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At least 487 records · Page 27Linked to original sources
PubMed2001

Feature localization and identification.

Theories on visual search differ substantially with respect to the relationship they assume between localization and identification processes. The aim of the present study was to rigorously compare the alternative theoretical notions on how localization and identification processes are related. In two experiments, participants searched for a target with a unique line orientation among distractors containing another orientation. Localization and identification performance were measured in combination, as function of display size and target eccentricity. To compare the alternative theories, formal binomial models were developed and compared with respect to their goodness of fit to the individual data. The formal analyses showed that the model assuming identification processes to be conditioned on localization processes provided the best fit to the individual data. Furthermore, maximum likelihood estimates of the parameter corresponding to identification processes were differently affected by display size than identification performance was. The results were discussed in terms of their implication for current theories on visual search.

Fixation, Ocular↗
PubMed2002

Olfactory identification and apolipoprotein E epsilon 4 allele in mild cognitive impairment.

To investigate olfactory identification and apolipoprotein E epsilon 4 allele in patients with mild cognitive impairment (MCI), we used Cross-Cultural Smell Identification Test (CC-SIT) from University of Pennsylvania to assess olfactory identification performance and polymerase chain reaction (PCR) to detect apolipoprotein E epsilon 4 (ApoE epsilon 4) allele in 28 patients with MCI and the 30 age-matched control subjects in present study. The Mann-Whitney U test demonstrated that the MCI group performed significantly worse on CC-SIT than the normal aging group (P<0.01). For MCI patients olfaction scores correlated positively with CAMCOG-C (r=0.61, P<0.01), but not with age, gender or years of education. In normal subjects, the CC-SIT score showed no significant associations with age, gender, years of education, or CAMCOG-C. As the least common allele in Chinese, epsilon 4 was found in 13.3% of controls and in 35.8% of MCI in this study. ApoE epsilon 4 was significantly higher in MCI group than normal group (chi(2)=4.65, P<0.01). There was a significant effect of allele status on odor identification: subjects with epsilon 4 allele were not able to identify as many odors as the subjects without epsilon 4 allele (P<0.01). These results suggested that the decreased olfactory identification in MCI may be a marker for the early diagnosis of Alzheimer's disease, and ApoE genotype may be part of the basis of olfactory identification decline.

Age Factors↗
PubMedDate not supplied

[Personality tests and gender identification in male transsexuals].

The aim of this research project was to study gender identification in male transsexuals compared to male and female controls, using the Rorschach test and the MMPI. In the international literature, many researches have shown that the nature of the human response on Rorschach card III is linked to gender identification, as is the MMPI Mf scale. Ten untreated male homosexual transsexuals and 18 treated and operated male homosexual transsexuals were compared to 10 male and 12 female controls regarding verbal IQ, human content on Rorschach card III and the MMPI Mf scale. Absence of hormonal treatment for the first group of transsexuals was checked by a blood test at the time of the psychological testing. Responses on Rorschach card III were scored according to different kinds of human contents: male (M), female (F), gender-unidentified/neutral (N), bisexual (B), feminine then masculine or the opposite (M/F), and nonhuman (NH). N, B, M/F and NH responses were rare in all Rorschach protocols. As expected, responses given by participants in the control group were significantly more consistent with their anatomical sex than with the opposite sex. Untreated transsexuals do not differ from treated and operated transsexuals on Rorschach data, and both transsexual groups give significantly more female human representations than male controls. Transsexuals' results are similar to female controls. Untreated transsexuals' mean score on the MMPI Mf scale is significantly higher than that of treated and operated transsexuals' score, in the male profile (biological sex). Both groups of transsexuals score higher on the Mf scale in the male profile than in the female profile. The mean Mf score in the male profile is significantly higher than that of male controls, whereas, in the female profile, the mean Mf score is similar to that of female controls. This study shows that for both groups of transsexuals, results are homogenous in respect of Rorschach and MMPI, showing hyper-conformism to self-perceived gender. Results in both groups are similar to results of female controls, but tend to show even more feminine gender identification. The absence of any significant difference between untreated and treated and operated transsexuals seems surprising, suggesting that the hormonal treatment has not had a major impact on gender identification processes. It would doubtless be interesting to study gender identification using even more kinds of data: all human contents in the Rorschach protocol (not just the responses given to card III), MMPI Mf scale, Draw-A-Person Test and Animal-and-Opposite Drawing Test. This would enhance result liability and could provide useful information about how gendter identification processes evolve after surgical sex reassigment.

