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Two cross-linguistic factors underlying tongue shapes for vowels.

Desirable characteristics of a vocal-tract parametrization include accuracy, low dimensionality, and generalizability across speakers and languages. A low-dimensional, speaker-independent linear parametrization of vowel tongue shapes can be obtained using the PARAFAC three-mode factor analysis procedure [Harshman et al., J. Acoust. Soc. Am. 62, 693-707 (1977)]. Harshman et al. applied PARAFAC to midsagittal x-ray vowel data from five English speakers, reporting that two speaker-independent factors are required to accurately represent the tongue shape measured along anatomically normalized vocal-tract diameter grid lines. Subsequently, the cross-linguistic generality of this parametrization was brought into question by the application of PARAFAC to Icelandic vowel data, where three nonorthogonal factors were reported [Jackson, J. Acoust. Soc. Am. 84, 124-143 (1988)]. This solution is shown to be degenerate; a reanalysis of Jackson's Icelandic data produces two factors that match Harshman et al.'s factors for English vowels, contradicting Jackson's distinction between English and Icelandic language-specific "articulatory primes". To obtain vowel factors not constrained by artificial measurement grid lines, x-ray tongue shape traces of six English speakers were marked with 13 equally spaced points. PARAFAC analysis of this unconstrained (x,y) coordinate data results in two factors that are clearly interpretable in terms of the traditional vowel quality dimensions front/back, high/low.

Cross-Cultural Comparison↗

Compensation strategies for the perturbation of French [u] using a lip tube. II. Perceptual analysis.

A perceptual analysis of the French vowel [u] produced by 10 speakers under normal and perturbed conditions (Savariaux et al., 1995) is presented which aims at characterizing in the perceptual domain the task of a speaker for this vowel, and, then, at understanding the strategies developed by the speakers to deal with the lip perturbation. Identification and rating tests showed that the French [u] is perceptually fairly well described in the [F1, (F2-F0)] plane, and that the parameter (((F2-F0) + F1)/2) (all frequencies in bark) provides a good overall correlate of the "grave" feature classically used to describe the vowel [u] in all languages. This permitted reanalysis of the behavior of the speakers during the perturbation experiment. Three of them succeed in producing a good [u] in spite of the lip tube, thanks to a combination of limited changes on F1 and (F2-F0), but without producing the strong backward movement of the tongue, which would be necessary to keep the [F1,F2] pattern close to the one measured in normal speech. The only speaker who strongly moved his tongue back and maintained F1 and F2 at low values did not produce a perceptually well-rated [u], but additional tests demonstrate that this gesture allowed him to preserve the most important phonetic features of the French [u], which is primarily a back and rounded vowel. It is concluded that speech production is clearly guided by perceptual requirements, and that the speakers have a good representation of them, even if they are not all able to meet them in perturbed conditions.

Adult↗

Modeling the metabolism of idarubicin to idarubicinol in rat heart: effect of rutin and phenobarbital.

Since the severe cardiotoxicity of anthracyclines has been attributed to the intramyocardial formation of C-13 alcohol metabolites, the kinetics of cardiac metabolite formation and disposition as well as the effect of carbonyl reductase inhibitors are of specific interest. This study was designed to investigate the effect of rutin and phenobarbital on the pharmacokinetics of idarubicin (IDA) and its conversion to idarubicinol (IDOL) in the single-pass perfused rat heart. After infusion of IDA (0.5 mg) during 1min, the venous outflow concentrations of IDA and IDOL were measured up to 80 min in the presence and absence of rutin and phenobarbital. A kinetic model was developed to help to interpret the concentration profiles in terms of compartmentation of IDOL formation and to estimate parameters quantitatively descriptive of the transport and biotransformation processes. Rutin and phenobarbital significantly reduced the residual amount of IDOL in heart to 64 and 47% of control, respectively. Pharmacokinetic modeling of the data revealed that IDOL is generated in two different compartments, besides the tissue compartment characterized by saturable uptake, also the compartment that accounts for the quasi-instantaneous initial distribution process is involved. The efflux rate constant of IDOL, k(21,IDOL,) was much smaller than that of IDA. Rutin and phenobarbital significantly reduced IDOL production. Additionally, phenobarbital competitively inhibited the saturable uptake of both IDA and IDOL (increase in apparent Michaelis constants). Reanalysis of data obtained in previous experiments showed that P-glycoprotein inhibitors (verapamil and amiodarone) reduced IDOL uptake in a similar way as already shown for IDA. The present study further supports the utility of pharmacokinetic modeling in identifying sites of drug interactions within the heart.

Amiodarone↗

Recombination in the hemagglutinin gene of the 1918 "Spanish flu".

