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At least 577 records · Page 32Linked to original sources
PubMed1998

[Contribution of fast-sequence three-dimensional MRI angiography with Gadolinium injection in the evaluation of supra-aortic vessels].

Sixty-nine patients with cervical atherosclerotic disease were evaluated by Magnetic Resonance (MR) angiography using a coronal 3D gradient echo gadolinium enhanced sequence. The image quality was evaluated for each artery and ostium on MIP reconstructions. A comparison with conventional angiography was achieved in 27 patients. All MR examinations were assessable; a second injection was performed in ten patients. All carotid bifurcations were visualized. The ostium of the common carotid artery was not assessable in 44% of cases due to the limited coverage. The evaluation of the posterior circulation was good in 90% of cases. The agreement between MR angiography and conventional angiography was good despite a tendency to overestimate moderate stenoses. Stenoses greater than 70%, carotid occlusions and vertebral stenoses greater than 50% were correctly detected.

Adolescent↗
PubMed2006

Dark lumen MR colonography: can high spatial resolution VIBE imaging improve the detection of colorectal masses?

PURPOSE: To assess whether the detection of colorectal lesions can be improved using high spatial resolution VIBE imaging. MATERIALS AND METHODS: 48 patients underwent same-day dark lumen MR colonography (MRC) and conventional colonoscopy (CC) as the standard for the detection of colorectal masses. MRC was performed using contrast-enhanced standard and high spatial resolution T1-weighted 3D VIBE sequences. The findings and the image quality of the standard and high spatial resolution VIBE sequences were compared qualitatively and quantitatively. The findings of both sequences regarding colorectal lesions were compared to those of a subsequently performed colonoscopy. RESULTS: The high spatial resolution VIBE sequence significantly improved the quantitative image quality (CNR 54.0 vs. 36.8). However, high spatial resolution VIBE imaging did not detect more colorectal lesions than the standard VIBE sequence. In addition, none of the sequences employed was able to detect lesions with a diameter of less than 5 mm (CC 40 lesions). However, 13 colorectal lesions with a diameter of greater than 5 mm were detected by both sequences (CC 15). CONCLUSION: High spatial resolution VIBE imaging did not improve the detection of colorectal masses and MRC fails to detect colorectal lesions with a diameter of less than 5 mm.

Adult↗
PubMed2004

3DCoffee: combining protein sequences and structures within multiple sequence alignments.

Most bioinformatics analyses require the assembly of a multiple sequence alignment. It has long been suspected that structural information can help to improve the quality of these alignments, yet the effect of combining sequences and structures has not been evaluated systematically. We developed 3DCoffee, a novel method for combining protein sequences and structures in order to generate high-quality multiple sequence alignments. 3DCoffee is based on TCoffee version 2.00, and uses a mixture of pairwise sequence alignments and pairwise structure comparison methods to generate multiple sequence alignments. We benchmarked 3DCoffee using a subset of HOMSTRAD, the collection of reference structural alignments. We found that combining TCoffee with the threading program Fugue makes it possible to improve the accuracy of our HOMSTRAD dataset by four percentage points when using one structure only per dataset. Using two structures yields an improvement of ten percentage points. The measures carried out on HOM39, a HOMSTRAD subset composed of distantly related sequences, show a linear correlation between multiple sequence alignment accuracy and the ratio of number of provided structure to total number of sequences. Our results suggest that in the case of distantly related sequences, a single structure may not be enough for computing an accurate multiple sequence alignment.

Protein Conformation↗
PubMed2025

JG2: an updated version of the Japanese population-specific reference genome.

Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website ( https://jmorp.megabank.tohoku.ac.jp/ ).

Journal Article↗
PubMed2001

A mini-greedy algorithm for faster structural RNA stem-loop search.

