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Results for “Sequencing quality”

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At least 721 records · Page 40Linked to original sources
PubMed1993

Fast spin-echo MR images of the pelvis obtained with a phased-array coil: value in localizing and staging prostatic carcinoma.

OBJECTIVE: The fast spin-echo pulse sequence allows T2-weighted MR images to be acquired more rapidly than is possible with conventional spin-echo sequences, and phased-array coils can provide a higher signal-to-noise ratio than is possible with the body coil. The combination of these methods permits higher resolution images to be obtained with more signal averages despite shorter imaging times. In this study, initial technical comparisons designed to confirm the advantage of combining fast spin-echo pulse sequences with a pelvic phased-array multicoil were followed by an assessment of the value of these methods for the localization and staging of prostatic carcinoma. SUBJECTS AND METHODS: Seventy-one men with known (60) or suspected (11) prostatic carcinoma were imaged with T2-weighted fast spin-echo pulse sequences in the axial and coronal planes with a phased array of four surface coils (multicoil) for signal reception. Four of these men also were imaged with fast spin-echo sequences and the body coil, and six of these men also were imaged with T2-weighted conventional spin echo sequences and the multicoil; image qualities achieved with these techniques were compared. The use of IV glucagon (42 of 71 studies) before fast spin-echo sequences was correlated with the subsequent presence or absence of peristaltic artifacts on MR images. MR images were analyzed for the presence or absence of prostatic cancer in the right and left sides of the gland and for evidence of spread either through the capsule, into the seminal vesicles, or to lymph nodes or bone. Findings at MR imaging were compared with results of radical prostatectomy (20), lymph node dissection without prostatectomy (seven), and biopsy (67). RESULTS: Image quality obtained with the combination of the fast spin-echo sequence with the multicoil was judged superior to that obtained with either the conventional spin-echo sequence with the multicoil or the fast spin-echo sequence with the body coil. Significant motion artifacts were noted in 45% of studies (13/29) performed without glucagon vs 7% of studies (3/42) performed with glucagon. In the 58 patients for whom information concerning the location of tumor in either the right or left side of the gland was obtained from biopsy (39) or surgery (19), MR images allowed cancer to be detected with 89% sensitivity and 77% specificity. Among the 20 patients undergoing prostatectomy and seven others undergoing lymph node dissection, MR imaging permitted high accuracies in predicting involvement of the seminal vesicles (100%), local transcapsular spread (85%), and involvement of pelvic lymph nodes (85%). CONCLUSION: Fast spin-echo imaging with a pelvic phased-array multicoil provides high-resolution images of the prostate that may obviate an endorectal coil for the detection, localization, and staging of prostatic carcinoma.

Aged↗
PubMed2001

[Study on allele-specific diagnostic PCR of the traditional Chinese medicines of the deers].

AIM: To develop a convenient and accurate method of DNA molecular marker for the identification of traditional Chinese medicines made of deers, consisting of pilose antler, penis and testis, tendon and foetus. METHODS: Based on the analysis of DNA sequence of mitochondrial Cyt b gene from original animals of both genuine crude drugs, Cervus nippon and Cervus elaphus, and adulterants, a pair of allele-specific primers named as ILu01-L and ILu01-H were designed for distinguishing geniune crude drugs of deers from their adulterants. RESULTS: The results of diagnostic PCR annealing at 64 degrees C for original animals showed that a 365 bp fragment was only amplified from DNA templates of Cervus nippon and Cervus elaphus. For the identification of medicinal materials total of 43 samples from 6 packages were tested under the same reaction conditions except for DNA templates extracted from these crude drugs. Only 9 samples mentioned above was shown to generate positive amplificon. The result indicate that of 8 samples from 1 package of pilose antler and only 1 sample of deer tendon was genuine crude drug. After that, 3 amplified fragments selected randomly were performed with sequencing analysis with the purpose of verifying the results from diagnostic PCR. Data from sequencing confirmed the reliability of diagnostic PCR identification. CONCLUSION: The diagnostic primers designed in the present study were highly specific for Cervus nippon and Cervus elaphus, and they could be used for the authentication of traditional Chinese medicines made from the deer. The quality of the crude drugs of the deer in the current market is a problem and more effective quality control for these traditional Chinese medicines is urgently needed.

