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PubMedDate not supplied

Identification power of a standardized HPLC-DAD system for systematic toxicological analysis.

High-performance liquid chromatography with photodiode-array detection (HPLC-DAD) provides two identification parameters: retention and UV spectral data. The identification power of these two parameters, expressed in standardized form (retention index and absorption maximum with the highest wavelength), is calculated using two approaches: discriminating power (DP) and mean list length (MLL). Our own HPLC database, which comprises data for more than 370 substances, is used as the basis of calculations. The identification power of both parameters applied separately is low but increases substantially when the combination of retention and spectral data is applied. Additionally, the DP and MLL values obtained for 56 acidic or neutral and 76 basic drugs examined by means of HPLC-DAD and other analytical methods (thin-layer chromatography, gas chromatography (GC), and ultraviolet (UV) detection) are compared. The on-line combination of HPLC retention index values and UV spectra, registered by means of DAD, creates an identification system in which the identification potential is slightly lower than the off-line combination of capillary GC and UV spectroscopy.

Chromatography, Gas↗
PubMed2005

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array.

One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.

Base Sequence↗
PubMed1997

Phosphor-stimulated computed cephalometry: reliability of landmark identification.

The aim of this randomized, controlled, prospective study was to determine the reliability of computed lateral cephalometry (Fuji Medical Systems, Tokyo, Japan) in terms of landmark identification compared to conventional lateral cephalometry (CAWO, Schrobenhausen, Germany). To assess the reliability of landmark identification on lateral cephalographs, 20 computed images, taken at 30 per cent reduced radiation (70 kV, 15 mA, 0.35 s) were compared to 20 conventional images (70 kV, 15 mA, 0.5 s). The 40 lateral cephalographs were taken from 20 orthodontic patients at immediate post-treatment and 1 year after retention. The order and type of imaging was randomized. Five orthodontists identified eight skeletal, four dental and five soft tissue landmarks on each of the 40 films. The error of identification was analysed in the XY Cartesian co-ordinate following digitization. Skeletal landmarks exhibited characteristic dispersion with respect to the Cartesian co-ordinates. Root apices were more variable than crown tips. Soft tissue landmarks were more consistent in the X co-ordinate. Two-way ANOVA shows that there is no significant difference between the two imaging systems in both co-ordinates (P > 0.05). Moreover, the differences are generally small (< 0.5 mm), and are unlikely to be of clinical significance. Most of the variables attained statistical power of at least 0.8 in the X-co-ordinate while only the dental landmarks achieved statistical power of at least 0.78 in the Y-co-ordinate. Based on the results of the study: (1) computed lateral cephalographs can be taken at 30 per cent radiation reduction, compared to conventional lateral cephalograph; (2) each anatomical landmark exhibits its characteristic dispersion of error in both the Cartesian co-ordinates; (3) there is no trend between the two imaging systems, with equivocal result, and none of the landmarks attained statistical significance when both raters and imaging systems are considered as factorial variables; (4) the random error of raters in landmark identification after replicate tracing was highlighted and needs to be taken into consideration in all studies involving landmark identification.

Adolescent↗
PubMed2002

Comparative study of efficiency of dental methods for identification of burn victims in two bus accidents in Spain.

This article deals with the usefulness and limitations of dental identification methods of human burn victims of two buses accidents in Spain. The first accident happened in Bailen in 1996 and involved 28 badly burned Spanish victims. In the second, in Illescas in 1997, 8 Japanese and 2 Spanish victims lost their lives. In both accidents, postmortem forensic procedures for identification were used, including external and internal examination, routine photographs, and dental examination. Dental identification was established in 57% of the cases in the Bailen accident and 80% in the Illescas accident. The success rate of dental identification varies considerably depending on the nature of the accident, the nationality and country of residence of the victims, the incidence of dental treatment, the availability of adequate dental records, and the degree of dental injuries. A discussion of procedures and methods for identification recommended when dealing with burn victims is included.

Accidents, Traffic↗
PubMed1997

Effects of formant bandwidth on the identification of synthetic vowels by cochlear implant recipients.

