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PubMed1996

Comparison of a commercial biochemical kit and an oligonucleotide probe for identification of environmental isolates of Vibrio vulnificus.

Methods for the identification and isolation of environmental isolates of Vibrio vulnificus were evaluated. Alkaline peptone water supplemented with polymyxin B and colistin-polymyxin B-cellobiose agar were employed for the isolation of suspected V. vulnificus from water, sediment and shellfish samples. When comparing the identification of putative V. vulnificus obtained with the API 20E assay and an oligonucleotide probe, 29 API 20E profiles were obtained with only four profiles (representing 20 isolates) reaching the identification threshold of V. vulnificus among a total of 66 isolates hybridizing with the probe. The results indicated that, compared with colony hybridization, the API 20E assay was not adequate for the identification of environmental isolates of V. vulnificus.

Bacterial Typing Techniques↗

PubMed2006

Fast identification of ten clinically important micro-organisms using an electronic nose.

AIMS: To evaluate the electronic nose (EN) as method for the identification of ten clinically important micro-organisms. METHODS AND RESULTS: A commercial EN system with a series of ten metal oxide sensors was used to characterize the headspace of the cultured organisms. The measurement procedure was optimized to obtain reproducible results. Artificial neural networks (ANNs) and a k-nearest neighbour (k-NN) algorithm in combination with a feature selection technique were used as pattern recognition tools. Hundred percent correct identification can be achieved by EN technology, provided that sufficient attention is paid to data handling. CONCLUSIONS: Even for a set containing a number of closely related species in addition to four unrelated organisms, an EN is capable of 100% correct identification. SIGNIFICANCE AND IMPACT OF THE STUDY: The time between isolation and identification of the sample can be dramatically reduced to 17 h.

Bacteria↗

PubMed2005

A chart-based method for identification of delirium: validation compared with interviewer ratings using the confusion assessment method.

OBJECTIVES: To validate a chart-based method for identification of delirium and compare it with direct interviewer assessment using the Confusion Assessment Method (CAM). DESIGN: Prospective validation study. SETTING: Teaching hospital. PARTICIPANTS: Nine hundred nineteen older hospitalized patients. MEASUREMENTS: A chart-based instrument for identification of delirium was created and compared with the reference standard interviewer ratings, which used direct cognitive assessment to complete the CAM for delirium. Trained nurse chart abstractors were blinded to all interview data, including cognitive and CAM ratings. Factors influencing the correct identification of delirium in the chart were examined. RESULTS: Delirium was present in 115 (12.5%) patients according to the CAM. Sensitivity of the chart-based instrument was 74%, specificity was 83%, and likelihood ratio for a positive result was 4.4. Overall agreement between chart and interviewer ratings was 82%, kappa=0.41. By contrast, using International Classification of Diseases, Ninth Revision, Clinical Modification, administrative codes, the sensitivity for delirium was 3%, and specificity was 99%. Independent factors associated with incorrect chart identification of delirium were dementia, severe illness, and high baseline delirium risk. With all three factors present, the chart instrument was three times more likely to identify patients incorrectly than with none of the factors present. CONCLUSION: A chart-based instrument for delirium, which should be useful for patient safety and quality-improvement programs in older persons, was validated. Because of potential misclassification, the chart-based instrument is not recommended for individual patient care or diagnostic purposes.

Aged↗

PubMed2003

Identification of yeast species from orange fruit and juice by RFLP and sequence analysis of the 5.8S rRNA gene and the two internal transcribed spacers.

Yeast isolates from orange fruit and juice in a spontaneous fermentation were identified and classified by two molecular techniques. The first was analysis of the restriction pattern generated from the polymerase chain reaction (PCR)-amplified 5.8S rRNA gene and the two internal transcribed spacers (ITS) using specific primers. The second technique was sequence analysis of the ITS regions using the same two primers. Nine different restriction profiles were obtained from the size of the PCR products and the restriction analyses with three endonucleases (CfoI, HaeIII and HinfI). These groups were identified as Candida tropicalis, Clavispora lusitaniae, Hanseniaspora uvarum, Pichia anomala, Pichia fermentans, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Saccharomyces unisporus, and Trichosporon asahii. Checking against identification according to morphological, physiological and biochemical traits corroborated this molecular identification. A total concordance was found in the identification with PCR-restriction fragment length polymorphism of the ITS region after analysing certified yeast strains from two different culture collections. Consequently, a rapid and reliable identification of the yeast populations was achieved by using molecular techniques.

