Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data reproducibility”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources
PubMed1975

[Heart diagnosis using M-mode echocardiography. Continuing registration of transverse left ventricular inner diameters. I. Measurement in healthy persons].

Transversal internal diameters of the left ventricle can be determined simply, quickly, precisely and continuously by external application of impulse reflected ultrasound. These measurements permit the calculation of "relative cross-sectional area differences" between end-diastole and end-systole (RCD); peak and mean velocity of circumferential fiber contraction can be equally determined. The present report gives an analysis of 133 measurements on 81 healthy individuals. All persons were examined at rest, a part of them during exercise. All measurements were taken while supine position. The transversal internal diameters averaged 4.9 cm with considerable standard deviations. There was only a trend showing diminution of diameters during exercise. The "relative cross-sectional area differences" (RCD) between end-diastole and end-systole have only small standard deviations compared with the diameters. The average 58.3% and show a slight increase during exercise. The RCD were only slightly influenced by heart rate at rest. In contrast, peak and mean velocity of circumferential fiber contraction are obviously dependent on the heart rate. The results indicate a linear correlation between mean velocity and heart rate. The "relative mean velocities of contraction" (RVC), defined by normalization of the values to a rate of 60/min, average 1.0 and have small standard deviations like the RCD. The small physiological variety and the excellent reproducibility of data offer RCD and RVC determined by echocardiography as sensitive dynamic heart parameters applicable in clinical cardial diagnosis without any stress for the patient.

Anthropometry↗
PubMed1999

[HPLC determination of uracil xanthine, hypoxanthine and uridine in species of animal drugs].

OBJECTIVE: To make further studies on the water-soluble components in animal drugs by determining the contents of uracil, xanthine, hypoxanthine and uridine from ten species of animal drugs. METHOD: The determination was affected by RP-HPLC, using Shim-pack CLC-ODS column(150 mm x 6 mm), 0.05 mol/L dibasic ammonium phosphate solution as mobile phase, flow rate 0.8 ml/min and detection at 254 nm. RESULTS: This method is accurate, rapid and reproducible. Analytical data for Hirudo nipponia, Eupolyphaga sinensis, Scolopendra subspinipes mutilans, Buthus martensii, Bombyx mori, Mylabris cicorri, Aspongopus chinensis, Lytta caraganae, Tabanus bivittatus and Huechys sanguinea are given. CONCLUSION: There are marked discrepancies in the contents of the four components as shown on the chromatograms, a point that may be helpful in identifying the above-cited ten species of animal drugs.

Animals↗
PubMed1999

[The comparison of contents of uracil, xanthine and hypoxanthine in five species of leech].

Three constituents(uracil, xanthine, hypoxanthine) were isolated from five species of leech and determined by reversed phase HPLC. The column employed was Shim-pack CLC-ODS C18(150 mm x 6 mm). The mobile phase was 0.05 mol/l ammonium phophate dibasic solution(pH = 8.4). The flow rate was 0.8 ml/min and detection was effected at 254 nm. This method is accurate, rapid and reproducible. Analytical data for five species and Whitmania pigra samples from different places were given.

Animals↗
PubMed2003

Transgenic animal technology: alternatives in genotyping and phenotyping.

Over the past decade, breakthrough technologies in transgenic animal technology and functional genomics have played a central role in the explosive growth of rodent modeling and in scientific innovation. Various noninvasive alternatives to routine surgical biopsy have been described for genotypic and phenotypic analyses of laboratory animals. A number of options are available to refine or replace potentially painful and invasive procedures ranging from tissue biopsies (including tail biopsies and toe docking) to several blood sampling techniques. Unfortunately, adoption of many non- or minimally invasive alternatives has proven difficult on a number of fronts ranging from historical reservations to procedural expectations and actual experimental productivity. Similarly, a variety of phenotyping considerations have addressed throughput efficiencies and the health and well being of research animals. From an animal welfare perspective, marked increases in laboratory animal populations have accompanied rapid advancements spanning the life sciences. As described for rodent modeling, but with applications across many laboratory animal species, diverse procedural refinements are available that will readily aid in the analysis of whole animal models. Ultimately, non-invasive technologies and complementary refinements have bearing on the quality and reproducibility of data that are reported, as well as of critical importance to the well being and ethical management of animals at all developmental stages: from fetal existence, to the neonatal period, and on through adulthood.

