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PubMed2002

Use of 16S-23S rRNA spacer-region (SR)-PCR for identification of intestinal clostridia.

The suitability of a species identification technique based on PCR analysis of 16S-23S rRNA spacer region (SR) polymorphism for human intestinal Clostridium species was evaluated. This SR-PCR based technique is highly reproducible and successfully differentiated the strains tested, which included 17 ATCC type strains of Clostridium and 152 human stool Clostridium isolates, at the species or intraspecies level. Ninety-eight of 152 stool isolates, including C. bifermentans, C. butyricum, C. cadaveris, C. orbiscindens, C. paraputrificum, C. pefringens, C. ramosum, C. scindens, C. spiroforme, C. symbiosum and C. tertium, were identified to species level by SR-PCR patterns that were identical to those of their corresponding ATCC type strains. The other 54 stool isolates distributed among ten SR-PCR patterns that are unique and possibly represent ten novel Clostridium species or subspecies. The species identification obtained by SR-PCR pattern analysis completely agreed with that obtained by 16S rRNA sequencing, and led to identification that clearly differed from that obtained by cellular fatty acid analysis for 23/152 strains (15%). These results indicate that SR-PCR provides an accurate and rapid molecular method for the identification of human intestinal Clostridium species.

Base Sequence↗

PubMed2002

Species specific identification of nine human Bifidobacterium spp. in feces.

Based on the 16S rDNA sequences, species specific primers were designed for the rapid identification by DNA amplification of nine human Bifidobacterium spp., namely B. adolescentis, B. angulatum, B. bifidum, B. breve, B. catenulatum, B. dentium, B. infantis, B. longum, B. pseudocatenulatum. B. lactis currently included in dairy products was added to the series. The primers were designed to target different positions of the 16S rDNA, allowing the simultaneous identification of these ten species of Bifidobacterium using two mixtures of primers. The identification procedure described in this paper was validated by establishing a correlation with an AluI restriction pattern of the different full length amplified 16S rDNA. This multiple primer DNA amplification technique was applied for the identification of pure colonies of Bifidobacterium spp. or directly from total bacteria recovered from human fecal samples. The technique was shown to be useful to detect dominant species and, when primers were used in separate reactions, underrepresented species could be identified as well.

Adult↗

PubMed2002

Associative priming in a masked perceptual identification task: evidence for automatic processes.

Two experiments investigated the influence of automatic and strategic processes on associative priming effects in a perceptual identification task in which prime-target pairs are briefly presented and masked. In this paradigm, priming is defined as a higher percentage of correctly identified targets for related pairs than for unrelated pairs. In Experiment 1, priming was obtained for mediated word pairs. This mediated priming effect was affected neither by the presence of direct associations nor by the presentation time of the primes, indicating that automatic priming effects play a role in perceptual identification. Experiment 2 showed that the priming effect was not affected by the proportion (.90 vs. .10) of related pairs if primes were presented briefly to prevent their identification. However, a large proportion effect was found when primes were presented for 1000 ms so that they were clearly visible. These results indicate that priming in a masked perceptual identification task is the result of automatic processes and is not affected by strategies. The present paradigm provides a valuable alternative to more commonly used tasks such as lexical decision.

Association↗

PubMedDate not supplied

Mother-daughter identification: Polish and Polish-American mothers and their adult daughters.

Toward the goal of furthering our understanding of the mother-daughter relationship, we investigated one aspect of the mother-daughter relationship, the mutual identification that occurs within it. Mutual identification was defined as the process by which a mother and her daughter internalize characteristics of each other. A convenience sample of 81 Polish and 81 Polish-American mother-daughter dyads was studied. Mother-daughter identification was measured using a semantic differential (SD) scale that included 12 concepts. Analyses using paired t tests revealed that there was no significant difference between the ratings of the Polish-American mothers and those of their daughters on 7 of the 12 concepts and no significant difference between the ratings of the Polish mothers and those of their daughters on 10 of the 12. There were, however, statistically significant differences between the Polish and Polish-American women's ratings of the concepts. These data are interpreted as support for the theory of mother-daughter identification.

