Biomedical subjects

R Marabini

Publications and source records attributed to R Marabini.

8 recordsLinked to original sources

PubMed1998

3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs).

Algebraic reconstruction techniques (ART) are iterative procedures for solving systems of linear equations. They have been used in tomography to recover objects from their projections. In this work we apply an ART approach in which the basis functions used to describe the objects are not based on voxels, but are much smoother functions named "blobs". The data collection studied in this work follows the so-called "conical tilt geometry" that is commonly used in many applications of three-dimensional electron microscopy of biological macromolecules. The performance of ART with blobs is carefully compared with a currently well-known three dimensional (3D) reconstruction algorithm (weighted back projection) using a methodology which assigns a level of statistical significance to a claim of relative superiority of one algorithm over another for a particular task. The conclusion we reach is that ART with blobs produces high-quality reconstructions and is, in particular, superior to weighted backprojection in recovering features along the "vertical" direction. For the exact implementation recommended in this paper, the computational costs of ART are almost an order of magnitude smaller than those of WBP.

Image Processing, Computer-Assisted↗

PubMed1997

Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection.

In this work we propose a reconstruction algorithm (ART with blobs) that has not been previously used in electron Tomography and we compare it with the standard method in the field (weighted back projection, WBP). We assume that only a limited set of very noisy images, collected around a single axis tilt, is available; which is a typical situation in Electron Tomography. In general, the reconstruction problem is underdetermined (due to the limited number of projections) and the data are inconsistent (due to the high level of noise). The evaluation of the results is performed in a rigorous way by a task-oriented approach which makes use of numerical observers. ART with blobs outperforms WBP for a number of key tasks. Results are presented both for simplified line integral data and for realistic simulations of macromolecular structures embedded in amorphous ice.

Algorithms↗

PubMed1996

Xmipp: An Image Processing Package for Electron Microscopy

We present in this article a specialized suite of image processing programs primarily aimed at obtaining the three-dimensional reconstruction of biological specimens from large sets of projection images obtained by transmission electron microscopy. The programs are written in ANSI-C and use X-Windows for graphical output. A number of parallel extensions using PVM and PARMACS are provided. The programs are freely available by anonymous ftp at ftp.cnb.uam.es.

Journal Article↗

PubMed1996

Galactosylhydroxylysine and pyridinium cross links in monitoring the bone response to hormone replacement therapy.

Aim of the study was to compare urinary galactosyl-hydroxylysine (GHyl), deoxypyridinoline (D-Pyr) and pyridinoline (Pyr) before and after 5 to 9 months of hormone replacement therapy (HRT) in postmenopausal women. The urinary markers were measured by HPLC in the second void of fasting samples and were expressed as ratio to creatinine. GHyl was also expressed as a ratio to glucosylgalactolysyl-hydroxylysine (GGHyl). After short-term hormone replacement therapy, urinary D-Pyr fell significantly, but Pyr and GHyl, also when expressed as a ratio to GGHyl, remained unmodified. We conclude that GHyl and Pyr are not useful markers in monitoring the bone response to HRT in postmenopausal women.

Alkaline Phosphatase↗

PubMed1994

Pattern recognition and classification of images of biological macromolecules using artificial neural networks.

The goal of this work was to analyze an image data set and to detect the structural variability within this set. Two algorithms for pattern recognition based on neural networks are presented, one that performs an unsupervised classification (the self-organizing map) and the other a supervised classification (the learning vector quantization). The approach has a direct impact in current strategies for structural determination from electron microscopic images of biological macromolecules. In this work we performed a classification of both aligned but heterogeneous image data sets as well as basically homogeneous but otherwise rotationally misaligned image populations, in the latter case completely avoiding the typical reference dependency of correlation-based alignment methods. A number of examples on chaperonins are presented. The approach is computationally fast and robust with respect to noise. Programs are available through ftp.

Algorithms↗

PubMed1992

Flow cytometric diagnosis of partial mole.

To differentiate histologically partial hydatidiform moles (PM) and complete hydatidiform moles (CM) may be difficult. Cytogenetic studies have shown that PMs often had a triploid karyotype while CMs were always diploid. We assessed the DNA content of 31 paraffin-embedded cases of trophoblastic disease with flow cytometry. Twenty-four cases were histologically diagnosed as PM, 3 cases as CM; the others as hydropic abortion (2 cases), choriocarcinoma (1 case), and persistent trophoblastic disease (1 case). Four normal term placentas were used as diploidy controls. In 9 cases the results of the cytogenetic analysis were available. All placental specimens included also maternal tissue as an internal control. Eight of the 24 histologically diagnosed PMs were triploid; there was agreement in 8 cases out of 9 (90%) between the flow cytometric analysis and the karyotypic determination of ploidy. All normal controls as well as the hydropic abortion, the CM and the persistent trophoblastic disease were diploid. Abnormal content of DNA (DI = 1.3) was observed in the choriocarcinoma. Our results show that flow cytometric analysis of DNA content is a reliable and fast method of diagnosing PM on paraffin-embedded material.

Choriocarcinoma↗

PubMed1988

The problem of identification of prognostic factors for persistent trophoblastic disease.

The role of anamnestic and clinical factors in defining the high group at risk of developing persistent trophoblastic disease (PTD) has been analyzed in 301 cases of hydatidiform mole. Patients age 40 or more years with AB blood, and a previous history of molar pregnancy had an elevated risk of developing PTD. The presence of various risk factors increased the frequency of PTD. However, with discriminant analysis, correct classification of outcome was obtained for only 69% of cases. Despite the magnitude of risk of PTD for women with three or more risk factors, the clinical relevance of prognostic variables in the prediction of outcome was limited by the low proportion of women classified in the low- and high-risk groups, making the identification at diagnosis of the women who could benefit of prophylactic chemotherapy extremely difficult and hence of little clinical importance.

ABO Blood-Group System↗

PubMedDate not supplied

Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy.

In this work we address the problem of information access that arises in the field of three-dimensional structure determination, by means of image processing, from data obtained by various types of microscopy. A prototype of a distributed database containing three-dimensional structural information is presented. In this database the volume information is linked, if possible, to other sources of catalogued information such as sequence data, atomic coordinates, and bibliographies. The solution we propose is sufficiently general to be applicable to data in other fields of biomedical science.

Computer Communication Networks↗