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At least 217 records · Page 12Linked to original sources
PubMed2025

Development and Validation of Amplicon-Based Protocol for Sequencing of Respiratory Syncytial Virus Genome.

The most prevalent cause of severe respiratory infections in children is the human respiratory syncytial virus (RSV). The advent of next-generation sequencing (NGS) has made it possible to incorporate this technology into pathogen monitoring and surveillance. Whole-genome sequencing (WGS) of RSV has now become a relatively widely used method for tracking viral evolution. Here we report an improved high-throughput RSV-WGS assay performed directly on clinical samples that is suitable for short-read sequencing platforms. A total of 100 RSV-positive samples collected between November 2022 and March 2024 fulfilled the inclusion cycle quantification criteria and were randomly included in the validation process. The WGS protocol was designed to amplify three distinct amplicons to cover the entire RSV genome. The protocol described here can be successfully replicated in several instances (approximately 95%) in samples with a relatively low viral load, typically corresponding to cycle of quantification values of 27-32. The amplicon-based protocol produced meaningful sequencing results in terms of median depth of coverage (more than 12000×) and median of mapped reads (> 1 × 106 reads). The sequences that had passed the filters showed a coverage of at least 98% across the entire genome, with cycle quantification values of 32. Based on the obtained data resulting in an easy-to-perform protocol helpful for the molecular epidemiology surveillance of RSV.

Humans↗
PubMedDate not supplied

DIAGNOdent measurements and correlation with the depth and volume of minimally invasive cavity preparations.

In this clinical study, DIAGNOdent (KaVo) was used to assess previously diagnosed carious lesions in the pits and fissures of first and second molars. The measurements from this device were correlated with the depth and volume of the cavity preparations that resulted from minimal intervention to remove occlusal carious lesions. Twenty-five patients, 18 years of age and older, who were previously scheduled for an occlusal restoration due to caries, were recruited and enrolled in this clinical study. These patients had 48 qualifying teeth without previous restorations, sealants or other carious lesions. The occlusal surface of each study tooth was cleaned utilizing ProphyFlex2 (KaVo). Two dentists separately traced the pit and fissure system of each tooth using DIAGNOdent for two 15-second periods each. The peak reading of each of the four measurements was recorded. An impression of the occlusal surface of each tooth was recorded with a polyvinyl siloxane bite registration material. The carious lesions were removed with an air abrasion unit employing a 0.015-inch nozzle opening utilizing minimal operative intervention. A low viscosity polyvinyl siloxane was used to take an impression of the cavity preparation impression, using the bite registration impression to form the occlusal surface of the preparation impression. The preparation impression volume was calculated from its weight, using the known density of the impression material. The greatest depth of the preparation was measured. The Pearson correlation coefficient was used to investigate any relationship between depth or volume of the preparation impression and the DIAGNOdent measurements. The correlation for preparation volume and maximum DIAGNOdent measurement was 0.191 (p = 0.189). Other logical subsets of cases also did not result in any statistically significant correlations between the DIAGNOdent readings and the depth or volume of the final cavity preparations.

Adolescent↗
PubMedDate not supplied

Intra- and interexaminer variability and validity of laser fluorescence and electrical resistance readings on root surface lesions.

The purpose of this study was to investigate the validity and reproducibility of laser fluorescence and electrical resistance readings on root carious lesions. One hundred and three freshly extracted human teeth with various forms of natural root caries were investigated by 6 operators using the laser fluorescence device DIAGNOdent (DD) and the Electronic Caries Monitor (ECM III). As a reference, a caries-free root area of each tooth was also examined. Specimens were classified as to colour, surface texture and cavitation depth. Teeth were sectioned through the centre of the lesion and prepared for polarising light microscopy. Histological depth of the lesions was defined as the distance between the surface and zone of translucency. Depths ranged from 0.1 to 3.1 mm. Statistical analysis of the interexaminer reproducibility revealed a significant correlation (Kendall's W) for DD measurements of 0.85 and 0.76 for ECM readings. Moderate correlation between the histological depth and DD (r(s) = 0.45) or ECM scores (r(s) = -0.48) could be demonstrated. Electrical resistance readings revealed a positive correlation (r(s) = 0.43) with the thickness of the remaining dentine, whereas this was negative for laser fluorescence readings (r(s) = -0.43). However, scatter plots suggested that most lesions had very low resistance. This investigation suggests that laser fluorescence and electrical conductance measurements can be obtained reproducibly by different operators and correlate moderately with histological lesion depth and remaining thickness of the dentine bridge.

