Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Signature”

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 793 records · Page 44Linked to original sources
PubMed2003

Spectral fluorescence signatures and partial least squares regression: model to predict dissolved organic carbon in water.

Spectro-fluorescence signature (SFS) of water samples contains information that may be used to quantify dissolved organic carbon (DOC) if combined with multivariate analyses. A model was built through SFS and partial least squared (PLS) regression. The SFSs of 219 samples of natural water along the Raritan River and Millstone River watersheds located in central New Jersey, and their corresponding DOC concentrations were used to build the model. Calibration, full cross-validation, and prediction performances of various models were statistically compared before optimal model selection. The final selected model, tested on the Passaic River watershed in northern New Jersey, provided a bias of 0.028 mg/l and a root mean squared error of prediction (RMSEP) of 0.35 mg/l. Linked to PLS, SFS can be a quality and cost effective method to perform on-line rapid DOC measurements.

Carbon↗
PubMed2003

Comparison of spectral fluorescent signatures-based models to characterize DOM in treated water samples.

Statistical procedures enable a multivariate analysis of the measurements to identify specific characteristics of the dissolved organic matter (DOM) fractions in raw natural water, including the concentrations. In this work, three already established models were used to predict the concentrations of fractions of DOM from spectral fluorescent signatures (SFSs): a general linear regression (GLR), loadings and scores of a principal components analysis (PCA), and a partial least squares regression (PLS). Details about the method undertaken to prepare the fractions were given. Water samples from surface water treatment plants in New Jersey were used for the testing. In all cases, PLS have shown much better biases and accuracies than GLR and PCA models. Hydrophilic neutral, however, showed poor performances (bias 33%) due to the isolation technique used. Recommendations were provided in order to improve the DOM characterization through SFS, which linked to PLS make a powerful and cost-effective surrogate parameter to characterize DOM.

Organic Chemicals↗
PubMed1999

Clinical relevance of age-dependent EEG signatures in the detection of neonates at high risk for apnea.

Age dependent EEG signatures were detected in the EEG of 71 neonates of 28-100 weeks of conceptional age (CA). Using the new method presented, neonates were automatically classified in three age groups (28-35 weeks CA), (36-40 weeks CA) and (41-100 weeks CA). Analysis was performed employing relative distance functions for the complete frequency spectra of the EEG registered by electrodes in C3 and C4 positions. The analysis was successful in automatic identification of individuals showing EEG anomalies. Polysomnographic analysis demonstrated these to be apnea risk patients. Accordingly, a purely EEG based detection of neonates that are medically at risk becomes feasible.

Age Factors↗
PubMed2004

Identification of Mycobacterium marinum virulence genes using signature-tagged mutagenesis and the goldfish model of mycobacterial pathogenesis.

Mycobacterium marinum, a causative agent of fish tuberculosis, is one of the most closely related Mycobacterium species (outside the M. tuberculosis complex) to M. tuberculosis, the etiologic agent of human tuberculosis. Signature-tagged mutagenesis was used to identify genes of M. marinum required for in vivo survival in a goldfish model of mycobacterial pathogenesis. Screening the first 1008 M. marinum mutants led to the identification of 40 putative virulence mutants. DNA sequence analysis of these 40 mutants identified transposon insertions in 35 unique loci. Twenty-eight out of 33 (85%) loci encoding putative virulence genes have homologous genes in M. tuberculosis.

Animals↗
PubMed2001

Two Arabidopsis homologs of the animal trithorax genes: a new structural domain is a signature feature of the trithorax gene family.

Two Arabidopsis genes have been characterized as first examples of plant genes homologous to the animal trithorax genes. The Arabidopsis genes are highly similar but display different tissue and development expression patterns. One of them was ubiquitously expressed, with highest levels registered in young seedlings. The other gene was less active in all tested tissues, was not expressed in mature leaves but was highly expressed in roots. A new structural motif common to all TRX-related proteins has been identified. This new architectural element was found only in genes of multicellular species and is present in all genes belonging to the trithorax family. Along with the SET domain and the PHD fingers, this new element is a signature feature for the trithorax gene family.

Amino Acid Sequence↗
PubMed2000

Strategy for qualitative and quantitative analysis in proteomics based on signature peptides.

