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 Microarray methods have become a basic tool in studies of global gene expression and changes in transcript levels. Affymetrix microarrays from the HGU133 series contain multiple probe-sets complementary to the same gene (4742 genes are represented by more than one probe-set in a microarray HGU133A). Individual probe-sets annotated to the same gene often show different hybridization signals and even opposite trends, which may result from some of them matching transcripts of more than one gene and from the existence of different splice-variant transcripts. Existing methods that redefine probe-sets and develop custom probe-set definitions use mathematical tools such as Matlab or the R statistical environment with the Bioconductor package (Gentleman et al., 2004, Genome Biol. 5: 280) and thus are directed to researchers with a good knowledge of bioinformatics. We propose here a new approach based on the principle that a probe-set which hybridizes to more than one transcript can be recognized because it produces a signal significantly different from others assigned to the particular gene, allowing it to be detected as an outlier in the group and eliminated from subsequent analyses. A simple freeware application has been developed (available at http://www.bioinformatics.aei.polsl.pl) that detects and removes outlying probe-sets and calculates average signal values for individual genes using the latest annotation database provided by Affymetrix. We illustrate this procedure using microarray data from our experiments aiming to study changes of transcription profile induced by ionizing radiation in human cells.
A population study is reported in which the DNA damage induced by y-radiation (2 Gy) and the kinetics of the subsequent repair were estimated by the comet and micronucleus assays in isolated lymphocytes of 82 healthy donors and patients with head and neck cancer before radiotherapy. The parameters of background and radia­tion-induced DNA damage, rate of repair, and residual non-repaired damage were measured by comet assay, and the repair kinetics for every donor were com­puter-fitted to an exponential curve. The level of background DNA damage before ir­radiation measured by comet assay as well as the level of micronuclei were signifi­cantly higher in the head and neck cancer patient group than in the healthy donors, while the parameters of repair were widely scattered in both groups. Cancer patient group contained significantly more individuals, whose irradiated lymphocytes showed high DNA damage, low repair rate and high non-repaired DNA damage level. Lymphocytes of donors belonging to this subgroup showed significantly lower inhibi­tion of cell cycle after irradiation.
Continuous subcutaneous insulin infusion (CSII) is a commonly used, safe intensive insulin therapy method effective in maintaining normoglycaemia. The disadvantage of CSII are skin infections of the catheter injection site. The aim of the study was to gain insight on the colonization of subcutaneous insulin pump catheters by skin flora and to investigate the correlation between Staphylococcus aureus carrier state (presence in the nose), its presence on the skin and catheter. 141 catheters obtained from 94 children with T1DM and CSII were examined using the semi quantitative culture technique of Maki. The result was positive in 34 examinations (24.1%) in 30 children (31.9%). Most often coagulase negative staphylococci were isolated (30), mainly Staphylococcus epidermidis, 1/3 of the staphylococci were methicillin resistant. S. aureus was detected in 7 examinations in 6 children. S. aureus carrier state was proved in 31.9% of all examined patients, more often in children with a positive catheter culture (41.4%), there were no MRSA. No correlation between S. aureus carrier state and catheter colonization was shown. Statistically significant correlations between: coagulase negative staphylococci presence, including the methicillin resistant strains, on the skin and on the catheter surface (p<0.0001); glycosylated hemoglobin (HbA1c) and bacteria catheter colonization (p = 0.0335) were observed. Subcutaneous catheter colonization by microorganisms often occurs in CSII. Microorganisms found on the skin are the most frequent cause of the subcutaneous catheter infection.
Progressive decline in fertility and sperm quality has been reported over the last few decades, especially in industrialized nations. It has been proposed that exposure to factors that induce damage in DNA of spermatogenic cells may significantly contribute to impaired fertility. Here, the 32P-postlabelling method was used to analyze the levels of bulky DNA adducts in sperm cells in a group of 179 volunteers, either healthy subjects or patients with an impaired fertility. The levels of DNA adducts were 1.35-fold higher in the infertile group as compared to healthy individuals (P = 0.012). Similarly, a significant negative correlation between the levels of DNA adducts and measures of semen quality (sperm concentration and motility) has been observed (P < 0.001). In addition, the levels of bulky DNA adducts in sperm cells positively corre­lates with amounts of leukocytes in semen, which were significantly higher in semen of infertile subjects.
A case of a widespread neoplastic process, originating from the mammary gland in mongrel bitch, weighing 27 kg and aging 7 years, was described. In the patient, blood morphology, blood biochemical parameters, gasometry of arterial blood, chest X-ray, and heart ECG and USG were determined. ECG record demonstrated elevation of ST-T segment by 0.2-0.3 mV in I, aVL leads and a downward- sloping depression in III and aVR leads. The alterations pointed with high probability to infarction in the lateral wall of the left ventricle. Following demonstration by imaging tests of numerous tumours in the chest, the dog was subjected to euthanasia. Upon autopsy, apart from the primary tumour in the mammary gland, numerous tumours were demonstrated in inner organs, including myocardium. Histopathology confirmed neoplastic growth of adenocarcinoma type. In the vicinity of the tumour localised in the left cardiac ventricle, microscopic examination disclosed regions of cardiomyocyte necrosis, which corroborated the preliminary diagnosis of infarction.
There is a 10–30% prevalence of HP infection in the general pediatric population in Poland. This study aimed to determine its prevalence in T1DM children in Upper Silesia, Poland and estimate its influence on metabolic control of patients. We studied 149(82♀) children with T1DM (duration > 12 months, mean HbA1c) and 298(164♀) age-matched controls. In all cases height and weight z-scores and Cole’s index were assessed. In T1DM patients additionally glycated hemoglobin A1c and T1DM duration were analyzed. Presence of HP infection was determined using 13C-isotope-labeled urea breath test (UBT) (fasting and 30min after ingestion 75 mg of 13C urea). HP infection was present in 17 (11.4%) T1DM patients and in 49 (16.4%) controls (p > 0.05). T1DM patients presented higher values of anthropometric parameters than healthy controls (weight SDS 0.25[–0.46÷0.84] vs. –0.25[–1.06÷0.26], height SDS 0.09[–0.60÷0.69] vs. –0.31[–1.17÷0.48]and Cole’s index 103%[93÷111%] vs. 97%[86÷106%]; for all p < 0001). Within both groups – T1DM children and controls – no differences regarding sex, age and any of the anthropometric parameters were determined. T1DM duration and HbA1c showed no relationto prevalence of HP infection. Prevalence of HP infection in pediatric T1DM patients is similar to that of healthy peers and shows no relation to glycemic control.
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