Adult↗

PubMed2002

Comparison of intraparenchymal and intradermal injection for identification of the sentinel node in patients with breast cancer.

BACKGROUND: Sentinel lymph node (SLN) mapping with radioisotope and blue dye has been advocated for the staging of clinically negative axillae in patients with breast cancer. The optimal radiotracer injection technique is still being defined. This study compares the results of intraparenchymal and intradermal injection of technetium 99m (Tc 99m) sulfur colloid to establish an optimal method for SLN localization. METHODS: Consecutive patients (n = 435) with clinically T0-2N0 breast cancer had SLN biopsy performed by a single surgeon. All patients but one received injections of both blue dye and Tc 99m sulfur colloid; one patient had injection of blue dye only and was excluded from analysis. Blue dye injections were intraparenchymal in all patients. The results of intraparenchymal (n = 107) and intradermal (n = 327) injections of radioisotope were compared for the following endpoints: 1) successful SLN identification, 2) false-negative rate, and 3) ratio of SLN/axillary background isotope counts. RESULTS: Intradermal radioisotope injection was as effective as intraparenchymal radioisotope injection, identifying the SLN in 99.4% and 92.5% of cases, respectively. False-negative rates for both radioisotope injection techniques were < or = 5%. Ratios of SLN/axillary background isotope counts were higher with intradermal than with intraparenchymal injection (193/1 vs 41/1). Patient follow-up has revealed no axillary recurrence of tumor. CONCLUSIONS: Intradermal radioisotope injection for SLN identification appears to be a highly accurate technique with acceptable false-negative and SLN identification rates. Compared with intraparenchymal isotope injection, the intradermal technique is associated with higher levels of isotope uptake by the SLN, facilitating SLN identification.

Journal Article↗

PubMed1993

An examination of the effects of axis foreshortening, monocular depth cues, and visual field on object identification.

Four experiments are reported on the identification of line drawings of common objects. In each experiment, performance on "unconventional" views of the objects, in which the major axis of the object was foreshortened, was compared to performance on more "conventional" views without appreciable foreshortening. In each experiment, except Experiment 2, where performance on the two views was experimentally equated, the foreshortened views were more difficult to identify than were the conventional views. Experiments 1 and 2 showed that if the foreshortened views were presented on a background with strong monocular depth cues, object identification was improved. This result suggests that part of the difficulty in identifying objects depicted from such a view stems from an improper depth interpretation of the object depictions. Experiments 3 and 4 examined visual field differences in the identification of the two types of object view. Results reported in the neuropsychological literature have shown that people with right-hemisphere damage have particular difficulty with the identification of unconventional views of objects that foreshorten major axes. Accordingly, it was expected that there would be a left visual field advantage for the foreshortened views. Neither experiment yielded any visual field effects consistent with this expectation. Possible reasons for the lack of a field effect are discussed.

Cues↗

PubMed2000

Determining the significance of coagulase-negative staphylococci isolated from blood cultures at a community hospital: a role for species and strain identification.

OBJECTIVES: To determine the degree to which species identification or strain relatedness assessment of successive blood culture isolates of coagulase-negative staphylococci (CNS) may improve the clinical diagnosis of bloodstream infection (BSI). SETTING: 400-bed community hospital. DESIGN: Prospective laboratory survey during which all CNS blood culture isolates obtained between mid-August 1996 and mid-February 1997 (study period) were saved and later identified to the species level; selected isolates were genotyped using pulsed-field gel electrophoresis at the Centers for Disease Control and Prevention (CDC). Retrospective review of medical records of 37 patients with multiple cultures positive for CNS. RESULTS: During the study period, 171 patients had blood cultures positive for CNS; 130 had single positive cultures and 41 had > or =2 positive cultures. Of these 41, 23 (62%) were from patients with signs and symptoms of BSI according to CDC surveillance definitions. Species identification and strain clonality of CNS isolates from patients with > or =2 positives revealed 3 (13%) of the 23 patients did not have a consistent CNS species, and another 3 (13%) did not have a consistent genotype in the > or =2 positive cultures, suggesting that CNS from these patients probably were contaminants. Thus, species identification and strain clonality assessment reduced by 27% the number of patients with BSI diagnosed based on the presence of symptoms and > or =2 positive blood cultures. CONCLUSIONS: Routine species identification and selected strain genotyping of CNS may reduce the misinterpretation of probable contaminants among patients with > or =2 positive blood cultures.

