Biomedical subjects

M Astrand

Publications and source records attributed to M Astrand.

3 recordsLinked to original sources

PubMed2003

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

MOTIVATION: When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations. RESULTS: We present three methods of performing normalization at the probe intensity level. These methods are called complete data methods because they make use of data from all arrays in an experiment to form the normalizing relation. These algorithms are compared to two methods that make use of a baseline array: a one number scaling based algorithm and a method that uses a non-linear normalizing relation by comparing the variability and bias of an expression measure. Two publicly available datasets are used to carry out the comparisons. The simplest and quickest complete data method is found to perform favorably. AVAILABILITY: Software implementing all three of the complete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html

Algorithms↗

PubMed1999

Endocrine and behavioral traits in low-avoidance Sprague-Dawley rats.

In the present series of experiments, we have examined the endocrine profile of two stable colonies of Sprague-Dawley rats, here labeled Stock A, and Stock B, differing markedly in their ability to acquire a conditioned avoidance response. On separate occasions, the animals were subjected to five daily sessions (approximately 20 trials per 15 min session) of conditioned avoidance training, measurements of startle reactivity to an auditory stimulation and open-field spontaneous locomotor activity observations. The experiments were concluded by taking blood samples for later analysis of plasma glucose and plasma levels of the following hormones: insulin, gastrin, CCK, glucagon, somatostatin, oxytocin and corticosterone. The low-performing Stock B animals were characterized by [1] being more reactive to sensory stimulation: higher startle amplitude and shorter startle latency; [2] having higher plasma insulin and corticosterone levels, whereas plasma gastrin and oxytocin were significantly lowered and a strong tendency for a decrease also in plasma CCK. There were no differences in spontaneous locomotor activity between the two substrains. Taking total variability in avoidance performance into account, there was a statistically significant positive correlation between plasma oxytocin, as well as gastrin, levels and avoidance performance. The evidence obtained here, and in other laboratories, suggests that the Stock B animals display hormonal changes indicative of a submissive-defensive reaction pattern. Thus, the avoidance acquisition deficits displayed by the present Sprague-Dawley stocks A and B, are in all probability caused by emotional reactions when challenged with external stimuli requiring active responding.

Acoustic Stimulation↗

PubMed1997

[Decreasing number of orchiectomies in prostatic cancer. Results of 9-year registration of the disease are reviewed].

There are several controversies regarding the management of prostate cancer. Whether curative treatment (e.g. radiotherapy and total prostatectomy) prolongs survival remains uncertain. Conservative management is beset with such unresolved issues as the effect on tumour progression of early instituted hormonal treatment and of treatment deferral. Since the outcome of the different types of treatment is unclear the value of screening and early detection remains uncertain. Owing to such issues as these, and the divergent views on prostate cancer, there is an urgent need of auditing. To co-ordinate prostate cancer care in the South-east Region of Sweden, a local management programme with principles for investigation and treatment has been used since 1987. An important feature of the programme is a register containing information on all cases of prostate cancer in the region, including the patient's national registration number, date of diagnosis, basis of diagnosis (cytology, pathology), tumour stage, histological grade, first line treatment, and date and cause of death. Secondary treatment has also been recorded since 1990, and treatment with prostate specific antigen since 1992. From 1987 to 1995, a total of 5,939 cases of prostate cancer were registered, the annual total increasing from 531 to 779 in 1993, after which there was a slight overall decrease but a small increase in the proportion of local tumours. The proportion of incidental tumours followed the same pattern as the transurethral prostatectomy rate in the region. M- and N-categorisation were done to a greater extent in the under-70 than in the over-70 age group. Orchidectomy is rapidly being replaced by treatment with GnRH (gonadotrophin-releasing hormone) analogues. Over the 9-year period, the total prostatectomy rate decreased from 12.5 to 4.6 per cent. All units responsible for prostate cancer care in the south-east region regularly receive processed updates from the register providing information on diagnostic and therapeutic methods used and their effect on mortality, thus providing a basis for improving the quality of prostate cancer care. Starting in 1997, a similar registration system is to be extended to cover the entire country.

Humans↗