A program for logistic prediction modelling

A computer program has been developed that can be used for analysing a binary outcome variable and a set of regressors of type interval with a logistic (i.e. nonlinear) model.     

VisiCoor: A simple program for visualization of proteins

A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.     

A robust co-localisation measurement utilising z-stack image intensity similarities for biological studies

Background

Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method

In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results

The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.     

A simple stereoselective synthesis and biological evaluation of FR181157: orally active prostacyclin mimetic

Synthetic method of novel prostaglandin (PG) mimetic: FR181175 without PG skeleton are described. The key to success is creation of a chiral epoxide using Sharpless AD reaction with high ee yield. FR181157 shows high potency and agonist efficacy at the IP receptor and has good bioavailability.     

A simple biological assay for relaxin measurement.

1. Relaxin (R) is considered a gestation hormone with an insulin-like molecular structure. Its physiological importance is significant in the reproduction process. 2. Different methods of biologically assaying R have been published but electrophysiology techniques on uterus and ileum of rat have never been used. 3. A protein fraction was obtained from ovarian tissue of the rat and used to measure electrophysiological activity in vivo and in vitro. 4. Protein recovered with R activity was similar to that in previous reports. 5. Reduction of 100% in contraction strength and 50% in its frequency was observed in ileum and in uterus respectively; it was only of 60%, but its frequency increased 43%. 6. Methodological considerations and some physiological aspects are discussed.     

A simple image analysis program for quantitative dot assays

Summary Dot assays are versatile, and are widely used for determining antigens and proteins. Because they require expensive equipment to be quantitative, often only qualitative dot results are reported. However, because the dot pattern is so regular, a simple image analysis program can determine mean dot grey levels, while handling irregular dot outlines, radial variations in colour within a dot, and varying or noisy sheet backgrounds. We describe a dot analysis program that runs on PCs under Windows, and permits quantitative dot assays to be run with inexpensive grayscale scanner input. The program is available from us as source and executable files. We present demonstration results for antigen and protein determinations.     

A simple method for estimation of phospholipids in biological objects

A simple method to estimate phospholipids is elaborated. This method is based on determination of optical density of phospholipid-molybdate complexes in chloroform. The method is used for the quantitative determination of phospholipids in biomembranes, liposomes and blood serum without their preliminary extraction, as well as in chloroform, methanol and chloroform-methanol solutions. It is also modified for the phospholipids determination in chromatographic fractions on silufol plates.     

A simple program for a phaseless recursive digital filter

A brief comparison of several types of digital filters is made and a simple subroutine implementing a recursive digital phaseless low and high pass filter is described. The subroutine, written in standard Fortran, is suitable for any computer with a Fortran IV compiler.     

A simple model for phase locking of biological oscillators

Summary A mathematical model is presented for phase locking of a biological oscillator to a sinusoidal stimulus. Analytical, numerical and topological considerations are used to discuss the patterns of phase locking as a function of the amplitude of the sinusoidal stimulus and the relative frequencies of the oscillator and the sinusoidal stimulus. The sorts of experimental data which are needed to make comparisons between theory and experiment are discussed.     

A HyperCard program for the identification of biological specimens

The authors with to make the following corrections to the abovepaper:

• page 64 and References: Omodeo, (1956) not (1965)
• page 68and References: Rosa, (1893) not (1981)
• Table I. Line 1. Cognetti,not Cogneni Line 20. delete (1906) Line 28. Kvavadze (1985)not (1975) Line 29. Kvavadze (1971) not (1981) Line 44.delete (1906) Line 52. delete (1906)
• page 68 in Note sectionthe address given should read ‘A.Colosimo,Departmentof Biochemical Sciences, University of Rome (La Sapienza),PiazzaleA.Moro I-00185, Rome, Italy.’

     

Diagrammatic representations for modelling biological knowledge

The contemporary research and development context in multidisciplinary biology has a serious requirement for integrating knowledge from disparate sources, and facilitating much-needed inter- and intra-disciplinary dialogue. A multiplicity of models arises when pluralistic approaches to modelling are followed, and also when there is not only a requirement to model systems and data, but also knowledge of systems and data. The challenges of addressing this multiplicity do not only include articulating the structure of complex systems, but also placing modelling within the framework of a process as well as a product. The graph representations presented here facilitate dialogue, modelling, clarification and specification of concepts, and the sharing of terms. This paper explores relationships between collections of graph representations. It is hoped that in future, when readers look at a node or a process in a graph, they will have a much deeper appreciation of relationships and context.     

A Hypercard program for the identification of biological specimens

A Hypercard-based software tool developed to provide help inthe identification of biological specimens is presented. Thepackage implements a matching algorithm that compares alphanumericstrings and runs on Macintosh computers, though its simple architecturecan be transferred to other computers and/or other programmingenvironments. The overall performance of the program and itseasy customization to specific problems are demonstrated bydiscussing at length one application in the field of earthwormidentification. Received on June 26, 1990; accepted on September 21, 1990     

Genetic distance: A simple quantitative measure of biological relatedness

We propose a new quantitative method of establishing the biological relatedness of two organisms, by means of comparison of the experimentally observed, differential-melting-curves of their DNAs which are assumed to depend on the detailed structure of the corresponding base pair sequences. In the light of recent experimental and theoretical results discussed in this paper, this assumption seems to be well justified. In the case of viruses and bacteria, analysis of available experimental data, demonstrates the straightforward applicability of the method in quantitative determinations of relatedness. In spite of certain difficulties arising in the application of the method to eucaryotes, we believe that it still could serve in obtaining at least first-order estimates of eucaryotic relatedness.     

A simple convenient biological dosimeter for monitoring solar UV-B radiation

The use of dry Bacillus subtilis spores as a biological dosimeter for the monitoring of solar UV-B (290-330 nm) radiation was described. Our field tests had supported the utility of this dosimeter as a reproducible and reliable sunlight dosimeter.