Adult↗
PubMed1999

Use of PCR-restriction fragment length polymorphism analysis of the hsp65 gene for rapid identification of mycobacteria in Brazil.

Polymerase chain reaction amplification of part of the gene coding for the heat shock protein hsp65 followed by restriction enzyme analysis (PRA) is a recently described tool for rapid identification of mycobacteria. In this study, the speed and simplicity of PRA for identification of isolates of mycobacteria from patients with clinical symptoms of tuberculosis was evaluated and compared with identification results obtained by commercially available methods. Established PRA patterns were observed for nineteen isolates of Mycobacterium tuberculosis, eleven belonging to the complex M. avium-intracellulare, four of M. kansasii, one of M. fortuitum, one of M. abscessus, three of M. gordonae and one of the recently described species M. lentiflavum, as identified by commercially available methods. Two isolates of M. fortuitum and one of M. gordonae had unique and so far undescribed PRA patterns, suggesting geographically-related intra-species variation within the hsp65 sequence. We propose the inclusion of these new patterns in the PRA identification algorithm and have defined more accurately the molecular weight values of the restriction fragments. This is the first report on the isolation of M. lentiflavum in Brazil suggesting that identification by means of PRA could be useful for detection of mycobacterial species that are usually unnoticed. Where the use of several commercial techniques in combination was necessary for correct identification, PRA demonstrated to be a simple technique with good cost-benefit for characterization of all mycobacterial isolates in this study.

Bacterial Proteins↗
PubMed1997

An identification procedure for foodborne microbial hazards.

A stepwise and interactive identification procedure for foodborne microbial hazards has been developed in which use is made of several levels of detail ranging from rough hazard identification to comprehensive hazard identification. This approach allows one to tackle the most obvious hazards first, before focusing on less obvious hazards. The interactive character of the identification procedure is based on the use of several knowledge sources. Combination of knowledge sources, expressed in the use of knowledge rules, supports the user in systematically selecting hazards which may pose a real risk to the consumer. Due to the structured method and the clear definitions of the knowledge rules, the procedure is transparent and may be changed if necessary. The hazard identification procedure has been implemented as a computer program, resulting in a decision-supporting identification system. It provides a way to efficiently assess those hazards which may cause harm if not brought under control during processing. The procedure forms a basis for quantitative risk assessments.

Animals↗
PubMed2000

Discriminative power of fatty acid methyl ester (FAME) analysis using the microbial identification system (MIS) for Candida (Torulopsis) glabrata and Saccharomyces cerevisiae.

Candida (Torulopsis) glabrata is frequently isolated in cases of fungal infection and commonly shows acquired or innate fluconazole resistance. Saccharomyces cerevisiae, an emerging opportunistic yeast pathogen, causes serious systemic infections in immunocompromised, and vaginitis and superficial infections in immunocompetent patients. For both species reliable identification in the routine laboratory is mandatory, but species identification of strains, e.g. trehalose-negative C. glabrata, may be difficult. Therefore, gas-liquid chromatography (GLC) of whole cell fatty acid methyl ester (FAME) profiles, that is independent of assimilation profiles of strains and suitable for reliable and rapid identification of clinically important yeasts, was applied. However, frequent misidentification of C. glabrata as S. cerevisiae has been reported when using the Yeast Clinical Database of MIS. Accuracy of MIS identification may be strongly influenced by the amounts of cell mass analyzed. Therefore, the present study compared the MIS results of these two yeasts achieved with different cell masses. Primarily we optimized, especially with respect to cost-effectiveness, the recommended streaking technique yielding a maximal recovery of 90-130 mg of cell mass from one plate, enabling testing of poor growing strains of C. glabrata. For all C. glabrata strains tested (n = 10) the highest identification scores (SI [Similarity Index] range 0.525-0.963, median 0.832) were achieved with 30 to 45 mg of cell mass. Only 5 of 10 S. cerevisiae strains revealed good library comparisons (SI > or = 0.5) when using 30 mg of cell mass, whereas with 45 mg all strains but two revealed this SI-level. For S. cerevisiae a higher amount of cell mass processed (up to 90 mg) was correlated with better identification scores (SI range using 90 mg: 0.464-0.870, median, 0.737). Several passages prior to FAME analysis of C. glabrata strains on recommended media revealed narrowing of SI ranges, but differences in SI values were not statistically significant.