Adolescent↗

PubMed2004

Blind identification of the kinetic parameters in three-compartment models.

Quantified knowledge of tissue kinetic parameters in the regions of the brain and other organs can offer information useful in clinical and research applications. Dynamic medical imaging with injection of radioactive or paramagnetic tracer can be used for this measurement. The kinetics of some widely used tracers such as [18F]2-fluoro-2-deoxy-D-glucose can be described by a three-compartment physiological model. The kinetic parameters of the tissue can be estimated from dynamically acquired images. Feasibility of estimation by blind identification, which does not require knowledge of the blood input, is considered analytically and numerically in this work for the three-compartment type of tissue response. The non-uniqueness of the two-region case for blind identification of kinetic parameters in three-compartment model is shown; at least three regions are needed for the blind identification to be unique. Numerical results for the accuracy of these blind identification methods in different conditions were considered. Both a separable variables least-squares (SLS) approach and an eigenvector-based algorithm for multichannel blind deconvolution approach were used. The latter showed poor accuracy. Modifications for non-uniform time sampling were also developed. Also, another method which uses a model for the blood input was compared. Results for the macroparameter K, which reflects the metabolic rate of glucose usage, using three regions with noise showed comparable accuracy for the separable variables least squares method and for the input model-based method, and slightly worse accuracy for SLS with the non-uniform sampling modification.

Algorithms↗

PubMed2002

Computational Analysis of Gene Identification with SAGE.

SAGE is one of the few techniques capable of uniformly probing gene expression at a genome level irrespective of mRNA abundance and without a priori knowledge of the transcripts present. However, individual SAGE tags can match many sequences in the reference database, complicating gene identification. We perform a baseline evaluation of gene identification with SAGE using UniGene Human as the reference database by analyzing 1) the distributions of tags for various length tag sets formed for UniGene Human and 2) the tag-to-sequence mapping using a SAGE tag set consisting of 37,522 tags derived from human myeloid cells. The extensive multiplicity of the dbEST component of UniGene significantly detracts from gains that might be expected by extending tags within the scope of the SAGE protocol. In order to achieve reasonable sequence specificity for gene identification with the content of the commonly used UniGene sequence collection, tags on the order of hundreds of bases in length are required. One way to produce tags of such lengths is with GLGI, which extends SAGE tags to the 3' end of cDNA. We show that the longer sequences produced by GLGI relieve significantly the multiple match condition. In the myeloid sample, we also found a correlation between multiple match severity and high copy number. We extrapolate these findings, providing insights into the use of UniGene Human as a reference for gene identification.

Animals↗

PubMed2005

Optimal construction of theoretical spectra for MS/MS spectra identification.

We derive the optimal number of peaks (defined as the minimum number that provides the required efficiency of spectra identification) in the theoretical spectra as a function of (i) the experimental accuracy, sigma, of the measured ratio m/z; (ii) experimental spectrum density; (iii) size of the database; (iv) number of peaks in the theoretical spectra; and (v) types of ions that the peaks represent. We show that if theoretical spectra are constructed including b and y ions alone, then for sigma = 0.5, which is typical for high-throughput data, peptide chains of eight amino acids or longer can be identified based on the positions of peaks alone, at a rate of false identification below 1%. To discriminate between shorter peptides, additional (e.g., intensity-inferred) information is necessary. We derive the dependence of the probability of false identification on the number of peaks in the theoretical spectra and on the types of ions that the peaks represent. Our results suggest that the class of mass spectrum identification problems, for which more elaborate development of fragmentation rules (such as intensity model) is required, can be reduced to the problems that involve homologous peptides.

Mass Spectrometry↗

PubMed1980

A comparison of four commercial systems for the identification of nonfermentative gram-negative bacilli.

