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At least 1,261 records · Page 70Linked to original sources
PubMed2002

XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis.

This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein from Klebsiella pneumoniae nitrogenase (Kp1) using the 1.6 A-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by approximately 0.1 A) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo.

Absorptiometry, Photon↗
PubMed2006

Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70.

Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542-640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to approximately 3.4 A. Crystals belong to space group I2(1)2(1)2(1), with unit-cell parameters a = b = 197, c = 200 A. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein-solvent boundary. Further density-modification, model-building and refinement are currently under way.

Animals↗
PubMed2005

Fat and hydration monitoring by abdominal bioimpedance analysis: data interpretation by hierarchical electrical modeling.

In a previous publication, it was demonstrated that the abdominal subcutaneous fat layer thickness (SFL) is strongly correlated with the abdominal electrical impedance when measured with a transversal tetrapolar electrode arrangement. This article addresses the following questions: 1) To which extent do different abdominal compartments contribute to the impedance? 2) How does the hydration state of tissues affect the data? 3) Can hydration and fat content be assessed independently? For simulating the measured data a hierarchical electrical model was built. The abdomen was subdivided into three compartments (subcutaneous fat, muscle, mesentery). The true anatomical structure of the compartment boundaries was modeled using finite-element modeling (FEM). Each compartment is described by an electrical tissue model parameterized in physiological terms. Assuming the same percent change of the fat fraction in the mesentery and the SFL the model predicts a change of 1,24 omega/mm change of the SFL compared to 1,1 omega/mm measured. 42% of the change stem from the SFL, 56% from the mesentery and 2% from changes of fat within the muscle compartment. A 1% increase of the extracellular water in the muscle is not discernible from a 1% decrease of the SFL. The measured data reflect not only the SFL but also the visceral fat. The tetrapolar electrode arrangement allows the measurement of the abdominal fat content only if the hydration remains constant.

Abdomen↗
PubMed2002

DNASER I: layout and data analysis.

We present the DNA analyzer (DNASER), a novel bioinstrumentation for real-time acquisition and elaboration of images from fluorescent DNA microarrays. A white light beam illuminates the target sample allowing the images grabbing on a high sensibility and wide-band charge-coupled device camera (ORCA II-Hamamatsu). This high-performance device permits to acquire images faster and of higher quality than the traditional systems. The DNA microarrays images are processed to recognize the DNA chip spots, to analyze their superficial distribution on the glass slide and to evaluate their geometric and intensity properties. Differently form conventional techniques, the spots analysis is fully automated and the DNASER does not require any additional information about the DNA microarray geometry. The DNASER hardware and software architecture is illustrated. Preliminary results are shown from experiments performed on real DNA samples.

Algorithms↗
PubMed2003

A data analysis competition to evaluate machine learning algorithms for use in brain-computer interfaces.

We present three datasets that were used to conduct an open competition for evaluating the performance of various machine-learning algorithms used in brain-computer interfaces. The datasets were collected for tasks that included: 1) detecting explicit left/right (L/R) button press; 2) predicting imagined L/R button press; and 3) vertical cursor control. A total of ten entries were submitted to the competition, with winning results reported for two of the three datasets.

Algorithms↗
PubMed2000

Bivariate binary data analysis with nonignorably missing outcomes.

One of the objectives in the Northern Manhattan Stroke Study is to investigate the impact of stroke subtype on the functional status 2 years after the first ischemic stroke. A challenge in this analysis is that the functional status at 2 years after stroke is not completely observed. In this paper, we propose a method to handle nonignorably missing binary functional status when the baseline value and the covariates are completely observed. The proposed method consists of fitting four separate binary regression models: for the baseline outcome, the outcome 2 years after the stroke, the product of the previous two, and finally, the missingness indicator. We then conduct a sensitivity analysis by varying the assumptions about the third and the fourth binary regression models. Our method belongs to an imputation paradigm and can be an alternative to the weighting method of Rotnitzky and Robins (1997, Statistics in Medicine 16, 81-102). A jackknife variance estimate is proposed for the variance of the resulting estimate. The proposed analysis can be implemented using statistical software such as SAS.

Biometry↗
PubMedDate not supplied

Some interrelationships between plasma levels of LH, FSH, oestradiol 17beta, androgens and semen analysis data in male infertility patients.