Animal Use Alternatives↗
PubMedDate not supplied

Exhaled biomarkers in COPD: their potential role in diagnosis, treatment and prognosis.

Several diagnostic tools have been developed for diagnosing, monitoring and evaluating Chronic Obstructive Pulmonary Disease (COPD). There is an increasing interest in the use of non or less invasive biological markers (biomarkers) which reflect the character and intensity of the pathological processes in the lungs of COPD patients. The main goal of this review was to discuss the origin and current role of exhaled biomarkers in the diagnosis, evaluation of treatment and prognosis of COPD. Data of cross-sectional, cohort and intervention studies on exhaled biomarkers were studied. These studies were identified by a Medline search on papers in the English language published from 1990 to November 2001. The following markers were discussed: exhaled nitric oxide (NO), exhaled carbon monoxide (CO), exhaled alkanes, exhaled hydrogen peroxide (H2O2), exhaled isoprostanes, exhaled NO metabolites and exhaled thiobarbituric acid-reactive substances (TBARs). Data on these markers were summarized. The origin of each marker, the technique of analysis, the values in healthy controls and COPD patients, the effect of treatment and the correlation with other parameters were presented. Most studies, however, were cross-sectional studies with small populations. It was also difficult to compare studies because of differences in technique and study population. This review shows that exhaled biomarkers need to be studied further before using them in clinical practice. There is a need for standardization of the measurements, for comparison of COPD patients with healthy persons matched for age and smoking-status, for data on reproducibility and variability of all markers, for correlation of exhaled markers with other parameters and for intervention studies.

Biomarkers↗
PubMed2003

Automated real-time PCR to determine K-ras codon 12 mutations in non-small cell lung cancer: comparison with immunohistochemistry and clinico-pathological features.

A real-time PCR technique with automated computerized analysis (TaqMan ) was tested to detect K-ras mutations in 66 patients suffering from NSCLC. This technology is characterized by high reproducibility of data and a time-saving analysis procedure. In 11% (7/66) of the tumour specimens and 2% (1/58) of adjacent tumour-free lung specimens a K-ras codon 12 mutation was detected. In adenocarcinomas containing > or =40% tumour cells, however, K-ras mutations were seen in 25% of the cases. The point mutations detected in tumours were GGT right curved arrow TGT in five cases and GGT right curved arrow GTT in two cases. As compared with immunohistochemical parameters, the K-ras mutated group was characterized by a c-erbB-2 negativity (p=0.04) and a smaller number of c-erbB-3 (p=0.02) positive cases. EGFR, bcl-2, p53, Ki-67 and p120 expression did not differ significantly. Determination of the K-ras point mutations by automated TaqMan PCR in NSCLC tumour specimens is feasable and highly specific. Due to its high throughput capacity this method represents a valuable tool for routine screening.

Carcinoma, Non-Small-Cell Lung↗
PubMed1992

[Indications for, technique and interpretation of arterial Doppler sonography from the vascular surgeon's viewpoint].

Doppler sonography is one of the most important diagnostic tools for angiologists and vascular surgeons and also for general practitioners with an interest in vascular disease. It can be carried out easily and at low cost and, at the same time, provides reproducible, quantitative data on which further diagnostic and therapeutic decisions can be based. First, systolic arterial pressures in the anterior and posterior tibial and in the peroneal arteries are measured, with the Doppler probe placed at ankle level. A cuff is wrapped around the lower leg and inflated until the Doppler signal disappears. The highest value measured in each leg is termed ankle pressure. Division of the latter by systolic brachial pressure results in the so-called ankle-brachial index or "ABI". Ankle pressure and ABI correlate well with clinical findings. In normal individuals it is greater than 1. In claudication it ranges between 0.3 and 0.9, in patients with resting pain between 0.1 and 0.5 and with ischemic tissue loss between 0.0 and 0.2. After angioplastic or surgical revascularization procedures, a fall of the ABI by 0.15 or more is an indication of relevant hemodynamic deterioration and, therefore, calls for further investigation by arteriography or color duplex sonography.

Arm↗
PubMedDate not supplied

Computerized image analysis of nails affected by fungal infection: evaluation using digital photographs and manually defined areas.