Four commercial systems for the identification of glucose nonfermentative, gram-negative bacilli and the conventional system used in our laboratory were compared. The API 20E, Roche Oxi/Ferm Tube, BBL Minitek, Flow N/F System, and our system were compared for accuracy, time needed for identification and number of isolates needing additional testing. A total of 241 different isolates were used. The API 20E identified 86.7% correctly; Oxi/FermTube, 83.0%; Minitek, 93.4%; N/F System, 90.5%; and our system, 90.0%. Within 24 hours after isolation, the API 20E identified 25.7%; Oxi/Ferm Tube and Minitek, 0%; N/F System 27.3%; and our system, 35.7%. After 48 hours, the API 20E identified 74.7%; Oxi/Ferm Tube, 35.7%; Minitek, 45.2%; N/F System, 83.0%; and our system, 94.6%. The number of isolates that required additional testing for identification by the API 20E was 119; Oxi/Ferm Tube, 161; Minitek, 88; N/F System, 43; and our system, 36. Ease of performance, technologist time, and level of identification required by individual laboratories are discussed.

Bacteriological Techniques↗

PubMed1981

Four-hour presumptive identification of Enterobacteriaceae from blood cultures.

A modification of the Minitek identification system for the four-hour identification of gram-negative bacilli recovered from blood cultures was developed. This method enabled our laboratory to identify correctly 99 of 100 consecutive isolates of all members of Enterobacteriaceae representing seven genera and nine species. All rapid identifications were confirmed using conventional biochemical methods. The procedure employs 11 Minitek biochemical discs inoculated with 0.1 ml of a dense organism suspension. Two-tenths milliliter of this suspension was added to a blank well for motility testing. In most instances, identification reactions were identical to those routinely used for the Minitek system. Only with the biochemical citrate disc does the interpretation vary from the Minitek standard. In addition to the blood culture isolates, 22 unknown organisms were also tested. All were correctly identified within four hours of the detection of visible turbidity in broth. This method offers a convenient, economic, and rapid means of identifying gram-negative bacilli isolated from blood cultures.

Bacteriological Techniques↗

PubMed1988

A comparison of the identification of group A streptococci and enterococci by two rapid pyrrolidonyl aminopeptidase methods.

Group A streptococci and enterococci can be differentiated from other streptococci by their ability to cleave L-pyrrolidonyl-beta-napthylamide (PYR). The authors evaluated two pyrrolidonyl aminopeptidase (PYRase) systems--Minitek (BBL Microbiology Systems, Cockeysville, MD) and Identicult-AE (Scott Laboratories, Inc., Fiskeville, RI)--for the presumptive identification of Group A streptococci and enterococci. Eighty-three Group A streptococci, 77 beta-hemolytic non-Group A streptococci, 74 enterococci, 56 nonenterococcal non-beta-hemolytic streptococci, 1 Streptococcus pneumoniae, and 1 Aerococcus were tested. Compared with results obtained with reference methods (bile esculin agar and 6.5% [w/v] sodium chloride for identification of enterococci, and latex agglutination tests by Streptex [Burroughs Wellcome, NC] for grouping of beta-hemolytic streptococci) both the Identicult-AE and MInitek systems were 100% sensitive and specific for identification of both enterococci and Group A beta-hemolytic streptococci. Advantages of the Identicult-AE system compared with Minitek were the use of a smaller inoculum for which subculture was not necessary, incubation at room temperature rather than at 37 degrees C, and lower cost. Both PYRase kits tested, and in particular the Identicult-AE system, were very easy to use and should be considered as rapid, reliable, and cost-effective alternative methods for the presumptive identification of Group A streptococci and enterococci in the clinical laboratory.

Aminopeptidases↗

PubMed2004

Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins.

