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Rafał Adamczak

Publications and source records attributed to Rafał Adamczak.

10 recordsLinked to original sources
PubMed2006

[The results of cytogenetic and molecular genetic examinations in 35 couples with primary sterility].

UNLABELLED: The causes of primary sterility are complex and frequently difficult to elucidate. Cytogenetic anomalies are responsible for sterility in 5-10% infertile couples. OBJECTIVES: Analysis of genetic background of primary sterility in 35 infertile couples. MATERIALS AND METHODS: 72h cultures of peripheral blood lymphocytes, GTG and CBG banding, fluorescence in situ hybrydization (FISH) with whole chromosome painting (WCP) probes. Karyotype analysis was performed in each patient out of 35 infertile couples referred to genetic counsel. SRY and CFTR gene mutation analysis by PCR was performed in all men with abnormal sperm. RESULTS: Chromosome aberrations were found in 6 couples. Klinefelter syndrome (47,XXY) was disclosed in 2 men. Isochromosome i(Xq) was found in 1 woman. The structural balanced translocations were found in 2 men; t(15;16)(q13;p13.3), t(1;19)(p35;q13.3) and a robertsonian translocation t(14;21)(q10;q10) in one. All men with chromosome aberrations had sperm anomalies: oligozoospermia, astenozoospermia, cryptozoospermia or azoospermia. There was a CFTR mutation, deltaF508, in one man and no SRY mutation in molecularly examined men with sperm abnormalities. CONCLUSIONS: In couples with primary sterility mainly the men are carriers of chromosome aberrations (CA). Because of 17.14% risk of the presence of chromosome aberrations in these couples, cytogenetic analysis should be an obligatory element of infertility diagnosis.

Adult↗
PubMed2005

Combining prediction of secondary structure and solvent accessibility in proteins.

Owing to the use of evolutionary information and advanced machine learning protocols, secondary structures of amino acid residues in proteins can be predicted from the primary sequence with more than 75% per-residue accuracy for the 3-state (i.e., helix, beta-strand, and coil) classification problem. In this work we investigate whether further progress may be achieved by incorporating the relative solvent accessibility (RSA) of an amino acid residue as a fingerprint of the overall topology of the protein. Toward that goal, we developed a novel method for secondary structure prediction that uses predicted RSA in addition to attributes derived from evolutionary profiles. Our general approach follows the 2-stage protocol of Rost and Sander, with a number of Elman-type recurrent neural networks (NNs) combined into a consensus predictor. The RSA is predicted using our recently developed regression-based method that provides real-valued RSA, with the overall correlation coefficients between the actual and predicted RSA of about 0.66 in rigorous tests on independent control sets. Using the predicted RSA, we were able to improve the performance of our secondary structure prediction by up to 1.4% and achieved the overall per-residue accuracy between 77.0% and 78.4% for the 3-state classification problem on different control sets comprising, together, 603 proteins without homology to proteins included in the training. The effects of including solvent accessibility depend on the quality of RSA prediction. In the limit of perfect prediction (i.e., when using the actual RSA values derived from known protein structures), the accuracy of secondary structure prediction increases by up to 4%. We also observed that projecting real-valued RSA into 2 discrete classes with the commonly used threshold of 25% RSA decreases the classification accuracy for secondary structure prediction. While the level of improvement of secondary structure prediction may be different for prediction protocols that implicitly account for RSA in other ways, we conclude that an increase in the 3-state classification accuracy may be achieved when combining RSA with a state-of-the-art protocol utilizing evolutionary profiles. The new method is available through a Web server at http://sable.cchmc.org.

Amino Acid Sequence↗
PubMed2005

Linear regression models for solvent accessibility prediction in proteins.