Despite the relevant increase in clinical trials on the efficacy of various systemic and/or topical antifungal agents in onychomycosis therapy, the evaluation of the results is largely subjective. The aim of this study was to set up and ensure an objective, reproducible and reliable method to measure nail plate involvement in onychomycosis. In order to validate a specifically designed software for the computerized image analysis of affected areas of the nail, standardized clinical pictures of onychomycosis were prepared by six different clinicians using a sample of 11 affected nails. Diseased areas and total nail plates were measured both on the clinical pictures and on their drawings traced by the different clinicians on transparent tapes adhering to sample nails. The computerized procedure was undertaken by a trained operator who was not a dermatologist. The variation coefficients of measurements on clinical pictures (automatically detected) and on drawings were compared. In addition, the agreement between automatic evaluation and drawing was evaluated by means of Bland-Altman analysis. To consider the effect of possible variations linked to different operators using the computerized method, 11 clinical pictures (one for each clinical case considered) were selected and submitted to computerized image analysis by six different trained operators. The computerized detection of affected nail areas showed a coefficient of variation (vc=8.5%) lower than that observed on drawings (vc=14.7%). The two methods showed appreciable agreement, as demonstrated by Bland-Altman plot. The coefficient of variation of image analysis conducted by six different operators was very low for the total area calculation (vc=0.9%) and acceptable for pathological area detection (vc=4.8%). Based on the results obtained, we conclude that automatic evaluation is a reliable and helpful method for the measurement of the clinical involvement of the nail plate in onychomycosis and for the evaluation of therapies, since it can increase the objectivity and reproducibility of data. However, in a minority of difficult cases, expert dermatological evaluation is needed.

Humans↗
PubMed2005

Assessment of dyssynchrony in patients with severe heart failure by nuclear imaging: paradise lost and regained or lost and gone forever?

Cardiac resynchronization therapy, based on biventricular and/or left ventricular preexcitation, is a recently introduced therapeutic option for patients with severe heart failure and intraventricular conduction disturbances. The invasive nature and expense of resynchronization therapy has highlighted the need to prospectively identify optimal candidates, because of the poor correlation of QRS duration with patient response. Scintigraphy and positron emission tomography made it possible the research investigation of the pathophysiological consequences of cardiac conduction disturbances on myocardial contraction, metabolism, and perfusion. Increasing evidence shows that nuclear imaging techniques allow a comprehensive evaluation of the candidates to resynchronization. In fact, phase analysis of equilibrium radionuclide angiography enables a simple, quick and reliable measurement of both of inter- and intraventricular mechanical dyssynchrony, affording an optimal predictive accuracy of the response. In addition, being scintigraphic data highly reproducible, they are suitable for sequential longitudinal follow-up of the ventricular performance and mechanical dyssynchrony in patients implanted with devices.

Arrhythmias, Cardiac↗
PubMed2002

Fast and sensitive algorithm for aligning ESTs to human genome.

There is a pressing need to align growing set of expressed sequence tags (ESTs) to newly sequenced human genome. The problem is, however, complicated by the exon/intron structure of eucaryotic genes, misread nucleotides in ESTs, and millions of repeptive sequences in genomic sequences. Indeed, to solve this, algorithms that use dynamic programming have been proposed, but in reality, these algorithms require an enormous amount of processing time. In an effort to improve the computational efficiency of these classical DP algorithms, we develop software that fully utilizes the lookup-table for allowing the efficient detection of the start- and endpoints of an EST within a given DNA sequence, and subsequently, the prompt identification of exons and introns. In addition, high sensitivity and accuracy must be achieved by calculating locations of all spliced sites correctly for more ESTs while retaining high computational efficiency. This goal is hard to accomplish in practice, owing to misread nucleotides in ESTs and repeptive sequences in the genome, but we present a couple of heuristics effective in settling this issue. Experimental results have confirmed that our technique improves the overall computation time by orders of magnitude compared with common tools such as sim4 and BLAT, and attains high sensitivity and accuracy against datasets of clean and documented genes at the same time.

Algorithms↗
PubMed2002

Fast and sensitive alignment of large genomic sequences.