When gene sequences from the influenza virus that caused the 1918 pandemic were first compared with those of related viruses, they yielded few clues about its origins and virulence. Our reanalysis indicates that the hemagglutinin gene, a key virulence determinant, originated by recombination. The "globular domain" of the 1918 hemagglutinin protein was encoded by a part of a gene derived from a swine-lineage influenza, whereas the "stalk" was encoded by parts derived from a human-lineage influenza. Phylogenetic analyses showed that this recombination, which probably changed the virulence of the virus, occurred at the start of, or immediately before, the pandemic and thus may have triggered it.

Animals↗

Contributions of anthropogenic and natural forcing to recent tropopause height changes.

Observations indicate that the height of the tropopause-the boundary between the stratosphere and troposphere-has increased by several hundred meters since 1979. Comparable increases are evident in climate model experiments. The latter show that human-induced changes in ozone and well-mixed greenhouse gases account for approximately 80% of the simulated rise in tropopause height over 1979-1999. Their primary contributions are through cooling of the stratosphere (caused by ozone) and warming of the troposphere (caused by well-mixed greenhouse gases). A model-predicted fingerprint of tropopause height changes is statistically detectable in two different observational ("reanalysis") data sets. This positive detection result allows us to attribute overall tropopause height changes to a combination of anthropogenic and natural external forcings, with the anthropogenic component predominating.

Journal Article↗

Computational improvements reveal great bacterial diversity and high metal toxicity in soil.

The complexity of soil bacterial communities has thus far confounded effective measurement. However, with improved analytical methods, we show that the abundance distribution and total diversity can be deciphered. Reanalysis of reassociation kinetics for bacterial community DNA from pristine and metal-polluted soils showed that a power law best described the abundance distributions. More than one million distinct genomes occurred in the pristine soil, exceeding previous estimates by two orders of magnitude. Metal pollution reduced diversity more than 99.9%, revealing the highly toxic effect of metal contamination, especially for rare taxa.

Bacteria↗

Comment on "Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot".

Latimer et al. (Reports, 9 September 2005, p. 1722) used an approximate likelihood function to estimate parameters of Hubbell's neutral model of biodiversity. Reanalysis with the exact likelihood not only yields different estimates but also shows that two similar likelihood maxima for very different parameter combinations can occur. This reveals a limitation of using species abundance data to gain insight into speciation and dispersal.

Animals↗

Comment on "A keystone mutualism drives pattern in a power function".

Vandermeer and Perfecto (Reports, 17 February 2006, p. 1000) reported a general power law pattern in the distribution of a common agricultural pest. However, there is an exact analytical solution for the expected cluster distribution under the proposed null model of density-independent growth in a patchy landscape. Reanalysis of the data shows that the system is not in a critical state but confirms the importance of a mutualism.

Animals↗

Comment on "A keystone mutualism drives pattern in a power function".

Vandermeer and Perfecto (Reports, 17 February 2006, p. 1000) maintain that a mutualist ant disrupts the power law distribution of scale insect abundances. However, reanalysis of the data reveals that ants cause an increase in the range of the power law and modify its exponent. We present a tentative, but more realistic, model that is suitable for quantitative predictions.

Animals↗

Radiation and the sex ratio in man.

An analysis of new data concerning the sex of children born to the survivors of the atomic bombings of Hiroshima and Nagasaki, together with a reanalysis of the data previously presented by Neel and Schull (9), reveals significant changes in the sex ratio of these children, changes in the direction to be expected if exposure had resulted in the induction of sex-linked lethal mutations (16).

Child↗

A fossil snake with limbs.

A 95-million-year-old fossil snake from the Middle East documents the most extreme hindlimb development of any known member of that group, as it preserves the tibia, fibula, tarsals, metatarsals, and phalanges. It is more complete than Pachyrhachis, a second fossil snake with hindlimbs that was recently portrayed to be basal to all other snakes. Phylogenetic analysis of the relationships of the new taxon, as well as reanalysis of Pachyrhachis, shows both to be related to macrostomatans, a group that includes relatively advanced snakes such as pythons, boas, and colubroids to the exclusion of more primitive snakes such as blindsnakes and pipesnakes.

Animals↗

Proteomics identify disease-associated variants in patients with rare diseases undiagnosed after genome sequencing.