OBJECTIVE: The main objective was to investigate whether the broadening and narrowing of formant bandwidths had a significant effect on the identification of vowels often confused by Nucleus cochlear implant recipients using the Spectral Peak (SPEAK) speech coding strategy. Specifically, identification performance for synthetic vowels with the first two formants (F1 and F2) parametrically varied in bandwidth was explored. DESIGN: Eight implanted subjects identified synthetic versions of the isolated vowel sounds [I, epsilon, lambda, [symbol: see text]] with F1 and F2 bandwidth manipulations, as well as foil tokens of [i, u, a, ae, [symbol: see text]]. Identification performance was examined in terms of percent correct as well as error patterns. Further analyses compared patterns of electrode activation. RESULTS: In general, broader F1 bandwidths yielded poorer performance and narrower F1 bandwidths yielded better performance relative to identifications for the reference stimuli. However, similar manipulations of F2 bandwidths resulted in less predictable performance. Comparison of electrode activation patterns indicated a distinct sharpening or flattening in the F1 frequency region for subjects with the greatest performance extremes. CONCLUSIONS: Manipulation of F1 bandwidth can result in concomitant changes in electrode activation patterns and identification performance. This suggests that modifications in the SPEAK coding strategy for the F1 region may be a consideration. Similar manipulations of F2 bandwidth yielded less predictable results and require further investigation.

Adolescent↗
PubMed2000

The New York State universal newborn hearing screening demonstration project: ages of hearing loss identification, hearing aid fitting, and enrollment in early intervention.

OBJECTIVE: To determine the ages of hearing loss identification, hearing aid fitting, and enrollment in early intervention through a multi-center, state-wide universal newborn hearing screening project. DESIGN: Universal newborn hearing screening was conducted at eight hospitals across New York State. All infants who did not bilaterally pass hearing screening before discharge were recalled for outpatient retesting. Inpatient screening and outpatient rescreening were done with transient evoked otoacoustic emissions and/or auditory brain stem response testing. Diagnostic testing was performed with age appropriate tests, auditory brain stem response and/or visual reinforcement audiometry. Infants diagnosed with permanent hearing loss were considered for hearing aids and early intervention. Ages of hearing loss identification, hearing aid fitting, and enrollment in early intervention were investigated regarding nursery type, risk status, unilateral versus bilateral hearing loss, loss type, loss severity, and state regions. RESULTS: The prevalence of infants diagnosed with permanent hearing loss was 2.0/1000 (85 of 43,311). Of the 85 infants with hearing loss, 61% were from neonatal intensive care units (NICUs) and 67% were at risk for hearing loss. Of the 36 infants fitted with hearing aids, 58% were from NICUs and 78% were at risk for hearing loss. The median age at identification and enrollment in early intervention was 3 mo. Median age at hearing aid fitting was 7.5 mo. Median ages at identification were less for infants from the well-baby nurseries (WBNs) than for the NICU infants and for infants with severe/profound than for infants with mild/moderate hearing loss, but were similar for not-at-risk and at-risk infants. Median ages at hearing aid fitting were less for well babies than for NICU infants, for not-at-risk infants than for at-risk infants, and for infants with severe/ profound hearing loss than for infants with mild/ moderate hearing loss. However, median ages at early intervention enrollment were similar for nursery types, risk status, and severity of hearing loss. CONCLUSIONS: Early ages of hearing loss identification, hearing aid fitting, and enrollment in early intervention can be achieved for infants from NICUs and WBNs and for infants at risk and not at risk for hearing loss in a large multi-center universal newborn hearing screening program.

Age Factors↗
PubMed2005

Prevalence and early identification of language delays among at-risk three year olds.

The aims of this study were fourfold: to document the prevalence of language delays in a sample of at-risk 3 year olds; to assess the effectiveness of a home visiting program in preventing early language delays; to determine how often parents, pediatric providers, and home visitors identified early language delays; and to assess the effectiveness of a home visiting program in improving early identification of language delays. The Preschool Language Scale, Third Edition (PLS-3) was administered to 513 at-risk 3 year olds participating in a randomized trial of home visiting services. Families randomized to home visiting were expected to receive weekly to quarterly visits throughout the 3 years of this study. The content of home visits included teaching parents about child development, role-modeling parenting skills, and linking families to a medical home. Identification of delays was measured using structured parent interviews and review of primary care and home visiting records. At age 3 years, 10% of children had severe language delays, defined as scoring >or=2 SD below the national mean on the PLS-3, whereas 49% scored >or=1 SD below the national mean. No differences in prevalence were seen between children who did and did not receive home visiting. Among children with severe delays, 42% were identified by parents, 33% by pediatric providers, and 24% by home visitors. Among children with any delays, 24% were identified by parents, 25% by pediatric providers, and 17% by home visitors. No differences in rates of identification were seen between children who did and did not receive home visiting. Thus, while language delays were highly prevalent among these at-risk children, rates of identification were low, even among children with severe delays. Home visiting was not effective in either preventing language delays or improving early identification. This suggests that pediatric providers and home visiting programs need to reexamine their approaches to recognizing and intervening with early language delays.