Beverages↗

PubMed2006

Partial rpoB gene sequencing for identification of Leptospira species.

The usual target for sequence-based identification of Leptospira species is the 16S rRNA gene. However, because the 16S rRNA gene is not polymorphic enough, it is necessary to sequence a 1500 bp segment of this gene for accurate identification. Based on the alignment of previously determined rpoB of three Leptospira strains, we designed and tested a primer pair that enabled us to amplify and sequence a 600 bp segment of Leptospira rpoB. This segment was species-specific for the 16 species tested, but was unable to separate Leptospira interrogans serovars accurately. For the 11 L. interrogans serovars tested, only seven genotypes could be determined. We thus think that analysis of partial rpoB may be useful as an initial screening test for the identification of a new isolate of Leptospira and detection or identification of Leptospira in clinical or environmental samples, but not for serovar determination.

Bacterial Typing Techniques↗

PubMed2005

Lack of agreement between biochemical and genetic identification of Aeromonas spp.

Biochemical and genetic identification by RFLP (restriction fragment length polymorphism) of the PCR-amplified 16S r-RNA sequence were compared for a selection of 171 clinical and environmental isolates of Aeromonas spp. The investigation revealed large differences between the two methods. The species phenotypic identification scheme and the genetic technique applied to the environmental strains gave divergent results for 96% of the strains tested. There was 46% discrepancy between the two methods for the clinical isolates. The distribution of species differed between clinical and environmental isolates. A. hydrophila, A. caviae, A. jandaei and A. veronii dominated the clinical material (81% of isolates by RFLP), whilst only 21% of the environmental isolates belonged to those four species. From the environmental group A. salmonicida, A. bestiarum, A. sobria, A. media, and A. encheleia contributed 72% of the strains tested. The poor parity between the biochemical and the genetic identification of the environmental isolates, and to a lesser extent for the clinical isolates, underlines the fact that our current biochemical methods cannot adequately differentiate Aeromonas spp. This work also shows that the biochemical schemes derived from clinical isolates are incomplete for the identification of environmental strains.

Aeromonas↗

PubMed2000

Isolation and identification of Candida from the oral cavity.

A number of methods of sampling the oral cavity for the presence of candida have been developed. Such techniques play an important role in the diagnosis and management of oral candidosis. In the past, identification of candida isolated from the oral cavity has usually been limited to the genus Candida or to the species C. albicans. However, with the recognition that Candida species differ in the production of putative virulence factors and sensitivity to antifungal agents, greater emphasis has been placed on identification of isolates to species level. As a result a range of commercially available systems for yeast identification can now be used in conjunction with traditional identification procedures.

Antifungal Agents↗

PubMed1993

Comparison of various methods and reagents for species identification of Staphylococcus aureus positive or negative for the mecA gene.

The reliability of various methods for species identification of Staphylococcus aureus was evaluated. A total of 135 coagulase-positive (SA) or -negative (SS) staphylococcal isolates were tested, including methicillin-resistant (MR) and -susceptible (MS) strains. When the nuc gene which encodes the S. aureus thermonuclease (TNase) was amplified in a multiplex PCR simultaneously with the mecA gene which encodes for the MR-associated penicillin-binding protein 2a of staphylococci, the nuc amplification showed full agreement with the results of the coagulase test. TNase detected by an enzymatic method or as protein in a sandwich ELISA identified S. aureus with nearly the same precision as the PCR. The Staphylase, Monostaph and Staphaurex agglutination kits were all reliable for identification of MSSA, but not for MRSA. Most of the negative MRSA strains were identified by the Pastorex agglutination kit, in which reagents for fibrinogen receptor and protein A detection have been supplemented with antibodies for capsular polysaccharides of the serotypes 5 and 8. These results show that detection of the nuc gene or its TNase product is highly reliable for identification of both MRSA and MSSA strains, while various widely used agglutination kits do not show the same reliability for identification of MRSA strains.

Agglutination Tests↗

PubMed1994

Identification of coryneform and other gram-positive rods with several methods.

