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At least 793 records · Page 44Linked to original sources
PubMed2003

Can an in silico drug-target search method be used to probe potential mechanisms of medicinal plant ingredients?

Medicinal plants have been explored therapeutically in traditional medicines and are a valuable source for drug discovery. Insufficient knowledge about the molecular mechanism of these medicinal plants limits the scope of their application and hinders the effort to design new drugs using the therapeutic principles of herbal medicines. This problem can be partially alleviated if efficient methods for rapid identification of protein targets of herbal ingredients can be introduced. Efforts have been directed at developing efficient computer methods for facilitating target identification. Various methods being explored or under investigation are reviewed here. So far, one computer method, INVDOCK, has been specifically used for automated drug target identification. Its usefulness in the identification of therapeutic targets of medicinal herbal ingredients as well as synthetic chemicals is reviewed. The majority of INVDOCK identified therapeutic targets of several well-known medicinal herbal ingredients have been found to be confirmed or implicated by experiments, which suggests the potential of in silico methods in facilitating the study of molecular mechanism of medicinal plants.

Algorithms↗
PubMed2003

Clinical brain MR imaging prescriptions in Talairach space: technologist- and computer-driven methods.

BACKGROUND AND PURPOSE: Variability in patient head positioning may yield substantial interstudy image variance in the clinical setting. We describe and test three-step technologist and computer-automated algorithms designed to image the brain in a standard reference system and reduce variance. METHODS: Triple oblique axial images obtained parallel to the Talairach anterior commissure (AC)-posterior commissure (PC) plane were reviewed in a prospective analysis of 126 consecutive patients. Requisite roll, yaw, and pitch correction, as three authors determined independently and subsequently by consensus, were compared with the technologists' actual graphical prescriptions and those generated by a novel computer automated three-step (CATS) program. Automated pitch determinations generated with Statistical Parametric Mapping '99 (SPM'99) were also compared. RESULTS: Requisite pitch correction (15.2 degrees +/- 10.2 degrees ) far exceeded that for roll (-0.6 degrees +/- 3.7 degrees ) and yaw (-0.9 degrees +/- 4.7 degrees ) in terms of magnitude and variance (P <.001). Technologist and computer-generated prescriptions substantially reduced interpatient image variance with regard to roll (3.4 degrees and 3.9 degrees vs 13.5 degrees ), yaw (0.6 degrees and 2.5 degrees vs 22.3 degrees ), and pitch (28.6 degrees, 18.5 degrees with CATS, and 59.3 degrees with SPM'99 vs 104 degrees ). CATS performed worse than the technologists in yaw prescription, and it was equivalent in roll and pitch prescriptions. Talairach prescriptions better approximated standard CT canthomeatal angulations (9 degrees vs 24 degrees ) and provided more efficient brain coverage than that of routine axial imaging. CONCLUSION: Brain MR prescriptions corrected for direct roll, yaw, and Talairach AC-PC pitch can be readily achieved by trained technologists or automated computer algorithms. This ability will substantially reduce interpatient variance, allow better approximation of standard CT angulation, and yield more efficient brain coverage than that of routine clinical axial imaging.

Adolescent↗
PubMedDate not supplied

Computer-interactive method for quantifying cerebrospinal fluid and tissue in brain CT scans: effects of aging.

Presented here is a modification of a previously developed, computed, semiautomated system for quantifying the amount of CSF and tissue on brain CT scans. The technique automatically strips skull from brain and applies a two-dimensional high-pass filter to reduce spectral-shift artifact. The resultant images are presented along with the raw images, section by section, on a screen for fluid-tissue differentiation by a human scorer. This is accomplished by adjusting a one-bit display of the filtered image until a satisfactory separation threshold is found. Data can be summed within or across sections to provide measures of CSF volume in specific regions of interest such as the ventricles and sulci. A major advantage is the improved accuracy of sulcal measurement. This method has been applied to scans of 57 community volunteers, 20-84 years old. High correlations have been established between rankings performed by an experienced clinician and automated rankings (r = 0.88 with rankings based on ventricular size, and r = 0.83 with rankings based on sulcal size). Furthermore, significant correlations were found between computed measures of ventricular size and age and between sulcal widening and age.

Adult↗
PubMed1995

Discovering the intelligence in molecular biology.

