Biomedical subjects

Christian Baumgartner

Publications and source records attributed to Christian Baumgartner.

10 recordsLinked to original sources

PubMed2006

Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data.

MOTIVATION: Classification is an important data mining task in biomedicine. In particular, classification on biomedical data often claims the separation of pathological and healthy samples with highest discriminatory performance for diagnostic issues. Even more important than the overall accuracy is the balance of a classifier, particularly if datasets of unbalanced class size are examined. RESULTS: We present a novel instance-based classification technique which takes both information of different local density of data objects and local cluster structures into account. Our method, which adopts the basic ideas of density-based outlier detection, determines the local point density in the neighborhood of an object to be classified and of all clusters in the corresponding region. A data object is assigned to that class where it fits best into the local cluster structure. The experimental evaluation on biomedical data demonstrates that our approach outperforms most popular classification methods. AVAILABILITY: The algorithm LCF is available for testing under http://biomed.umit.at/upload/lcfx.zip.

Algorithms↗

PubMed2006

Different patterns of aortic wall elasticity in patients with Marfan syndrome: a noninvasive follow-up study.

OBJECTIVE: Aortic complications determine the life expectancy of most patients with Marfan syndrome. To find out whether there is heterogenous aortic involvement among patients and, if there is, to characterize aortic patterns and response to long-term beta-blocker therapy, we investigated aortic elastic properties before and during beta-blocker treatment. METHODS: In 46 patients with Marfan syndrome (age, 17.4 +/- 11.1 years) and 46 healthy control subjects, ascending and descending aortic elastic parameters were determined noninvasively before and after 39 +/- 16 months of beta-blocker treatment with atenolol. RESULTS: Aortic diameters and distensibility distinguished Marfan patients and controls with a sensitivity of 85% and a specificity of 87%. Cluster analysis revealed 4 patterns of aortic phenotypic expression: (1) reduced ascending aortic elasticity (46% of patients), (2) diminished ascending and descending aortic elasticity (17%), (3) minimal alterations of ascending and descending aortic elasticity (20%), and (4) reduced descending aortic elasticity (17%). During follow-up, aortic elastic properties improved in 21 (70%) of 30 patients and deteriorated in 9 (30%) irrespective of beta-blocker dosage. Improvement was observed in 100% of patients (n = 7; age, 5.3 +/- 4.2 years) with end-diastolic aortic root diameters between 20 and 30 mm and in 61% of patients (14/23; age, 20.5 +/- 10.0 years) with root diameters between 30 and 52 mm. CONCLUSIONS: Aortic elastic parameters distinguish between patients with Marfan syndrome and healthy controls and show the pattern of regional aortic involvement. Improvement or deterioration during follow-up can influence therapeutic decisions to prevent aortic dissection and rupture. Young age, small root diameter, and high distensibility are favorable prognostic factors.

Adolescent↗

PubMed2005

Biomarker discovery, disease classification, and similarity query processing on high-throughput MS/MS data of inborn errors of metabolism.

In newborn errors of metabolism, biomarkers are urgently needed for disease screening, diagnosis, and monitoring of therapeutic interventions. This article describes a 2-step approach to discover metabolic markers, which involves (1) the identification of marker candidates and (2) the prioritization of them based on expert knowledge of disease metabolism. For step 1, the authors developed a new algorithm, the biomarker identifier (BMI), to identify markers from quantified diseased versus normal tandem mass spectrometry data sets. BMI produces a ranked list of marker candidates and discards irrelevant metabolites based on a quality measure, taking into account the discriminatory performance, discriminatory space, and variance of metabolites' concentrations at the state of disease. To determine the ability of identified markers to classify subjects, the authors compared the discriminatory performance of several machine-learning paradigms and described a retrieval technique that searches and classifies abnormal metabolic profiles from a screening database. Seven inborn errors of metabolism-- phenylketonuria (PKU), glutaric acidemia type I (GA-I), 3-methylcrotonylglycinemia deficiency (3-MCCD), methylmalonic acidemia (MMA), propionic acidemia (PA), medium-chain acylCoAdehydrogenase deficiency (MCADD), and 3-OH long-chain acyl CoA dehydrogenase deficiency (LCHADD)-were investigated. All primarily prioritized marker candidates could be confirmed by literature. Some novel secondary candidates were identified (i.e., C16:1 and C4DC for PKU, C4DC for GA-I, and C18:1 forMCADD), which require further validation to confirm their biochemical role during health and disease.

Acyl-CoA Dehydrogenase↗

PubMed2005

Reduced aortic elastic properties in a child with Takayasu arteritis: case report and literature review.