Comparative analysis of syntenic genome sequences can be used to identify functional sites such as exons and regulatory elements. Here, the first step is to align two or several evolutionary related sequences and, in recent years, a number of computer programs have been developed for alignment of large genomic sequences. Some of these programs are extremely fast but often time-efficiency is achieved at the expense of sensitivity. One way of combining speed and sensitivity is to use an anchored-alignment approach. In a first step, a fast heuristic identifies a chain of strong sequence similarities that serve as anchor points. In a second step, regions between these anchor points are aligned using a slower but more sensitive method. We present CHAOS, a novel algorithm for rapid identification of chains of local sequence similarities among large genomic sequences. Similarities identified by CHAOS are used as anchor points to improve the running time of the DIALIGN alignment program. Systematic test runs show that this method can reduce the running time of DIALIGN by more than 93% while affecting the quality of the resulting alignments by only 1%. The source code for CHAOS is available at http://www.stanford.edu/~brudno/chaos/ An integrated program package containing CHAOS and DIALIGN is available at http://bibiserv.techfak.uni-bielefeld.de/dialign/

Algorithms↗
PubMed2005

Improvement in the accuracy of multiple sequence alignment program MAFFT.

In 2002, we developed and released a rapid multiple sequence alignment program MAFFT that was designed to handle a huge (up to approximately 5,000 sequences) and long data (approximately 2,000 aa or approximately 5,000 nt) in a reasonable time on a standard desktop PC. As for the accuracy, however, the previous versions (v.4 and lower) of MAFFT were outperformed by ProbCons and TCoffee v.2, both of which were released in 2004, in several benchmark tests. Here we report a recent extension of MAFFT that aims to improve the accuracy with as little cost of calculation time as possible. The extended version of MAFFT (v.5) has new iterative refinement options, G-INS-i and L-INS-i (collectively denoted as [GL]-INS-i in this report). These options use a new objective function combining the weighted sum-of-pairs (WSP) score and a score similar to COFFEE derived from all pairwise alignments. We discuss the improvement in accuracy brought by this extension, mainly using two benchmark tests released very recently, BAliBASE v.3 (for protein alignments) and BRAliBASE (for RNA alignments). According to BAliBASE v.3, the overall average accuracy of L-INS-i was higher than those of other methods successively released in 2004, although the difference among the most accurate methods (ProbCons, TCoffee v.2 and new options of MAFFT) was small. The advantage in accuracy of [GL]-INS-i became greater for the alignments consisting of approximately 50-100 sequences. By utilizing this feature of MAFFT, we also examined another possible approach to improve the accuracy by incorporating homolog information collected from database. The [GL]-INS-i options are applicable to aligning up to approximately 200 sequences, although not applicable to thousands of sequences because of time and space complexities.

Amino Acid Sequence↗
PubMed1991

Experience with the particulate prostaglandin endoperoxide synthase assay for testing non-steroidal antiinflammatory drugs.

A microsomal prostaglandin endoperoxide synthase preparation was obtained from sheep vesicular glands and used as a test system for non-steroidal antiinflammatory drugs. The activity was measured oxygraphically with arachidonic acid as substrate. The assay conditions were optimized with respect to the concentrations of enzyme, substrate and hydroperoxidase co-substrate as well as preincubation. The validity of the test was assessed by eight known prostaglandin H synthase inhibitors and two antiinflammatory drugs not acting on this enzyme. Sodium diclofenac proved to be the most potent inhibitor. As shown with indometacin as example the test shows a good reproducibility. The data were fitted to a kinetic mathematical model assuming two distinct inhibitor binding sites with different affinities. This model gave in most cases a good fitting of the experimental data.

Animals↗
PubMed1991

A new approach to a damage risk criterion for weapons impulses.

Existing damage-risk criteria for weapons impulses suffer from their lack of a theoretical basis, thereby limiting their generalizability and utility. Furthermore, a number of studies now indicate that they may be inaccurate for impulses with energy in the low frequency region (Dancer & al., 1985; Patterson & al., 1985; Price & al., 1989). We have approached the problem by modeling the ear mathematically as a means of gaining insight into the loss processes. In the model, the external and middle ears are linear at lower intensities; however, the stapes displacement is limited to 20 microns, as would be expected on anatomical/physical grounds. Susceptibility, in the inner ear, is modeled as mechanical stress, a function of basilar membrane displacement and number of flex cycles. The model, which is executable on a PC-based computer, reproduces the data on the ear that can be measured at lower intensities. It also ranks the known hazard from impulses in the correct order, explains the finding of loss in mid-cochlea regardless of spectral location of the weapons impulse, and suggests that the greatest hazard comes from that portion of the acoustic wave in which pressures cross through ambient and at a rate consistent with energy in the mid-range. Because the model is theoretically based, it has the potential for use as the basis for a damage risk criterion for impulse noise as well as for a design criterion for weapons.

