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At least 667 records · Page 37Linked to original sources
PubMed2005

Comparison of fat-suppressed T2-weighted fast spin-echo sequence and modified STIR sequence in the evaluation of the rotator cuff tendon.

OBJECTIVE: This study was performed to determine whether a modified version of the classic STIR sequence provides similar information about the integrity of the rotator cuff tendon as the commonly used fat-suppressed T2-weighted fast spin-echo sequence. SUBJECTS AND METHODS: Sixty-one consecutive MRI examinations of the shoulder in 57 patients were performed using a coronal oblique T1-weighted spin-echo sequence, a modified version of the STIR sequence, and a fat-suppressed T2-weighted fast spin-echo sequence. Three reviewers independently assessed the rotator cuff tendon using the coronal oblique modified inversion recovery sequence and T1-weighted spin-echo sequence. After a minimum of 4 weeks, reviewers assessed the rotator cuff tendon using the fat-suppressed T2-weighted fast spin-echo sequence and T1-weighted spin-echo sequence. The kappa statistic was used to measure the degree of concordance between interpretations when each sequence was used independently. The conditional probability that a full- and a partial-thickness tear would be diagnosed on both sequences was calculated. Image quality was assessed in a side-by-side comparison. RESULTS: The overall weighted kappa score was 0.82, which indicates excellent concordance between the two sequences. If a full-thickness tear of the rotator cuff tendon was found on the fat-suppressed T2-weighted fast spin-echo sequence, there was a 94.1% probability that the same conclusion would be reached using the modified inversion recovery sequence. If a partial-thickness tear was found on the fat-suppressed T2-weighted fast spin-echo sequence, there was an 80.3% probability that the same conclusion would be reached with the modified inversion recovery sequence. Fat suppression in the modified inversion recovery sequence was superior to that in the T2-weighted fast spin-echo sequence in 26-39% of the examinations. CONCLUSION: The modified inversion recovery sequence and fat-suppressed T2-weighted fast spin-echo sequence provide similar information about the integrity of the rotator cuff tendon.

Adult↗
PubMed2002

Construction of optimal quality control for oligo arrays.

MOTIVATION: Oligo arrays are important experimental tools for the high throughput measurement of gene expression levels. During production of oligo arrays, it is important to identify any faulty manufacturing step. RESULTS: We describe a practical algorithm for the construction of optimal quality control designs that identify any faulty manufacturing step. The algorithm uses hillclimbing, a search technique from combinatorial optimization. We also present the results of using this algorithm on all practical quality control design sizes. AVAILABILITY: On request from the authors.

Algorithms↗
PubMed2000

Insulin aspart: a new rapid-acting insulin analog.

OBJECTIVE: To examine the pharmacology, therapeutics, pharmacokinetics, dosing guidelines, adverse effects, and drug interactions of insulin aspart, and summarize the clinical trials of efficacy and safety in patients with type or type 2 diabetes mellitus. DATA SOURCES: A MEDLINE database search (1985-May 2000) was performed to identify all applicable published articles and abstracts; in some cases, Novo Nordisk unpublished information was also obtained. Review articles on insulin analogs were also identified, as well as review chapters in medical textbooks. STUDY SELECTION: The majority of the studies identified were in abstract form. These studies reported information on the pharmacokinetics of insulin aspart in healthy volunteers and in those with diabetes, as well as the therapeutic utility, safety, and clinical efficacy in patients with diabetes. A limited number of randomized studies were reported as artices in the medical literature DATA EXTRACTION: All published clinical studies were reviewed. DATA SYNTHESIS: Insulin aspart, the second Food and Drug Administration-approved rapid-acting insulin analog, is produced by recombinant technology that replaces the proline at position 28 on the B chain of insulin with negatively charged aspartic acid. Insulin aspart exists as hexamers that rapidly dissociate into monomers and dimers on subcutaneous injection. When administered immediately prior to a meal, insulin aspart is at least as effective as regular human insulin in control of postprandial blood glucose concentrations. Insulin aspart achieves higher peak insulin concentrations in less time and with a shorter duration of action than regular human insulin. CONCLUSIONS: Insulin aspart is a convenient premeal insulin for use by patients requiring mealtime insulin. Furthermore, due to favorable pharmacokinetics, insulin aspart controls postprandial blood glucose concentrations at least as well as regular human insulin and contributes to improved quality of life.