The identification of 202 isolates of aerobically growing Gram-positive rods from clinical material was attempted by using a combination of "traditional" morphological and biochemical tests (Hollis & Weaver (20)) plus patterns of cellular and metabolic fatty acids. This system served as the "gold standard" for three others, i.e. API Coryne (Rapid Coryne), MIDI TSBA and MIDI CLIN Aerobic. In addition, several growth, biochemical and susceptibility tests (growth on cystine-tellurite blood agar, DNase, hippurate and starch hydrolysis, methanethiol formation, API ZYM, CAMP reaction, susceptibility to O/129 and to six antimicrobials) were done in order to check their usefulness for the identification of this group of bacteria. Our system, with the help of chemotaxonomic tests (m-DAP and mycolic acids), was able to identify 154/202 (76%) of the isolates by species and an additional 41/202 (21%) by genus only; 7 (3%) could not be identified. The API Coryne system identified to species or genus level 140/195 isolates (72%). Corresponding figures for the MIDI TSBA and CLIN systems were 63/195 (32%) and 88/195 (45%); further details of species and genus identification are presented in the text. The main drawback of the commercial systems is the extent and probably the numerical depth of the data base. We recommend the use of our multisystem approach for the identification of Gram-positive rods until commercial systems are based on a broader and numerically more extensive data base. The additional tests did not prove species- or genus-specific.

Culture Media↗

PubMed1998

Apolipoprotein E status is associated with odor identification deficits in nondemented older persons.

Alzheimer's disease (AD) patients with moderate dementia show losses in olfactory threshold, odor identification and odor memory. Sensitivity and specificity of olfactory testing is significant, with the greatest power of accurate diagnosis in the more cognitively loaded olfactory tasks. In patients with very mild AD or in patients at risk for the disease because of their mild cognitive impairment, losses are apparent for odor identification, odor recognition memory and odor threshold, with the best sensitivity in the identification task. Persons who are either heterozygous or homozygous for the epsilon 4 allele of apolipoprotein E (ApoE) have an increased risk of Alzheimer's disease, although they show no dementia in the preclinical period. Evidence of olfactory dysfunction in this population might be reflective of an incipient dementing process. We have recently examined olfactory function in a group of normal elderly persons who have undergone genetic testing for the Apoe4 allele. These individuals consisted of all normal control subjects at the University of California, San Diego (UCSD) Alzheimer's Disease Research Center (ADRC) who had undergone both the genetic testing and testing for olfactory function. All had been diagnosed as normal control participants by two different neurologists who applied the National Institute of Neurological Disorders and Stroke and the Alzheimer's Disease and Related Disorders Association (NINDS-ADRDA) criteria for dementia. Persons with a history of alcoholism, drug abuse, learning disability or neurologic or psychiatric illness (including depression) were excluded. In this population, persons with the Apoe4 allele showed significantly poorer odor identification than those without an epsilon 4 allele. Early appearance of olfactory deficits in the progression to AD in persons with the epsilon 4 allele suggests diagnostic utility in olfactory testing.

Aged↗

PubMed2000

Identification and psychic closure. A dynamic structuralist approach of the psyche

In this paper, the emergence of psychic structures is conceived within a dynamic structuralist framework, developed in dialogue with the semiotic and dynamic viewpoint on levels from evolutionary systems theory. If psychic structures emerge, it is because they are particular kinds of organizationally closed systems that interpret the variety from below (the biological level) for the level above (the social level). The mechanism of psychic closure is presented as the key mechanism for the constitution of psychic structures, and is interpreted in terms of identification: an identificatory judgment is a self-referential, closing judgment that involves a reinterpretation of the level below (the organic body) and is addressed to the level above (the fellow human being). The way in which identification has worked determines the kinds of psychic structures that are formed and also leads to different kinds of signifying practices. Different types of identification are discussed and a brief presentation of clinical arguments serves to illustrate the determinative role of identification in the formation of psychic structures.

Journal Article↗

PubMed2002

A new approach to closed-loop linear system identification via a vector autoregressive model.

