Method for epitope selection of antisera for immunohistology

Polyclonal anti-laminin serum was affinity-purified on paraformaldehyde-fixed laminin on a nitrocellulose filter. The purified antibodies were tested for their specificity in immunohistological stainings on frozen sections of paraformaldehyde-fixed tissue. As compared to the initial polyclonal serum, the purified antibodies increased the specificity of antigen detection, since all background caused by nonspecific reactions was eliminated. This technique promises to be very useful for immunohistological analysis using light and electron microscopy.     

Protocols for data generation for predictive modeling

Summary Essential to the development of useful predictive models for foods is the collection of appropriate data. Within the UK Predictive Food Microbiology Program, a series of documents have been produced to aid the standardization of data collection by a number of laboratories. Documents include a protocols form, notes on experimental design, notes on the accuracy of counts by plating, the preferred method of calculating a plate count value, preferred MPN tables and the preferred methods of recording data values. These documents have proven useful in aiding collaboration between laboratories.     

Method for Coding Data on Protozoan Strains for Computers

SYNOPSIS. Traditionally, observations on the nature of protozoa have been published in periodicals or books, or remain buried in research notebooks. The retrieval and processing of information on a particular species or strain are dependent solely upon individual investigators. Although various modern methods have been applied to the study of protozoa, no attempt has been made to develop a system with which information on protozoan strains can be stored, retrieved easily, and processed for various analyses by computer technology. Based upon an existing system for encoding data on bacterial strains, a complementary system applicable to protozoan strains was developed and is described herein.     

Reward for Bdellovibrio bacteriovorus for preying on a polyhydroxyalkanoate producer

Bdellovibrio bacteriovorus HD100 is an obligate predator that invades and grows within the periplasm of Gram‐negative bacteria, including mcl‐polyhydroxyalkanoate (PHA) producers such as Pseudomonas putida. We investigated the impact of prey PHA content on the predator fitness and the potential advantages for preying on a PHA producer. Using a new procedure to control P. putida KT2442 cell size we demonstrated that the number of Bdellovibrio progeny depends on the prey biomass and not on the viable prey cell number or PHA content. The presence of mcl‐PHA hydrolysed products in the culture supernatant after predation on P. putida KT42Z, a PHA producing strain lacking PhaZ depolymerase, confirmed the ability of Bdellovibrio to degrade the prey's PHA. Predator motility was higher when growing on PHA accumulating prey. External addition of PHA polymer (latex suspension) to Bdellovibrio preying on the PHA minus mutant P. putida KT42C1 restored predator movement, suggesting that PHA is a key prey component to sustain predator swimming speed. High velocities observed in Bdellovibrio preying on the PHA producing strain were correlated to high intracellular ATP levels of the predator. These effects brought Bdellovibrio fitness benefits as predation on PHA producers was more efficient than predation on non‐producing bacteria.     

Cercariometry for detection of transmission sites for schistosomiasis

Cercariometry provided information on diurnal fluctuation, seasonal and spatial distribution of cercariae in the suitable natural water bodies. There was an apparent mismatch between the results of cercariometry and snail sampling. Water, which cercariometry showed to contain cercariae was potentially infective, although the resultant worm load of sentinel rodents may not bear a linear relationship with cercarial density. Cercariometry has some weakness in practices and analysis of data, however, it provides the valuable information on the active transmission sites of schistosomiasis.     

A Decision-Tree Strategy for Combining Diagnostic Tests for Prediction

In the context of medical screening, various diagnostic tests have been developed for determining whether a disease is present in an individual. Similarly, in the context of toxicological screening, a variety of short-term assays have been developed to predict whether a chemical would be carcinogenic if tested in a long-term bioassay. In both contexts, it is a challenge to combine the results of several predictive tests in a way that improves on the predictivity of the individual tests. Increases in positive predictivity can be accompanied by decreases in negative predictivity, and vice versa. This article presents a decision-tree classification model for combining results from several independent short-term or diagnostic tests to quantify the likelihood of a true positive result (patient has disease, or chemical is carcinogenic). The decision-tree strategy determines the most advantageous sequence for conducting the predictive tests. The classification model is based on statistical confidence limits on the predictive probability of disease (carcinogenicity) rather than on the central estimate of the predictive probability. This model is applied to the assessment of the abilities of four short-term tests in the prediction of chemical carcinogenicity under the assumption of independence among the four tests, and is used to demonstrate a testing strategy for the application of three pancreatic cancer diagnostic tests.     