Age Factors↗
PubMed2006

Identification of the unidentified deceased: turnaround times, methods, and demographics in Fulton County, Georgia.

CONTEXT: Multiple methods may be employed in an attempt to identify deceased individuals who are unidentified when reported to the medical examiner or coroner. The success and turnaround times of various methods differ. OBJECTIVE: To determine the number of deaths initially involving unidentified individuals, their demographics, the methods used and turnaround times for cases in which identification was successful and the portion of cases that remain unidentified for significant periods of time. DESIGN, SETTING, AND PARTICIPANTS: Retrospective case review of all decedents who were initially unidentified when death was reported to the Fulton County Medical Examiner in Atlanta, Georgia, during a 1-year period between May 2003 and May 2004. MAIN OUTCOME MEASURES: Rate per 1000 deaths which involved an unidentified decedent, tabulation of methods used to make identifications, and rate of cases remaining unidentified. RESULTS: Of 2279 deaths reported to the office, 100 were originally unidentified, resulting in a rate of 44 unidentified decedents per 1000 deaths reported. Those who remained unidentified involved 6 cases, resulting in a "cold case" rate of 2.6 per 1000 deaths. Seventy-eight percent were identified within 2 days, and the most common successful methods were visual identification (52%) and fingerprints (31%). Dental (10%), x-ray (4%), and other methods (6%) were least commonly used. Of the 94 persons identified, all identifications occurred within 29 days. DNA procedures were not needed in most cases, and in the few cases where such tests were needed, results were either unavailable or failed to show a match with known samples. CONCLUSIONS: The majority of unidentified deceased individuals were identified within 2 days, with visual verification or fingerprints accounting for about 83% of methods successfully employed. The medical examiner noted a rate of 44 unidentified deceased persons per 1000 death reports, with an ultimate "cold case" (long-term unidentified) rate of about 2.6 cases per 1000 death reports. These data may be useful in developing office policy and procedure regarding the procedural and temporal aspects of investigations centered on achieving identification and making dispositions of unidentified deceased bodies.

Adolescent↗
PubMed1983

A probability matrix for identification of some Streptomycetes.

The character state data obtained for clusters defined at the 77.5% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a probabilistic identification matrix. The 23 phena included were the major clusters (19 Streptomyces, 2 Streptoverticillium and 'Nocardia' mediterranea) and one minor cluster (Streptomyces fradiae). The characters most diagnostic for these clusters were selected using Sneath's CHARSEP and DIACHAR programs. The resulting matrix consisted of 41 characters x 23 phena. Identification scores, determined by Sneath's MATIDEN program were used to evaluate the matrix. Theoretical assessment was achieved by determination of the cluster overlap (OVERMAT), the identification scores for the Hypothetical Medium Organism of each cluster (MOSTTYP), and the scores for randomly selected cluster representatives using the classification data of Williams et al. (1983). The matrix was evaluated practically by the independent re-determination of the characters for the same cluster representatives, which also provided a measure of test error. Finally it was used to identify unknown isolates from a range of habitats. The results showed that the matrix was theoretically sound. Test error was within acceptable limits and did not distort identifications. Of the unknown isolates, 80% were clearly identified with a cluster. It is suggested that the matrix could form the basis for a more objective identification and grouping of the large number of Streptomyces species which have been described.

Drug Resistance, Microbial↗
PubMed1988

A frequency matrix for probabilistic identification of some bacilli.

A matrix comprising frequencies for positive results for 44 Bacillus taxa for 30 characters has been constructed. The 44 taxa include most of the common species and several clusters of environmental isolates including those described as B. firmus-B. lentus intermediates. The tests, which were chosen for their high diagnostic value, included some of the traditional tests used for identification of bacilli supplemented with a range of sugar fermentations and other characterization tests. The matrix was evaluated by identifying hypothetical median organisms, cluster representatives and a panel of 23 reference strains. All reference strains achieved Willcox probabilities above 0.995. Fifty-eight environmental isolates were also subjected to the 30 tests and identification was attempted. Forty-one strains (70%) achieved a Willcox probability greater than 0.95, which was considered an acceptable identification, and were assigned to 12 taxa. If the SE of taxonomic distance was also considered in the identification score (an acceptable value being less than 7.0), the number of acceptable identifications was reduced to 34 (59%). It was encouraging that bacteria from garden soils identified to the common species such as B. subtilis, B. cereus and B. licheniformis whereas some of the bacteria from an estuarine habitat were identified as species such as B. firmus which are normally identified with that habitat.