When a set of coregulated genes share a common structural RNA motif, e.g. a hairpin, most motif search approaches fail to locate the covarying but structurally conserved motif. There do exist methods that can locate structural RNA motifs, like FOLDALIGN, but the main problem with these methods is that they are computationally expensive. In FOLDALIGN, a major contribution to this is the use of a greedy algorithm to construct the multiple alignment. To ensure good quality many redundant computations must be made. However, by applying the greedy algorithm on a carefully selected subset of sequences, near full greedy quality can be obtained. The basic idea is to estimate the order in which the sequences entered a good greedy alignment. If such a ranking, found from all pairwise alignments, is in good agreement with the order of appearance in the multiple alignment, the core structural motif can be found by performing the greedy algorithm on just the top sequences in the ranking. The ranking used in this mini-greedy algorithm is found by using two complementing approaches: 1) When interpreting the FOLDALIGN score as an inner product (kernel), the sequences can be ranked according to their distance to their center of mass; 2) We construct an algorithm that attempts to find the K closest sequences in the vector space associated with the inner product, and the remaining sequences can be ranked by their minimum distance to any of the sequences, or to the center of mass in this set. The two approaches arecompared and merged, and the results discussed. We also show that structural alignments of near full greedy quality can found in significantly reduced time, using these methods. The algorithm is being included in the SLASH (Stem-Loop Align SearcH) server available at http://www.bioinf.au.dk/slash.

Algorithms↗
PubMed2001

[The influential factors on DNA cycle sequencing and data evaluation of practical example].

OBJECTIVE: To study some factors that may influence DNA sequencing by analyzing 2040 sequencing samples retrospectively. METHODS: The effects of DNA templates, primers, cycle sequencing reactions as well as purification methods were comparatively analyzed. RESULTS: 70 percent of sequencing failure is caused by DNA template. Characteristics of data from poor template preparation include top-heavy with a short read length, acceptable signal with some noise peaks (Ns), weak signal, overall noise and flat lines or no signal. The ineffective primers can cause 15.4 percent sequencing failure. Possible explanations include primer mismatches and low Tm value. CONCLUSIONS: The quality of template DNA can have a major impact on the quality of the DNA sequencing. Purification of the extension products is absolutely necessary in DNA sequencing, and isopropanol precipitation is highly recommended for this procedure.

Animals↗
PubMed2004

Evaluation of balanced steady-state free precession (TrueFISP) and K-space segmented gradient echo sequences for 3D coronary MR angiography with navigator gating at 3 Tesla.

PURPOSE: To test the feasibility of k-space segmented gradient-echo pulse sequences for free-breathing coronary magnetic resonance angiography (cMRA) on a clinical 3T system. MATERIALS AND METHODS: T2-prepared, fat-suppressed turbo field echo (TFE, turboFLASH, SFPGR) as well as balanced TFE (b-TFE, trueFISP, FIESTA, segmented SSFP) sequences with navigator gating for prospective motion correction were applied on a 3T system equipped with a six-element phased-array cardiac coil. In 15 healthy volunteers, the right coronary artery (RCA) was examined with TFE and b-TFE sequences. Due to examination time limitations, the left coronary artery (LM/LAD) was examined exclusively with the TFE sequence in ten volunteers. Image quality was graded on a five point scale (0 = not visualized to 4 = excellent). The length, diameter and sharpness of the vessels and the contrast-to-noise ratios (CNR) were measured. RESULTS: 98 % of all major segments (proximal/middle/distal) of the RCA could be seen with the TFE sequence and 82 % with the b-TFE sequence. The image quality for the three segments was graded higher for the TFE sequence (2.7/2.7/1.5) than for the b-TFE sequence (1.9/1.6/0.9) with P: (< or = 0.001/< or = 0.004/< or = 0.056). The kappa of the interobserver variability was 0.75 for the TFE sequence and 0.8 for the b-TFE sequence. The measured vessel lengths were longer for the TFE sequence (95 +/- 22 mm) than for the b-TFE sequence (80 +/- 40 mm; P < or = 0.115). No significant changes (P < or = 0.074, P < or = 0.145) in diameter and vessel sharpness of the RCAs were observed between the TFE (2.4 +/- 0.3 mm, 60 % +/- 5) and b-TFE sequences (2.4 +/- 0.3 mm, 62 % +/- 6). The CNR was higher for the TFE sequence (10.1 +/- 3.4) than for the b-TFE sequence (6.6 +/- 2.1; P < or = 0.014). All ten main and proximal segments of the LM/LAD, which were examined exclusively with the TFE sequence, were visible with grade 2.5 and 2.1. The middle segment was visible in seven cases with grade 1.3. In three cases, the distal segment was visible with grade 0.5. The vessel length was 78 +/- 27 mm and the CNR 11.9 +/- 2.4. CONCLUSION: The conventional TFE technique has demonstrated good feasibility for cMRA at 3T. In its operational availability at 3T, the b-TFE sequence is inferior to the TFE sequence.

