Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “IDENTIFICATION”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 721 records · Page 40Linked to original sources
PubMed1997

rpoB sequence analysis as a novel basis for bacterial identification.

Comparison of the sequences of conserved genes, most commonly those encoding 16S rRNA, is used for bacterial genotypic identification. Among some taxa, such as the Enterobacteriaceae, variation within this gene does not allow confident species identification. We investigated the usefulness of RNA polymerase beta-subunit encoding gene (rpoB) sequences as an alternative tool for universal bacterial genotypic identification. We generated a database of partial rpoB for 14 Enterobacteriaceae species and then assessed the intra- and interspecies divergence between the rpoB and the 16S rRNA genes by pairwise comparisons. We found that levels of divergence between the rpoB sequences of different strains were markedly higher than those between their 16S rRNA genes. This higher discriminatory power was further confirmed by assigning 20 blindly selected clinical isolates to the correct enteric species on the basis of rpoB sequence comparison. Comparison of rpoB sequences from Enterobacteriaceae was also used as the basis for their phylogenetic analysis and demonstrated the genus Klebsiella to be polyphyletic. The trees obtained with rpoB were more compatible with the currently accepted classification of Enterobacteriaceae than those obtained with 16S rRNA. These data indicate that rpoB is a powerful identification tool, which may be useful for universal bacterial identification.

DNA-Directed RNA Polymerases↗
PubMed2001

Rapid species identification of coagulase negative Staphylococci by rRNA spacer length polymorphism analysis.

OBJECTIVES: The identification of coagulase-negative staphylococci (CNS) is carried out mainly through conventional methods, commercial identification kits, and molecular biology-based methods. We evaluated the efficiency of PCR analysis of tRNA intergenic spacer length polymorphism (tDNA-ILP) and 16S-23S intergenic spacer length polymorphism (16S-23S ILP), and also that of restriction analysis of 16S-23S intergenic spacer amplification products (RA 16S-23S), for the rapid and accurate identification of CNS species. METHODS: The PCR assays of rRNA spacer length polymorphisms were tested with nine reference type strains and 122 clinical isolates. The results were compared with those obtained by conventional methods and the Vitek system for clinical isolates. RESULTS: Seventy-eight (63.9%) of 122 strains were identified as the same species with conventional identification, the Vitek GPI system, tDNA-ILP, and RA 16S-23S. The 16S-23S ILP analysis did not produce distinguishable PCR fragments. The results of tDNA-ILP analysis were in agreement with those of RA 16S-23S to the species level for 98.2% except for unknown patterns (eight isolates). CONCLUSIONS: These results indicate that tDNA-ILP and RA 16S-23S analysis are potentially valuable tools for rapid and accurate CNS identification.

Coagulase↗
PubMed2001

16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory.

For many years, sequencing of the 16S ribosomal RNA (rRNA) gene has served as an important tool for determining phylogenetic relationships between bacteria. The features of this molecular target that make it a useful phylogenetic tool also make it useful for bacterial detection and identification in the clinical laboratory. Sequence analysis of the 16S rRNA gene is a powerful mechanism for identifying new pathogens in patients with suspected bacterial disease, and more recently this technology is being applied in the clinical laboratory for routine identification of bacterial isolates. Several studies have shown that sequence identification is useful for slow-growing, unusual, and fastidious bacteria as well as for bacteria that are poorly differentiated by conventional methods. The technical resources necessary for sequence identification are significant. This method requires reagents and instrumentation for amplification and sequencing, a database of known sequences, and software for sequence editing and database comparison. Commercial reagents are available, and laboratory-developed assays for amplification and sequencing have been reported. Likewise, there are an increasing number of commercial and public databases. Despite the availability of resources, sequence-based identification is still relatively expensive. The cost is significantly reduced only by the introduction of more automated methods. As the cost decreases, this technology is likely to be more widely applied in the clinical setting.

Bacteria↗
PubMed1997

DNA diagnosis and identification of carriers of infantile and juvenile neuronal ceroid lipofuscinoses.

