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PubMed2004

Pitch modulates lexical identification in spoken word recognition: ERP and behavioral evidence.

Event-related potentials (ERPs) were recorded in cross-modal word fragment priming (CMWP) to address the function of pitch for the identification of spoken words. In CMWP fragments of spoken words (e.g., re taken from Regal [Engl. shelves]) are immediately followed by visual targets. Together with reduced reaction times (RTs), an ERP deflection named P350 has been found to be reduced for targets, which match the primes (e.g., in the prime-target pair re-REGAL) as compared to unrelated targets (e.g., re-WIRBEL [Engl. burble]). The P350 has been related to facilitated lexical identification [Friedrich, Kotz, Friederici and Gunter (in press), ERPs reflect lexical identification in word fragment priming, JOCN]. In the present study, we presented syllable primes with different pitch contours. One version of each prime bore a stressed pitch contour (e.g., re_1), the other an unstressed pitch contour (e.g., re_2). Primes were combined with targets being either stressed on the first syllable (e.g., REgel [Engl. rule]) or on the second syllable (e.g., reGAL [Engl. shelves]). We found a reduced amplitude of the P350 and slightly faster reactions for targets with a stress pattern that matched the pitch of the primes (e.g., re_1-REgel) as compared to targets with a stress pattern that did not match the pitch of the primes (e.g., re_1-reGAL). The present study replicates the P350 effect with different material, and indicates that pitch is used for lexical identification in spoken word recognition.

Adult↗

PubMed2005

Assessment of RAISUS, a novel system for identification and antimicrobial susceptibility testing for enterococci.

RAISUS, a system developed by Nissui Pharmaceutical (Tokyo, Japan), is a novel fully automated system for rapid identification and antimicrobial susceptibility testing. The aim of this study was to compare RAISUS with VITEK systems and microdilution tests based on the National Committee for Clinical Laboratory Standards, with regard to the identification and susceptibility of 64 enterococci. The agreement rate between RAISUS and VITEK was 98.4% (63/64) for bacterial identification. One strain was identified as E. faecalis by RAISUS, but as E. faecium by VITEK. Regarding susceptibility tests, the range of essential agreement and agreement in clinical categories for RAISUS and VITEK ranged from 70.3% to 95.3% and from 68.8% to 96.9%, respectively. Results of antimicrobial susceptibility testing for vancomycin (VAN) showed very major, major, and minor errors in 0%, 3.1% (2/64), and 0%, respectively. RAISUS could provide reports of detection of VAN-resistant enterococci (VRE) within 5 h by using fluorogenic substances and redox. In conclusion, RAISUS could be useful in a clinical setting because it allows rapid identification of enterococci and the potential ability to detect VRE more promptly than the VITEK system.

Bacterial Typing Techniques↗

PubMed2006

Rapid identification of fungal pathogens in BacT/ALERT, BACTEC, and BBL MGIT media using polymerase chain reaction and DNA sequencing of the internal transcribed spacer regions.

We report a direct polymerase chain reaction/sequence (d-PCRS)-based method for the rapid identification of clinically significant fungi from 5 different types of commercial broth enrichment media inoculated with clinical specimens. Media including BacT/ALERT FA (BioMérieux, Marcy l'Etoile, France) (n = 87), BACTEC Plus Aerobic/F (Becton Dickinson, Microbiology Systems, Sparks, MD) (n = 16), BACTEC Peds Plus/F (Becton Dickinson) (n = 15), BACTEC Lytic/10 Anaerobic/F (Becton Dickinson) (n = 11) bottles, and BBL MGIT (Becton Dickinson) (n = 11) were inoculated with specimens from 138 patients. A universal DNA extraction method was used combining a novel pretreatment step to remove PCR inhibitors with a column-based DNA extraction kit. Target sequences in the noncoding internal transcribed spacer regions of the rRNA gene were amplified by PCR and sequenced using a rapid (24 h) automated capillary electrophoresis system. Using sequence alignment software, fungi were identified by sequence similarity with sequences derived from isolates identified by upper-level reference laboratories or isolates defined as ex-type strains. We identified Candida albicans (n = 14), Candida parapsilosis (n = 8), Candida glabrata (n = 7), Candida krusei (n = 2), Scedosporium prolificans (n = 4), and 1 each of Candida orthopsilosis, Candida dubliniensis, Candida kefyr, Candida tropicalis, Candida guilliermondii, Saccharomyces cerevisiae, Cryptococcus neoformans, Aspergillus fumigatus, Histoplasma capsulatum, and Malassezia pachydermatis by d-PCRS analysis. All d-PCRS identifications from positive broths were in agreement with the final species identification of the isolates grown from subculture. Earlier identification of fungi using d-PCRS may facilitate prompt and more appropriate antifungal therapy.