Adult↗
PubMed1993

Large-scale sequencing library production: an adaptor-based strategy.

A significant bottleneck in large-scale DNA sequencing projects is the creation of high-quality random libraries suitable for sequencing. We have utilized an adaptor-based strategy and developed a simple protocol to reliably generate single-insert random subclone M13 libraries yielding uniform coverage and > 10(3) clones per microgram of DNA. Of the resulting white plaques, 95% contained inserts, < 0.5% were due to adaptors with no insert, and none of the clones were found to contain extraneous DNA (0/600) or multiple inserts (0/300).

Base Sequence↗
PubMed2004

Structural and functional analysis of rice genome.

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

Chromosomes, Plant↗
PubMed2006

Species-specific identification of Leptospiraceae by 16S rRNA gene sequencing.

The genus Leptospira is classified into 13 named species and 4 genomospecies based upon DNA-DNA reassociation studies. Phenotypic tests are unable to distinguish between species of Leptospira, and there is a need for a simplified molecular approach to the identification of leptospires. 16S rRNA gene sequences are potentially useful for species identification of Leptospira, but there are a large number of sequences of various lengths and quality in the public databases. 16S rRNA gene sequences of near full length and bidirectional high redundancy were determined for all type strains of the species of the Leptospiraceae. Three clades were identified within the genus Leptospira, composed of pathogenic species, nonpathogenic species, and another clade of undetermined pathogenicity with intermediate 16S rRNA gene sequence relatedness. All type strains could be identified by 16S rRNA gene sequences, but within both pathogenic and nonpathogenic clades as few as two or three base pairs separated some species. Sequences within the nonpathogenic clade were more similar, and in most cases < or =10 bp distinguished these species. These sequences provide a reference standard for identification of Leptospira species and confirm previously established relationships within the genus. 16S rRNA gene sequencing is a powerful method for identification in the clinical laboratory and offers a simplified approach to the identification of Leptospira species.

Bacterial Typing Techniques↗
PubMedDate not supplied

A theory-based approach to analysing conversation sequences.

AIMS: To assess the quality of communication generally two procedures are used: one defines categories of utterances and counts their frequency, the other uses global observer ratings. We investigated whether a sequence analysis of utterances yields results which more precisely reflect the process of a conversation. METHODS: We re-examined data from a randomised controlled intervention study in which residents' interviews with simulated patients were analysed with the Maastricht History and Advice Checklist (MAAS-R) and the Roter Interaction Analysis System (RIAS). Using the U-file of the RIAS we studied the effect of different types of physician questions (open, closed questions, facilitators, other physician actions) on the length of uninterrupted patients' speech and content of utterances. We investigated also whether reciprocity indices improve after a communication skills training, and whether they correlate with global scores form MAAS-R. RESULTS: Patients respond to a closed question with a mean of 1.78 (+/- 1.49) utterances as compared to 2.75 (+/- 2.72) utterances after an open question. The likelihood of a concern was more than 10 fold higher after an open question compared to closed questions. Reciprocal sequences make up less than 2 percent of the conversation, Still, they correlate with global items form MAAS-R. The 'empathy index' improves after the training.

Communication↗
PubMedDate not supplied

Breath-held MR cholangiopancreatography with half-averaged single shot hybrid rapid acquisition with relaxation enhancement sequence: comparison of fast GRE and SE sequences.

PURPOSE: Our goal was to determine whether half-averaged single shot hybrid rapid acquisition with relaxation enhancement (single shot hybrid RARE) sequence can improve image quality, duct conspicuity, signal intensity ratio (SIR), and contrast-to-noise ratio (CNR) of MR cholangiopancreatography (MRCP) by comparing it with two other MRCP sequences: fast SE (FSE) and contrast-enhanced Fourier-acquired steady-state technique (CE-FAST). METHOD: MRCP with three sequences was obtained in 46 people (10 volunteers, 36 patients with pancreatobiliary disease). Overall image quality and duct conspicuity were graded. SIR and CNR were also measured. RESULTS: Overall image quality was graded excellent or good in all 46 patients (100%) with single shot hybrid RARE, in 38 of 46 (83%) with FSE, and in 5 of 46 (11%) with CE-FAST. Duct conspicuity was the best in single shot hybrid RARE statistically. SIR was the highest in FSE, while CNR was highest statistically in single shot hybrid RARE of three sequences. CONCLUSION: Single shot hybrid RARE can provide consistently higher quality MRCP than FSE and CE-FAST because sequential images by single shot hybrid RARE minimize respiratory, bowel, and cardiac motion artifacts.