Alleles↗
PubMed2001

Sources of nonlinearity in cDNA microarray expression measurements.

BACKGROUND: A key assumption in the analysis of microarray data is that the quantified signal intensities are linearly related to the expression levels of the corresponding genes. To test this assumption, we experimentally examined the relationship between signal and expression for the two types of microarrays we most commonly encounter: radioactively labeled cDNAs on nylon membranes and fluorescently labeled cDNAs on glass slides. RESULTS: We uncovered two sources of nonlinearity. The first, which led to discrepancies in analysis affecting the fluorescent signals, was signal quenching associated with excessive dye concentrations. The second, affecting the radioactive signals, was a nonlinear transformation of the raw data introduced by the scanner. Correction for this transformation was made by some, but not all, image-quantification software packages. CONCLUSIONS: The second type of nonlinearity is more troublesome, because it could not have been predicted a priori. Both types of nonlinearities were detected by simple dilution series, which we recommend as a quality-control step.

Calibration↗
PubMed2003

Consistency checks for characterizing protein forms.

Proteomics enforces the reverse chronological order on the gene to protein dogma and imposes amino acid sequences as a starting point of an investigation relative to function. By this approach, proteomics data can confirm the presence of multiple forms of a protein. Notwithstanding variations attributed specific individual features of organisms and tissues, from two to over ten protein forms can be identified in a given sample. The present work describes some guidelines for tracking the origin of alternative protein forms and attempts to tag the details of sequence data in the literature. Working via these guidelines we have uncovered a third alternative form of the Pim subfamily of oncogenes. The term form is here combined with the qualification alternative to describe any product of a given gene including closely related paralogs. This paper also emphasizes the need for consistency checks in annotation processes, such as gene clustering, to avoid losing important details describing protein alternative forms. By identifying alternative protein forms, we illustrate the fact that rationalizing of protein function via the identification of protein-protein interactions should in reality be that of identifying (alternative) form-form interactions.

Amino Acid Sequence↗
PubMed2002

Protein sequence threading: Averaging over structures.

Multiple sequence alignments are a routine tool in protein fold recognition, but multiple structure alignments are computationally less cooperative. This work describes a method for protein sequence threading and sequence-to-structure alignments that uses multiple aligned structures, the aim being to improve models from protein threading calculations. Sequences are aligned into a field due to corresponding sites in homologous proteins. On the basis of a test set of more than 570 protein pairs, the procedure does improve alignment quality, although no more than averaging over sequences. For the force field tested, the benefit of structure averaging is smaller than that of adding sequence similarity terms or a contribution from secondary structure predictions. Although there is a significant improvement in the quality of sequence-to-structure alignments, this does not directly translate to an immediate improvement in fold recognition capability.

Animals↗
PubMed1996

Quantitative magnetic resonance methods for in vivo investigation of the human liver and spleen. Technical aspects and preliminary clinical results.