Costs and Cost Analysis↗

PubMed2005

Evaluation of (GTG)5-PCR for identification of Enterococcus spp.

A set of reference strains and a group of previously unidentified enterococci were analysed by rep-PCR with the (GTG)(5) primer to evaluate the discriminatory power and suitability of this method for typing and identification of enterococcal species. A total of 49 strains representing all validly described species were obtained from bacterial collections. For more extensive evaluation of this identification approach 112 well-defined and identified enterococci isolated from bryndza cheese were tested. The (GTG)(5)-PCR fingerprinting assigned all strains into well-differentiated clusters representing individual species. Subsequently, a group including 44 unidentified enterococci isolated from surface waters was analysed to evaluate this method for identification of unknown isolates. Obtained band patterns allowed us to identify all the strains clearly to the species level. This study proved that rep-PCR with (GTG)(5) primer is a reliable and fast method for species identification of enterococci.

Bacterial Typing Techniques↗

PubMed2004

Comparison of cultural methods for the identification and molecular investigation of yeasts from sourdoughs for Italian sweet baked products.

Twenty-five yeast strains isolated from sourdough samples for Panettone, Pandoro and Cornetto brioche manufactured by eight different bakeries in northern Italy were characterised. Classification was performed by the simplified identification method (SIM), Kurtzman and Fell's identification protocol, the API system from bioMérieux (France) and the MicroLog system from Biolog (USA). Genetic diversity was investigated by randomly amplified polymorphic DNA fingerprinting and mitochondrial-DNA restriction enzyme analysis. Sequences of the internal transcribed spacers between 18S and 26S rDNA genes were analysed. Candida humilis was the predominant species (56% of isolates), whereas the remaining strains (44%) were related to the Saccharomyces cerevisiae sensu stricto group. Identification systems based on phenotypic analysis proved to be unreliable to identify yeasts from sourdough. Either RAPD-PCR or mtDNA restriction analysis showed to be suitable for the identification of species, but could not be used to differentiate among the isolates at the strain level. Sequencing of the ITS region permitted a consistent classification of the sourdough yeasts.

Bread↗

PubMed2005

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.

Base Sequence↗

PubMed2005

Contextual information renders experts vulnerable to making erroneous identifications.

We investigated whether experts can objectively focus on feature information in fingerprints without being misled by extraneous information, such as context. We took fingerprints that have previously been examined and assessed by latent print experts to make positive identification of suspects. Then we presented these same fingerprints again, to the same experts, but gave a context that suggested that they were a no-match, and hence the suspects could not be identified. Within this new context, most of the fingerprint experts made different judgements, thus contradicting their own previous identification decisions. Cognitive aspects involved in biometric identification can explain why experts are vulnerable to make erroneous identifications.

Bias↗

PubMed2005

Some mathematical problems in the DNA identification of victims in the 2004 tsunami and similar mass fatalities.

