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Algorithm Consisting (algorithm + consisting)

Distribution by Scientific Domains

Medical Sciences	75%

Selected Abstracts

Extending Ellenberg's indicator values to a new area: an algorithmic approach

JOURNAL OF APPLIED ECOLOGY, Issue 1 2000
Mark O. Hill
Summary 1.,Ellenberg's indicator values scale the flora of a region along gradients reflecting light, temperature, continentality, moisture, soil pH, fertility and salinity. They can be used to monitor environmental change. 2.,Ellenberg values can be extended from central Europe, for which they were defined, to nearby parts of Europe. Given a database of quadrat samples, they can be repredicted by a simple algorithm consisting of two-way weighted averaging, followed by local regression. 3.,A database of British samples was assembled from two large surveys. Ellenberg values were repredicted. 4.,Except for the indicator of continentality, the correlation of repredicted and original values was in the range 0·72 (light) to 0·91 (moisture). The continentality indicator could not be adequately repredicted by the algorithm, and is unusable in Britain. 5.,Discrepancies between original and repredicted values can be attributed to various causes, including wrong original values, differing ecological requirements in Britain and central Europe, biased sampling of the British range of habitats, and the occurrence of small plants in shaded or basic microhabitats within well illuminated or predominantly acid quadrats. 6.,The repredicted values were generally reliable, but a small proportion was clearly wrong. Wrong values were due to either inadequate sampling of species' realized niches in Britain or sampling with quadrats that were too large and included species that were not close associates. [source]

Protocol for clinical neurophysiologic examination of the pelvic floor

NEUROUROLOGY AND URODYNAMICS, Issue 6 2001
Simon Podnar
Abstract Clinical neurophysiologic examination of the pelvic floor is performed worldwide, but there is no consensus on the choice of tests, nor on technical details of individual methods. Standardized methods are, however, necessary to obtain their valid application in different laboratories for the purpose of collection of normative data, comparison of patient data and organization of multi-center studies. It is proposed that in patients with suspected "lower motor neuron" type lesions concentric needle electromyography (CNEMG) is the most informative test to detect pelvic floor denervation/reinnervation, and the external anal sphincter (EAS) muscle is the most appropriate muscle to be examined (either in isolation,when a selective lesion is suspected,or in addition to examination of other muscles). An algorithm consisting of standardized tests including a standardized approach to CNEMG examination of the EAS is presented. The proposed electrophysiologic assessment consists of a computer-assisted analysis of denervation and reinnervation features of the CNEMG signal, a qualitative assessment of reflex and voluntary activation of EAS motor units, and of electrical (or mechanical) elicitation of the bulbocavernosus reflex in those patients in whom manual anogenital stimulation failed to elicit a robust response in the EAS. The proposed protocol could serve as a basis for further studies on validity, sensitivity and specificity of electrophysiologic assessment in patients with different types of "lower motor neuron" involvement of pelvic floor muscles and sacral dysfunction. Neurourol. Urodynam. 20:669,682, 2001. © 2001 Wiley-Liss, Inc. [source]

Use of Quantitative Broad-based Polymerase Chain Reaction for Detection and Identification of Common Bacterial Pathogens in Cerebrospinal Fluid

ACADEMIC EMERGENCY MEDICINE, Issue 7 2010
Richard Rothman MD
ACADEMIC EMERGENCY MEDICINE 2010; 17:741,747 © 2010 by the Society for Academic Emergency Medicine Abstract Background:, Conventional laboratory diagnosis of bacterial meningitis based on microscopy followed by culture is time-consuming and has only moderate sensitivity. Objectives:, The objective was to define the limit of detection (LOD), analytic specificity, and performance characteristics of a broad-based quantitative multiprobe polymerase chain reaction (PCR) assay for rapid bacterial detection and simultaneous pathogen-specific identification in patients with suspected meningitis. Methods:, A PCR algorithm consisting of initial broad-based detection of Eubacteriales by a universal probe, followed by pathogen identification using either pathogen-specific probes or Gram-typing probes, was employed to detect pathogens. The 16S rRNA gene, which contains both conserved and variable regions, was chosen as the target. Pathogen-specific probes were designed for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, and Listeria monocytogenes. Gram-positive and -negative typing probes were designed based on conserved regions across all eubacteria. The LOD and time to detection were assessed by dilutional mocked-up samples. A total of 108 convenience cerebrospinal fluid (CSF) clinical samples obtained from the Johns Hopkins Hospital (JHH) microbiology laboratory were tested, and results were compared with hospital microbiologic culture reports. Results:, The LOD of the assay ranged from 101 to 102 colony-forming units (CFU)/mL. Pathogen-specific probes showed no cross-reactivity with other organisms. Time to detection was 3 hours. In clinical specimens, the universal probe correctly detected 16 of 22 culture-positive clinical specimens (sensitivity = 72.7%; 95% confidence interval [CI] = 49.8% to 89.3%), which were all correctly characterized by either pathogen-specific or Gram-typing probes. Adjusted sensitivity after removing probable microbiologic laboratory contaminants was 88.9% (95% CI = 65.3% to 98.6%). The universal probe was negative for 86 of 86 culture-negative specimens. Conclusions:, A broad-based multiprobe PCR assay demonstrated strong analytic performance characteristics. Findings from a pilot clinical study showed promise in translation to human subjects, supporting potential utility of the assay as an adjunct to traditional diagnostics for early identification of bacterial meningitis. [source]

Rapid Polymerase Chain Reaction-based Screening Assay for Bacterial Biothreat Agents

ACADEMIC EMERGENCY MEDICINE, Issue 4 2008
Samuel Yang MD
Abstract Objectives:, To design and evaluate a rapid polymerase chain reaction (PCR)-based assay for detecting Eubacteria and performing early screening for selected Class A biothreat bacterial pathogens. Methods:, The authors designed a two-step PCR-based algorithm consisting of an initial broad-based universal detection step, followed by specific pathogen identification targeted for identification of the Class A bacterial biothreat agents. A region in the bacterial 16S rRNA gene containing a highly variable sequence flanked by clusters of conserved sequences was chosen as the target for the PCR assay design. A previously described highly conserved region located within the 16S rRNA amplicon was selected as the universal probe (UniProbe, Integrated DNA Technology, Coralville, IA). Pathogen-specific TaqMan probes were designed for Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Performance of the assay was assessed using genomic DNA extracted from the aforementioned biothreat-related organisms (inactivated or surrogate) and other common bacteria. Results:, The UniProbe detected the presence of all tested Eubacteria (31/31) with high analytical sensitivity. The biothreat-specific probes accurately identified organisms down to the closely related species and genus level, but were unable to discriminate between very close surrogates, such as Yersinia philomiragia and Bacillus cereus. Conclusions:, A simple, two-step PCR-based assay proved capable of both universal bacterial detection and identification of select Class A bacterial biothreat and biothreat-related pathogens. Although this assay requires confirmatory testing for definitive species identification, the method has great potential for use in ED-based settings for rapid diagnosis in cases of suspected Category A bacterial biothreat agents. [source]