This project was initiated with the introduction of magnetic resonance (MR) in Denmark in order to evaluate the possibilities of this technique as a diagnostic aid in non-focal liver and splenic diseases. The signal intensities in the MR image are sensitive to the longitudinal relaxation (T1), the transverse relaxation (T2), flow and chemical shift. All these parameters may be quantified by developing specific pulse sequences sensitive to the parameter in question. Previous studies had indicated that relaxation time measurements might be of value in the diagnosis of liver cirrhosis and haemochromatosis. Measuring relaxation times in these 2 groups of patients posed different challenges. In patients with liver cirrhosis a method had to be developed for simultaneous T1 and T2 relaxation time measurements, which was robust to the respiratory motion of the liver. A combination of multi-echo pulse sequences with different repetition times was chosen, because motion effects were partly refocused. Multi-acquisition was used to improve the signal-to-noise ratio in the heavily saturated experiments with short repetition times, to further reduce the sensitivity to motion. To test the quality of this pulse sequence, phantom experiments were performed, and sensitivity to motion was tested by measuring with and without respiratory synchronization. Respiratory synchronization gave a marked improvement in focal liver diseases, whereas no difference was found in non-focal diseases. Standard imaging sequences with a minimum echo time of 30 ms could not be used to measure the short T2 relaxation times found in patients with increased liver iron. A volume-selective multi-echo spectroscopic pulse was developed with a minimum echo time of 4 ms. Biexponential signal decay could be shown in patients with increased liver iron by using this sequence. Patients with liver cirrhosis, as a group, had increased T1 relaxation times compared to normal volunteers, but an overlap in T1 values was found. No correlation between the degree of fibrosis and the T1 relaxation time was found. Liver iron concentration could be quantified either by using the fast component of the T2 signal decay or by using the decreased signal in spin-echo and gradient echo images. Patients with leukemias and myeloproliferative disorders had prolonged T1 relaxation times in the spleen, but a considerable overlap was found between this group and a group of patients with benign hyperplasia and patients with splenomegaly secondary to portal hypertension. Volume-selective proton spectroscopy was developed and used to quantify the liver fat concentration. The accuracy of the method was about 3 g/100 g. With the implementation of a second generation scanner system it became possible to develop a pulse sequence, using the phase information in the MR signal, to measure portal vein flow during breath-holding. This method made it possible to estimate the portal vein flow during fasting, and the flow increase after eating. Quantitative MR methods may contribute to the diagnosis of non-focal liver diseases by estimation of liver fat and liver iron and by assessment of portal vein blood flow. Increased T1 relaxation time is a sign of a disease process in the liver rather than specific for any liver disease.

Humans↗
PubMed2000

Application of LCModel for quality control and quantitative in vivo 1H MR spectroscopy by short echo time STEAM sequence.

The linear combination of model spectra (LCModel) calculation of a parameter for long-term quality control, kT, was introduced, representing the ratio of the temporal and nominal intensities of CH3 groups of lactate and acetate in a quality control phantom. This procedure is a part of the quality assurance of the scanner using fully automatic measurement and calculation of kT parameters, and utilizing Shewhart regulation control charts for continuous evaluation of the magnetic resonance (MR) scanner setting. The application of the kT parameter for the correction of in vivo data increases the precision of molar concentration determination by about 4%. This was tested by the quantitative in vivo MR determination of the molar concentrations of 13 prominent metabolites (N-acetylaspartate (NAA), N-acetylaspartylglutamate, creatine and phosphocreatine (Cr), choline-containing compounds (Cho), myo-inositol, scyllo-inositol, gamma-aminobutyric acid, glutamine, glutamate, glucose, lactate, alanine, taurine) in the white matter and hippocampus of the brain in groups of volunteers, using a short echo time stimulated echo acquisition mode sequence (echo time = 10 ms) and the LCModel technique. The repeatability of the measurement of prominent metabolites such as NAA, Cr and Cho was found to be around 10% (relative standard deviation, n = 6); precision in a group of volunteers (n = 20 and 28, respectively) was in the range of approximately 13-20%. For other metabolites, which are measured with a lower signal-to-noise ratio, the precision can be much lower.

Acetates↗
PubMed2003

Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction.

Data preprocessing including proper normalization and adequate quality control before complex data mining is crucial for studies using the cDNA microarray technology. We have developed a simple procedure that integrates data filtering and normalization with quantitative quality control of microarray experiments. Previously we have shown that data variability in a microarray experiment can be very well captured by a quality score q(com) that is defined for every spot, and the ratio distribution depends on q(com). Utilizing this knowledge, our data-filtering scheme allows the investigator to decide on the filtering stringency according to desired data variability, and our normalization procedure corrects the q(com)-dependent dye biases in terms of both the location and the spread of the ratio distribution. In addition, we propose a statistical model for false positive rate determination based on the design and the quality of a microarray experiment. The model predicts that a lower limit of 0.5 for the replicate concordance rate is needed in order to be certain of true positives. Our work demonstrates the importance and advantages of having a quantitative quality control scheme for microarrays.

Algorithms↗
PubMed2005

MASQOT: a method for cDNA microarray spot quality control.