DNA is a major and essential identification tool for mass fatality incidents including the hundreds of thousands of victims of the 2004 Indian Ocean tsunami. Mathematical complications characteristic of this sort of mass fatality include prevalence of related victims, the many races represented among the victims, and various identification modalities in tandem with DNA. Four mathematical problems of interest are discussed in this paper. (1) Other quantifiable factors (i.e. geography) can be formally accounted for by including a likelihood ratio that can be thought of as reducing the "effective number of victims." (2) When a victim is found and tentatively identified as V, but then it comes to light that the victim has a relative W who is also missing, confidence in the identity is depressed. To account for the existence of W, increment the effective number of victims by the likelihood ratio supporting W as the identity of the victim. (3) When several apparently related victims are found, their mutual identities should be calculated simultaneously. Compared to one-at-a-time, serial identifications, this is both logical and may lead to much more confidence in the identities. (4) Although there may be many different population groups represented among the missing, it is generally sufficient to consider population statistics for only a few of them in deciding whether to declare an identification.

DNA↗

PubMed2006

Post-mortem radiological CT identification based on classical ante-mortem X-ray examinations.

Radiological identification is important in forensic medicine. Identification using comparison of individualising structures with ante- and post-mortem conventional radiographs has been known for a long time. New radiological procedures such as computed tomography (CT) and magnetic resonance imaging (MRI) are being increasingly used for identification. In this paper, a new comparative approach using various radiological methods is described and its application demonstrated. This new approach is the comparison of ante-mortem conventional radiographs with projected images calculated from post-mortem CT data. The identification procedure will be illustrated with reference to the frontal sinus and the pelvis.

Forensic Anthropology↗

PubMed2006

Improved repeat identification and masking in Dipterans.

Repetitive sequences are a major constituent of many eukaryote genomes and play roles in gene regulation, chromosome inheritance, nuclear architecture, and genome stability. The identification of repetitive elements has traditionally relied on in-depth, manual curation and computational determination of close relatives based on DNA identity. However, the rapid divergence of repetitive sequence has made identification of repeats by DNA identity difficult even in closely related species. Hence, the presence of unidentified repeats in genome sequences affects the quality of gene annotations and annotation-dependent analyses (e.g. microarray analyses). We have developed an enhanced repeat identification pipeline using two approaches. First, the de novo repeat finding program PILER-DF was used to identify interspersed repetitive elements in several recently finished Dipteran genomes. Repeats were classified, when possible, according to their similarity to known elements described in Repbase and GenBank, and also screened against annotated genes as one means of eliminating false positives. Second, we used a new program called RepeatRunner, which integrates results from both RepeatMasker nucleotide searches and protein searches using BLASTX. Using RepeatRunner with PILER-DF predictions, we masked repeats in thirteen Dipteran genomes and conclude that combining PILER-DF and RepeatRunner greatly enhances repeat identification in both well-characterized and un-annotated genomes.

Animals↗

PubMed2006

[Interpretation of sentinel node identification in vulvar cancer].

OBJECTIVE: Sentinel node (SN) identification in vulvar carcinoma would avoid groin dissection and its complications in early stages, but we first have to validate the method, as an unrecognised node metastasis is detrimental to survival. PATIENTS AND METHODS: Since June 2002, 38 patients with T1 or T2 lesions underwent SN identification by radioactive tracer injection and scintigraphy with, on the following day, per operative use of a handheld probe +/- patent blue dye. In case of a midline lesion, a bilateral inguinal dissection was performed whatever the result of SN identification. SN free from disease were ultrastaged with immunohistochemistry. RESULTS: 1 or more SN were identified in 36 out of 38 patients. 64 groins were analysed, 15 with node metastases. In 9 out of these 15 cases the SN was metastatic, in 5 it had not been identified, and in 1 it was a false negative. In these last 6 cases, there were massively metastatic nodes in the groin. In 19 out of the 26 midline lesions the surgeon identified only unilateral SN. The side without SN contained metastatic nodes in 5 cases. DISCUSSION AND CONCLUSION: Failure in SN identification is sometimes related to a massively invaded node. This should be taken into account especially in the management of midline tumors where a seemingly unilateral drainage at scintigraphy warrants nevertheless a surgical assessment of the mute groin.