Bacillus↗
PubMed1989

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. II. Identification.

The data from an integrated numerical classification was used to construct identification schemes for some fasciculate penicillia. The identification schemes were presented as a synoptic key and a frequency matrix for computer-assisted identification. Statistical testing of the frequency matrix showed that although character separation values were generally low, only four pairs of taxa showed overlap greater than that expected for a rectangular distribution. The identification schemes were tested practically with 52 previously studied strains and 51 further cultures. A synoptic key based on 10 and 90% cutoff limits was used to correctly identify 44 of the 51 additional strains, although this proved very sensitive to single test discrepancies. The frequency matrix was used to correctly identify 45 of the additional strains with a Willcox probability score and this was compared to identifications based on the modal likelihood fraction.

Numerical Analysis, Computer-Assisted↗
PubMed1997

Rapid identification by specific PCR of coagulase-negative staphylococcal species important in hospital infection.

Polymerase chain reaction (PCR) identification assays were designed for eight major species of coagulase-negative staphylococci (CNS) on the basis of three variable regions found in the 16S rRNA gene. The PCR assays were tested with 41 staphylococcal strains representing the diversity of staphylococci defined by classical biotyping schemes. Each PCR result was compared with species-specific polymorphism in and around the 16S rRNA gene (i.e., 16S ribotype) and the phenotypic identification of the strain in a miniaturised biochemical test gallery (bioMerieux ATB 32 Staph). Twenty-six of the 41 strains were identified by PCR as belonging to one of the eight species for which primers had been designed and none of the remaining strains was misidentified. For 22 of the 26 strains there was complete agreement between the PCR identification, 16S ribotype and ATB identification. For the remaining four strains there was agreement between PCR identification and 16S ribotype. Two National Collection of Type Culture strains were re-assigned to different species and 10 previously unassigned strains were formally speciated for the first time. These PCR assays are suitable for rapid and definitive speciation of CNS.

Bacterial Typing Techniques↗
PubMed2003

Species identification of medically important fungi by use of real-time LightCycler PCR.

Invasive fungal infection has become a major cause of morbidity and mortality in immunocompromised patients. Rapid identification of pathogenic fungi to species level is critical for disease treatment. A real-time LightCycler assay aiming at rapid detection and species identification of pathogenic fungi from clinical isolates was developed. Template DNAs of different species were amplified and detected in real time by employing SYBR Green fluorescent dye. The target sequences for species-level detection were located between the 18S and 28S rDNA. Seven fungal species encountered frequently in the clinical setting, Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis, Candida guilliermondii and Cryptococcus neoformans, could be discriminated by species-specific primers and confirmed by melting-curve analyses. The range of linearity was from 1 ng to 1 pg (microl(-1) water) and the sensitivity was 1 pg fungal DNA microl(-1). Identification by this real-time PCR method matched biochemical identification for all 58 clinical strains. Therefore, the method is simple, rapid and sensitive enough for detection and identification of several fungal species.

Fungi↗
PubMed2006

Identification and molecular characterization of mannitol salt positive, coagulase-negative staphylococci from nasal samples of medical personnel and students.

The identification of mannitol salt positive, coagulase-negative staphylococci (CNS) is often disregarded when Staphylococcus aureus is screened in clinical samples using mannitol salt agar. However, the emergence of CNS as important human pathogens has indicated that reliable methods for the identification of clinically significant CNS are of great importance in understanding the epidemiology of infections caused by them. The identification and molecular characterization of mannitol salt positive CNS from nasal samples of medical personnel and students is reported here. A total of 84 mannitol salt positive staphylococcal isolates were obtained from 240 nasal samples, of which 15 were CNS. The API STAPH system classified the CNS isolates into six species, and one-third of the isolates were identified with confidence levels of <80 %. 16S-23S rRNA intergenic spacer length polymorphism analysis (ITS-PCR) identified only two species (Staphylococcus haemolyticus and Staphylococcus saprophyticus). This identification was confirmed by antibiotyping, species-specific PCR and PFGE. The results from this study indicate that ITS-PCR is a potentially useful and reliable tool, enabling hospital laboratories to obtain rapid, full and accurate identification of CNS at the species level.

Bacterial Typing Techniques↗
PubMed2001

Efficiency of database search for identification of mutated and modified proteins via mass spectrometry.