The relative solvent accessibility (RSA) of an amino acid residue in a protein structure is a real number that represents the solvent exposed surface area of this residue in relative terms. The problem of predicting the RSA from the primary amino acid sequence can therefore be cast as a regression problem. Nevertheless, RSA prediction has so far typically been cast as a classification problem. Consequently, various machine learning techniques have been used within the classification framework to predict whether a given amino acid exceeds some (arbitrary) RSA threshold and would thus be predicted to be "exposed," as opposed to "buried." We have recently developed novel methods for RSA prediction using nonlinear regression techniques which provide accurate estimates of the real-valued RSA and outperform classification-based approaches with respect to commonly used two-class projections. However, while their performance seems to provide a significant improvement over previously published approaches, these Neural Network (NN) based methods are computationally expensive to train and involve several thousand parameters. In this work, we develop alternative regression models for RSA prediction which are computationally much less expensive, involve orders-of-magnitude fewer parameters, and are still competitive in terms of prediction quality. In particular, we investigate several regression models for RSA prediction using linear L1-support vector regression (SVR) approaches as well as standard linear least squares (LS) regression. Using rigorously derived validation sets of protein structures and extensive cross-validation analysis, we compare the performance of the SVR with that of LS regression and NN-based methods. In particular, we show that the flexibility of the SVR (as encoded by metaparameters such as the error insensitivity and the error penalization terms) can be very beneficial to optimize the prediction accuracy for buried residues. We conclude that the simple and computationally much more efficient linear SVR performs comparably to nonlinear models and thus can be used in order to facilitate further attempts to design more accurate RSA prediction methods, with applications to fold recognition and de novo protein structure prediction methods.

Amino Acids↗
PubMed2005

[The results of cytogenetic investigations in 107 couples with recurrent spontaneous abortions from Pomerania-Kujawy region of Poland].

About 10-15% of clinically diagnosed pregnancies end by spontaneous abortion. One of the causes of recurrent abortions is the presence of chromosome aberrations in a parent. The paper presents the results of cytogenetic investigations in 107 couples referred to genetic council clinic because of at least 2 spontaneous abortions. Cytogenetic analysis was performed on peripheral blood lymphocytes after standard 72h PHA-stimulated culture. At least 20 GTG- and CBG-banded metaphases were analyzed in each patient. Fluorescence in situ hybridization technique was used as to precisely define cytogenetic results. Chromosome aberrations were found in 7 couples (6.54%), exclusively in women. Numerical aberration (47,XXX) was present in 1 woman, and balanced structural aberrations in 6 (5.61%). In 3 of them balanced translocations were disclosed: t(7; 19)(p13;p13.3), t(8;16)(q24;q22), and t(3;8)(q21;p21), in 2--inversions: inv(2)(p25q31), inv(17)(p12p13.3), and in 1--der(20). Pericentric inversion of chromosome 9 was found in 3 men. The analysis of nongenetic factors showed that neither age, nor congenital anomalies of uterus could be an important factor causing abortions in analyzed couples with aberrations. However, infections and muta- or teratogenic exposure could contribute to loss of pregnancies in some cases. Authors conclude that karyotype analysis should be an integral part of diagnostics in couples with recurrent abortions.

Abortion, Spontaneous↗
PubMed2004

Accurate prediction of solvent accessibility using neural networks-based regression.

