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Results for “Sequencing quality”

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At least 361 records · Page 20Linked to original sources
PubMed1987

Optimizing single- and double-contrast colon examinations.

Recent technical advances have greatly increased the effectiveness of barium enema examinations for detection of common diseases of the colon. As documented in the literature, the double-contrast enema may equal or exceed colonoscopy in detection of colonic neoplasms and, with proper technique, the single-contrast enema may also closely approach these results. This presentation reviews recent technical improvements in the areas of radiographic-fluoroscopic equipment, fluoroscopic images, film-screen combinations, barium suspensions, examination techniques, filming sequences, and quality controls. These are employed to optimize both the double- and single-contrast barium enemas to where their sensitivities are competitive with endoscopy.

Air↗
PubMed1994

[An expert system for the planning of whole-body irradiation treatments].

Total body irradiation (TBI) combined with intensive chemotherapy and bone marrow transplantation is used with increasing success for the treatment of hematologic malignancies with severe prognosis. An expert system, developed on the basis of the experience acquired during the last years in our department, has been designed to optimize the different treatment steps. The choice of an expert system is based on its capabilities in reconstructing a rule-based reasoning through the combination of theoretical and empirical knowledge. Particularly, a subsystem dealing with the steps to be taken to optimize treatment in TBI has been designed using medical and physical data. Our system can determine radiation treatment variables together with a sequence of quality control procedures. Moreover, indications are given about short, medium and long term damage probabilities and toxicity estimates, both derived from literature data and our personal series of cases. Treatment quality can be assessed and the different techniques compared using these data. This project is aimed at providing physicians and physicists with useful clinical suggestions for TBI setting for bone marrow transplantation.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1997

Construction and analysis of a detailed three-dimensional model of the ligand binding domain of the human B cell receptor CD40.

The interaction between the human B cell receptor CD40 and its ligand on T cells is critical for B cell proliferation and the regulation of humoral immune responses. CD40 is a member of the tumor necrosis factor receptor (TNFR) family. We report here the construction and analysis of a detailed three-dimensional model of the TNFR-homologous extracellular region of CD40. This study provides an example for structure-based model building in the presence of low sequence similarity. The assessment of model quality and sequence-structure compatibility is emphasized, and limitations of the model are discussed. The current CD40 model predicts structural details beyond the backbone level. Features of the CD40 ligand binding site are discussed in conjunction with the results of a previous mutagenesis study.

Amino Acid Sequence↗
PubMed2005

Analysis of expressed sequence tags from Musa acuminata ssp. burmannicoides, var. Calcutta 4 (AA) leaves submitted to temperature stresses.

In order to discover genes expressed in leaves of Musa acuminata ssp. burmannicoides var. Calcutta 4 (AA), from plants submitted to temperature stress, we produced and characterized two full-length enriched cDNA libraries. Total RNA from plants subjected to temperatures ranging from 5 degrees C to 25 degrees C and from 25 degrees C to 45 degrees C was used to produce a COLD and a HOT cDNA library, respectively. We sequenced 1,440 clones from each library. Following quality analysis and vector trimming, we assembled 2,286 sequences from both libraries into 1,019 putative transcripts, consisting of 217 clusters and 802 singletons, which we denoted Musa acuminata assembled expressed sequence tagged (EST) sequences (MaAES). Of these MaAES, 22.87% showed no matches with existing sequences in public databases. A global analysis of the MaAES data set indicated that 10% of the sequenced cDNAs are present in both cDNA libraries, while 42% and 48% are present only in the COLD or in the HOT libraries, respectively. Annotation of the MaAES data set categorized them into 22 functional classes. Of the 2,286 high-quality sequences, 715 (31.28%) originated from full-length cDNA clones and resulted in a set of 149 genes.

Base Sequence↗
PubMed2005

Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control.

We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings.

Asian People↗
PubMed2026

QCatch: a framework for quality control assessment and analysis of single-cell sequencing data.

MOTIVATION: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (and augmented execution context for the alevin-fry), offer flexibility and computational efficiency to process single-cell data, this ecosystem will further benefit from a standardized QC reporting tailored for its outputs. RESULTS: We introduce QCatch, a Python-based command-line tool that generates comprehensive and interactive HTML QC reports designed specifically for single-cell quantification results. Taking the output directory of alevin-fry or simpleaf as the input, QCatch is able to perform essential processing steps, like cell calling, and generate detailed QC reports that contain informative visualizations and statistics, including unique molecular identifier (UMI) count distributions, sequencing saturation estimates, and splicing status information, for QC assurance. Built for seamless integration into downstream analysis workflows, QCatch exports the processed results in a richly-annotated H5AD format file, a widely used data format common among many downstream single-cell data analysis tools. AVAILABILITY AND IMPLEMENTATION: The source code and documentation of QCatch are available on GitHub at https://github.com/COMBINE-lab/QCatch. QCatch can be installed via both Bioconda and PyPI.

Single-Cell Analysis↗
PubMed1995

DMSO resolves certain compressions and signal dropouts in fluorescent dye labeled primer-based DNA sequencing reactions.