Biomass↗
PubMed1997

Dynamical Neural Networks that Ensure Exponential Identification Error Convergence.

Classical adaptive and robust adaptive schemes, are unable to ensure convergence of the identification error to zero, in the case of modeling errors. Therefore, the usage of such schemes to "black-box" identification of nonlinear systems ensures-in the best case-bounded identification error. In this paper, new learning (adaptive) laws are proposed which when applied to recurrent high order neural networks (RHONN) ensure that the identification error converges to zero exponentially fast, and even more, in the case where the identification error is initially zero, it remains equal to zero during the whole identification process. The parameter convergence properties of the proposed scheme, that is, their capability of converging to the optimal neural network model, is also examined; it is shown to be similar to that of classical adaptive and parameter estimation schemes. Finally, it is mentioned that the proposed learning laws are not locally implementable, as they make use of global knowledge of signals and parameters. Copyright 1997 Elsevier Science Ltd. All Rights Reserved.

Journal Article↗
PubMed1992

Computer-assisted identification of mycobacteria using code lists--results of a multi-centric study. German Working Group on Mycobacteria.

The frequency of isolation of environmental mycobacteria from clinical specimens has increased significantly in the course of the last years. Assessment of the medical importance of such isolates always depends on a correct identification of any of these strains. In a multicentric study, the efficacy of a standardized, computer-aided system for identification has been evaluated. 13 Laboratories received 24 strains of mycobacteria each and were asked to test all these strains for 16 different features. The results were coded in a standardized way. For the evaluation of these tests, the laboratories were supplied with a list containing all possible codes, which might be indicative of one or another identification. The results proved the logic of the approach. However, the application of the system lead to a correct identification in only 74% of all attempts. It is concluded that such a standardized approach is not useful for mycobacteria, because it requires too much working time and material. It will be more practical to concentrate on a smaller number of tests in the peripheral laboratories, which might allow the identification of M. tuberculosis and a few other species and to leave the definitive identification to reference laboratories. The development of faster, simpler and more reliable methods remains highly desirable.

Bacterial Typing Techniques↗
PubMed1989

Evaluation of the Cobas-Bact system for direct and rapid identification and antimicrobial susceptibility testing of Enterobacteriaceae from positive urine specimens.

A direct antimicrobial susceptibility test and a direct identification of Gram-stained urine specimens positive for Enterobacteriaceae using a new instrument (Cobas-Bact) were compared by means of the conventional Kirby-Bauer agar diffusion disk method and the spot indole test, an in-house set of identification tests or API 20E. Bacteria from 191 cases of monomicrobial bacteriuria due to members of the family Enterobacteriaceae were tested. Direct susceptibility testing was performed in 180 cases (94%), providing 1649 antibiotic-microorganism combinations. A complete agreement was reached in 82% and essential agreement in 92% of cases. Minor discrepancies were found in 163 (9.9%) major ones in 125 (7.6%) and very major ones in 10 (0.6%) of examinations. 72% of all minor and 71% of all major discrepancies were caused by two antibiotics: cephalothin and nitrofurantoin. Of the very major discrepancies, 50% were due to amoxicillin. Of 171 direct identifications obtained, 130 (76%) were "high-confidence" correct identifications (percentage of likelihood p greater than or equal to 80%), 25 (14.6%) "low-confidence" identifications (percentage of likelihood p less than 80%) and 16 (9.4%) misidentifications. On the whole, this direct and rapid Cobas-Bact identification and susceptibility testing procedure provided satisfying information within 5-6 h after collection of urine specimens positive for members of the Enterobacteriaceae family.