BACKGROUND: cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more. RESULTS: A novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies. CONCLUSION: The proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.

Data Interpretation, Statistical↗
PubMed1989

Phase-distortion-free in vivo surface coil proton spectroscopy.

A 1-11 water suppression pulse sequence for phase-distortion-free surface coil NMR spectroscopy was constructed and tested in vivo on cat brain. The sequence produces brain spectra free of phase distortions, but some degradation of water suppression quality compared to closely related sequences which produce phase distortions was observed.

Animals↗
PubMed2006

Fingerprint multicast in secure video streaming.

Digital fingerprinting is an emerging technology to protect multimedia content from illegal redistribution, where each distributed copy is labeled with unique identification information. In video streaming, huge amount of data have to be transmitted to a large number of users under stringent latency constraints, so the bandwidth-efficient distribution of uniquely fingerprinted copies is crucial. This paper investigates the secure multicast of anticollusion fingerprinted video in streaming applications and analyzes their performance. We first propose a general fingerprint multicast scheme that can be used with most spread spectrum embedding-based multimedia fingerprinting systems. To further improve the bandwidth efficiency, we explore the special structure of the fingerprint design and propose a joint fingerprint design and distribution scheme. From our simulations, the two proposed schemes can reduce the bandwidth requirement by 48% to 87%, depending on the number of users, the characteristics of video sequences, and the network and computation constraints. We also show that under the constraint that all colluders have the same probability of detection, the embedded fingerprints in the two schemes have approximately the same collusion resistance. Finally, we propose a fingerprint drift compensation scheme to improve the quality of the reconstructed sequences at the decoder's side without introducing extra communication overhead.

Algorithms↗
PubMed2004

High-resolution MR-imaging of the liver with T2-weighted sequences using integrated parallel imaging: comparison of prospective motion correction and respiratory triggering.

PURPOSE: To compare high-resolution T2-weighted images of the liver with and without integrated parallel acquisition techniques (iPAT) using either breath-hold sequences in combination with prospective acquisition motion correction (PACE) or respiratory triggering. MATERIALS AND METHODS: Ten volunteers and 10 patients underwent each four different high-resolution fast spin echo (FSE) T2-weighted sequences with 5 mm slice thickness and a full 320 matrix: a multi-breath-hold FSE sequence with and without iPAT and PACE and a respiratory-triggered FSE sequence with and without iPAT. Image quality was rated with a five-point scale by two independent readers. Signal intensity measurements were performed on a water phantom. RESULTS: The sequences with iPAT required a substantially shorter acquisition time without loss of image quality. Overall image quality was rated equal for all sequences by both readers. Image time for nine slices with iPAT was 13 seconds (19 seconds without iPAT) with multi-breath-hold and on average 4:00 minutes (7:02 minutes without iPAT) with respiratory triggering. Imaging with the PACE technique resulted in more correct positioning of the image stacks. CONCLUSION: T2-weighted fast imaging with iPAT is feasible and results in high-quality images within a short acquisition time. Overall image quality is not negatively affected by iPAT.

Adult↗
PubMed2002

Theoretical analysis of alternative splice forms using computational methods.

Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper, we explain the approach of using the different available databases and software tools to start a large scale investigation of alternative splice forms. To collect information about alternative splicing we investigated known data in the databases using different computational methods. The investigations proceeded from the genomic sequence data to structural protein data. Then, we interpreted those data to find the relationship between alternative splice forms and protein function and structure. We found some interesting features of alternative splicing which are presented here. We discuss the results of one chosen example. They concern the coverage quality of the protein sequence of a known structure, an EST analysis, the validation of splice variants, the determination of the alternative splice type, and finally the link between alternative splicing and disease.

Algorithms↗
PubMed2001

Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.

The crystal structure of affinity-purified Thermomonospora fusca beta-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.7% of the mannanase gene sequence was obtained from genomic T. fusca DNA by PCR. The structure-derived sequence was then compared with the DNA-derived sequence and corrected when necessary. Applying the presented protocol, there was no need to manually build a model at an early stage of structure determination, an erroneous and tedious process, especially in the absence of the amino-acid sequence. Using the DNA sequence information and the current version of ARP/wARP, 281 residues, or 93% of the polypeptide chain (including side chains), were built and refined to an R factor of 16.5% without any manual intervention.