Despite the introduction of genome sequencing (GS) for rare disease diagnostics, a genetic cause is not identified in most patients. Here, we explored the potential of proteomics to improve the diagnostic yield in 424 patients with rare diseases from the 100,000 Genomes Project (100kGP) without a genetic diagnosis. Serum proteomic profiling was performed using the Olink Explore 1536 assay (N&#xa0;=&#xa0;1463 proteins). For 13 patients without genetic diagnoses, detection of lower serum protein "outliers" (z-score&#xa0;<&#xa0;-2) led to confirmed genetic diagnoses by resolving variants of uncertain significance or prioritizing genes for targeted GS reanalysis. For 23 additional patients without genetic diagnoses (64% of findings), we identified candidate gene-disease links and variants through convergent evidence from lower protein outliers and variants ranked through the variant prioritization tool Exomiser. For example, we identified a candidate heterozygous missense variant [Genome Aggregation Database (gnomAD) minor allele frequency&#xa0;=&#xa0;0.006%] in tyrosine kinase with immunoglobulin-like and epidermal growth factor homology domains 1 (TIE1) that was only present in a patient with lower TIE1 serum abundance (z-score&#xa0;=&#xa0;-5.12) and their father, both of whom were affected by the same monogenic cardiac disorder, but in no other individuals from the 100kGP. Missense (52.5%) and splice region (27.5%) variants accounted for most diagnostic or candidate variants prioritized. This proof-of-principle study demonstrated that serum proteomics can support rare disease diagnosis and identify disease-causing genes in patients undiagnosed after GS, although successful implementation will likely depend on tissue specificity of protein expression, detectability in blood, proteomic platform coverage, and sensitivity.

Humans↗

Retrospective study of Gen-Probe rapid diagnostic system for detection of legionellae in frozen clinical respiratory tract samples.

The Gen-Probe Rapid Diagnostic System for legionellae, which uses 125I-labeled cDNA directed against the rRNAs of legionellae, was evaluated for its ability to detect members of the genus by using clinical specimens which had been frozen at -70 degrees C for 2 to 8 years. Culture and direct immunofluorescence (DFA) results obtained at the time of specimen collection were used to categorize samples. The specimens tested were 112 samples culture positive for legionellae and 230 samples negative on culture and DFA tests. They were tested in a blinded and randomized fashion. Results were expressed in terms of the ratio of counts per minute of the sample to the counts per minute of the provided negative control. A ratio of greater than or equal to 4.0 was picked for optimal specificity. Of the 112 previously positive specimens, 63 (57%) were positive by the probe assay, and of the 230 previously negative samples, 228 (99.1%) were negative. The 51 discrepant specimens were reexamined by culture and DFA testing if adequate amounts remained; this was possible for 34 specimens. On repeat culture, 22 of 33 previously culture-positive samples yielded legionellae and 11 were negative. Ten of the positive repeat cultures yielded two or fewer colonies per plate. One probe-positive but previously culture-negative sample was overgrown by contaminants on repeat culture. Reanalysis of data after exclusion of the 17 unavailable, 11 repeat culture-negative, and 1 unevaluable specimen gave a probe sensitivity of 74% and specificity of 100%. The Gen-Probe test is therefore specific and is of useful sensitivity.

DNA↗

Evaluation of Syva enzyme immunoassay for detection of Chlamydia trachomatis in genital specimens.

Detection of Chlamydia trachomatis infection was evaluated by culture and a new Syva enzyme immunoassay (EIA) in 1,012 patients at two Baltimore, Md., sexually transmitted disease clinics. The overall chlamydia prevalence determined by culture was 12%. For 506 fresh cervical and urethral specimens, the sensitivity of Syva EIA was 90% and its specificity was 94% compared with culture. Discordant Syva EIA results were further evaluated by staining the sediment in centrifuged culture transport media and Syva EIA transport tubes with a fluorescent monoclonal antibody to C. trachomatis to detect elementary bodies. Reanalysis of the data after use of this technique to resolve discordant results increased sensitivity and specificity to 92 and 96%, respectively. A subsample of 307 fresh cervical specimens was also tested in a three-way comparison using Abbott Chlamydiazyme, Syva EIA, and culture. In this sample, compared with culture, the sensitivity and specificity of Syva EIA were 87 and 95%, respectively, and for Chlamydiazyme they were 77 and 98%, respectively. Syva EIA is a 4-h, easy-to-perform enzyme-linked immunosorbent assay which has a high sensitivity with fresh genital specimens and offers an excellent alternative to culture.

Adolescent↗

Comparison of the QUANTIPLEX HIV-1 RNA 2.0 assay with the AMPLICOR HIV-1 MONITOR 1.0 assay for quantitation of levels of human immunodeficiency virus type 1 RNA in plasma of patients receiving stavudine-didanosine combination therapy.