Experimental evidence for a semi-flexible conformation for arabinoxylans

Purified water-soluble arabinoxylans from wheat flour were deferuloylated and fractionated into six fractions by graded ethanol precipitation. Further fractionation by HPSEC on Sephacryl S500 resulted in 48 subfractions with low polydispersity index. Conformational characteristics (persistence length q, hydrodynamic parameter v and Mark-Houwink exponent a) were similar among all subfractions and fitted with a semi-flexible conformation, whatever their structural characteristics. Substitution degree of the xylan backbone by arabinose residues has no influence on the conformation of arabinoxylans.     

Testing for density dependence allowing for weather effects

A test for density dependence in time-series data allowing for weather effects is presented. The test is based on a discrete time autoregressive model for changes in population density with a covariate for the effects of weather. The distribution of the test statistic on the null hypothesis of density independence is obtained by parametric bootstrapping. A computer simulation exercise is used to demonstrate the gain in statistical power by allowing for weather effects. Application of the method to time-series data on three species of butterflies and two species of songbirds showed stronger evidence of density dependence than two standard tests. Received: 4 October 1996 / Accepted: 4 August 1997     

Analysis of Bead Sizes for MR Capsules Labeled for Sprinkle

The bead sizes used in approved modified release capsules labeled for sprinkling on food was investigated to generate bead size guidelines for generic products labeled for sprinkling. The conclusions from a survey of FDA databases were corroborated with experimental data obtained by measuring the bead sizes of several reference-listed drugs on the market labeled for administration by sprinkling on food. The experimental data show that majority of the marketed products were found to have bead sizes of less than 1,500 microm (1.5 mm). Based on this information, a bead size of less than 1,500 microm should generally be considered acceptable for use in generic products labeled for sprinkling.     

The surface-based approach for DNA computation is unreliable for SAT

Previous research presented DNA computing on surfaces, which applied to each clause three operations:"mark","destroy", and "unmark", and demonstrated how to solve a four-variable four-clause instance of the 3-SAT. It was claimed that only the strands satisfying the problem remained on the surface at the end of the computation and the surface-based approach was capable of scaling up to larger 3-SAT problems. Accordingly, the identities of the strands were only determined in the"readout" step for the correct solutions to the problem without checking if the strands really satisfied the problem. Thus, based on the claim above, the surface-based approach became a polynomial-time algorithm. In this paper, we show that for some instance of SAT, at the end of the computation all the remaining strands falsify the instance. However, by the previous claim all the strands falsifying the problems would be regarded as the correct solutions to the problems. Therefore, the DNA computing on surfaces is unreliable. For this reason, it is necessary to add a "verify" step after the "readout" step to check if the strands remaining on the surface at the end of the computation really satisfy the problem.     

Modeling for Understanding v. Modeling for Numbers

I draw a distinction between Modeling for Numbers, which aims to address how much, when, and where questions, and Modeling for Understanding, which aims to address how and why questions. For-numbers models are often empirical, which can be more accurate than their mechanistic analogues as long as they are well calibrated and predictions are made within the domain of the calibration data. To extrapolate beyond the domain of available system-level data, for-numbers models should be mechanistic, relying on the ability to calibrate to the system components even if it is not possible to calibrate to the system itself. However, development of a mechanistic model that is reliable depends on an adequate understanding of the system. This understanding is best advanced using a for-understanding modeling approach. To address how and why questions, for-understanding models have to be mechanistic. The best of these for-understanding models are focused on specific questions, stripped of extraneous detail, and elegantly simple. Once the mechanisms are well understood, one can then decide if the benefits of incorporating the mechanism in a for-numbers model is worth the added complexity and the uncertainty associated with estimating the additional model parameters.     

Perspectives for subunit vaccines for the control of ticks

For the first time, successful vaccination against a tick has been carried out using a single defined antigen. Further, it has been shown that it is feasible to produce active antigenic material by recombinant DNA technology. This represents a significant advance towards the development of an alternative means of tick control. Nevertheless, as with any new product and new technology, much developmental work still has to be done before one can be confident that a practical means of tick control will result. From the published information, it does not seem that research on vaccines against other tick species is as advanced as that on Boophilus microplus. The work on B. microplus may, however, provide a short cut to the development of further tick vaccines.     