The recent identification of the genes and the mutations underlying infantile neuronal ceroid lipofuscinosis and juvenile onset neuronal ceroid lipofuscinosis facilitates specific DNA-based diagnostics for the disorders. We have developed a solid-phase minisequencing test for the identification of the major Finnish INCL mutation, an A to T transversion at nucleotide position 364 of the palmitoyl protein thioesterase gene on chromosome 1. This test has been applied for prenatal diagnosis and for identification of disease carriers in INCL families. For population-based screening for INCL carriers the coverage of the test would be 98%. In addition, by combining the solid-phase minisequencing test with whole genome preamplification, we have developed a procedure that allows reliable identification of the INCLFin-mutation in single blastomeres from in-vitro-fertilized embryos. This method is applicable for preimplantation diagnosis, and thus it offers an alternative to early prenatal diagnosis in the prevention of INCL. A modification of the solid-phase minisequencing test was devised for detection of the major INCL mutation, a 1.02 kb deletion in the CLN3 gene on chromosome 16. The coverage of this test for diagnosis of INCL and identification of carriers is 90% in Finland and > 80% worldwide.

Adolescent↗
PubMed1996

Target localisation and identification in rapid visual search.

In recent models of visual search in has been proposed that, in rapid parallel search, information about the location of a target pattern among distractors and information about its identity would not be available simultaneously, but that target location is represented at earlier stages of visual processing than target identity. In the present study, the priority of location information over identity information in parallel visual search was investigated by means of one identification and two localisation tasks of different levels of difficulty. In all three tasks, the stimulus display was identical An oblique line segment, randomly 45 degrees or 135 degrees in orientation, was presented randomly at one quadrant of the display. In the identification task, the observer reported the orientation of the oblique line irrespective of its location. In the easy localisation task, the observer indicated whether the oblique line was at the left or right side of the display, and in the difficult localisation task whether it was in the upper or lower part of the display. In both localisation tasks, the observer ignored the orientation of the target line. The oblique line was accompanied by one, five, seventeen, or thirty-nine vertical distractor line segments in all tasks. The results showed that the response speed in the left vs right localisation was faster than in the identification task, whereas performance in the up vs down localisation was inferior. When the response factors (stimulus-response compatibility) in the left vs right localisation were taken into account, there were no performance differences between localisation and identification. Thus, these results demonstrated that direct performance comparisons between localisation and identification may be somewhat arbitrary, and they do not solve the issue of priority of location or identity information in rapid visual search.

Adult↗
PubMed2005

Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry.

Identification of proteins by MS/MS is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein data base. The search engine assigns each spectrum a score indicating how well the experimental data complies with the expected one; a higher score means increased confidence in the identification. One problem is the false-positive identifications, which arise from incomplete data as well as from the presence of misleading ions in experimental mass spectra due to gas-phase reactions, stray ions, contaminants, and electronic noise. We employed a novel technique of reduction of false positives that is based on a combined use of orthogonal fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation (CAD). Since ECD and CAD exhibit many complementary properties, their combined use greatly increased the analysis specificity, which was further strengthened by the high mass accuracy (approximately 1 ppm) afforded by Fourier transform mass spectrometry. The utility of this approach is demonstrated on a whole cell lysate from Escherichia coli. Analysis was made using the data-dependent acquisition mode. Extraction of complementary sequence information was performed prior to data base search using in-house written software. Only masses involved in complementary pairs in the MS/MS spectrum from the same or orthogonal fragmentation techniques were submitted to the data base search. ECD/CAD identified twice as many proteins at a fixed statistically significant confidence level with on average a 64% higher Mascot score. The confidence in protein identification was hereby increased by more than 1 order of magnitude. The combined ECD/CAD searches were on average 20% faster than CAD-only searches. A specially developed test with scrambled MS/MS data revealed that the amount of false-positive identifications was dramatically reduced by the combined use of CAD and ECD.

Cyclotrons↗
PubMed2004

Quality test of the MicroSeq D2 LSU Fungal Sequencing Kit for the identification of fungi.

Fungal contaminants may be health risk factors in general indoor and occupational environments. The identification of microfungi by macro- and micro-morphological characters is known to be very difficult and time consuming. An alternative method for identification of fungi using a molecular biological method based on a commercially available kit is described. The method is based on the DNA-extraction and subsequent amplification of the D2 expansion region of the large subunit of the fungal rDNA. DNA extraction, amplification, sequencing and database screening can be performed within 24 hours. A total of 28 different fungal species were identified on a morphological basis and compared with identification by the molecular biological method. The database comparison revealed identification down to the species for 12 samples and to the genus level of 11 samples. Five samples could not be identified. It is concluded that the identification of fungi by molecular biological method needs to be improved. This can partly be reached by expanding the fungal DNA-sequence datasets.