Automated base calling algorithms are more sensitive to the quality of the DNA sequencing data than are the labor intensive visual methods of base calling. To improve this quality, data from DNA sequencing reactions have been compared in order to determine the effects of the inclusion of dimethyl sulfoxide (DMSO). Inclusion of 10% DMSO into the reaction cocktail resolves at least one type of sequence compression. This compression may be due to the lack of ability in T7 DNA polymerase to read through certain sequences correctly. The poor quality of these data is seen as radioactive bands or fluorescent signal peaks that have an abnormal alignment, either in the wrong order or as single bands/peaks. The inclusion of DMSO also resolves sequences where the peak signal is absent or severely diminished, leading to a "gap" in the chromatogram profile. DMSO is better than deaza-dITP for resolving certain compressions. Addition of DMSO is a cheaper and more efficient method for high-throughput DNA sequencing than repeating reactions with base analogs.

Algorithms↗
PubMedDate not supplied

Sequential use of ferumoxide particles and gadolinium chelate for the evaluation of focal liver lesions on MRI.

This study describes the sequential use of ferumoxide (superparamagnetic iron oxide) particles and nonspecific extracellular gadolinium chelate (Gd) for evaluation of focal liver lesions on MRI to evaluate order of contrast administration and imaging effect of the first contrast agent on sequences acquired after the second contrast agent. Thirteen patients underwent MR examinations that included ferumoxide and Gd. The order and timing of administration were as follows: separate sessions (three patients; Gd study 4-19 days before ferumoxide study), same session, Gd first (seven patients; Gd study 1-2 hours before ferumoxide study), and same session, ferumoxide first (three patients; ferumoxide administered less than 1 hour before Gd study). Postcontrast sequences were reviewed in a randomized, blinded fashion by two separate investigators. Determination was made regarding whether (a) the presence of the first agent administered could be detected on sequences obtained after the second agent and (b) the presence of the first agent interfered with the image quality of those sequences. No evidence for the presence of Gd was appreciated by either observer on postferumoxide sequences acquired in separate session studies. In same session, Gd first studies, the presence of Gd was observed in six of seven patients on T1-weighted spoiled gradient-echo (SGE) images obtained after ferumoxide administration. The presence of Gd was not apparent in seven of seven patients on T2-weighted fat-suppressed images obtained after ferumoxide. In same session, ferumoxide first studies, the presence of ferumoxide was appreciated on post-Gd sequences in two of three patients. The presence of ferumoxide did not appreciably diminish image quality on those sequences. Exact agreement was achieved by the independent investigators. Our results suggest that Gd and ferumoxide can be administered sequentially within one study session without substantial loss of diagnostic information obtained on sequences performed after administration of the second contrast agent. Administrating Gd first resulted in less of an effect of the visualization of the first agent on sequences acquired after the second agent.

Adult↗
PubMed2005

INTERALIGN: interactive alignment editor for distantly related protein sequences.

SUMMARY: Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence.

Algorithms↗
PubMed2005

Time-resolved echo-shared parallel MRA of the lung: observer preference study of image quality in comparison with non-echo-shared sequences.

The aim of this study was to evaluate the image quality of time-resolved echo-shared parallel MRA of the lung. The pulmonary vasculature of nine patients (seven females, two males; median age: 44 years) with pulmonary disease was examined using a time-resolved MRA sequence combining echo sharing with parallel imaging (time-resolved echo-shared angiography technique, or TREAT). The sharpness of the vessel borders, conspicuousness of peripheral lung vessels, artifact level, and overall image quality of TREAT was assessed independently by four readers in a side-by-side comparison with non-echo-shared time-resolved parallel MRA data (pMRA) previously acquired in the same patients. Furthermore, the SNR of pulmonary arteries (PA) and veins (PV) achieved with both pulse sequences was compared. The mean voxel size of TREAT MRA was decreased by 24% compared with the non-echo-shared MRA. Regarding the sharpness of the vessel borders, conspicuousness of peripheral lung vessels, and overall image quality the TREAT sequence was rated superior in 75-76% of all cases. If the TREAT images were preferred over the pMRA images, the advantage was rated as major in 61-71% of all cases. The level of artifacts was not increased with the TREAT sequence. The mean interobserver agreement for all categories ranged between fair (artifact level) and good (overall image quality). The maximum SNR of TREAT did not differ from non-echo-shared parallel MRA (PA: TREAT: 273+/-45; pMRA: 280+/-71; PV: TREAT: 273+/-33; pMRA: 258+/-62). TREAT achieves a higher spatial resolution than non-echo-shared parallel MRA which is also perceived as an improved image quality.

Adolescent↗
PubMedDate not supplied

High resolution breath-holding MR imaging of the abdomen with a phased-array multicoil.

We prospectively compared standard resolution and high resolution breath-hold T1- and T2-weighted images of the upper abdomen with use of a body phased-array multicoil in 30 patients. The image quality of high resolution T1-weighted FLASH sequence was equal to that of standard resolution sequence, while the quality of high resolution T2-weighted turbo spin-echo sequence was slightly inferior to that of standard resolution sequence. The merit of high resolution image is appreciated especially on a T1-weighted FLASH sequence.