This paper describes a new analytical strategy for identifying proteins in concentration flux based on isotopic labeling peptides in tryptic digests. Primary amino groups in peptides from control and experimental samples were derivatized with acetate and trideuteroacetate, respectively. After mixing samples thus labeled from these two sources, the relative concentration of peptides was determined by isotope ratio analysis with MALDI and ESI mass spectrometry. More than a 100-fold difference in relative concentration could be detected. Simplification of complex tryptic digests prior to mass spectral analysis was achieved by selection of histidine-containing peptides with immobilized metal affinity sorbents or of glycopeptides by lectin columns. Because most of these peptides have sequences that are unique to a single protein, they are a signature of the protein from which they were derived; providing a facile route to protein analysis.

Chromatography, Affinity↗
PubMed2002

Mutations of the p53 and PTCH gene in basal cell carcinomas: UV mutation signature and strand bias.

Mutations of p53 and PTCH gene, two candidate tumor suppressor genes for basal cell carcinoma (BCC), were screened in 15 cases of sporadic BCCs that developed in sun-exposed skin region in a Korean population. p53 and PTCH mutations were detected at a frequency of 33 and 40%, respectively, and the mutations were predominantly UV-signature transition, C-->T transitions at dipyrimidine sites and CC-->TT tandem mutations. In both genes, the most common mutations were missense mutations resulting in amino acid substitution, which is different than the results from Caucasian BCCs where mutations are frequently predicted to make truncated or absent proteins. All mutations, except for one, occurred on the nontranscribed strand where is little efficient removal of UV-induced pyrimidine dimers relative to the transcribed strand. Loss of heterozygocity (LOH) of 9q22 for PTCH loci was found in eight of 15 informative cases of BCCs (53%), but none of the cases were informative for LOH of 17p13 for p53 loci. Not only do our data indicate the key role played by p53 and PTCH in the development of BCCs, these findings also suggest that UVB may significantly contribute to BCC tumorigenesis. Moreover, molecular epidemiology composed of incidence of p53 and PTCH mutations, difference in the type of mutation and repair bias of UV-induced DNA lesions might affect the distinct features of BCCs between different racial population.

Aged↗
PubMed2000

Detection of genes essential in specific niches by signature-tagged mutagenesis.

Variations of the signature-tagged mutagenesis (STM) technique are now possible and the method can be applied to most pathogens that have an STM-selectable phenotype in a host system. STM screening of 15,040 mutants from 11 bacterial species identified 323 in vivo attenuated mutants. As a genome-scanning tool, STM will yield information about genes with unknown functions as well as information crucial for understanding microbial pathogenesis.

Animals↗
PubMed2003

Self-representation: searching for a neural signature of self-consciousness.

Human self-consciousness operates at different levels of complexity and at least comprises five different levels of representational processes. These five levels are nonconceptual representation, conceptual representation, sentential representation, meta-representation, and iterative meta-representation. These different levels of representation can be operationalized by taking a first-person-perspective that is involved in representational processes on different levels of complexity. We refer to experiments that operationalize a first-person-perspective on the level of conceptual and meta-representational self-consciousness. Interestingly, these experiments show converging evidence for a recruitment of medial cortical and parietal regions during taking a first-person-perspective, even when operating on different degrees of complexity. These data lend support for the speculative hypothesis, that there exist a neural signature for human self-consciousness that is recruited independent from the degree of representational complexity to be performed.

Awareness↗
PubMed2000

Signature-tagged mutagenesis in the identification of virulence genes in pathogens.

Signature-tagged mutagenesis is a functional genomics technique that identifies microbial genes required for infection within an animal host, or within host cells. The application of this technique to a range of microbial pathogens has resulted in the identification of novel virulence determinants in each screen performed to date, so that cumulatively several hundred genes have been ascribed a role in virulence.

Candida↗
PubMed2000

Brain chirps: spectrographic signatures of epileptic seizures.

OBJECTIVE: A chirp is a brief signal within which the frequency content changes rapidly. Spectrographic chirps are found in signals produced from many biological and physical phenomena. In radar and sonar engineering, signals with chirps are used to localize direction and range to the signal source. Although characteristic frequency changes during epileptic seizures have long been observed, the correlation with chirps and chirp technology seems never to have been made. METHODS: We analyzed 19404 s (1870 s of which were from 43 seizures) of intracranially (subdural and depth electrode) recorded digital EEG from 6 patients for the presence of spectral chirps. Matched filters were constructed from methods in routine use in non-medical signal processing applications. RESULTS: We found that chirps are very sensitive detectors of seizures (83%), and highly specific as markers (no false positive detections). The feasibility of using spectral chirps as matched filters was demonstrated. CONCLUSIONS: Chirps are highly specific and sensitive spectrographic signatures of epileptic seizure activity. In addition, chirps may serve as templates for matched filter design to detect seizures, and as such, can demonstrate localization and propagation of seizures from an epileptic focus.