Air Pollution, Indoor↗
PubMed2004

Eliminating the dichotomy between theory and practice in talent identification and development: considering the role of psychology.

It is acknowledged that appropriate support and training are essential if talented individuals are to fulfil their potential. The early identification of talented athletes is an increasingly important consideration for researchers and practitioners alike. Once talented individuals have been detected, crucial but limited support resources can be optimally deployed to ensure that their needs are met and that their gifts are developed. However, there is considerable disagreement among experts on what talent is, and which factors can reliably be used within talent identification processes. This paper explores prerequisites to success in sport, and the comparative efficacy of employing these prerequisites within talent identification schemes. It is proposed that talent needs to be reconceptualized so that talent identification and talent development processes are perceived to be dynamic and interrelated. Additionally, the need to place greater emphasis on the capacity of a child to develop in sport and the psychological factors that underpin this process is highlighted. To this end, it is advocated that talent identification and development schemes, while emphasizing the multidimensional nature of talent, need to recognize the essential role of psychology in the ability of individuals to fulfil their sporting potential.

Humans↗
PubMed1999

Microbiological and chemical identification of antimicrobial drugs in kidney and muscle samples of bovine cattle and pigs.

Microbiological and chemical identification of antimicrobial drug residues was attempted in 95 kidney and 76 muscle samples from 58 cattle, 36 pigs and one horse which had revealed kidneys positive to an inhibitor test. Information on pre-slaughter medication with one antimicrobial drug was available for 63% of the carcasses. Microbiological identification was performed by agar diffusion using 17 or 18 combinations of eight test bacteria, varying medium pH and three substances blocking the action of certain antimicrobials. Sample activity patterns compiled from inhibition zone diameters on test plates were compared with those obtained with standard antimicrobial solutions both visually and by locating the minimal sum of absolute pairwise differences over the tests. Chemical identification of residues was based on liquid chromatography. In kidney samples containing one microbiologically-identified antimicrobial the two methods gave fully consistent results with tetracyclines (15/15) and fluoroquinolenes (8/8). Preparation and storage of the kidney samples before chemical analyses appeared to influence the chemical identification of penicillin G. The results were consistent in 37 of the 41 samples stored without homogenization at -70 degrees C. The residue was identified by chemical means only in six and neither microbiologically nor chemically in four kidney samples with information on pre-slaughter medication. The same residue as in the kidney samples was identifiable microbiologically in 41% of the muscle samples of the same carcasses. The results show that the microbiological method is well suited for identification of antibiotic residues. They indicate further that an enhanced resolution with a reduced combination of plates is attainable.

Animals↗
PubMed2002

Attentional cueing effect in the identification of words and pseudowords of different length.

Three experiments studied the influence of spatial attention on familiar and unfamiliar letter string identification. Siéroff and Posner's (1988) cueing procedure was used: A cue indicated in advance either the beginning (left) or the end (right) of a foveally presented letter string that participants were instructed to read aloud. Results showed that the precue had a stronger influence on pseudoword than on word identification. Similar results were obtained when participants were instructed to report the identity of the cue or not. For pseudowords, a cueing effect was obtained regardless of length (6, 8, and 10 letters), whereas only 10-letter words showed such an effect, though to a lesser degree than pseudowords of the same length. However, results showed that shorter words were also influenced by the cue location when the exposure duration was reduced. Results are compatible with an early role of spatial attention in letter string processing, but they also suggest that the lexical status of a letter string can directly influence the distribution of attention before the identification process is completely achieved. Although orienting of spatial attention seems heavily involved in a pseudoword identification, some spatial attention mechanism could also take place in the case of familiar words. The results are discussed within two theoretical frameworks concerning the involvement of spatial attention in word identification: The "replacement" theory and the "redistribution" theory.

Adolescent↗
PubMed2004

Development of a novel, simple and rapid molecular identification system for clinical Candida species.

Identification of clinical yeast isolates causing candidiasis is routinely performed by commercial yeast identification systems based on biochemical, morphological and physiological tests. These systems require 3-5 days and the proportion of identifications that are incorrect is high. Our novel and rapid molecular identification system for clinical Candida species is based on the analysis of restriction patterns obtained from PCR-generated ribosomal DNA sequences using five restriction enzymes. A software package (CandID) was designed to include a database of restriction fragment length polymorphism (RFLP) patterns for 29 Candida species. For 'in-house' validation, 122 clinical isolates that had previously identified in clinical laboratories were typed by this system. These clinical isolates were also independently re-identified by the API 20C AUX system. The ribosomal DNA RFLP database in the context of supporting analytical software allowed simple and rapid (1 work day) identification.