A new vector autoregressive (VAR) model algorithm is developed for closed-loop identification. The new VAR approach is an extension of a recently developed algorithm, named the optimal parameter search (OPS), thus, we call the new technique VOPS, for vector OPS. Monte Carlo simulations of closed-loop systems were performed to compare the performance of VOPS to the widely utilized vector least squares (VLS) and vector fast orthogonal search (VFOS) approaches. In addition, we examined the effect on parameter estimates obtained via open-loop identification techniques, when using data from closed-loop systems. Comparative results show that both the VOPS and VFOS algorithms produce far more accurate parameter estimates than does the VLS. Furthermore, open-loop identification via univariate OPS and to a lesser extent univariate FOS for closed-loop systems, does not adversely affect the accuracy of the parameter estimates. An open-loop identification via the univariate least-squares method for closed-loop systems showed the most deleterious effect on the accuracy of the parameter estimates. In addition to developing the VOPS algorithm, we also developed approaches termed constrained OPS (COPS) and constrained FOS (CFOS). For closed-loop systems considered in this paper, both COPS and CFOS resulted in more accurate parameter estimates (less biased and more efficient) than did VLS, VFOS, and VOPS.

Algorithms↗

PubMed2003

Prostate brachytherapy seed identification on post-implant TRUS images.

TRUS is a conceptually appealing alternative to CT-based dosimetry, offering the substantial practical advantage of being readily available intraoperatively. To test the feasibility and reliability of seed identification on post-implant TRUS using standard two-dimensional images, ten patients treated with I-125 or Pd-103 brachytherapy were studied. A set of transverse images (6 MHz) were taken immediately following completion of the implant procedure. Original thermal images were sent to four physicians and the sources were identified independently by placing marks on a cellophane overlay, with grids to match the axial TRUS images. The number and type of seed implanted were not revealed to the investigators. Instead, they were instructed to mark the positions of what they would consider, with reasonable certainty, to be seeds. The overlays were then manually compared for source identification and agreement between observers regarding each alleged source. The actual number of implanted seeds ranged from 44 to 108 (median: 60). In contrast, the mean number of seeds allegedly identified per patients ranged from 26 to 82 (median: 43). The average percent of the seeds allegedly identified per patient ranged from 51% to 83% (mean: 74%). The four physician investigators--KW, JS, BH, and GM--identified an alleged median of 90%, 44%, 63%, and 91% of the total seeds, respectively. There were five instances in which investigators alleged more seeds than were actually implanted. The consistency of seed identification among the investigators was evaluated by noting how many investigators identified each bright spot on the images. The percent of bright spots identified by all four investigators ranged from 8% to 33% (median: 20%). Despite considerable interest among some of our clinical and commercial colleagues in developing TRUS-based intraoperative post-implant dosimetry, the use of TRUS-based seed identification for post-implant dosimetry should be viewed with skepticism.

Brachytherapy↗

PubMed2005

Phonetic identification in quiet and in noise by listeners with cochlear implants.

This study examined the effect of noise on the identification of four synthetic speech continua (/ra/-/la/, /wa/-/ja/, /i/-/u/, and say-stay) by adults with cochlea implants (CIs) and adults with normal-hearing (NH) sensitivity in quiet and noise. Significant group-by-SNR interactions were found for endpoint identification accuracy for all continua except /i/-/u/. The CI listeners showed the least NH-like identification functions for the /ra/-/la/ and /wa/-/ja/ continua. In a second experiment, NH adults identified four- and eight-band cochlear implant stimulations of the four continua, to examine whether group differences in frequency selectivity could account for the group differences in the first experiment. Number of bands and SNR interacted significantly for /ra/-/la/, /wa/-/ja/, and say-stay endpoint identification; strongest effects were found for the /ra/-/la/ and say-stay continua. Results suggest that the speech features that are most vulnerable to misperception in noise by listeners with CIs are those whose acoustic cues are rapidly changing spectral patterns, like the formant transitions in the /wa/-/ja/ and /ra/-/la/ continua. However, the group differences in the first experiment cannot be wholly attributable to frequency selectivity differences, as the number of bands in the second experiment affected performance differently than suggested by group differences in the first experiment.

Acoustic Stimulation↗

PubMed2006

The influence of perceived sexual orientation on fricative identification.