Adult↗

PubMed2005

Rapid detection and identification of pathogens in blood cultures by fluorescence in situ hybridization and flow cytometry.

Septicemia is one of the leading causes of death in hospitalized patients. The timely detection and identification of microorganisms from the patient's blood has great diagnostic, prognostic and economic significance. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been proven to be a fast method for the identification of human pathogenic bacteria and yeasts. Data presented herein reveal that the combination of FISH and flow cytometry (FC-FISH) is a rapid and reliable technique for identification of pathogens (Gram-negative rods, Candida spp.) directly from blood cultures without further cultivation and biotyping. Moreover, detection of growing pathogens (e.g., Stenotrophomonas maltophilia) in blood cultures is achieved more rapidly by FC-FISH compared to standard detection methods. Therefore, FC-FISH allows rapid detection and identification of pathogens in blood cultures.

Bacteria↗

PubMed2026

Identification Matters: How Data Sharing Affects Pupil Honesty and Engagement in Universal School Well-Being Assessments.

PURPOSE: Universal well-being assessments in schools may support early identification of pupils needing mental health support. However, little is known about how privacy and confidentiality concerns influence pupils' acceptability of assessments and willingness to engage authentically. This study examined how hypothetical identification, where responses are linked to pupils and shared with key stakeholders, affects pupils' anticipated honesty and engagement, and whether known help-seeking barriers predict negative responses. METHODS: Cross-sectional data were collected from 12,377 primary (ages 8-10) and secondary pupils (ages 11-17) across 55 schools in England. Pupils reported whether their responses would change if identifiable and shared with school staff, parents/guardians, or external professionals. Responses indicating reduced honesty or likelihood of disengagement were coded as negative. Predictors were examined using mixed-effects logistic regression models, including demographics, school connectedness, and mental well-being. RESULTS: Identification and data sharing influenced pupils' anticipated engagement, particularly in secondary schools. Identification by school staff elicited the highest proportion of negative responses in both phases, whereas external professionals elicited the fewest. Most primary pupils reported they would respond authentically, while a larger proportion of secondary pupils indicated they would respond less honestly or disengage when responses were identifiable and shared. Across primary and secondary samples, low well-being, low school connectedness, and being female were associated with greater likelihood of negative response. DISCUSSION: Pupils' anticipated engagement with well-being assessments is shaped by who accesses their data, with marked developmental differences. Strengthening trust, privacy, and connectedness, and supporting pupils' autonomy, may improve the acceptability and response accuracy.

Humans↗

PubMed2006

On the risk of false positive identification using multiple ion monitoring in qualitative mass spectrometry: large-scale intercomparisons with a comprehensive mass spectral library.

Analysts involved in qualitative mass spectrometry have long debated the minimum data requirements for demonstrating that signals from an unknown sample are identical to those from a known compound. Often this process is carried out by comparing a few selected ions acquired by multiple ion monitoring (MIM), with due allowance for expected variability in response. In a few past experiments with electron-ionization mass spectrometry (EI-MS), the number of ions selected and the allowable variability in relative abundance were tested by comparing one spectrum against a library of mass spectra, where library spectra served to represent potential false positive signals in an analysis. We extended these experiments by carrying out large-scale intercomparisons between thousands of spectra and a library of one hundred thousand EI mass spectra. The results were analyzed to gain insights into the identification confidence associated with various numbers of selected ions. A new parameter was investigated for the first time, to take into account that a library spectrum with a different base peak than the search spectrum may still cause a false positive identification. The influence of peak correlation among the specific ions in all the library mass spectra was also studied. Our computations showed that (1) false positive identifications can result from similar compounds, or low-abundance peaks in unrelated compounds if the method calls for detection at very low levels; (2) a MIM method's identification confidence improves in a roughly continuous manner as more ions are monitored, about one order of magnitude for each additional ion selected; (3) full scan spectra still represent the best alternative, if instrument sensitivity is adequate. The use of large scale intercomparisons with a comprehensive library is the only way to provide direct evidence in support of these conclusions, which otherwise depend on the judgment and experience of individual analysts. There are implications for residue chemists who would rely on standardized confirmation criteria to assess the validity of a given confirmatory method. For example, standardized confirmation criteria should not be used in the absence of interference testing and rational selection of diagnostic ions.

