propose and employ a new test for detecting subtle periodicities in time series data based on a signal coherence function. The technique is applied to a set of seven half-hourly exchange rate series. Overall, we find the signal coherence to be maximal at the 8-h and 12-h frequencies. Retaining only the most coherent frequencies for each series, we implement a trading rule that is based on these observed periodicities. Our results demonstrate in all cases except one that, in gross terms, the rules can generate returns that are considerably greater than those of a buy-and-hold strategy, although they cannot retain their profitability net of transactions costs. We conjecture that this methodology could constitute an important tool for financial market researchers which will enable them to detect, quantify and rank the various periodic components in financial data better.