The Third International Conference on Intelligent Systems in Molecular Biology was truly an outstanding event. Computational methods in molecular biology have reached a new level of maturity and utility, resulting in many high-impact applications. The success of this meeting bodes well for the rapid and continuing development of computational methods, intelligent systems and information-based approaches for the biosciences. The basic technology, originally most often applied to 'feasibility' problems, is now dealing effectively with the most difficult real-world problems. Significant progress has been made in understanding protein-structure information, structural classification, and how functional information and the relevant features of active-site geometry can be gleaned from structures by automated computational approaches. The value and limits of homology-based methods, and the ability to classify proteins by structure in the absence of homology, have reached a new level of sophistication. New methods for covariation analysis in the folding of large structures such as RNAs have shown remarkably good results, indicating the long-term potential to understand very complicated molecules and multimolecular complexes using computational means. Novel methods, such as HMMs, context-free grammars and the uses of mutual information theory, have taken center stage as highly valuable tools in our quest to represent and characterize biological information. A focus on creative uses of intelligent systems technologies and the trend toward biological application will undoubtedly continue and grow at the 1996 ISMB meeting in St Louis.

Algorithms↗
PubMed1998

NICE, a new cause of death classification for stillbirths and neonatal deaths. Neonatal and Intrauterine Death Classification according to Etiology.

BACKGROUND: Stillbirths and neonatal deaths are often the result of a complicated chain of events. For epidemiological purposes a classification into single cause of death groups is essential. For large-scale studies, a method is needed which enables such grouping based on available register data. METHODS: A cause of death classification system called NICE is presented. It is hierarchical and is aetiologically orientated. A computerized method is adapted which makes use of data in four central Swedish registries. A validation of the computer method has been made from the medical records on a 10% sample of all stillbirths and neonatally dead infants in Sweden from 1983 to 1990. RESULTS: The specificity of the computer method is high, sensitivity is less satisfactory for some subgroups. A time trend analysis illustrates the usefulness of the classification system and shows a decline with time for two groups: placental abruption and obstetric complications. CONCLUSIONS: The NICE classification system fulfils the criteria of an aetiologically orientated classification system which can be used in a computerized environment.

Cause of Death↗
PubMed2005

Quantification of aortic elasticity: development and experimental validation of a method using computed tomography.

Aortic distensibility depending on aortic cross-sectional area changes is an important parameter for the grading of vascular diseases. This study measured aortic area changes by multidetector computed tomography. An image reconstruction algorithm was developed to assess aorta diameter and area as a function of the cardiac cycle with sufficient time resolution along the entire length of the aorta by four-detector row computed tomography. The algorithm was tested on porcine aortic specimens and compared with an optical reference method. The error of the relative vessel area change comparing the two methods was found to be about 3%. Initial tests on patient datasets indicate that clinical application is feasible. The proposed method has the advantage that it can easily be integrated into a modified routine CT angiography study and allows the measurement of aortic cross-sectional area changes.

Anatomy, Cross-Sectional↗
PubMed1976

A computer-based method for the quantification of leukocyte chemotaxis.

A computerized method for the counting of polymorphonuclear leukocytes (PMN's) on chemotactic membranes is described. Through the use of an optical scanner-computer accurate objective quantification is obtained which is similar to the results generated by visual tabulation of the same membranes. Futhermore, the electronic quantification method is both less time consuming and highly reproducible.

Adult↗
PubMed2005

Characterization of heterologous hemoglobin and flavohemoglobin promoter regulation in Escherichia coli.

Bacterial hemoglobins and flavohemoglobins have been used to improve cell growth and productivity in biotechnological applications. The expression of globin genes can be induced by reducing the oxygen supply or applying external stressors, which provide a simple and inexpensive mechanism for induction of heterologous protein production. It is in the interest of the biotechnological industry to seek new promoters, which are non-patented, cheap and simple to induce. Therefore, new globin gene promoters have been isolated from Campylobacter jejuni, Bacillus subtilis, Deinococcus radiodurans, Streptomyces coelicolor, and Salmonella typhi. The goal was to obtain insights about the regulation mechanisms of these promoters in Escherichia coli using in silico and experimental methods. The recognition of these promoters by the E. coli transcriptional machinery was first analyzed by computational methods. Computer analysis revealed that all the promoters, except the promoter of S. coelicolor, should be functional in E. coli and most of them also contain putative binding sites for ArcA, CRP, and FNR global regulators. Furthermore, the expression profiles of the promoters fused to the chloramphenicol acetyl transferase gene were analyzed under various conditions using E. coli mutants devoid of regulatory molecules. In vivo regulation studies of globin promoters mainly verified the in silico predictions.

Bacteria↗