Amino Acid Sequence↗
PubMed2005

Water-saturated three-dimensional balanced steady-state free precession for fast abdominal fat quantification.

PURPOSE: To compare the performance of a novel water-saturated b-SSFP sequence with that of a conventional T1-weighted turbo spin echo (T1W TSE) sequence for abdominal fat quantification. MATERIALS AND METHODS: A water-saturated, segmented, three-dimensional balanced steady-state free precession (b-SSFP) sequence and a traditional T1W TSE sequence were both employed on phantom and human studies. For phantom studies, a dual-layered phantom with known internal/external oil volumes was imaged using the two sequences. Images obtained by the two sequences were both processed using a computer-aided semiautomatic program for oil volume quantification. For human studies, six volunteers were scanned axially, centered at L2-L3 levels. Signal-to-noise ratio (SNR)(fat), contrast-to-noise ratio (CNR)(fat-muscle), CNR(fat-large bowel), and CNR(fat-small bowel) were calculated on hand-drawn regions of interest (ROIs), and averaged over all six slices for each subject. Statistical analyses were then performed to determine the SNR and CNR differences between images obtained by the two techniques. RESULTS: The phantom studies show that water-saturated b-SSFP offers a significantly closer estimation of true oil volumes compared with that of T1W TSE (P < 0.0001), as well as a more accurate internal/external volume ratio (P = 0.0001). In human studies, three-dimensional water-saturated b-SSFP images demonstrated higher CNR than that of T1W TSE (P < 0.0005), and very close SNR(fat) (P = 0.045). CONCLUSION: The proposed three-dimensional water-saturated b-SSFP sequence can generate high quality fat-only abdominal images with high CNR and SNR in shorter scan duration than the conventional T1W TSE approach. As images generated by this sequence suffer from no flow artifacts, and are less sensitive to bulk, respiratory, and bowel motion, three-dimensional water-saturated b-SSFP is a faster and more robust method for improving abdominal fat quantification using MRI.

Abdomen↗
PubMed2001

LD-PCR coupled to long-read direct sequencing: an approach for mutation detection in genes with compact genomic structures.

A number of techniques have been developed as primary screens to scan for DNA sequence variants, including denaturing gradient gel electrophoresis, denaturing high-performance liquid chromatography, single-strand conformation polymorphism and heteroduplex analysis. Variant alleles detected by these assays are subsequently characterised by DNA sequencing. Sequencing itself is rarely used as a primary screen because of labour intensity, cost, and, upon automation, occasional inaccuracy in identifying heterozygous sites. We have previously developed an approach based on coupling long-distance PCR (LD-PCR) to long-read direct sequencing to allow the detection of mutations in the approximately 1.1 kb exon 3 of MECP2. Our use of dye-labelled primers generated high-quality bi-directional sequence runs > 650 bp and allowed easy discrimination of heterozygous bases. We now describe the application of this approach to the detection of mutations in a considerably larger 6.35 kb LD-PCR fragment spanning 10 exons (exons 32-41) of the structurally complex, but genomically compact, TSC2 gene. In a blind analysis, 15/15 previously characterised mutations were successfully identified using seven overlapping bi-directional sequencing reactions. Our approach of long-read sequencing of long-distance PCR products may allow rapid sequencing of multiple exons of compact genes and may be appropriate as a highly sensitive primary screen for mutations.

Base Sequence↗
PubMed2002

Comparison of microarray designs for class comparison and class discovery.

