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 127 records · Page 7Linked to original sources
PubMed2006

The distinctive signatures of promoter regions and operon junctions across prokaryotes.

Here we show that regions upstream of first transcribed genes have oligonucleotide signatures that distinguish them from regions upstream of genes in the middle of operons. Databases of experimentally confirmed transcription units do not exist for most genomes. Thus, to expand the analyses into genomes with no experimentally confirmed data, we used genes conserved adjacent in evolutionarily distant genomes as representatives of genes inside operons. Likewise, we used divergently transcribed genes as representative examples of first transcribed genes. In model organisms, the trinucleotide signatures of regions upstream of these representative genes allow for operon predictions with accuracies close to those obtained with known operon data (0.8). Signature-based operon predictions have more similar phylogenetic profiles and higher proportions of genes in the same pathways than predicted transcription unit boundaries (TUBs). These results confirm that we are separating genes with related functions, as expected for operons, from genes not necessarily related, as expected for genes in different transcription units. We also test the quality of the predictions using microarray data in six genomes and show that the signature-predicted operons tend to have high correlations of expression. Oligonucleotide signatures should expand the number of tools available to identify operons even in poorly characterized genomes.

Bacillus subtilis↗
PubMed2004

Characterization of palmprints by wavelet signatures via directional context modeling.

The palmprint is one of the most reliable physiological characteristics that can be used to distinguish between individuals. Current palmprint-based systems are more user friendly, more cost effective, and require fewer data signatures than traditional fingerprint-based identification systems. The principal lines and wrinkles captured in a low-resolution palmprint image provide more than enough information to uniquely identify an individual. This paper presents a palmprint identification scheme that characterizes a palmprint using a set of statistical signatures. The palmprint is first transformed into the wavelet domain, and the directional context of each wavelet subband is defined and computed in order to collect the predominant coefficients of its principal lines and wrinkles. A set of statistical signatures, which includes gravity center, density, spatial dispersivity and energy, is then defined to characterize the palmprint with the selected directional context values. A classification and identification scheme based on these signatures is subsequently developed. This scheme exploits the features of principal lines and prominent wrinkles sufficiently and achieves satisfactory results. Compared with the line-segments-matching or interesting-points-matching based palmprint verification schemes, the proposed scheme uses a much smaller amount of data signatures. It also provides a convenient classification strategy and more accurate identification.

Algorithms↗
PubMed2006

Examination of a "velasco" signature on an oil painting.

In September 2003, an investor bought an oil painting at auction in Denmark. The painting was signed "José Maria Velasco." The investor attempted to sell the painting in the United States, but found that he needed confirmation that this was an authentic Velasco painting. The provenance of the painting was questionable because it came to Europe from Cuba without appropriate documentation including the date of its entry into the European market. If the signature was determined to be authentic, the painting would have an approximate value of 1 million dollars. Initial research on the life and works of the artist and a literature review resulted in the preparation of an "Art Worksheet." Known signature specimens were obtained from reputable sources. A comparison of the known signatures with the questioned signature concluded the questioned signature was very probably not executed by José Maria Velasco.

Journal Article↗
PubMed2004

Function of the ABC signature sequences in the human multidrug resistance protein 1.

Human multidrug resistance protein 1 (MRP1) is a membrane ATP-binding cassette transporter that confers multidrug resistance to tumor cells by effluxing intracellular drugs in an ATP-dependent manner. The mechanisms by which transport occurs and by which ATP hydrolysis is coupled to drug transport are not fully elucidated. In particular, the function of the signature sequences in the nucleotide binding domains (NBDs) of MRP1 is unknown. We therefore investigated the effect of mutation of the signature sequences (G771D and G1433D) and of the Walker A motifs (K684M and K1333M) in the NBDs on the 8-azido-[alpha-32P]ATP photolabeling and 8-azido-[alpha-32P]ADP vanadate trapping of MRP1. Both mutations in the Walker A motif almost completely inhibited the labeling of the mutated NBD with 8-azido-[alpha-32P]ATP but not the labeling of the other intact NBD. In contrast, the G771D mutation in the signature sequence of NBD1 enhanced the labeling of NBD1 but slightly decreased the labeling of NBD2. The G1433D mutation in the signature motif of NBD2 enhanced the labeling of NBD2 but did not affect the labeling of NBD1. These effects were all substrate-independent. Photolabeling of NBD2 and a very slight photolableing of NBD1 were detectable under vanadate trapping conditions with 8-azido-[alpha-32P]ATP. Trapping at both NBD1 and NBD2 was almost completely inhibited by K684M and K1333M mutations and by the K684M/K1333M double mutation. The G771D mutation completely inhibited trapping at NBD2 and considerably inhibited trapping at NBD1. However, whereas the G1433D mutation also considerably inhibited trapping at NBD1, it only partially inhibited trapping of NBD2, and the trapping could still be enhanced by leukotriene C4. Our findings suggest that both signature sequences of MRP1 are involved in ATP hydrolysis and must be intact for the ATP hydrolysis and the transport by MRP1.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti.

