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At least 37 records · Page 2Linked to original sources
PubMed1975

Computer method for the analysis of evoked motor unit potentials. 2. Duchenne, limb-girdle, facioscapulohumeral and myotonic muscular dystrophies.

Single motor unit potentials recorded from surface electrodes over the extensor digitorum brevis muscle and evoked by stimulation of the anterior tibial nerve at the ankle were obtained by a computer subtraction method. Their latencies, durations, amplitudes, and areas were measured in control subjects and patients with Duchenne, limb-girdle, facioscapulohumeral, and myotonic muscular dystrophy. Lateral popliteal motor nerve conduction velocities were also recorded. In the muscular dystrophies there was a significant increase in both the latencies and durations of motor unit potentials, the latter in notable contrast with the findings of conventional needle electromyography. Fastest motor conduction velocities were significantly reduced in the limb-girdle, facioscapulohumeral, and myotonic muscular dystrophy patients, while the shortest distal motor latencies were significantly prolonged in these patients and those with Duchenne muscular dystrophy. The results support the presence of a definitive neurogenic influence in the muscular dystrophies.

Adolescent↗
PubMed1975

[Study of interventricular septal defects with equal aortic and pulmonary artery pressures. Classification by clinical and computer methods of 70 cases].

Application of various methods of classification to a group of 70 cases of ventricular septal defect with high pulmonary artery hypertension allowed a comparative study between the various methods aiming at distinguishing the forms with low from high pulmonary artery resistance. The reference clinical classification provides supplementary informations derived from the natural or post-operative course and eventually from the microscopic examination. The first automatic classification relies on the study of a single criterion: the pulmonary arteriolar resistance and the systemic resistance ratio. A second classification is based on the attribution of points to some clinical or haemodynamic signs resulting in a score orienting the classification of every individual. Multifactorial analysis methods deal with all the available informations for the overall group, and suppose the use of a computer. The informatic methods make it possible to study the classifying value of every sign. Correlations were established between these various techniques and the medical classification.

Adolescent↗
PubMed1978

Simple computer method for equivalent square therapy field determination.

A simple BASIC computer program allows rapid determination of the equivalent squares of irregular radiation therapy fields. A port film or scale drawing of the irregular field is outlined manually on a spark tablet digitizer, and the side length of the square of equivalent area to perimeter ratio is rapidly calculated and returned by the computer.

Computers↗
PubMed2025

Prediction and Evaluation of Protein Aggregation with Computational Methods.

Protein and peptide aggregation has recently become one of the most studied biomedical problems due to its central role in several neurodegenerative disorders and of biotechnological importance. Multiple in silico methods, databases, tools, and algorithms have been developed to predict aggregation of proteins and peptides to better understand fundamental mechanisms of various aggregation diseases. Here, we attempt to provide a brief overview of bioinformatic methods and tools to better understand molecular mechanisms of aggregation disorders. Furthermore, through a better understanding of protein aggregation mechanisms, it might be possible to design novel therapeutic agents to treat and hopefully prevent protein aggregation diseases.

Computational Biology↗
PubMed2026

Development of a multi-copy integration platform in Kluyveromyces marxianus enabled by a computational method for genome-wide identification of multi-copy integration loci.

Multi-copy integration is a core strategy for redirecting metabolic flux toward target compounds. However, its application has been hampered by the absence of methods for systematically identifying native multi-copy genomic loci. To overcome this, we developed a computational procedure for genome-wide identification of such loci. Theoretically, this method is potentially applicable to any genome-sequenced species as it only requires the genomic assembly of the target species as input. Applying the procedure to Kluyveromyces marxianus, we identified four groups of loci (KmCS1-4). Combining these loci-KmCS1-4 and the traditional 26S rDNA-with 14 markers with graded selection strengths, we established a versatile multi-copy integration toolkit comprising 70 plasmids. Each plasmid exhibits a unique integration pattern, collectively forming an integration profile. This profile serves as a manual, enabling users to select appropriate tools tailored to the expression requirements of rate-limiting enzymes in their pathways. Applying representative plasmids exhibiting low-, medium-, and high-copy integration patterns to lycopene biosynthesis modules resulted in lycopene titers of 3.5, 6.8 and 40.5 mg/L, corresponding to 2, 6 and 9 genomic copies, respectively, demonstrating a positive correlation between lycopene titers, genomic copy numbers and integration patterns, which highlights the versatility of the toolkit and its supporting manual. Our study not only provides a broadly applicable methodology for genome-wide identification of multi-copy loci, but also an efficient integration platform for K. marxianus.

Kluyveromyces marxianus↗
PubMed1992

Computer methods in child language research: four principles for the use of archived data.