Brain↗
PubMed2002

Computational selection of distinct class- and subclass-specific gene expression signatures.

In this investigation we used statistical methods to select genes with expression profiles that partition classes and subclasses of biological samples. Gene expression data corresponding to liver samples from rats treated for 24 h with an enzyme inducer (phenobarbital) or a peroxisome proliferator (clofibrate, gemfibrozil or Wyeth 14,643) were subjected to a modified Z-score test to identify gene outliers and a binomial distribution to reduce the probability of detecting genes as differentially expressed by chance. Hierarchical clustering of 238 statistically valid differentially expressed genes partitioned class-specific gene expression signatures into groups that clustered samples exposed to the enzyme inducer or to peroxisome proliferators. Using analysis of variance (ANOVA) and linear discriminant analysis methods we identified single genes as well as coupled gene expression profiles that separated the phenobarbital from the peroxisome proliferator treated samples and discerned the fibrate (gemfibrozil and clofibrate) subclass of peroxisome proliferators. A comparison of genes ranked by ANOVA with genes assessed as significant by mixedlinear models analysis [J. Comput. Biol. 8 (2001) 625] or ranked by information gain revealed good congruence with the top 10 genes from each statistical method in the contrast between phenobarbital and peroxisome proliferators expression profiles. We propose building upon a classification regimen comprised of analysis of replicate data, outlier diagnostics and gene selection procedures to utilize cDNA microarray data to categorize subclasses of samples exposed to pharmacologic agents.

Algorithms↗
PubMed2003

SETting the stage. Eed-Enx1 leaves an epigenetic signature on the inactive X chromosome.

Despite evidence implicating the Polycomb group protein, Eed (embryonic ectoderm development protein) in imprinted X inactivation, a similar role in random X inactivation in the embryo has remained an open question. Brockdorff and colleagues now report that Eed, along with its binding partner Enx1, transiently associates with the inactive X chromosome (Xi) and likely contributes to the epigenetic signature and long-term stability of the Xi heterochromatin.

Animals↗
PubMed2001

An extended structural signature for the tRNA anticodon loop.

Anticodon hairpins are structural motifs with contradictory functions. The recognition by aminoacyl synthetases implies extended interactions with the anticodon base triplet and thus, usually, an unfolding of the anticodon loop. The recognition by the ribosome and cognate interaction with a mRNA codon implies, on the other hand, the formation of a mini-helix with a canonical anticodon hairpin structure as observed by crystallography and NMR. To be able to understand the various properties of this motif, a precise description of its structural conservation is required. Here, on the basis of phylogenetic, structural, and molecular dynamics data, we discuss a conserved interaction established between the ribose of the U33 and the base at position 35, either a purine or a pyrimidine. This interaction involves the hydrogen bonding donor or acceptor potential of the hydroxyl group of U33 and has to be integrated in an extended definition of the anticodon hairpin. The extended structural signature provides also an explanation for the role played by pseudouridines at position 35.

Anticodon↗
PubMed2001

Phosphopeptide derivatization signatures to identify serine and threonine phosphorylated peptides by mass spectrometry.

The development of rapid, global methods for monitoring states of protein phosphorylation would provide greater insight for understanding many fundamental biological processes. Current best practices use mass spectrometry (MS) to profile digests of purified proteins for evidence of phosphorylation. However, this approach is beset by inherent difficulties in both identifying phosphopeptides from within a complex mixture containing many other unmodified peptides and ionizing phosphopeptides in positive-ion MS. We have modified an approach that uses barium hydroxide to rapidly eliminate the phosphoryl group of serine and threonine modified amino acids, creating dehydroamino acids that are susceptible to nucleophilic derivatization. By derivatizing a protein digest with a mixture of two different alkanethiols, phosphopeptide-specific derivatives were readily distinguished by MS due to their characteristic ion-pair signature. The resulting tagged ion pairs accommodate simple and rapid screening for phosphopeptides in a protein digest, obviating the use of isotopically labeled samples for qualitative phosphopeptide detection. MALDI-MS is used in a first pass manner to detect derivatized phosphopeptides, while the remaining sample is available for tandem MS to reveal the site of derivatization and, thus, phosphorylation. We demonstrated the technique by identifying phosphopeptides from beta-casein and ovalbumin. The approach was further used to examine in vitro phosphorylation of recombinant human HSP22 by protein kinase C, revealing phosphorylation of Thr-63.