Anti-Bacterial Agents↗
PubMed1998

Landmark identification error in submentovertex cephalometrics. A computerized method for determining the condylar long axis.

The purpose of this study was to examine the identification error of certain submentovertex landmarks and to compare three different methods of determining horizontal condylar angulation in submentovertex radiographs. To determine landmark identification error, a random sampling of 12 submentovertex radiographs from preorthodontic patients between the ages of 10 and 17 years was used to determine both intraexaminer and interexaminer reliability. The error associated with the identification of each of 11 landmarks varied between specific landmarks, between the same landmarks bilaterally, and between the vertical and horizontal components of the same landmark. In general, intraexaminer data showed less landmark identification error in both vertical and horizontal directions than did interexaminer data. The foramen spinosum landmarks demonstrated the lowest identification error in both horizontal and vertical direction (intraexaminer), whereas greater identification error was associated with the condylar lateral poles and posterior condylar points (both intraexaminer and interexaminer). A comparison of three different methods of condylar angulation determination was undertaken through the use of two tracings of each of 101 submentovertex radiographs. A computer-derived method representing the principal axis of minimum moment of inertia of the condyle was shown to be more reliable (p < 0.05) with respect to describing condylar angulation than both a method that used a best-fit line through the anterior condylar border and an interpolar axis method.

Adolescent↗
PubMedDate not supplied

Associated postmortem dental findings as an aid to personal identification.

The use of the unique features of the human dentition to aid in personal identification is well accepted within the forensic field. Indeed, despite advances in DNA and other identification methodologies, comparative dental identifications still play a major role in identifying the victims of violence, disaster or other misfortune. The classic comparative dental identification employs the use of postmortem and antemortem dental records (principally written notes and radiographs) to determine similarities and exclude discrepancies. In many cases the tentative identification of the individual is unknown and therefore antemortem records cannot be located. In such a situation a dental profile of the individual is developed to aid the search for the individual's identity. With such a profile a forensic odontologist can identify and report indicators for age at time of death, race (within the four major ethnic groups) and sex. In addition to these parameters the forensic dentist may be able to give more insight into the individual. This paper outlines, for the non-expert, some of the additional personal information that can be derived from the teeth of the deceased, and which may assist in their ultimate identification.

Forensic Dentistry↗
PubMed2003

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes.

This paper investigates the use of survival functions and expectation values to evaluate the results of protein identification experiments. These functions are standard statistical measures that can be used to reduce various protein identification scoring schemes to a common, easily interpretably representation. The relative merits of scoring systems were explored using this approach, as well as the effects of altering primary identification parameters. We would advocate the widespread use of these simple statistical measures to simplify and standardize the reporting of the confidence of protein identification results, allowing the users of different identification algorithms to compare their results in a straightforward and statistically significant manner. A method is described for measuring these distributions using information that is being discarded by most protein identification search engines, resulting in accurate survival functions that are specific to any combination of scoring algorithms, sequence databases, and mass spectra.

Mass Spectrometry↗
PubMed2003

Reliable detection and identification of genetically modified maize, soybean, and canola by multiplex PCR analysis.