MOTIVATION: Two-color microarray experiments in which an aliquot derived from a common RNA sample is placed on each array are called reference designs. Traditionally, microarray experiments have used reference designs, but designs without a reference have recently been proposed as alternatives. RESULTS: We develop a statistical model that distinguishes the different levels of variation typically present in cancer data, including biological variation among RNA samples, experimental error and variation attributable to phenotype. Within the context of this model, we examine the reference design and two designs which do not use a reference, the balanced block design and the loop design, focusing particularly on efficiency of estimates and the performance of cluster analysis. We calculate the relative efficiency of designs when there are a fixed number of arrays available, and when there are a fixed number of samples available. Monte Carlo simulation is used to compare the designs when the objective is class discovery based on cluster analysis of the samples. The number of discrepancies between the estimated clusters and the true clusters were significantly smaller for the reference design than for the loop design. The efficiency of the reference design relative to the loop and block designs depends on the relation between inter- and intra-sample variance. These results suggest that if cluster analysis is a major goal of the experiment, then a reference design is preferable. If identification of differentially expressed genes is the main concern, then design selection may involve a consideration of several factors.

Algorithms↗
PubMed2004

A new algorithm for detecting low-complexity regions in protein sequences.

MOTIVATION: Pair-wise alignment of protein sequences and local similarity searches produce many false positives because of compositionally biased regions, also called low-complexity regions (LCRs), of amino acid residues. Masking and filtering such regions significantly improves the reliability of homology searches and, consequently, functional predictions. Most of the available algorithms are based on a statistical approach. We wished to investigate the structural properties of LCRs in biological sequences and develop an algorithm for filtering them. RESULTS: We present an algorithm for detecting and masking LCRs in protein sequences to improve the quality of database searches. We developed the algorithm based on the complexity analysis of subsequences delimited by a pair of identical, repeating subsequences. Given a protein sequence, the algorithm first computes the suffix tree of the sequence. It then collects repeating subsequences from the tree. Finally, the algorithm iteratively tests whether each subsequence delimited by a pair of repeating subsequences meets a given criteria. Test results with 1000 proteins from 20 families in Pfam show that the repeating subsequences are a good indicator for the low-complexity regions, and the algorithm based on such structural information strongly compete with others. AVAILABILITY: http://bioinfo.knu.ac.kr/research/CARD/ CONTACT: swshin@bioinfo.knu.ac.kr

Algorithms↗
PubMed2006

Routes to improving the reliability of low level DNA analysis using real-time PCR.

BACKGROUND: Accurate quantification of DNA using quantitative real-time PCR at low levels is increasingly important for clinical, environmental and forensic applications. At low concentration levels (here referring to under 100 target copies) DNA quantification is sensitive to losses during preparation, and suffers from appreciable valid non-detection rates for sampling reasons. This paper reports studies on a real-time quantitative PCR assay targeting a region of the human SRY gene over a concentration range of 0.5 to 1000 target copies. The effects of different sample preparation and calibration methods on quantitative accuracy were investigated. RESULTS: At very low target concentrations of 0.5-10 genome equivalents (g.e.) eliminating any replicates within each DNA standard concentration with no measurable signal (non-detects) compromised calibration. Improved calibration could be achieved by eliminating all calibration replicates for any calibration standard concentration with non-detects ('elimination by sample'). Test samples also showed positive bias if non-detects were removed prior to averaging; less biased results were obtained by converting to concentration, including non-detects as zero concentration, and averaging all values. Tube plastic proved to have a strongly significant effect on DNA quantitation at low levels (p = 1.8 x 10(-4)). At low concentrations (under 10 g.e.), results for assays prepared in standard plastic were reduced by about 50% compared to the low-retention plastic. Preparation solution (carrier DNA or stabiliser) was not found to have a significant effect in this study.Detection probabilities were calculated using logistic regression. Logistic regression over large concentration ranges proved sensitive to non-detected replicate reactions due to amplification failure at high concentrations; the effect could be reduced by regression against log (concentration) or, better, by eliminating invalid responses. CONCLUSION: Use of low-retention plastic tubes is advised for quantification of DNA solutions at levels below 100 g.e. For low-level calibration using linear least squares, it is better to eliminate the entire replicate group for any standard that shows non-detects reasonably attributable to sampling effects than to either eliminate non-detects or to assign arbitrary high Ct values. In calculating concentrations for low-level test samples with non-detects, concentrations should be calculated for each replicate, zero concentration assigned to non-detects, and all resulting concentration values averaged. Logistic regression is a useful method of estimating detection probability at low DNA concentrations.