Animals↗
PubMed2002

Cis-trans signatures of proline-containing tryptic peptides in the gas phase.

High-resolution ion mobility/time-of-flight techniques were used to measure collision cross sections for 968 tryptic digest peptide ions obtained from digestion of common proteins. Here, we report a mobility signature that aids in identifying proline-containing peptides containing 4-10 residues. Of 129 peptides (< or = 10 residues in length) in the database that contain proline residues, 57% show multiple resolved features in the ion mobility distribution for at least one of the [M + H]+ or [M + 2H]2+ ions. These multiple features are attributed to different conformations that arise from populations of cis and trans forms of proline. The number of resolved peaks in the ion mobility distribution appears to be correlated with the peptide ion charge state and the number of proline residues in the peptide.

Animals↗
PubMed2005

Comprehensive assignment of mass spectral signatures from individual Bacillus atrophaeus spores in matrix-free laser desorption/ionization bioaerosol mass spectrometry.

We have fully characterized the mass spectral signatures of individual Bacillus atrophaeus spores obtained using matrix-free laser desorption/ionization bioaerosol mass spectrometry (BAMS). Mass spectra of spores grown in unlabeled, 13C-labeled, and 15N-labeled growth media were used to determine the number of carbon and nitrogen atoms associated with each mass peak observed in mass spectra from positive and negative ions. To determine the parent ion structure associated with fragment ion peaks, the fragmentation patterns of several chemical standards were independently determined. Our results confirm prior assignments of dipicolinic acid, amino acids, and calcium complex ions made in the spore mass spectra. The identities of several previously unidentified mass peaks, key to the recognition of Bacillus spores by BAMS, have also been revealed. Specifically, a set of fragment peaks in the negative polarity is shown to be consistent with the fragmentation pattern of purine nucleobase-containing compounds. The identity of m/z = +74, a marker peak that helps discriminate B. atrophaeus from Bacillus thuringiensis spores grown in rich media is [N1C4H12]+. A probable precursor molecule for the [N1C4H12]+ ion observed in spore spectra is trimethylglycine (+N(CH3)3CH2COOH), which produces a m/z = +74 peak when ionized in the presence of dipicolinic acid. A clear assignment of all the mass peaks in the spectra from bacterial spores, as presented in this work, establishes their relationship to the spore chemical composition and facilitates the evaluation of the robustness of "marker" peaks. This is especially relevant for peaks that have been used to discriminate Bacillus spore species, B. thuringiensis and B. atrophaeus, in our previous studies.

Amino Acids↗
PubMed2026

Plasma Proteome Signatures in Sickle Cell Anemia and the Effect of Hydroxyurea Treatment.

Sickle Cell Anaemia (SCA) is a monogenic blood disorder caused by a mutation in the &#x3b2;-globin gene, yet it presents with marked clinical variability. Although hydroxyurea (HU) is an established therapy, its precise mechanism of action remains incompletely understood. Plasma proteins represent valuable biomarkers for elucidating disease mechanisms and treatment responses. In this study, plasma proteome profiling of 31 healthy controls and 76 SCA patients identified 43 differentially abundant proteins (DAPs) that form a highly interconnected interaction network. Proteins with increased abundance in SCA were largely associated with immune and inflammatory responses, whereas those with reduced levels were linked to coagulation and proteolytic pathways. HU therapy was associated with elevated levels of haptoglobin (HP) and hemopexin (HPX), key mediators of free hemoglobin scavenging. We also identified several previously unreported plasma proteins altered in SCA, broadening the landscape of potential biomarkers and HU-responsive targets. Many DAPs significantly correlated with clinical indices, such as transfusion frequency, vaso-occlusive crises, white blood cell counts, and platelet counts, offering insights into disease mechanisms and potential utility in disease management. Notably, overlap with &#x3b2;-thalassemia-associated signatures suggests shared pathophysiological pathways between these hemoglobinopathies. Collectively, these findings provide a strong foundation for translational validation in larger, independent cohorts.

Humans↗