Although protein identification by matching tandem mass spectra (MS/MS) against protein databases is a widespread tool in mass spectrometry, the question about reliability of such searches remains open. Absence of rigorous significance scores in MS/MS database search makes it difficult to discard random database hits and may lead to erroneous protein identification, particularly in the case of mutated or post-translationally modified peptides. This problem is especially important for high-throughput MS/MS projects when the possibility of expert analysis is limited. Thus, algorithms that sort out reliable database hits from unreliable ones and identify mutated and modified peptides are sought. Most MS/MS database search algorithms rely on variations of the Shared Peaks Count approach that scores pairs of spectra by the peaks (masses) they have in common. Although this approach proved to be useful, it has a high error rate in identification of mutated and modified peptides. We describe new MS/MS database search tools, MS-CONVOLUTION and MS-ALIGNMENT, which implement the spectral convolution and spectral alignment approaches to peptide identification. We further analyze these approaches to identification of modified peptides and demonstrate their advantages over the Shared Peaks Count. We also use the spectral alignment approach as a filter in a new database search algorithm that reliably identifies peptides differing by up to two mutations/modifications from a peptide in a database.

Algorithms↗
PubMed2006

Ligand identification using electron-density map correlations.

A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.

Algorithms↗
PubMed1991

Recursive parameter identification of constrained systems: an application to electrically stimulated muscle.

In the application of real-time identification methods for diagnosis or adaptive control of biomedical systems, there is often known model information that is ignored. Constraints on the allowable values of parameters, which may be based on physical considerations, are often neglected because the information does "fit" easily into commonly used parameter-identification algorithms. In this paper a method of incorporating constraints on model parameters is developed. This method is applicable to most recursive parameter-identification algorithms. It enforces linear equality constraints on identified parameters. The use of this method for the real-time identification of autoregressive moving-average-type time series models, subject to parameter constraints, is described in detail. These constraints may be time varying. At each time step, the parameter estimate obtained by a recursive least squares estimator is orthogonally projected onto the constraint surface. This simple idea, when appropriately executed, enhances the output prediction accuracy of estimated parameters. Using constraint information in this way is important when we do not wish to destroy a "natural" parameterization of the model (by an initial projection to incorporate equality constraints), or when we cannot use a single initial model simplification (because the constraints are time varying or involve inputs and outputs). Because it improves output prediction at future times, this method is advantageous for use in predictive adaptive controllers. The use of this algorithm is demonstrated in the identification of electrically stimulated quadriceps muscles in paraplegic human subjects, using percutaneous intramuscular electrodes. The nonlinear steady-state force versus pulsewidth recruitment characteristic of the electrode-muscle system is identified simultaneously with the input-output muscle response dynamics, using a Hammerstein-type model. Knowledge of the recruitment curve's shape is translated into constraints on the identified parameters. This information improves the experimental predictive quality of the identified model.

Adult↗
PubMed2005

A comparison of mycolic acid analysis for nontuberculous mycobacteria identification by thin-layer chromatography and molecular methods.

The development of fast, inexpensive, and reliable tests to identify nontuberculous mycobacteria (NTM) is needed. Studies have indicated that the conventional identification procedures, including biochemical assays, are imprecise. This study evaluated a proposed alternative identification method in which 83 NTM isolates, previously identified by conventional biochemical testing and in-house M. avium IS1245-PCR amplification, were submitted to the following tests: thin-layer chromatography (TLC) of mycolic acids and PCR-restriction enzyme analysis of hsp65(PRA). High-performance liquid chromatography (HPLC) analysis of mycolic acids and Southern blot analysis for M. avium IS1245 were performed on the strains that evidenced discrepancies on either of the above tests. Sixty-eight out of 83 (82%) isolates were concordantly identified by the presence of IS1245 and PRA and by TLC mycolic acid analysis. Discrepant results were found between the phenotypic and molecular tests in 12/83 (14.4%) isolates. Most of these strains were isolated from non-sterile body sites and were most probably colonizing in the host tissue. While TLC patterns suggested the presence of polymycobacterial infection in 3/83 (3.6%) cultures, this was the case in only one HPLC-tested culture and in none of those tested by PRA. The results of this study indicated that, as a phenotypic identification procedure, TLC mycolic acid determination could be considered a relatively simple and cost-effective method for routine screening of NTM isolates in mycobacteriology laboratory practice with a potential for use in developing countries. Further positive evidence was that this method demonstrated general agreement on MAC and M. simiae identification, including in the mixed cultures that predominated in the isolates of the disseminated infections in the AIDS patients under study. In view of the fact that the same treatment regimen is recommended for infections caused by these two species, TLC mycolic acid analysis may be a useful identification tool wherever molecular methods are unaffordable.

Bacterial Typing Techniques↗