Tests and diagnostic plots for detecting lack-of-fit for circular-linear regression models

Summary .   Regression diagnostics and lack-of-fit tests mainly focus on linear--linear regression models. When the design points are distributed on the circumference of a circle, difficulties arise as there is no natural starting point or origin. Most classical lack-of-fit tests require an arbitrarily chosen origin, but different choices may result in different conclusions. We propose a graphical diagnostic tool and a closely related lack-of-fit test, which does not require a natural starting point. The method is based on regional residuals which are defined on arcs of the circle. The graphical method formally locates and visualizes subsets of poorly fitting observations on the circle. A data example from the food technology is used to point out the before-mentioned problems with conventional lack-of-fit tests and to illustrate the strength of the methodology based on regional residuals in detecting and localizing departures from the no-effect hypothesis. A small simulation study shows a good performance of the regional residual test in case of both global and local deviations from the null model. Finally, the ideas are extended to the case of more than one predictor variable.     

A KPSS test for stationarity for spatial point processes

Summary .   We propose a formal method to test stationarity for spatial point processes. The proposed test statistic is based on the integrated squared deviations of observed counts of events from their means estimated under stationarity. We show that the resulting test statistic converges in distribution to a functional of a two-dimensional Brownian motion. To conduct the test, we compare the calculated statistic with the upper tail critical values of this functional. Our method requires only a weak dependence condition on the process but does not assume any parametric model for it. As a result, it can be applied to a wide class of spatial point process models. We study the efficacy of the test through both simulations and applications to two real data examples that were previously suspected to be nonstationary based on graphical evidence. Our test formally confirmed the suspected nonstationarity for both data.     

Networks for all

A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008.     

蛋白质二级结构预测方法的评价

目前评价蛋白质二级结构预测方法主要考虑预测准确率,并没有充分考虑方法自身参数对方法的影响。本文提出一种新型评价方法,将内在评价与外在评价相结合评价预测方法的优劣。以基于混合并行遗传算法的蛋白质二级结构预测方法为例,通过内在评价,合理选取内在参数——切片长度和组内类别数,有效提高预测准确率,同时,通过外在评价,与其他基于随机算法的蛋白质二级结构预测算法比较和与CASP所提供的结论比较,说明了方法的有效性与正确性,以此验证内在评价和外在评价的客观性、公正性和全面性。     

Correcting for single ascertainment by truncation for a quantitative trait.

Two methods for correcting for single ascertainment by truncation are compared. These methods are (1) conditioning on the phenotype of the proband and (2) conditioning on the event that the proband phenotype is greater than a threshold. The use of a constraint on model parameters is considered. The lack of robustness of this method to misspecifiction of the constraint has been demonstrated by Rao et al. It is noted that the constraint on model parameters used by Rao et al. is equivalent to an encoding of knowledge derived from a random sample, and an alternative representation of this information that has superior robustness properties is proposed.     

Guidelines for hurricane and disaster preparation for animal facilities

Animal facilities are vulnerable to hurricanes and other natural disasters, which can endanger lives and disrupt critical animal care routines. Facility managers must therefore prepare a rigorous emergency plan that ensures human safety while considering the specific needs of all animals on site. The author presents guidelines and recommendations for disaster preparedness based on her experience at a facility in Florida, where hurricanes are relatively common. An effective plan must include a priority system, a well-trained emergency response team, efficient communication methods and concrete provisions for animals and employees.     

Standards for Approval of Hospitals for Graduate Training

The assessment program for approval of hospitals for training in specialties has been augmented by survey visits. Surveyors for the Canadian Council on Hospital Accreditation have acted on behalf of the Royal College of Physicians and Surgeons of Canada and have assisted in the formulation of standard criteria for evaluation of teaching programs. Areas where considerable variation in program exists and where further standardization might profitably be developed are suggested. It is recommended that periodic on-the-site visits be made to all specialty training hospitals. Standards should be further elucidated to guide teachers, students and Royal College surveyors alike. It is emphasized that standards cannot be used to assess the calibre of teaching and learning, but can be employed to assist in evaluating the teachings and learning media that are likely to produce good (or poor) results.     

Searching for a model for use in vegetation analysis

Summary Indirect gradient analysis methods require an explicit vegetation model which must be based on direct gradient analysis studies. Various vegetation models are reviewed. Field evidence for the models is discussed. Experimental studies of species response to environmental gradients are reviewed and discussed. Three types of gradient are recognized as important for development of models: indirect environmental gradients where the environmental factor has no direct physiological influence on plant growth e.g. elevation; direct environmental gradients where the factor has a direct physiological effect on growth but is not an essential resource, e.g. pH; resource gradients where the factor is an essential resource for plant growth. The behaviour of the ecological carrying capacity and the role of competition along such gradients are shown to be important for developing vegetation models.