We compared the QUANTIPLEX HIV-1 RNA 2.0 assay with the AMPLICOR HIV-1 MONITOR 1.0 assay for quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in plasma in the Stadi trail, which evaluated a stavudine plus didanosine combination therapy in 52 patients. HIV-1 RNA baseline values measured with AMPLICOR HIV-1 MONITOR 1.0 were significantly higher than those measured with QUANTIPLEX HIV-1 RNA 2.0, and decreases in HIV-1 RNA levels from baseline were also found to be significantly higher when measured with the AMPLICOR HIV-1 MONITOR 1.0 assay. The frequency of HIV-1 RNA levels below the lower limit of quantitation was significantly higher with QUANTIPLEX HIV-1 RNA 2.0 than with AMPLICOR HIV-1 MONITOR 1.0. Reanalysis of these results by an ultrasensitive procedure of AMPLICOR HIV-1 MONITOR 1.0 or by a modified version of the test that included additional primers adapted for non-B HIV-1 clades yielded greater differences between the QUANTIPLEX HIV-1 RNA 2.0 assay and the AMPLICOR HIV-1 MONITOR 1.0 assay. Our results indicate that a valid comparison of the virological efficacies obtained with different antiretroviral drug regimens requires the use of the same viral load quantitation procedure; further standardization between the different HIV-1 RNA quantitation kits is therefore needed.

Anti-HIV Agents↗

Algorithmic approach to high-throughput molecular screening for alpha interferon-resistant genotypes in hepatitis C patients.

This study was designed to analyze the feasibility and validity of using Cleavase Fragment Length Polymorphism (CFLP) analysis as an alternative to DNA sequencing for high-throughput screening of hepatitis C virus (HCV) genotypes in a high-volume molecular pathology laboratory setting. By using a 244-bp amplicon from the 5' untranslated region of the HCV genome, 61 clinical samples received for HCV reverse transcription-PCR (RT-PCR) were genotyped by this method. The genotype frequencies assigned by the CFLP method were 44.3% for type 1a, 26.2% for 1b, 13.1% for type 2b, and 5% type 3a. The results obtained by nucleotide sequence analysis provided 100% concordance with those obtained by CFLP analysis at the major genotype level, with resolvable differences as to subtype designations for five samples. CFLP analysis-derived HCV genotype frequencies also concurred with the national estimates (N. N. Zein et al., Ann. Intern. Med. 125:634-639, 1996). Reanalysis of 42 of these samples in parallel in a different research laboratory reproduced the CFLP fingerprints for 100% of the samples. Similarly, the major subtype designations for 19 samples subjected to different incubation temperature-time conditions were also 100% reproducible. Comparative cost analysis for genotyping of HCV by line probe assay, CFLP analysis, and automated DNA sequencing indicated that the average cost per amplicon was lowest for CFLP analysis, at $20 (direct costs). On the basis of these findings we propose that CFLP analysis is a robust, sensitive, specific, and an economical method for large-scale screening of HCV-infected patients for alpha interferon-resistant HCV genotypes. The paper describes an algorithm that uses as a reflex test the RT-PCR-based qualitative screening of samples for HCV detection and also addresses genotypes that are ambiguous.

Algorithms↗

The p160 RhoA-binding kinase ROK alpha is a member of a kinase family and is involved in the reorganization of the cytoskeleton.

The GTPase RhoA has been implicated in various cellular activities, including the formation of stress fibers, motility, and cytokinesis. We recently reported on a p150 serine/threonine kinase (termed ROK alpha) binding RhoA only in its active GTP-bound state and on its cDNA; introduction of RhoA into HeLa cells resulted in translocation of the cytoplasmic kinase to plasma membranes, consistent with ROK alpha being a target for RhoA (T. Leung, E. Manser, L. Tan, and L. Lim, J. Biol. Chem. 256:29051-29054, 1995). Reanalysis of the cDNA revealed that ROK alpha contains an additional N-terminal region. We also isolated another cDNA which encoded a protein (ROK beta) with 90% identity to ROK alpha in the kinase domain. Both ROK alpha and ROK beta, which had a molecular mass of 160 kDa, contained a highly conserved cysteine/histidine-rich domain located within a putative pleckstrin homology domain. The kinases bound RhoA, RhoB, and RhoC but not Rac1 and Cdc42. The Rho-binding domain comprises about 30 amino acids. Mutations within this domain caused partial or complete loss of Rho binding. The morphological effects of ROK alpha were investigated by microinjecting HeLa cells with DNA constructs encoding various forms of ROK alpha. Full-length ROK alpha promoted formation of stress fibers and focal adhesion complexes, consistent with its being an effector of RhoA. ROK alpha truncated at the C terminus promoted this formation and also extensive condensation of actin microfilaments and nuclear disruption. The proteins exhibited protein kinase activity which was required for stress fiber formation; the kinase-dead ROK alpha K112A and N-terminally truncated mutants showed no such promotion. The latter mutant instead induced disassembly of stress fibers and focal adhesion complexes, accompanied by cell spreading. These effects were mediated by the C-terminal region containing Rho-binding, cysteine/histidine-rich, and pleckstrin homology domains. Thus, the multidomained ROK alpha appears to be involved in reorganization of the cytoskeleton, with the N and C termini acting as positive and negative regulators, respectively, of the kinase domain whose activity is crucial for formation of stress fibers and focal adhesion complexes.

Amino Acid Sequence↗