Adult↗
PubMed1990

[Clinical laboratory application of HPLC].

In clinical laboratory tests, high performance liquid chromatography (HPLC) has been widely used because of good reproducibility of data and easy automatization. In this workshop, separation of IgG and albumin in commercially available IgG preparation and determination of blood theophylline and serum uric acid levels were conducted by the HPLC method. In separation of IgG and albumin, HPLC analysis was carried out within 10 minutes by using the high-performance gel filtration column (TSK gel G 3,000 SWXL). Blood theophylline was fully automatically determined by using the pretreated column to separate small molecular material before application of the analytical column. A good correlation of blood theophylline levels between HPLC and ordinary EIA method was observed. In determination of serum uric acid, pretreatment for deproteinization of samples by acid was done to measure exactly the whole blood uric acid content. Eluent was adjusted to pH 2.2 to increase affinity to ODS phase of the reversed column (TSK gel ODS-80 TM). There was a good correlation of values of uric acid between HPLC and uricase-catalase method.

Albumins↗
PubMed1989

Evaluation and clinical significance of appendicular skeletal assessment by radiographic photodensitometry.

"Senile" or age-related bone loss affects cortical and trabecular bone and may be detected in the appendicular as well as the axial skeleton. This study presents radiographic photodensitometry as a precise and sensitive technique for evaluating appendicular skeletal status. Data from reproducibility studies indicate that the coefficient of variation for the technology is between 1.9% and 4.5% for the three bones analyzed. Evaluation of age-related changes in bone mass for over 800 subjects demonstrated a decline in mass vs. age after the fourth decade in women, with the slope of the decline being very similar to that seen in CT longitudinal studies. Applied serially to a patient over time, the technology identifies changes in bone mass and may be used to evaluate the response to intervention therapy.

Absorptiometry, Photon↗
PubMed1989

Functionally important regions of the factor IX gene have a low rate of polymorphism and a high rate of mutation in the dinucleotide CpG.

We have recently described genomic amplification with transcript sequencing (GAWTS), a three-step procedure that allows direct genomic sequencing. By GAWTS more than 100,000 bp of sequence have been generated from eight regions of the factor IX gene, which include the putative promoter region, the coding region, and the splice junctions. All eight regions were examined in 20 unrelated normal individuals of defined ethnicity and subsequently in 22 hemophiliacs in different families. The following three major conclusions emerge: (1) The rate of polymorphism in these eight regions of functional significance has been measured in an X-linked gene, and it is about one-third of the average rate observed for intronic and intergenic sequences on the X chromosome. The rate is low enough that the causative mutation should be the only sequence change seen in the overwhelming majority of hemophiliacs. (2) Transitions of CpG account for 31% (5/16) of the distinct mutations and for 38% (5/13) of the single-base changes. The rate of transitions at CpG is elevated by an estimated 77-fold, presumably owing to lack of repair of thymidine generated by the spontaneous deamination of 5-methylcytidine. (3) High-quality, reproducible sequence data can be obtained on a time scale that makes direct carrier testing and prenatal diagnosis feasible.

Amino Acid Sequence↗
PubMed1985

[Molecular biology of natural and constructed in vitro recombinants of human adenoviruses and SV40].

This review is devoted to the molecular and biological properties of natural and artificial Ad-SV40 hybrids. The conditions of adenovirus and SV40 recombinant formations are discussed. The principal one is the ability of the C-terminal portion of the SV40 T-antigen to carry a helper function for growing human adenoviruses in the cultures of simian cells, in which the adenoviruses themselves are not reproduced. The data about the structural and functional organization of the hybrid RNA and proteins, tumor properties of defective and nondefective Ad-SV40 recombinants are provided. A special chapter is devoted to the construction of Ad-SV40 hybrids in vitro. The possibility of using them not only for the investigation of adenoviral properties, but for the super production of different proteins is marked. Alongside the corresponding region of SV40 genome may perform the function of a selection marker for the creation of eucaryotic vectors on the basis of adenoviruses.

Adenoviruses, Human↗