Listeners are more likely to hear a synthetic fricative ambiguous between /s/ and /integral/ as /integral/ if it is appended to a woman's voice than a man's voice [Strand and Johnson, in Natural Language Processing and Speech Technology: Results of the 3rd KONVENS Conference (Mouton de Gruyter, Berlin, 1996), pp. 14-26]. This study expanded on this finding by replicating the result with a much larger group of male and female talkers than had been examined previously, by examining whether phonetic context mediates the influence of talker sex on fricative identification, and by examining whether talkers' perceived sexual orientation influences fricative identification. Stimuli were created by pairing a synthetic nine-step /s/-/integral/ continuum with tokens of /ae k/ and /Ip/ taken from productions of shack and ship by 44 talkers whose perceived sexual orientation had been reported previously [Munson et al., J. Phonetics (in press)]. Listeners participated in a series of two-alternative sack-shack and sip-ship identification experiments. Listeners identified more /integral/ tokens for women's voices than for men's voices for both continua. Lesbian/bisexual-sounding women elicited more sack and sip responses than heterosexual-sounding women. No consistent influence of perceived sexual orientation on fricative identification was noted for men's voices. Results suggest that listeners are sensitive to the association between fricatives' center frequencies and perceived sexual orientation in women's voices, but not in men's voices.

Adult↗

PubMed2006

Improving syllable identification by a preprocessing method reducing overlap-masking in reverberant environments.

Overlap-masking degrades speech intelligibility in reverberation [R. H. Bolt and A. D. MacDonald, J. Acoust. Soc. Am. 21(6), 577-580 (1949)]. To reduce the effect of this degradation, steady-state suppression has been proposed as a preprocessing technique [Arai et al., Proc. Autumn Meet. Acoust. Soc. Jpn., 2001; Acoust. Sci. Tech. 23(8), 229-232 (2002)]. This technique automatically suppresses steady-state portions of speech that have more energy but are less crucial for speech perception. The present paper explores the effect of steady-state suppression on syllable identification preceded by /a/ under various reverberant conditions. In each of two perception experiments, stimuli were presented to 22 subjects with normal hearing. The stimuli consisted of mono-syllables in a carrier phrase with and without steady-state suppression and were presented under different reverberant conditions using artificial impulse responses. The results indicate that steady-state suppression statistically improves consonant identification for reverberation times of 0.7 to 1.2 s. Analysis of confusion matrices shows that identification of voiced consonants, stop and nasal consonants, and bilabial, alveolar, and velar consonants were especially improved by steady-state suppression. The steady-state suppression is demonstrated to be an effective preprocessing method for improving syllable identification by reducing the effect of overlap-masking under specific reverberant conditions.

Adolescent↗

PubMed1978

Influence of the precedence effect on word identification by normally hearing and hearing-impaired subjects.

The influence of the precedence effect on word identification was investigated binaurally and monaurally with normally hearing and hearing-impaired subjects. The Modified Rhyme Test was processed through a PDP-12 computer to produce delay times of 0, 5, 10, 20, 40, 80, or 160 ms. The sounds were reproduced in a room by two loudspeakers positioned at +/-30 degrees azimuths in front of a subject at 50 dB SPL for normals and at the most comfortable level for impaireds. A babble of eight voices was added to reduce scores about 15% from the best values measured in quiet. Binaural and monaural word identification remained constant over a range of delays from 0 to 20 ms and declined for longer delays for both groups of subjects. The shapes of the word-identification curves were explained by self-masking (an overlap of consonants with their own repetitions) and masking (an overlap of consonants with preceding vowels or preceding and following words in sentence). Binaural responses for ten selected initial and final consonants showed various patterns of perception with delay. Some hearing impaireds showed more deterioration in word identification than others which might indicate that they experience more perceptual difficulties than normal listeners in places with reverberation or sound amplification.

Adult↗

PubMed1985

Phonetic identification by elderly normal and hearing-impaired listeners.

Young normal-hearing listeners, elderly normal-hearing listeners, and elderly hearing-impaired listeners were tested on a variety of phonetic identification tasks. Where identity was cued by stimulus duration, the elderly hearing-impaired listeners evidenced normal identification functions. On a task in which there were multiple cues to vowel identity, performance was also normal. On a/b d g/identification task in which the starting frequency of the second formant was varied, performance was abnormal for both the elderly hearing-impaired listeners and the elderly normal-hearing listeners. We conclude that errors in phonetic identification among elderly hearing-impaired listeners with mild to moderate, sloping hearing impairment do not stem from abnormalities in processing stimulus duration. The results with the /b d g/continuum suggest that one factor underlying errors may be an inability to base identification on dynamic spectral information when relatively static information, which is normally characteristic of a phonetic segment, is unavailable.

Adult↗