Candida↗
PubMed2005

Molecular methods for the identification of Aspergillus species.

Invasive aspergillosis (IA) is a leading cause of morbidity and mortality in immunocompromised hosts. In some institutions, species of Aspergillus less susceptible to amphotericin B than Aspergillus fumigatus are becoming more common, making an accurate identification of species important. However, species identification has traditionally relied on macroscopic colony characteristics and microscopic morphology, which may require several days of culture. Additional sub-culturing on specialized media may be required to induce conidia formation; in some cases conidia may never form, confounding identification. Therefore, rapid, nucleic acid-based methods that identify species of Aspergillus independent of morphology are now being developed to augment or replace phenotypic identification methods. The most successful methods to date have employed polymerase chain reaction (PCR) amplification of target sequences within the ribosomal RNA gene complex, including the 28S ribosomal subunit (D1-D2 region) and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). We therefore developed a PCR-based assay to differentiate medically important species of Aspergillus from one another, and from other opportunistic moulds and yeasts, by employing universal, pan-fungal primers directed to conserved ribosomal genes and species-specific DNA probes directed to the highly variable ITS2 region. Amplicons were then detected in a simple, colorimetric enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 and ITS2 regions and of the D1-D2 region was also conducted for the differentiation of species by comparative GenBank sequence analysis. The PCR-EIA method was found to be rapid, sensitive, and specific for the identification and differentiation of the most medically important species of Aspergillus. In addition, methods to identify species of Aspergillus by comparative GenBank sequence analysis were found to be more reliable using the ITS1 and ITS2 regions than the D1-D2 region.

Aspergillosis↗
PubMed2004

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery.

In Kellis et al. (2003), we reported the genome sequences of S. paradoxus, S. mikatae, and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae. Genomewide comparative analysis allowed the identification of functionally important sequences, both coding and noncoding. In this companion paper we describe the mathematical and algorithmic results underpinning the analysis of these genomes. (1) We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining ambiguities in the gene correspondence revealed recent gene family expansions in regions of rapid genomic change. (2) We present methods for the identification of protein-coding genes based on their patterns of nucleotide conservation across related species. We observed the pressure to conserve the reading frame of functional proteins and developed a test for gene identification with high sensitivity and specificity. We used this test to revisit the genome of S. cerevisiae, reducing the overall gene count by 500 genes (10% of previously annotated genes) and refining the gene structure of hundreds of genes. (3) We present novel methods for the systematic de novo identification of regulatory motifs. The methods do not rely on previous knowledge of gene function and in that way differ from the current literature on computational motif discovery. Based on genomewide conservation patterns of known motifs, we developed three conservation criteria that we used to discover novel motifs. We used an enumeration approach to select strongly conserved motif cores, which we extended and collapsed into a small number of candidate regulatory motifs. These include most previously known regulatory motifs as well as several noteworthy novel motifs. The majority of discovered motifs are enriched in functionally related genes, allowing us to infer a candidate function for novel motifs. Our results demonstrate the power of comparative genomics to further our understanding of any species. Our methods are validated by the extensive experimental knowledge in yeast and will be invaluable in the study of complex genomes like that of the human.

Algorithms↗
PubMed2005

Gender, Internet identification, and Internet anxiety: correlates of Internet use.

This paper reports a study that investigated the effects of gender, Internet anxiety, and Internet identification on use of the Internet. The study involved 608 undergraduate students (490 females and 118 males). We surveyed the students' experience with the Internet, as well as their levels of Internet anxiety and Internet identification. We found a number of gender differences in participants' use of the Internet. Males were proportionally more likely to have their own web page than were females. They used the Internet more than females; in particular, they were more likely to use game websites, to use other specialist websites, and to download material from the Internet. However, females did not use the Internet for communication more than males. There was a significant positive relationship between Internet identification and total use of the Internet, and a significant negative relationship between Internet anxiety and total use of the Internet. Controlling for Internet identification and Internet anxiety, we found a significant and negative correlation between gender and use of the Internet. In total, all three of our predictors accounted for 40% of the variance in general Internet use: with Internet identification accounting for 26%, Internet anxiety accounting for 11%, and gender accounting for 3%.