UNLABELLED: Takayasu arteritis (TA) is a chronic inflammatory vasculitis of the aorta and its major branches with a very low incidence in Europe and North America. Our objective was to determine the elastic properties of the affected ascending and descending aortic walls non-invasively in a 14-year-old Iraqi girl with a 3-year history of fever, fatigue, malaise and diffuse pain. Ultrasound and magnetic resonance angiography showed marked thickening of the aortic wall, dilatation of the aortic arch, and decreased luminal diameters of the abdominal aorta and both subclavian arteries, consistent with TA. Ascending and descending aortic elastic properties such as distensibility and stiffness index were markedly reduced compared to a group of healthy controls (n=39): ascending aortic distensibility was 20 kPa(-1) x 10(-3) versus 63+/-23 kPa(-1) x 10(-3) in controls, and the ascending aortic stiffness index 9.6 versus 3.5+/-1.3 in controls. Although the patient's general condition improved rapidly on oral prednisolone and azathioprine and inflammatory parameters normalised within 3 weeks, the aortic elastic parameters did not change during the first 2 weeks of anti-inflammatory treatment. Unfortunately, no further follow-up was possible. CONCLUSION: In patients with Takayasu arteritis, non-invasive quantification of reduced aortic elastic properties can help to assess aortic involvement, and possibly to follow disease activity and vascular response to therapy.

Abdominal Pain↗

PubMed2005

A bioinformatics framework for genotype-phenotype correlation in humans with Marfan syndrome caused by FBN1 gene mutations.

Mutations in the human FBN1 gene are known to be associated with the Marfan syndrome, an autosomal dominant inherited multi-systemic connective tissue disorder. However, in the absence of solid genotype-phenotype correlations, the identification of an FBN1 mutation has only little prognostic value. We propose a bioinformatics framework for the mutated FBN1 gene which comprises the collection, management, and analysis of mutation data identified by molecular genetic analysis (DHPLC) and data of the clinical phenotype. To query our database at different levels of information, a relational data model, describing mutational events at the cDNA and protein levels, and the disease's phenotypic expression from two alternative views, was implemented. For database similarity requests, a query model which uses a distance measure based on log-likelihood weights for each clinical manifestation, was introduced. A data mining strategy for discovering diagnostic markers, classification and clustering of phenotypic expressions was provided which enabled us to confirm some known and to identify some new genotype-phenotype correlations.

Computational Biology↗

PubMed2005

Impaired elastic properties of the ascending aorta in newborns before and early after successful coarctation repair: proof of a systemic vascular disease of the prestenotic arteries?

BACKGROUND: Despite successful surgical correction, morbidity of patients with coarctation of the aorta is increased. It is well known that these patients have impaired elastic properties of the prestenotic arteries. To find out whether these abnormalities are primarily present or develop later, we studied 17 newborns before and early after surgical repair. METHODS AND RESULTS: Aortic wall stiffness index and distensibility were calculated using ascending and abdominal aortic diameters determined by M-mode echocardiography and noninvasive estimation of aortic pulse pressure in the right arm and leg. Seventeen patients with aortic coarctation (mean age, 20+/-26 days) were compared with 17 normal neonates (mean age, 13+/-7 days) preoperatively and postoperatively (10+/-6 days after surgery). Ascending aortic distensibility in patients was significantly reduced preoperatively (79+/-58 versus 105+/-36; P=0.03) and postoperatively (65+/-24 versus 105+/-36; P<0.005). Preoperative and postoperative ascending aortic stiffness index was higher in patients (preoperative, 5.2+/-4.4 versus 2.7+/-0.9; P=0.04; postoperative, 4.0+/-1.6 versus 2.7+/-0.9; P<0.005). Elastic properties of the descending aorta did not differ preoperatively or postoperatively compared with those in normal subjects. CONCLUSIONS: Elastic properties of the prestenotic aorta of patients with coarctation seem to be impaired primarily, even in neonates, and remain unchanged early after successful operation. Surgical correction does not resolve inborn pathology of the prestenotic aortic vascular bed.

Aorta↗

PubMed2005

Functional cluster analysis of CT perfusion maps: a new tool for diagnosis of acute stroke?