MOTIVATION: Identification of potentially allergenic proteins is needed for the safety assessment of genetically modified foods, certain pharmaceuticals and various other products on the consumer market. Current methods in bioinformatic allergology exploit common features among allergens for the detection of amino acid sequences of potentially allergenic proteins. Features for identification still unexplored include the motifs occurring commonly in allergens, but rarely in ordinary proteins. In this paper, we present an algorithm for the identification of such motifs with the purpose of biocomputational detection of amino acid sequences of potential allergens. RESULTS: Identification of allergen-representative peptides (ARPs) with low or no occurrence in proteins lacking allergenic properties is the essential component of our new method, designated DASARP (Detection based on Automated Selection of Allergen-Representative Peptide). This approach consistently outperforms the criterion based on identical peptide match for predicting allergenicity recommended by ILSI/IFBC and FAO/WHO and shows results comparable to the alignment-based criterion as outlined by FAO/WHO. AVAILABILITY: The detection software and the ARP set needed for the analysis of a query protein reported here are properties of the Swedish National Food Agency and are available upon request. The protein sequence sets used in this work are publicly available on http://www.slv.se/templatesSLV/SLV_Page____9343.asp. Allergenicity assessment for specific protein sequences of interest is also possible via ulfh@slv.se

Algorithms↗

PubMed2004

Splice site identification by idlBNs.

MOTIVATION: Computational identification of functional sites in nucleotide sequences is at the core of many algorithms for the analysis of genomic data. This identification is based on the statistical parameters estimated from a training set. Often, because of the huge number of parameters, it is difficult to obtain consistent estimators. To simplify the estimation problem, one imposes independent assumptions between the nucleotides along the site. However, this can potentially limit the minimum value of the estimation error. RESULTS: In this paper, we introduce a novel method in the context of identifying functional sites, that finds a reasonable set of independence assumptions supported by the data, among the nucleotides, and uses it to perform the identification of the sites by their likelihood ratio. More importantly, in many practical situations it is capable of improving its performance as the training sample size increases. We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction.

Algorithms↗

PubMed2006

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

UNLABELLED: An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model-an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3% and 99.8% peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. AVAILABILITY: The software is available upon request.

Algorithms↗

PubMed1997

'Sniffin' sticks': olfactory performance assessed by the combined testing of odor identification, odor discrimination and olfactory threshold.

'Sniffin' Sticks' is a new test of nasal chemosensory performance based on pen-like odor dispensing devices. It comprises three tests of olfactory function, namely tests for odor threshold (n-butanol, testing by means of a single staircase), odor discrimination (16 pairs of odorants, triple forced choice) and odor identification (16 common odorants, multiple forced choice from four verbal items per test odorant). After extensive preliminary investigations the tests were applied to a group of 104 healthy volunteers (52 female, 52 male, mean age 49.5 years, range 18-84 years) in order to establish test-retest reliability and to compare them with an established measure of olfactory performance (the Connecticut Chemosensory Clinical Research Center Test, CCCRC). Performance decreased with increasing age of the subjects (P < 0.001). Coefficients of correlation between sessions 1 and 2 were 0.61 for thresholds, 0.54 for discrimination and 0.73 for identification. Butanol thresholds as obtained with the CCCRC increased as a function of age; this relation to the subjects' age was not found for the CCCRC odor identification task. The test-retest reliability for CCCRC thresholds was 0.36, for odor identification it was 0.60. It is concluded that 'Sniffin' Sticks' may be suited for the routine clinical assessment of olfactory performance.

Adult↗

PubMed2004

Demographic and cognitive predictors of cued odor identification: evidence from a population-based study.

This study investigated demographic and cognitive correlates of cued odor identification in a population-based sample from the Betula project: 1906 healthy adults varying in age from 45 to 90 years were assessed in a number of tasks tapping various cognitive domains, including cognitive speed, semantic memory and executive functioning. The results revealed a gradual and linear deterioration in cued odor identification across the adult life span. Overall, females identified more odors than men, although men and women performed at the same level in the oldest age cohort (85-90 years). Hierarchical regression analyses revealed that age, sex, education, cognitive speed and vocabulary were reliable correlates of performance in the odor identification task. In addition, age-related deficits in the included demographic and cognitive variables could not fully account for the observed age-related impairment in identification, suggesting that additional factors are underlying the observed deterioration. Likely candidates here are sensory abilities such as olfactory detection and discrimination.

Adult↗