Adolescent↗
PubMed2003

Maintaining data integrity in microarray data management.

Gene expression microarrays are a relatively new technology, dating back just a few years, yet they have already become a very widely used tool in biology, and have evolved to a wide range of applications well beyond their original design intent. However, while the use of microarrays has expanded, and the issues of performance optimization have been intensively studied, the fundamental issue of data integrity management has largely been ignored. Now that performance has improved so greatly, the shortcomings of data integrity control methods constitute a greater percent of the stumbling blocks for investigators. Microarray data are cumbersome, and the rule up to this point has mostly been one of hands-on transformations, leading to human errors which often have dramatic consequences. We show in this review that the time lost on such mistakes is enormous and dramatically affects results; therefore, mistakes should be mitigated in any way possible. We outline the scope of the data integrity issue, to survey some of the most common and dangerous data transformations, and their shortcomings. To illustrate, we review some case studies. We then look at the work done by the research community on this issue (which admittedly is meager up to this point). Some data integrity issues are always going to be difficult, while others will become easier-one of our goals is to expedite the use of integrity control methods. Finally, we present some preliminary guidelines and some specific approaches that we believe should be the focus of future research.

Algorithms↗
PubMed2002

Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.

A method is presented to refine models built by homology by the use of restricted molecular dynamics (MD) techniques. The basic idea behind this method is the use of structure validation software to determine for each residue the likelihood that it is modeled correctly. This information is used to determine constraints and restraints in an MD simulation including explicit solvent molecules, which is used for model refinement. The procedure is based on the idea that residues that the validation software identifies as correctly positioned should be strongly constrained or restrained in the MD simulations, whereas residues that are likely to be positioned wrongly should move freely. Two different protocols are compared: one (applied to CASP3 target T58) using full structural constraints with separate optimization of each short fragment and the other (applied to T47) allowing some freedom using harmonic restraining potentials, with automatic optimization of the whole molecule. Structures along the MD trajectory that scored best in structural checks were selected for the construction of models that appeared to be successful in the CASP3 competition. Model refinement with MD in general leads to a model that is less like the experimental structure (Levitt et al. Nature Struct Biol 1999;6:108-111). Actually, refined T47 was slightly improved compared to the starting model; changes in model T58 led not to further enhancement. After the X-ray structure of the modeled proteins became known, the procedure was evaluated for two targets (T47 and the CASP4 target T111) by comparing a long simulation in water with the experimental target structures. It was found that structural improvements could be obtained on a nanosecond time scale by allowing appropriate freedom in the simulation. Structural checks applied to fast fluctuations do not appear to be informative for the correctness of the structure. However, both a simple hydrogen bond count and a simple compactness measure, if averaged over times of typically 300 ps, correlate well with structural correctness and we suggest that criteria based on these properties may be used in computational folding strategies.

Amino Acid Sequence↗
PubMed2002

Improving the analysis of arteriovenous passage times.

PURPOSE: This study evaluated the effect of two techniques, time-based correction (TBC) and de-interlacing, on the quality of an image sequence from a scanning laser ophthalmoscope (SLO), and their impact on subsequent analysis for the determination of arteriovenous passage (AVP) times. METHODS: Fluorescein angiograms obtained from one patient participating in a concurrent study approved by an institutional review board (IRB) were analyzed before and after the serial connection of a TBC, and before and after de-interlacing of the images. Informed consent was obtained, and all tenets of the Declaration of Helsinki were followed. AVP times were determined and the variance in time per 100 frames was calculated. RESULTS: The average error in the determination of AVP times was significantly less after the application of these techniques ( p<0.05). Also, the coefficient of variance in the time elapsed per 100 frames was reduced after TBC and de-interlacing of the video sequence. CONCLUSION: The study showed that in addition to the subjective improvement in image quality after de-interlacing and TBC, quantitative parameters are improved. This leads to a more accurate analysis of the angiogram.

Arteries↗