Artifacts↗
PubMed2005

Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.

Dorsal is a sequence-specific transcription factor that is distributed in a broad nuclear gradient across the dorsal-ventral (DV) axis of the early Drosophila embryo. It initiates gastrulation by regulating at least 30-50 target genes in a concentration-dependent fashion. Previous studies identified 18 enhancers that are directly regulated by different concentrations of Dorsal. Here, we employ computational methods to determine the basis for these distinct transcriptional outputs. Orthologous enhancers were identified in a variety of divergent Drosophila species, and their comparison revealed several conserved sequence features responsible for DV patterning. In particular, the quality of Dorsal and Twist recognition sequences correlates with the DV coordinates of gene expression relative to the Dorsal gradient. These findings are entirely consistent with a gradient threshold model for DV patterning, whereby the quality of individual Dorsal binding sites determines in vivo occupancy of target enhancers by the Dorsal gradient. Linked Dorsal and Twist binding sites constitute a conserved composite element in certain "type 2" Dorsal target enhancers, which direct gene expression in ventral regions of the neurogenic ectoderm in response to intermediate levels of the Dorsal gradient. Similar motif arrangements were identified in orthologous loci in the distant mosquito genome, Anopheles gambiae. We discuss how Dorsal and Twist work either additively or synergistically to activate different target enhancers.

Animals↗
PubMed2002

Options available--from start to finish--for obtaining data from DNA microarrays II.

Microarray technology has undergone a rapid evolution. With widespread interest in large-scale genomic research, an abundance of equipment and reagents have now become available and affordable to a large cross section of the scientific community. As protocols become more refined, careful investigators are able to obtain good quality microarray data quickly. In most recent times, however, perhaps one of the biggest obstacles researchers face is not the manufacture and use of microarrays at the bench, but storage and analysis of the array data. This review discusses the most recent equipment, reagents and protocols available to the researcher, as well as describing data analysis and storage options available from the evolving field of microarray informatics.

DNA↗
PubMedDate not supplied

A method for optimization of pulse sequences in NMR-imaging.

The diagnostic quality of NMR-images is very much dependent on the pulse sequences and the associated parameters. Therefore, one could use pulse sequences as 'electronic contrast media', if one knew the interrelation between the appearance of pathological alterations in NMR-images and the pulse sequences used. A method is demonstrated which allows a simulation of NMR experiments in the computer, based upon two measurements of one single plane with different recovery times. During this procedure, proton density-, T1- and T2-pictures are calculated and a systematic parameter variation can be done with any programmed pulse sequence equation, by calculating new pictures with different contrast. Even virtual images which cannot be achieved by real NMR experiments can be created. In some cases these virtual images have advantages over real NMR-pictures which are demonstrated. The method may be helpful by answering the questions about optimal parameters and may be one step towards a standardization in NMR-imaging.

Brain Neoplasms↗
PubMed2003

A novel strategy for microarray quality control using Bayesian networks.