Accurate prediction of relative solvent accessibilities (RSAs) of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation. Toward that goal we developed a novel method for improved prediction of RSAs. Contrary to other machine learning-based methods from the literature, we do not impose a classification problem with arbitrary boundaries between the classes. Instead, we seek a continuous approximation of the real-value RSA using nonlinear regression, with several feed forward and recurrent neural networks, which are then combined into a consensus predictor. A set of 860 protein structures derived from the PFAM database was used for training, whereas validation of the results was carefully performed on several nonredundant control sets comprising a total of 603 structures derived from new Protein Data Bank structures and had no homology to proteins included in the training. Two classes of alternative predictors were developed for comparison with the regression-based approach: one based on the standard classification approach and the other based on a semicontinuous approximation with the so-called thermometer encoding. Furthermore, a weighted approximation, with errors being scaled by the observed levels of variability in RSA for equivalent residues in families of homologous structures, was applied in order to improve the results. The effects of including evolutionary profiles and the growth of sequence databases were assessed. In accord with the observed levels of variability in RSA for different ranges of RSA values, the regression accuracy is higher for buried than for exposed residues, with overall 15.3-15.8% mean absolute errors and correlation coefficients between the predicted and experimental values of 0.64-0.67 on different control sets. The new method outperforms classification-based algorithms when the real value predictions are projected onto two-class classification problems with several commonly used thresholds to separate exposed and buried residues. For example, classification accuracy of about 77% is consistently achieved on all control sets with a threshold of 25% RSA. A web server that enables RSA prediction using the new method and provides customizable graphical representation of the results is available at http://sable.cchmc.org.

Artificial Intelligence↗
PubMed2004

[Symptoms of andropausal syndrome in smoking and non-smoking males].

Symptoms of andropause syndrome such as: erectile dysfunction, somatovegetative and psychic symptoms have been examined in groups of smoking and non-smoking patients between 45 and 75 years of age Tests of testosterone, prolactin and SHBG levels have been carried out. Earlier andropause, a lower level of testosterone as well as more common arterial hypertension have been found in the group of smoking patients.

Aged↗
PubMed2003

[Clinical and cytogenetic evaluation of patients with disorders of somato-sexual development].

UNLABELLED: Congenital somato-sexual disturbances include wide range of classic syndromes, as well as different types of numerous or isolated developmental defects. 28 women with disorders of sexual development were clinically and cytogenetically analyzed. AIM: Clinical and cytogenetic evaluation of patients with disorders of somato-sexual development. MATERIAL AND METHODS: 28 women, 17-35 years old, were included in the study. Analysis data were performed on the basis of clinical records from Department of Obstetrics and Woman's Diseases of Medical University in Bydgoszczy. Cytogenetic investigations were carried out on standard lymphocyte culture method. RESULTS: Turner's syndrome was found in 12 women; 45, X in 7 mosaic karyotype 45, X/46, XX in 4, isochromosome i(Xq) in 1.3 women had normal, male karyotype, 46, XY. One of them had dysgenetic gonads of malignant dysplesia transformation. One patient's karyotype was 47, XXX. 12 women with gonadal dysgenesis--karyotype 46, XX. CONCLUSIONS: 1. Patients with congenital disorders of somato-sexual development are a heterogenous group. 2. Laparoscopy an effective diagnostic and treatment method in women with disorders of congenital somato-sexual development.

Adolescent↗
PubMedDate not supplied

[Antithrombin and protein C activity in the blood of premature newborns with intrauterine growth retardation].

UNLABELLED: Intrauterine growth retardation (IUGR) and prematurity are often correlated with higher mortality and morbidity in the first days of life especially due to complications such as: hypoglycemia, polycythemia, necrotizing enterocolitis, meconium aspiration syndrome. Disturbances in the haemostatic system could be responsible for poor outcome of these complications. AIM: To determine the activity of main inhibitor of coagulation-antithrombin, level of protein C, concentration of thrombin-antithrombin (TAT) complexes and fibrinogen in the blood of premature infants with intrauterine growth retardation (IUGR) in comparison with premature infants without IUGR. MATERIAL: 33 premature infants with symptoms of intrauterine growth retardation (IUGR) and 146 premature infants without IUGR were included in our trial. RESULTS: There were no statistical differences between the analyzed groups in the level of protein C, concentration of TAT and fibrinogen. Activity of antithrombin was higher within 1 hour after birth and lower on the third day of life in the group of children with IUGR. CONCLUSIONS: Higher activity of antithrombin after birth in the group of newborns with IUGR prevents excessive activation of coagulation. On the third or fourth day of life the activity of antithrombin decreases due to its higher consumption in the blood of newborns with IUGR.

Antithrombin III↗