Multiplex PCR procedures were developed for simultaneously detecting multiple target sequences in genetically modified (GM) soybean (Roundup Ready), maize (event 176, Bt11, Mon810, T14/25), and canola (GT73, HCN92/28, MS8/RF3, Oxy 235). Internal control targets (invertase gene in corn, lectin and beta-actin genes in soybean, and cruciferin gene in canola) were included as appropriate to assess the efficiency of all reactions, thereby eliminating any false negatives. Primer combinations that allowed the identification of specific lines were used. In one system of identification, simultaneous amplification profiling (SAP), rather than target specific detection, was used for the identification of four GM maize lines. SAP is simple and has the potential to identify both approved and nonapproved GM lines. The template concentration was identified as a critical factor affecting efficient multiplex PCRs. In canola, 75 ng of DNA template was more effective than 50 ng of DNA for the simultaneous amplification of all targets in a reaction volume of 25 microL. Reliable identification of GM canola was achieved at a DNA concentration of 3 ng/microL, and at 0.1% for GM soybean, indicating high levels of sensitivity. Nonspecific amplification was utilized in this study as a tool for specific and reliable identification of one line of GM maize. The primer cry1A 4-3' (antisense primer) recognizes two sites on the DNA template extracted from GM transgenic maize containing event 176 (European corn borer resistant), resulting in the amplification of products of 152 bp (expected) and 485 bp (unexpected). The latter fragment was sequenced and confirmed to be Cry1A specific. The systems described herein represent simple, accurate, and sensitive GMO detection methods in which only one reaction is necessary to detect multiple GM target sequences that can be reliably used for the identification of specific lines of GMOs.

Brassica napus↗
PubMedDate not supplied

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

Automation↗
PubMedDate not supplied

Two-dimensional mass spectra generated from the analysis of 15N-labeled and unlabeled peptides for efficient protein identification and de novo peptide sequencing.

Protein identification has been greatly facilitated by database searches against protein sequences derived from product ion spectra of peptides. This approach is primarily based on the use of fragment ion mass information contained in a MS/MS spectrum. Unambiguous protein identification from a spectrum with low sequence coverage or poor spectral quality can be a major challenge. We present a two-dimensional (2D) mass spectrometric method in which the numbers of nitrogen atoms in the molecular ion and the fragment ions are used to provide additional discriminating power for much improved protein identification and de novo peptide sequencing. The nitrogen number is determined by analyzing the mass difference of corresponding peak pairs in overlaid spectra of (15)N-labeled and unlabeled peptides. These peptides are produced by enzymatic or chemical cleavage of proteins from cells grown in (15)N-enriched and normal media, respectively. It is demonstrated that, using 2D information, i.e., m/z and its associated nitrogen number, this method can, not only confirm protein identification results generated by MS/MS database searching, but also identify peptides that are not possible to identify by database searching alone. Examples are presented of analyzing Escherichia coli K12 extracts that yielded relatively poor MS/MS spectra, presumably from the digests of low abundance proteins, which can still give positive protein identification using this method. Additionally, this 2D MS method can facilitate spectral interpretation for de novo peptide sequencing and identification of posttranslational or other chemical modifications. We envision that this method should be particularly useful for proteome expression profiling of organelles or cells that can be grown in (15)N-enriched media.

Amino Acid Sequence↗
PubMedDate not supplied

Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry.

We describe the application of a peptide retention time reversed phase liquid chromatography (RPLC) prediction model previously reported (Petritis et al. Anal. Chem. 2003, 75, 1039) for improved peptide identification. The model uses peptide sequence information to generate a theoretical (predicted) elution time that can be compared with the observed elution time. Using data from a set of known proteins, the retention time parameter was incorporated into a discriminant function for use with tandem mass spectrometry (MS/MS) data analyzed with the peptide/protein identification program SEQUEST. For singly charged ions, the number of confident identifications increased by 12% when the elution time metric is included compared to when mass spectral data is the sole source of information in the context of a Drosophila melanogaster database. A 3-4% improvement was obtained for doubly and triply charged ions for the same biological system. Application to the larger Rattus norvegicus (rat) and human proteome databases resulted in an 8-9% overall increase in the number of confident identifications, when both the discriminant function and elution time are used. The effect of adding "runner-up" hits (peptide matches that are not the highest scoring for a spectra) from SEQUEST is also explored, and we find that the number of confident identifications is further increased by 1% when these hits are also considered. Finally, application of the discriminant functions derived in this work with approximately 2.2 million spectra from over three hundred LC-MS/MS analyses of peptides from human plasma protein resulted in a 16% increase in confident peptide identifications (9022 vs 7779) using elution time information. Further improvements from the use of elution time information can be expected as both the experimental control of elution time reproducibility and the predictive capability are improved.