Abdomen↗
PubMed1986

Dynamic digital subtraction imaging using fast low-angle shot MR movie sequence.

High-quality magnetic resonance (MR) images can be recorded within seconds with the use of fast low-angle shot (FLASH) MR imaging. This technique also gives new access to the time evolution of both periodic functions, such as cardiac motion, and nonperiodic physiologic processes, such as flow within internal organs. The time course and regional distribution of dynamic processes detectable by FLASH MR movies are often demonstrated best within series of difference images obtained by digital subtraction of the original data, especially after the use of MR contrast agents. In addition, quantitative information is provided by the analysis of time-intensity profiles for selected regions of interest. Dynamic digital subtraction MR imaging was evaluated in rabbit brain and kidney using a 2.3-T, 40-cm-bore magnet. The time resolution was 1.5 seconds for brain studies and 28 seconds for kidney studies. The total examination times were 1.5 and 30 minutes, respectively.

Angiography↗
PubMed2006

HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.

HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.

Binding Sites↗
PubMed1993

Efficient DNA sequencing on microtiter plates using dried reagents and Bst DNA polymerase.

Sequenase, Taq DNA polymerase and Bst DNA polymerase were tested for sequencing of DNA on microtiter plates using dried down reagents. Several parameters were investigated to expedite the drying process while minimizing damage to the enzyme. Sequenase did not tolerate drying very well, and frequently generated sequences with weak signals and many sites of premature termination. With Taq DNA polymerase it was possible to obtain sequences of good quality. However, there was considerable variation of results between experiments and between batches of microtiter plates. Bst DNA polymerase generated sequences of excellent quality. It was stable for more than a week in dried-down state at -20 degrees C and at least overnight at room temperature. The method described here using Bst DNA polymerase is well suited for laboratory robots and workstations that typically employ 96-well microtiter plates.

Automation↗
PubMed2000

Applying quality control charts to the analysis of single-subject data sequences.

Techniques from the field of quality control can be used to classify the quality of individual samples of physical or cognitive performance. After stable baselines have been established for an individual, deviations in performance can be evaluated using control charts. The effectiveness of this approach in evaluating cognitive performance was tested using databases collected under a variety of risk factors. The sensitivity and specificity characteristics of Shewhart, cumulative-sum (CUSUM), and exponentially weighted moving average (EWMA) control charts were determined for a total of 174 trials involving 10 participants and 23 cognitive performance assessment measures. The most effective technique in each case was typically a function of the specific performance measure and the type of performance change being evaluated. Sensitivity and specificity for the best techniques were as high as 100%. This study demonstrated the usefulness of quality control charts as a tool to evaluate individual participant performance over time. Actual or potential applications of this research include readiness-to-perform screening of industrial workers in order to improve the health and safety of the workforce.

Data Interpretation, Statistical↗
PubMed2005

Improving sequence-based fold recognition by using 3D model quality assessment.

MOTIVATION: The ability of a simple method (MODCHECK) to determine the sequence-structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-like models. RESULTS: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile-profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information. CONTACT: d.jones@cs.ucl.ac.uk

Algorithms↗
PubMed1994

Variations on cycle sequencing.

Linear amplification or cycle sequencing is an advance that has made the use of automated fluorescent DNA sequencing instruments truly practical for large-scale genome analysis. We have investigated several variations of our standard cycle sequencing method. First, we have reduced the number of amplification cycles, which resulted in improved data quality and faster sequencing. Second, we have used different thermostable enzymes, which again improved data quality. Lastly, we have devised a method for precipitating reaction products in 96-tube trays. Together, these variations have allowed us to develop an improved cycle sequencing method that significantly increases sequencing throughput, improves efficiency and data quality, and reduces the cost of sequencing reactions.

Gene Amplification↗
PubMedDate not supplied

Fast T2-weighted liver MR imaging: comparison among breath-hold turbo-spin-echo, HASTE, and inversion recovery (IR) HASTE sequences.

BACKGROUND: To evaluate the diagnostic efficacy of fast T2-weighted magnetic resonance (MR) imaging sequences on image quality, hepatic lesion detection, and lesion conspicuity. METHODS: Three breath-hold, fast T2-weighted sequences with turbo-spin-echo (TSE), half-Fourier acquisition single-shot TSE (HASTE), and inversion recovery (IR) HASTE techniques were examined for 43 lesions in 20 consecutive patients. Evaluation was performed qualitatively on image quality and lesion detectability and quantitatively on lesion conspicuity by using lesion/liver signal-intensity and contrast-to-noise ratios. RESULTS: Artifacts were significantly less present on the HASTE sequence (p < 0.01). Both TSE and HASTE sequences detected 39 lesions (91% each); the IR HASTE sequence detected 37 (86%). IR HASTE sequence showed a significantly higher signal-intensity ratio than did the others (p < 0.01). CONCLUSIONS: Breath-hold TSE versus breath-hold HASTE or IR HASTE is still the most robust sequence in lesion detection, image quality, and lesion conspicuity. However, the HASTE sequence offers good lesion detection and image quality, and the IR HASTE has a better signal-intensity ratio.

Adolescent↗