With the increasing use of computers in language research, there is a need for caution concerning several new issues of data accountability. This paper presents four principles for archive-based language research: Maximum Readability and Minimum Bias; Consistent Encoding for exhaustive computer search; Systematic Contrastiveness; and Data Comparability in elicitation, transcription and coding. These and related principles are illustrated by examples from existing computer archives, and strategies are suggested for minimizing detrimental effects of violations. Finally, the paper describes some implications of the principles for properties of a field-wide and international standard of transcription of language data.

Archives↗
PubMed1991

Computational method for the design of enzymes with altered substrate specificity.

A combination of enzyme kinetics and X-ray crystallographic analysis of site-specific mutants has been used to probe the determinants of substrate specificity for the enzyme alpha-lytic protease. We now present a generalized model for understanding the effects of mutagenesis on enzyme substrate specificity. This algorithm uses a library of side-chain rotamers to sample conformation space within the binding site for the enzyme-substrate complex. The free energy of each conformation is evaluated with a standard molecular mechanics force field, modified to include a solvation energy term. This rapid energy calculation based on coarse conformation sampling quite accurately predicts the relative catalytic efficiency of over 40 different alpha-lytic protease-substrate combinations. Unlike other computational approaches, with this method it is feasible to evaluate all possible mutations within the binding site. Using this algorithm, we have successfully designed a protease that is both highly active and selective for a non-natural substrate. These encouraging results indicate that it is possible to design altered enzymes solely on the basis of empirical energy calculations.

Algorithms↗
PubMed1991

A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences.

We describe a new computer program that identifies conserved secondary structures in aligned nucleotide sequences of related single-stranded RNAs. The program employs a series of hash tables to identify and sort common base paired helices that are located in identical positions in more than one sequence. The program gives information on the total number of base paired helices that are conserved between related sequences and provides detailed information about common helices that have a minimum of one or more compensating base changes. The program is useful in the analysis of large biological sequences. We have used it to examine the number and type of complementary segments (potential base paired helices) that can be found in common among related random sequences similar in base composition to 16S rRNA from Escherichia coli. Two types of random sequences were analyzed. One set consisted of sequences that were independent but they had the same mononucleotide composition as the 16S rRNA. The second set contained sequences that were 80% similar to one another. Different results were obtained in the analysis of these two types of random sequences. When 5 sequences that were 80% similar to one another were analyzed, significant numbers of potential helices with two or more independent base changes were observed. When 5 independent sequences were analyzed, no potential helices were found in common. The results of the analyses with random sequences were compared with the number and type of helices found in the phylogenetic model of the secondary structure of 16S ribosomal RNA. Many more helices are conserved among the ribosomal sequences than are found in common among similar random sequences. In addition, conserved helices in the 16S rRNAs are, on the average, longer than the complementary segments that are found in comparable random sequences. The significance of these results and their application in the analysis of long non-ribosomal nucleotide sequences is discussed.

Base Composition↗
PubMed1991

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗
PubMed1991

A computer method for visual presentation and programmed evaluation of labor.

Manual graphing of the progress of labor is considered useful but is not often done. The early detection of some deviations requires special graphics aids. Our objective was to develop an easy-to-use computer program for the integrated visual presentation of information characterizing the progress of labor. Through the use of inexpensive personal computers equipped with graphics monitors, the program provides a combined graphics display of timed progressive cervical dilatation, fetal station, and stimulation of uterine activity (oxytocin infusion). For the early detection of abnormalities, phase-specific normal ranges (reference areas) are displayed. In addition, protraction/arrest as well as precipitate labor disorders are highlighted and computer messages are displayed. The program was evaluated through the assessment of 405 labors entered into a local area network of computers. On average, the program identified 1.5 abnormalities per recorded labor (2.0 for labors resulting in vaginal delivery). The graphic presentation of the labor curve, produced within 3 seconds, displayed 27% more information than the tabular format on the same screen area and provided a single-screen display of the labor curve even for patients with excessive data. The computer-generated display of labor curves facilitates visual presentation and interpretation of labor progress and can also help to translate quality assurance criteria into clinical practice.

Computer Graphics↗
PubMed1992

Computer methods for locating kinetoplastid cryptogenes.

RNA editing in the mitochondria of kinetoplastid protoza involves the insertion and/or deletion of precise numbers of uridine residues at precise locations in the numbers of uridine residues at precise locations in the transcribed RNA of certain genes. These genes are known as cryptogenes. In this paper we study computational algorithms to search for unknown cryptogenes and for the associated templates for insertion of uridines, gRNA sequences. The pairwise similarity search algorithm of Smith and Waterman (1) is modified to study this problem. The algorithm searches for unknown gRNAs given the cryptogene sequence. The method is tested on 4 known cryptogenes from L.tarentolae which are known to have 7 associated gRNAs. The statistical distribution of the longest gRNA when comparing random sequences is derived. Finally we develop an algorithm to search for cryptogenes using amino acid sequences from related proteins.

Algorithms↗