Animals↗
PubMed2006

In-gel isoelectric focusing of peptides as a tool for improved protein identification.

In the analysis of proteins in complex samples, pre-fractionation is imperative to obtain the necessary depth in the number of reliable protein identifications by mass spectrometry. Here we explore isoelectric focusing of peptides (peptide IEF) as an effective fractionation step that at the same time provides the added possibility to eliminate spurious peptide identifications by filtering for pI. Peptide IEF in IPG strips is fast and sharply confines peptides to their pI. We have evaluated systematically the contribution of pI filtering and accurate mass measurements on the total number of protein identifications in a complex protein mixture (Drosophila nuclear extract). At the same time, by varying Mascot identification cutoff scores, we have monitored the false positive rate among these identifications by searching reverse protein databases. From mass spectrometric analyses at low mass accuracy using an LTQ ion trap, false positive rates can be minimized by filtering of peptides not focusing at their expected pI. Analyses using an LTQ-FT mass spectrometer delivers low false positive rates by itself due to the high mass accuracy. In a direct comparison of peptide IEF with SDS-PAGE as a pre-fractionation step, IEF delivered 25% and 43% more proteins when identified using FT-MS and LTQ-MS, respectively. Cumulatively, 2190 non redundant proteins were identified in the Drosophila nuclear extract at a false positive rate of 0.5%. Of these, 1751 proteins (80%) were identified after peptide IEF and FT-MS alone. Overall, we show that peptide IEF allows to increase the confidence level of protein identifications, and is more sensitive than SDS-PAGE.

Animals↗
PubMed1998

Evolutionary distances and identification of Candida species in clinical isolates by randomly amplified polymorphic DNA (RAPD).

Fast and reliable identification of different species of the genus Candida is important to define adequate therapeutic decisions, because the different species have highly variable susceptibilities to antifungal drugs; azoles and amphothericin B. Accurate statistical records on case history and epidemiological studies also depend on effective identification. To address this problem we established a RAPD method that enabled direct identification of five very common species of Candida. Initially, reference band patterns were established for C. albicans, C. tropicalis, C. parapsilosis, C. glabrata and C. krusei. One of the primers, M2, showed remarkably conserved intra-specific patterns of approximately 10 bands each, ranging in size from 2.0 to 0.1 kb. These patterns were significantly different and species-specific. Few bands were conserved between different species of Candida, which was assumed to be consistent with their phylogenetic relatedness. In addition, band patterns were constant and reproducible and DNA isolated from single colonies yielded sufficient DNA for identification. The reference band patterns were then used, in blind experiments, to identify species of Candida in 50 randomly chosen samples, including clinical isolates and ATCC strains. RAPD results were 100% consistent with results obtained by conventional diagnostic methods and were achieved in one day instead of several days taken by conventional methods. Because ideal identification methods should be consistent with phylogeny and taxonomy we tested whether RAPD could be used to calculate genetic distances. Comparison of RAPD phylogenetic trees with 18S rRNA trees showed significant differences in tree topologies which indicated that RAPD data could not accurately measure the relative distances between different species. Also, computer simulations of RAPD random patterns were used to test whether the observed degree of RAPD band pattern similarities could occur at random. These simulations suggested that the level of inter-specific band pattern similarities observed in our data could be obtained at random, while intraspecific pattern similarities could not. RAPD would be helpful to discriminate between isolates but not to quantitate the differences. We suggest that the inaccurate estimate of genetic distances from RAPD is a general limitation of the technique and not a specific problem of our identification method. Because of the repetitive character of the target sequences, genetic distances calculated from RAPD could be affected by paralogy, namely, recombination and duplication events not parallel with speciation events.

Candida↗