Sinorhizobium meliloti genome sequence determination has provided the basis for different approaches of functional genomics for this symbiotic nitrogen-fixing alpha-proteobacterium. One of these approaches is gene disruption with subsequent analysis of mutant phenotypes. This method is efficient for single genes; however, it is laborious and time-consuming if it is used on a large scale. Here, we used a signature-tagged transposon mutagenesis method that allowed analysis of the survival and competitiveness of many mutants in a single experiment. A novel set of signature tags characterized by similar melting temperatures and G+C contents of the tag sequences was developed. The efficiencies of amplification of all tags were expected to be similar. Thus, no preselection of the tags was necessary to create a library of 412 signature-tagged transposons. To achieve high specificity of tag detection, each transposon was bar coded by two signature tags. In order to generate defined, nonredundant sets of signature-tagged S. meliloti mutants for subsequent experiments, 12,000 mutants were constructed, and insertion sites for more than 5,000 mutants were determined. One set consisting of 378 mutants was used in a validation experiment to identify mutants showing altered growth patterns.

Base Sequence↗
PubMed2004

Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum.

The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase beta' subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (sigma70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., sigma70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group.

Amino Acid Sequence↗
PubMed2002

Multi-resolution and wavelet representations for identifying signatures of disease.

Identifying physiological and anatomical signatures of disease in signals and images is one of the fundamental challenges in biomedical engineering. The challenge is most apparent given that such signatures must be identified in spite of tremendous inter and intra-subject variability and noise. Crucial for uncovering these signatures has been the development of methods that exploit general statistical properties of natural signals. The signal processing and applied mathematics communities have developed, in recent years, signal representations which take advantage of Gabor-type and wavelet-type functions that localize signal energy in a joint time-frequency and/or space-frequency domain. These techniques can be expressed as multi-resolution transformations, of which perhaps the best known is the wavelet transform. In this paper we review wavelets, and other related multi-resolution transforms, within the context of identifying signatures for disease. These transforms construct a general representation of signals which can be used in detection, diagnosis and treatment monitoring. We present several examples where these transforms are applied to biomedical signal and imaging processing. These include computer-aided diagnosis in mammography, real-time mosaicking of ophthalmic slit-lamp imagery, characterization of heart disease via ultrasound, predicting epileptic seizures and signature analysis of the electroencephalogram, and reconstruction of positron emission tomography data.

Algorithms↗
PubMed2005

Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy.

Protein signatures in disease, a portion of the protein complement of cells that directly reflects disease related changes, provide a unique data set that may be correlated with or be an aid to more effective diagnosis, prognosis, and response to therapy. A recent article in this Journal from the author's laboratory described the protein analysis of glioma tissue and the discovery of protein signatures for assessing the stage of disease as well as their correlation with patient survival. This investigation used direct proteomic analysis of glioma biopsies, the discovery of molecular signatures for stage and outcome, and identification of specific proteins of this signature group. This minireview discusses the background and present state of the technology used in this work and the role that direct tissue analysis can play in the discovery of high-quality protein signatures.

Humans↗
PubMed2005

A rare transporter associated with antigen processing polymorphism overpresented in HLAlow colon cancer reveals the functional significance of the signature domain in antigen processing.