Dental Caries Activity Tests↗
PubMed1994

Prelexical and postlexical strategies in reading: evidence from a deep and a shallow orthography.

The validity of the orthographic depth hypothesis (ODH) was examined in Hebrew by employing pointed (shallow) and unpointed (deep) print. Experiments 1 and 2 revealed larger frequency effects and larger semantic priming effects in naming with unpointed print than with pointed print. In Experiments 3 and 4, subjects were presented with Hebrew consonantal strings that were followed by vowel marks appearing at stimulus onset asynchronies ranging from 0 ms (simultaneous presentation) to 300 ms from the onset of consonant presentation. Subjects were inclined to wait for the vowel marks to appear even though the words could be named unequivocally using lexical phonology. These results suggested that prelexical phonology was the default strategy for readers in shallow orthographies, providing strong support for the ODH.

Adult↗
PubMed2004

Comparison of dynamic contour tonometry with goldmann applanation tonometry.

PURPOSE: The dynamic contour tonometer (DCT; Pascal tonometer) is a novel tonometer designed to measure intraocular pressure (IOP) independent of corneal properties. The purpose of this study was a comparison of the DCT with the Goldmann applanation tonometer (GAT) with respect to mean of IOP readings, the influence of ocular structural factors on IOP readings, and both intra- and interobserver variability, in a large group of healthy subjects. METHODS: In a prospective study of 228 eyes, IOP measurements by GAT and DCT were compared, and the effects of central corneal thickness (CCT), corneal curvature, axial length, and anterior chamber depth were analyzed. To evaluate intra- and interobserver variability, IOP was measured in eight eyes by four observers. RESULTS: There was a high concordance between the IOP readings obtained by DCT and GAT. However, IOP readings were consistently higher with DCT than with GAT (median difference: +1.7 mm Hg, interquartile range [25th-75th percentile] = 0.8-2.7 mm Hg). In contrast to GAT, multivariable regression analysis showed no significant effect of corneal thickness, corneal curvature, astigmatism, anterior chamber depth, and axial length on DCT readings. For repeated measurements the intraobserver variability was 0.65 mm Hg for the DCT and 1.1 mm Hg for the GAT (P = 0.008). Interobserver variability was 0.44 mm Hg for the DCT and 1.28 mm Hg for the GAT (P = 0.017). CONCLUSIONS: IOP measurements by DCT are highly concordant with IOP readings obtained from GAT but do not vary in CCT and have a lower intra- and interobserver variability. DCT seems to be an appropriate method of tonometry for routine clinical use.

Astigmatism↗
PubMed1997

Cognitive operations in the human caudate nucleus.

We have addressed the role of the head of caudate nucleus in taks of lexical decision, semantic categorization, reading aloud, memory retrieval and object naming by recording neuronal activity from depth electrodes in parkinsonism patients. The firing rate of cells was increased within 400-600 ms when semantic processing was required. Phonological differences increased firing from 1000 to 1200 ms. These responses were similar to those described earlier in Broca's area. Both reading aloud and explicit memory retrieval tasks elicited an inhibition in firing of the same cells with an onset around 800 ms. The results confirm earlier lesion and stimulation studies, and provide a basis for relating cellular activity to studies of blood flow and scalp electrical activity in similar cognitive tasks thus helping us to understanding the cellular mechanisms involved in human cognition.

Caudate Nucleus↗
PubMed1999

Coloured overlays, text, and texture.

In four studies children were asked to read aloud a passage of randomly ordered common words with and without a coloured sheet of plastic (overlay) placed upon the page. The children's rate of reading increased with the overlay, for some children more than for others. The children were also asked to undertake a test of texture segmentation in which targets consisting of a structured texture had to be distinguished from within a random background texture. The texture segmentation was improved when the overlay was used, again for some children more than for others. The improvement in texture segmentation was, in general, correlated with the improvement in rate of reading. Slower readers were generally poorer at texture segmentation. The implications for reading, for texture segmentation, and for clinical tests of vision are discussed.