Amino Acid Sequence↗
PubMedDate not supplied

[Manufacture of DNA chips in a laboratory for internal use: legislation and quality assurance].

Manufacturing and using DNA chips in a laboratory, while respecting legality and good practices, require a review of the regulatory framework and relevant documentation for implementing a quality assurance system. Using DNA chips, either as a research tool, or as an in vitro diagnostic medical device, does not come within the same regulations: none in the first case, and european directive 98/79/CE in the second one. It is the same for research practice, for which the law to be enforced has been primarily conditioned to ethics, while carrying out medical analyses has been framed in France by the GBEA. The regulatory approach laid down in the GBEA is a first step for implementing a quality assurance system, but this must be extended to the manufacturing process of DNA chips. International standards (ISO 9001: 2000, ISO/IEC 15189...) provide documentation to meet this last requirement, but also enable one to carry on the quality approach up to the certification of the laboratory or its accreditation.

Clinical Medicine↗
PubMedDate not supplied

The existence of sequence effect in cross-over bioequivalence trials.

A generic drug product (T) in order to be approved for marketing authorization a bioequivalence trial is required. In the trial the generic product is compared to the innovator product (R) in terms of the pharmacokinetic parameters AUC and Cmax. The regulatory requirement for bioequivalence is that the 90% confidence intervals for the ratio (T/R) of the generic to innovator product pharmacokinetic parameter averages lies within the limits (80%, 125%). The design of the trial is usually a two-period crossover. This design has the limitation that if the statistical analysis reveal significant sequence effect then the bioequivalence results may be biased and their interpretation is difficult. The sequence effect is confounding with the unequal residual effect and with the formulation by period interaction. Since the existence of the sequence effect questions the quality of the trial, the applicant should provide possible explanations and information on the subjects, the trial conditions, the clinical settings and the assay methodology. An additional statistical analysis on the data from the first period of the trial may support the bioequivalence. If it is proven that the sequence effect is a true effect then the generic may be approved for marketing authorization.

Biological Availability↗
PubMed2005

Protocols for the assurance of microarray data quality and process control.

Microarrays represent a powerful technology that provides the ability to simultaneously measure the expression of thousands of genes. However, it is a multi-step process with numerous potential sources of variation that can compromise data analysis and interpretation if left uncontrolled, necessitating the development of quality control protocols to ensure assay consistency and high-quality data. In response to emerging standards, such as the minimum information about a microarray experiment standard, tools are required to ascertain the quality and reproducibility of results within and across studies. To this end, an intralaboratory quality control protocol for two color, spotted microarrays was developed using cDNA microarrays from in vivo and in vitro dose-response and time-course studies. The protocol combines: (i) diagnostic plots monitoring the degree of feature saturation, global feature and background intensities, and feature misalignments with (ii) plots monitoring the intensity distributions within arrays with (iii) a support vector machine (SVM) model. The protocol is applicable to any laboratory with sufficient datasets to establish historical high- and low-quality data.

Artificial Intelligence↗
PubMedDate not supplied

Genetic methods for detection of antimicrobial resistance.

Accurate and rapid diagnostic methods are needed to guide antimicrobial therapy and infection control interventions. Advances in real-time PCR have provided a user-friendly, rapid and reproducible testing platform catalysing an increased use of genetic assays as part of a wider strategy to minimize the development and spread of antimicrobial-resistant bacteria. In this review we outline the principal features of genetic assays in the detection of antimicrobial resistance, their advantages and limitations, and discuss specific applications in the detection of methicillin-resistant Staphylococcus aureus, glycopeptide-resistant enterococci, aminoglycoside resistance in staphylococci and enterococci, broad-spectrum resistance to beta-lactam antibiotics in gram-negative bacteria, as well as genetic elements involved in the assembly and spread of antimicrobial resistance.

Bacteria↗