MOTIVATION: High-throughput microarray technologies enable measurements of the expression levels of thousands of genes in parallel. However, microarray printing, hybridization and washing may create substantial variability in the quality of the data. As erroneous measurements may have a drastic impact on the results by disturbing the normalization schemes and by introducing expression patterns that lead to incorrect conclusions, it is crucial to discard low quality observations in the early phases of a microarray experiment. A typical microarray experiment consists of tens of thousands of spots on a microarray, making manual extraction of poor quality spots impossible. Thus, there is a need for a reliable and general microarray spot quality control strategy. RESULTS: We suggest a novel strategy for spot quality control by using Bayesian networks, which contain many appealing properties in the spot quality control context. We illustrate how a non-linear least squares based Gaussian fitting procedure can be used in order to extract features for a spot on a microarray. The features we used in this study are: spot intensity, size of the spot, roundness of the spot, alignment error, background intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment. SUPPLEMENTARY INFORMATION: http://sigwww.cs.tut.fi/TICSP/SpotQuality/.

Algorithms↗
PubMed2002

Selecting signature oligonucleotides to identify organisms using DNA arrays.

MOTIVATION: DNA arrays are a very useful tool to quickly identify biological agents present in some given sample, e.g. to identify viruses causing disease, for quality control in the food industry, or to determine bacteria contaminating drinking water. The selection of specific oligos to attach to the array surface is a relevant problem in the experiment design process. Given a set S of genomic sequences (the target sequences), the task is to find at least one oligonucleotide, called probe, for each sequence in S. This probe will be attached to the array surface, and must be chosen in a way that it will not hybridize to any other sequence but the intended target. Furthermore, all probes on the array must hybridize to their intended targets under the same reaction conditions, most importantly at the temperature T at which the experiment is conducted. RESULTS: We present an efficient algorithm for the probe design problem. Melting temperatures are calculated for all possible probe-target interactions using an extended nearest-neighbor model, allowing for both non-Watson-Crick base-pairing and unpaired bases within a duplex. To compute temperatures efficiently, a combination of suffix trees and dynamic programming based alignment algorithms is introduced. Additional filtering steps during preprocessing increase the speed of the computation. The practicability of the algorithms is demonstrated by two case studies: The identification of HIV-1 subtypes, and of 28S rDNA sequences from >or=400 organisms.

Algorithms↗
PubMed2003

MicroPreP: a cDNA microarray data pre-processing framework.

The user-friendly MicroPreP framework was developed to transform raw intensity data from cDNA microarrays into high-quality data. The main features of this software are: LOWESS normalisation; merging of DNA microarray data from changing slide versions; outlier detection; and slide quality assessment.

Algorithms↗
PubMed2001

Quantitative quality control in microarray image processing and data acquisition.

A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal-background segmentation and defines five quality scores for each spot to record irregularities in spot intensity, size and background noise levels. A composite score q(com) is defined based on these individual scores to give an overall assessment of spot quality. Using q(com) we demonstrate that the inherent variability in intensity ratio measurements is closely correlated with spot quality, namely spots with higher quality give less variable measurements and vice versa. In addition, gauging data by q(com) can improve data reliability dramatically and efficiently. We further show that the variability in ratio measurements drops exponentially with increasing q(com) and, for the majority of spots at the high quality end, this improvement is mainly due to an improvement in correlation between the two dyes. Based on these studies, we discuss the potential of quantitative quality control for microarray data and the possibility of filtering and normalizing microarray data using a quality metrics-dependent scheme.

Algorithms↗
PubMed2004

New alleles in calpastatin gene are associated with meat quality traits in pigs.

Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and higher juiciness and, therefore, this haplotype is associated with higher eating quality. Some of the sequence variation identified may be associated with differences in phosphorylation of CAST by adenosine cyclic 3', 5'-monophosphate-dependent protein kinase and may in turn explain the meat quality phenotypic differences. The beneficial haplotype was present in all the commercial breeds tested and may provide significant improvements for the pig industry and consumers because it can be used in marker-assisted selection to produce naturally tender and juicy pork without additional processing steps.

Alleles↗