Adolescent↗
PubMed2024

An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.

Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.

DNA, Mitochondrial↗
PubMed1988

Description and clinical evaluation of a new computerized periodontal probe--the Florida probe.

A new periodontal probing system has been developed which incorporates the advantages of constant probing force, precise electronic measurement to 0.1 mm and computer storage of the data. The system includes a probe handpiece, displacement transducer with digital readout, foot switch, computer interface and personal computer. A unique movable arm design enables the probe handpiece to maintain smooth operation and makes it easy to clean and sterilize. Electronic recording of the data (actuated by pressing a foot switch) eliminates errors which occur when probe tip markings are read visually and the data are called to an assistant. Computer storage and analysis of the data facilitates detecting changes in pocket depth and attachment level by rapidly comparing data recorded at different visits. The system was evaluated in 3 experiments using a 0.4 mm diameter tip and a 25 g probing force. The standard deviation of repeated pocket depth measurement was less (0.58 mm versus 0.82 mm) than that of a common probe. With paired readings referenced to an occlusal stent, the standard deviation of repeated attachment level measurements was 0.28 mm. A loss of attachment level was detected to a certainty of 99% with less than a 1 mm change. This is a significant improvement over common probes, which require a 2-3 mm change for equivalent positive identification of change in attachment level.

Computers↗
PubMed2006

Sex differences in semantic processing: event-related brain potentials distinguish between lower and higher order semantic analysis during word reading.

Behavioral studies suggest that women and men differ in the strategic elaboration of verbally encoded information especially in the absence of external task demand. However, measuring such covert processing requires other than behavioral data. The present study used event-related potentials to compare sexes in lower and higher order semantic processing during the passive reading of semantically related and unrelated word pairs. Women and men showed the same early context effect in the P1-N1 transition period. This finding indicates that the initial lexical-semantic access is similar in men and women. In contrast, sexes differed in higher order semantic processing. Women showed an earlier and longer lasting context effect in the N400 accompanied by larger signal strength in temporal networks similarly recruited by men and women. The results suggest that women spontaneously conduct a deeper semantic analysis. This leads to faster processing of related words in the active neural networks as reflected in a shorter stability of the N400 map in women. Taken together, the findings demonstrate that there is a selective sex difference in the controlled semantic analysis during passive word reading that is not reflected in different functional organization but in the depth of processing.

Adult↗
PubMed2006

Assembling millions of short DNA sequences using SSAKE.

UNLABELLED: Novel DNA sequencing technologies with the potential for up to three orders magnitude more sequence throughput than conventional Sanger sequencing are emerging. The instrument now available from Solexa Ltd, produces millions of short DNA sequences of 25 nt each. Due to ubiquitous repeats in large genomes and the inability of short sequences to uniquely and unambiguously characterize them, the short read length limits applicability for de novo sequencing. However, given the sequencing depth and the throughput of this instrument, stringent assembly of highly identical sequences can be achieved. We describe SSAKE, a tool for aggressively assembling millions of short nucleotide sequences by progressively searching through a prefix tree for the longest possible overlap between any two sequences. SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets. AVAILABILITY: http://www.bcgsc.ca/bioinfo/software/ssake.

Algorithms↗
PubMed2006

Ocular pulse amplitude in healthy subjects as measured by dynamic contour tonometry.

OBJECTIVES: To test whether dynamic contour tonometry yields ocular pulse amplitude (OPA) measurements that are independent of corneal thickness and curvature, and to assess variables of observer agreement. METHODS: In a multivariate cluster analysis on 223 eyes, the relationship between central corneal thickness, corneal curvature, axial length, anterior chamber depth, intraocular pressure, sex, age, and OPA measurements was assessed. Intraobserver and interobserver variabilities were calculated from repeated measurements obtained from 8 volunteers by 4 observers. RESULTS: The OPA readings were not affected by central corneal thickness (P = .08), corneal curvature (P = .47), anterior chamber depth (P = .80), age (P = .60), or sex (P = .73). There was a positive correlation between OPA and intraocular pressure (0.12 mm Hg/1 mm Hg of intraocular pressure; P<.001) and a negative correlation between OPA and axial length (0.27 mm Hg/1 mm of length; P<.001). Intraobserver and interobserver variabilities were 0.08 and 0.02 mm Hg, respectively, and the intraclass correlation coefficient was 0.89. CONCLUSIONS: The OPA readings obtained with dynamic contour tonometry in healthy subjects are not influenced by the structure of the anterior segment of the eye but are affected by intraocular pressure and axial length. We found a high amount of agreement within and between observers.