Serum LH, FSH and immunoreactive testosterone-like substances (TLS) have been measured by radioimmunoassay in 130 male infertility patients and oestradiol 17beta in 26 cases. A weak but significant negative correlation was found between FSH and sperm count (rs = -0.19, p less than 0.05) but not LH and sperm count. However, LH and FSH were strongly correlated in the azoospermic (rs = 0.71, p less than 0.01) and oligozoospermic (rs = 0.53, p less than 0.01) groups and levels of both gonadotrophins were significantly elevated in the azoospermic and oligozoospermic as compared to the normozoospermic group. The elevated LH levels in the oligozoo- and azoospermic groups could not be explained by reduced negative feedback of testosterone or oestradiol 17beta since firstly, TLS and oestradiol 17beta levels were similar in all three groups and, secondly, within-group correlations between LH and TLS were either non-significant or positive (azoospermic group r = 0.37, p = 0.06). It is suggested that spermatogenesis-related feedback factor(s) may inhibit LH as well as FSH secretion. No role for oestradiol 17beta as a selective inhibitor of FSH secretion seemed likely as oestradiol 17beta levels were similar in the three groups and were correlated (r = 0.51, p less than 0.01) to TLS levels i.e. to leydig cell rather than spermatogenic function. Seminal fructose was negatively correlated (r = -0.26, p less than 0.01) with sperm count but not significantly with plasma TLS. It would thus seem unlikely that the tendency for seminal fructose levels to increase as sperm count decreases is due to increased androgen production or that seminal fructose can be used as an index of a patient's androgenic status. Patients with varicoceles had hormone levels similar to other patients of similar sperm count. Both sperm morphology and motility were strongly correlated to log sperm count (r = 0.84 and 0.55 respectively) and semen volume was significantly greater in oligozoospermic than normozoospermic patients (p less than 0.01).

Androgens↗
PubMed2004

Modeling of esophageal bolus flow by functional data analysis of scintigrams.

Peristaltic forces cause a topographic, time-dependent distribution of bolus mass during its esophageal transport. A two-dimensional spatial-temporal pattern (profile) of local transit times is constructed by computer-based double compression of scintigraphic images sampled from whole swallows. Reconstruction by Gaussian bands and modeling this pattern discloses transient ellipsoidal bolus structures. The structures studied in 10 healthy volunteers present highly reproducible quantitative parameters for marking a region-specificity of transit times, which is related to the known region-selectivity of esophageal functions. Correlation of bolus flow with the dynamics of peristalsis is essential for understanding the complex mechanisms of esophageal transport as well as for diagnostic discrimination of disturbances of bolus flow.

Adult↗
PubMed1993

Planar 201Tl scintigraphy in ischaemic heart disease: a critical re-evaluation of qualitative and quantitative data analysis.

The aims of the present study were to examine the observer agreement of qualitative (visual) and quantitative (computer-assisted) analysis of planar 201Tl imaging and to compare the diagnostic values of these methods in the detection of infarcted and exercise-induced ischaemic myocardium. The study population comprised of 119 patients (aged 24-77 years) referred consecutively for stress thallium scintigraphy for either diagnostic reasons (n = 42, 35%) or for further evaluation of known coronary artery disease (CAD) (n = 77, 65%). The interobserver agreement was low with the qualitative method and significantly higher with the quantitative method: Kappa-values 0.29-0.39 vs. 0.80-0.92, P < 0.00001. Sensitivity and specificity for the detection of previous Q-wave infarct was significantly higher with the quantitative method (94% and 94%) compared to the qualitative method (77% and 74%), P < 0.01. The corresponding predictive values of a positive and a negative test were 96% and 92% vs. 80% and 70% (P < 0.01). In 86 patients in whom coronary angiography was performed the two methods did not differ significantly regarding sensitivity, specificity and predictive values for the diagnosis of reversible ischaemia or rather CAD. However, when 22 patients with a maximal exercise heart rate < 80% of the predicted target heart rate were excluded the sensitivity was increased with both techniques and was significantly higher with the quantitative method. We conclude that qualitative image analysis has an unacceptably low reproducibility and that quantitative image analysis increases the diagnostic value of 201Tl scintigraphy considerably in both the detection of previous infarcts and, provided a sufficient exercise level is achieved, in the disclosure of reversible myocardial ischaemia.

Adult↗
PubMed2005

For debate: problems with the DMF index pertinent to dental caries data analysis.

The Decayed, Missing, Filled (DMF) index has been used for over 50 years and is well established as the key measure of caries experience in dental epidemiology. Despite its long history of use, there is debate about the most appropriate number of surfaces to include for a missing tooth. Assigning the maximum possible value for the 'M' component of DMFS (Surfaces) leads to overestimation of an individual's caries experience, and in any associated comparisons of in-caries experience, whereas assigning the minimum possible value for the 'M' component has the opposite effect. Alternative methods of assigning the number of caries-affected surfaces for an extracted tooth are considered. The net caries increment and adjusted caries increment (common methods of correction of the crude increment measure for reversals) are discussed, along with incidence density, a measure of caries extent. Problems exist with the adjusted caries increment, particularly among cohorts with low mean baseline caries experience. Development of an alternative method of estimating the relationship of 'true' and 'examiner' reversals is advocated, as well as greater utilization of incidence density in dental epidemiology.

Adolescent↗