CT perfusion imaging constitutes an important contribution to the early diagnosis of acute stroke. Cerebral blood flow (CBF), cerebral blood volume (CBV) and time-to-peak (TTP) maps are used to estimate the severity of cerebral damage after acute ischemia. We introduce functional cluster analysis as a new tool to evaluate CT perfusion in order to identify normal brain, ischemic tissue and large vessels. CBF, CBV and TTP maps represent the basis for cluster analysis applying a partitioning (k-means) and density-based (density-based spatial clustering of applications with noise, DBSCAN) paradigm. In patients with transient ischemic attack and stroke, cluster analysis identified brain areas with distinct hemodynamic properties (gray and white matter) and segmented territorial ischemia. CBF, CBV and TTP values of each detected cluster were displayed. Our preliminary results indicate that functional cluster analysis of CT perfusion maps may become a helpful tool for the interpretation of perfusion maps and provide a rapid means for the segmentation of ischemic tissue.

Adult↗

PubMed2005

Modelling of classification rules on metabolic patterns including machine learning and expert knowledge.

Machine learning has a great potential to mine potential markers from high-dimensional metabolic data without any a priori knowledge. Exemplarily, we investigated metabolic patterns of three severe metabolic disorders, PAHD, MCADD, and 3-MCCD, on which we constructed classification models for disease screening and diagnosis using a decision tree paradigm and logistic regression analysis (LRA). For the LRA model-building process we assessed the relevance of established diagnostic flags, which have been developed from the biochemical knowledge of newborn metabolism, and compared the models' error rates with those of the decision tree classifier. Both approaches yielded comparable classification accuracy in terms of sensitivity (>95.2%), while the LRA models built on flags showed significantly enhanced specificity. The number of false positive cases did not exceed 0.001%.

Algorithms↗

PubMed2005

Diagnostic power of aortic elastic properties in young patients with Marfan syndrome.

BACKGROUND: In patients with Marfan syndrome, progressive aortic dilation implicates a still-unpredictable risk of life-threatening aortic dissection and rupture. We sought to quantify aortic wall dysfunction noninvasively, determine the diagnostic power of various aortic parameters, and establish a diagnostic model for the early detection of aortic abnormalities associated with Marfan syndrome. METHODS: In 19 patients with Marfan syndrome (age, 17.7 +/- 9.5 years) and 19 age- and sex-matched healthy control subjects, computerized ascending and abdominal aortic wall contour analysis with continuous determination of aortic diameters was performed out of transthoracic M-mode echocardiographic tracings. After simultaneous oscillometric blood pressure measurement, aortic elastic properties were determined automatically. RESULTS: The following ascending aortic elastic parameters showed statistically significant differences between the Marfan group and the control group: (1) decreased aortic distensibility ( P < .001), (2) increased wall stiffness index ( P < .01), (3) decreased systolic diameter increase ( P < .01), and (4) decreased maximum systolic area increase ( P < .001). The diagnostic power of all investigated parameters was tested by single logistic regression models. A multiple logistic regression model including solely aortic parameters yielded a sensitivity of 95% and a specificity of 100%. CONCLUSIONS: In young patients with Marfan syndrome, a computerized image-analyzing technique revealed decreased aortic elastic properties expressed by parameters showing high diagnostic power. A multiple logistic regression model including merely aortic parameters can serve as useful predictor for Marfan syndrome.

Adolescent↗

PubMed2003

Tumor-inhibiting platinum(II) complexes with aminoalcohol ligands: comparison of the mode of action by capillary electrophoresis and electrospray ionization-mass spectrometry.

Capillary electrophoresis (CE) was used as an assay for studying the interaction of (SP-4-2)-bis[(R)-(-)-2-aminobutanol)dichloroplatinum(II) (1) and (SP-4-2)bis(4-aminobutanol)dichloroplatinum(II) (2) with guanosine 5'-monophosphate (GMP). CE kinetic measurements carried out at two physiological pH levels indicated that upon increasing the pH, 1 showed an appreciable change in binding behavior, with the rate of binding increased for more than 10 times as expressed by apparent half-life values of GMP (6.1 and 62.2 h at pH 6.0 and 7.4, respectively). The rate of GMP binding for 2 remained comparatively less affected by pH (half-lives of 8.5 and 10.6 h, respectively). Regardless of the nature of platinum complex and pH, the reaction with GMP tends to be decelerated at increased chloride concentrations in solution, this effect being particularly pronounced when changing from 4 mM (intracellular level) to 100 mM (extracellular level). The kinetic differences of platinum complexes were characterized in terms of the respective GMP-adducts structure, independently identified by means of off-line electrospray ionization-mass spectrometry. Also addressed was the interpretation of binding behavior as based on the structural features of the intact complexes, namely differing inclination to intramolecular chelation.

Antineoplastic Agents↗