Adult↗
PubMed1989

Clinical evaluation of a samarium/aluminum compound filter.

Rare earth compound filters, which offer reduced patient exposure during intraoral radiography, have not been clinically evaluated for their effect on diagnostic yield. This clinical study was conducted to compare the diagnostic yield of bitewing radiographs exposed with a conventional aluminum filter with matched bitewing radiographs exposed with a samarium/aluminum compound filter. One hundred sixty-three pairs of bitewing radiographs were read independently by two reviewers for absence or presence and depth of proximal carious lesions. Degree of agreement between films was assessed by means of the kappa statistic. Results showed good agreement between the radiographs exposed with each filter type. Thus, x-ray machines modified with a samarium/aluminum rare earth compound filter produce bitewing radiographs of comparable diagnostic yield and lower dose when compared with radiographs exposed with a conventional aluminum filter.

Adult↗
PubMed1978

Pandemonium and visual search.

Pandemonium-like models have played a central role in theories of perceptual recognition. One model is examined which asserts that information is sorted unidirectionally through a hierarchy of increasingly abstract levels only to a depth required by the logical demands of the task and read off from the appropriate level to control response decisions. The support originally claimed for the model in terms of its application to visual search performance is questioned. It is suggested that the pervasiveness of such models is not due to their competition with alternative theories but rather to methatheoretic considerations.

Feedback↗
PubMed2005

An improved method for constructing and selectively silanizing double-barreled, neutral liquid-carrier, ion-selective microelectrodes.

We describe an improved, efficient and reliable method for the vapour-phase silanization of multi-barreled, ion-selective microelectrodes of which the silanized barrel(s) are to be filled with neutral liquid ion-exchanger (LIX). The technique employs a metal manifold to exclusively and simultaneously deliver dimethyldichlorosilane to only the ion-selective barrels of several multi-barreled microelectrodes. Compared to previously published methods the technique requires fewer procedural steps, less handling of individual microelectrodes, improved reproducibility of silanization of the selected microelectrode barrels and employs standard borosilicate tubing rather than the less-conventional theta-type glass. The electrodes remain stable for up to 3 weeks after the silanization procedure. The efficacy of a double-barreled electrode containing a proton ionophore in the ion-selective barrel is demonstrated in situ in the leaf apoplasm of pea (Pisum) and sunflower (Helianthus). Individual leaves were penetrated to depth of approximately 150 microm through the abaxial surface. Microelectrode readings remained stable after multiple impalements without the need for a stabilizing PVC matrix.

Journal Article↗
PubMed2026

Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan.

Chloroplast genomes provide important insights into plant phylogeny, genome evolution, and molecular marker development. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of two endemic species from Uzbekistan, Astragalus nuratensis and Oxytropis pseudorosea. Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638&#xd7; and 1,725&#xd7;, respectively. The chloroplast genomes were 122,316&#xa0;bp in A. nuratensis and 122,708&#xa0;bp in O. pseudorosea. Both genomes encoded 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Consistent with members of the inverted repeat-lacking clade of Fabaceae, both species lacked the typical inverted repeat regions, resulting in a single-copy genome structure. Phylogenetic analysis based on 119 complete chloroplast genomes resolved major lineages within Astragalus and related genera with strong support. Astragalus nuratensis was placed within the Phaca clade, while Oxytropis pseudorosea formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes.

Genome, Chloroplast↗
PubMed1998

[Special schools for deaf children. Their status of hearing, speech and clinical history].

170 deaf school children were described with respect to the following conditions: depth of the hearing impairment, phonic speech ability and lip reading possibility. The anamnesis data were also analyzed. All children disclosed a profound hearing impairment. 60 from 170 (35%) had deaf parents. The phonic speech ability was possessed in an unsufficient degree by only 128 (75%) children. 69 (40%) children passed 3 years of speech and hearing rehabilitation before entering the school. 58 (34%) showed good lip reading ability.

Adolescent↗