Journal Article↗

PubMed2004

Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes.

About 63 species of Dendrobium are identified in China, making the identification of the origin of a particular Dendrobium species on the consumer market very difficult. We report evaluation of multiple species-specific probes screened from genomic DNA for closely related Dendrobium species identification, based on DNA array hybridization. Fourteen species-specific probes were screened from five closely related Dendrobium species, D. aurantiacum Kerr, D. officinale Kimura et Migo, D. nobile Lindl., D. chrysotoxum Lindl. and D. fimbriatum Hook., based on the SSH-Array technology we developed. Various commercial Dendrobium samples and unrelated samples were definitely identified. The specificity and accuracy of the multiple species-specific probes for species identification was assessed by identifying various commercial Dendrobium samples (Herba Dendrobii). Hybridization patterns of these multiple probes on digested genomic DNAs of Dendrobium species indicated that there are distinct polymorphic sequence fragment in the higher eukaryotes. This is the first report on detection and utilization of multiple species-specific probes of Dendrobium in whole genomic DNA, and this could be useful tools not only for a new technical platform for the closely related species identification but also for epidemiological studies on higher eukaryotes.

DNA↗

PubMed2004

Term identification in the biomedical literature.

Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is the terms (and their relationships) that convey knowledge across scientific articles. Due to the complexities of a dynamically changing biomedical terminology, term identification has been recognized as the current bottleneck in text mining, and--as a consequence--has become an important research topic both in natural language processing and biomedical communities. This article overviews state-of-the-art approaches in term identification. The process of identifying terms is analysed through three steps: term recognition, term classification, and term mapping. For each step, main approaches and general trends, along with the major problems, are discussed. By assessing previous work in context of the overall term identification process, the review also tries to delineate needs for future work in the field.

Abbreviations as Topic↗

PubMed2005

Human identification from the ankle with pre- and postsurgical radiographs.

Fifty-four sets of presurgical ("premortem") and postsurgical ("postmortem") foot and ankle radiographs were retrospectively evaluated to simulate a postmortem identification. The entire foot and ankle was examined in a previous study. The present study evaluates only the ankle for positive identification. Results are consistent with our earlier investigation of pre- and postsurgical foot and ankle radiographic comparisons and indicate that surgical intervention with subsequent healing does not preclude positive identification. However, the ankle contains fewer skeletal features unique to an individual than does the entire foot. Hence, the ankle may be less useful than the foot for establishing positive identification from radiographic comparisons.

Adult↗

PubMed2005

Protein identification assisted by the prediction of retention time in liquid chromatography/tandem mass spectrometry.

Two-dimensional liquid chromatography (2D-LC) coupled on-line with electrospray ionization tandem mass spectrometry (2D-LC-ESI-MS/MS) is a new platform for analysis and identification of proteome. Peptides are separated by 2D-LC and then performed MS/MS analysis by tandem MS/MS. The MS/MS data are searched against database for protein identification. In one 2D-LC-ESI-MS/MS run, we obtained not only the structural information of peptides directly from MS/MS, but also the retention time of peptides eluted from LC. Information on the chromatographic behavior of peptides can assist protein identification in the new platform for proteomics. The retention time of the matching peptides of the identified protein was predicted by the hydrophobic contribute of each amino acid on reversed-phase liquid chromatography (RPLC). By using this strategy proteins were identified by four types of information: peptide mass fingerprinting (PMF), sequence query, and MS/MS ions searched and the predicted retention time. This additional information obtained from LC could assist protein identification with no extra experimental cost.

Amino Acid Sequence↗