Anxiety↗
PubMed1988

Identification of viridans streptococci by three commercial systems.

The API 20S (Analytab Products, Plainview, NY), the GPI card (Vitek Systems, St. Louis, MO) and the RapSTR system (Innovative Diagnostics, Atlanta, GA) were compared with conventional biochemicals for the identification of viridans streptococci. One hundred nine clinical isolates were tested that included the following species: intermedius (38) sanguis II (20), bovis (variant) (14), mitis (14), salivarius (11), sanguis I (6), constellatus (3), mutans (2), and uberis (1). With initial testing, a correct species call was made with 72% of the isolates with the GPI card, 62% with the RapSTR, and 50% with the API 20S. Identifications of viridans streptococci group or those that needed additional biochemicals for species identification occurred with 28% of isolates with the API 20S, 8% with the RapSTR, and 9% with the GPI card. Incorrect identifications occurred with 6% of the isolates tested by the GPI card, 20% with the API 20S, and 30% with the RapSTR. Most discrepancies with the RapSTR were with 66% of the intermedius isolates, whereas most, 55%, of misidentifications with the API 20S were with sanguis II isolates. No identifications were made with 2% and 13% of isolates with the API 20S and GPI, respectively.

Humans↗
PubMed1991

Software for the development and evaluation of probabilistic identification matrices.

A number of programs are described for the development and evaluation of probabilistic identification matrices for use with computer-assisted identification. The program BEST reads an initial matrix of per cent probabilities for all the binary characters examined during a cluster analysis and determines the most useful set of tests for distinguishing taxa in the matrix. Program RESORT creates from the initial matrix an identification matrix in which the order of the tests may be different or the number of tests reduced. A printed version of a matrix can be produced by MATPRINT, which creates tables giving the per cent probability of a positive test result and the test results presented as '-', 'v' and '+' depending on a user-specified threshold. Program IDSC evaluates an identification matrix by calculating the best identification score for each taxon in the matrix using the expected result for each test. The programs were written in FORTRAN 77 and can be run on any micro-computer using the PC/MS-DOS operating system.

Algorithms↗
PubMed1999

Odor identification, consistency of label use, olfactory threshold and their relationships to odor memory over the human lifespan.

The purpose of this study was to investigate olfactory threshold, odor identification, consistency of label use and their relationships to odor memory in the context of semantic/episodic memory across the human lifespan. A total of 137 subjects aged 4-90 years were tested with several olfactory test procedures. We found that olfactory sensitivity was well developed in children despite the finding that their odor naming and odor memory were inferior to that of adults. In the elderly population, olfactory functions gradually declined, with odor memory and odor identification demonstrating the most significant decline. Semantic encoding was differentially related to odor memory over the human age span. Whereas consistency of label use was the main predictor for odor memory in children and young adults, olfactory identification ability was the main predictor in the elderly study group. We also calculated response bias for the separate age groups and found no differences between children, young adults and elderly. However, with age false alarm rates increased. We conclude that children possess equal olfactory sensitivity compared with adults; however, due to limitations in linguistic capabilities and familiarity to odorants, odor memory and odor identification performance was limited. Additionally, our data indicate major alterations of olfactory processing in advanced age with substantial losses in odor memory and odor identification performance.

Adolescent↗
PubMed2004

Usefulness of the odor stick identification test for Japanese patients with olfactory dysfunction.

The odor stick identification test (OSIT) is a new test of olfactory function recently developed for Japanese people. The purpose of the present study was to evaluate this test in relation to T&T olfactometry and the cross-cultural smell identification test (CC-SIT) by applying to 110 Japanese patients with olfactory disturbance. The averaged recognition thresholds for five odorants in T&T olfactometry, the number of correct answers in the CC-SIT and the rates of identification of 13 odorants in the OSIT were compared. The visual analogue scale (VAS) was also used to evaluate symptoms. The rate of identification of OSIT showed high and significant correlation coefficients with the averaged recognition thresholds of T&T olfactometry (-0.766, P < 0.001), with the number of correct answers in CC-SIT (0.754, P < 0.001) and with the VAS score (0.591, P < 0.001). In addition, on the identification performance measured by OSIT, we found significant differences between all pairs of four degrees of olfactory dysfunction except for one pair. Thus, we conclude that OSIT is useful for evaluating olfactory dysfunction in Japanese people.

Asian People↗