Transporter associated with antigen processing (TAP), a member of the ATP-binding cassette transporter superfamily, is composed of two integral membrane proteins, TAP-1 and TAP-2. Each subunit has a C-terminal nucleotide-binding domain that binds and hydrolyzes ATP to energize peptide translocation across the endoplasmic reticulum membrane. A motif comprising the sequence LSGGQ (called the signature motif) and the amino acid that is immediately C-terminal to this motif are highly conserved in the nucleotide-binding domains of ATP-binding cassette transporters. To search for natural variants of TAP-1 with alterations in or near the signature motif, we sequenced the TAP-1 exon 10 amplified from 103 human colon cancer samples. We found a rare TAP-1 allele with an R>Q alteration at a residue immediately C-terminal to the signature motif (R648) that occurred 17.5 times more frequently in colon cancers with down-regulated surface class I MHC than those with normal MHC levels (P = 0.01). Functional analysis revealed that the Q648 variant had significantly reduced peptide translocation activity compared with TAP-1 (R648). In addition, we found that mutations S644R, G645R, G646S, and G646D interfered with TAP-1 activity. TAP-1 G646D, which showed the most severe defect, resided normally in the endoplasmic reticulum and associated with the peptide loading complex, but failed to transport peptide across the endoplasmic reticulum membrane. Thus, a TAP-1 polymorphism adjacent to the signature motif may be a contributing factor for MHC class I down-regulation in colon cancer. Given the widespread defects in DNA mismatch repair in colon cancer, mutations at or near the signature domain can potentially modulate antigen processing.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2024

Stemness related lncRNAs signature for the prognosis and tumor immune microenvironment of ccRCC patients.

Long non-coding RNAs (lncRNAs) and cancer stem cells (CSCs) are crucial for the growth, migration, recurrence, and medication resistance of tumors. However, the impact of lncRNAs related to stemness on the outcome and tumor immune microenvironment (TIME) in clear cell renal cell carcinoma (ccRCC) is still unclear. In this study, we aimed to predict the outcome and TIME of ccRCC by constructing a stem related lncRNAs (SRlncRNAs) signature. We firstly downloaded ccRCC patients' clinical data and RNA sequencing data from UCSC and TCGA databases, and abtained the differentially expressed lncRNAs highly correlated with stem index in ccRCC through gene expression differential analysis and Pearson correlation analysis. Then, we selected suitable SRlncRNAs for constructing a prognostic signature of ccRCC patients by LASSO Cox regression. Further, we used nomogram and Kaplan Meier curves to evaluate the SRlncRNA signature for the prognose in ccRCC. At last, we used ssGSEA and GSVA to evaluate the correlation between the SRlncRNAs signature and TIME in ccRCC. Finally, We obtained a signtaure based on six SRlncRNAs, which are correlated with TIME and can effectively predict the ccRCC patients' prognosis. The SRlncRNAs signature may be a noval prognostic indicator in ccRCC.

Humans↗
PubMed2005

Analysis of significance patterns identifies ubiquitous and disease-specific gene-expression signatures in patient peripheral blood leukocytes.

The utilization of gene-expression microarrays in patient-based research creates new prospects for the discovery of diagnostic biomarkers and the identification of genes or pathways linked to pathogenesis. Gene-expression signatures in peripheral blood mononuclear cells isolated from over one hundred patients with conditions presenting a strong immunological component (patient with autoimmune, graft versus host and infectious diseases, as well as immunosuppressed transplant recipients) were generated. This dataset provides the opportunity to carry out comparative analyses and define disease signatures in a broader context. Transcriptional changes of 22,283 probe sets were evaluated through statistical group comparison performed systematically for seven diseases versus their respective healthy control group. Patterns of significance were generated by hierarchical clustering of P-values. This approach led to the identification of a SLE-specific "diagnostic signature," formed by genes that did not change compared to healthy subjects in the other six diseases. Conversely, a "sentinel signature" that was common to all seven diseases was characterized. These findings bring new perspectives for the application of blood leukocyte expression signatures for diagnosis and early disease detection.

Adult↗
PubMed2006

Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer.

PURPOSE: We previously identified in a single-center study a 76-gene prognostic signature for lymph node-negative (LNN) breast cancer patients. The aim of this study was to validate this gene signature in an independent more diverse population of LNN patients from multiple institutions. PATIENTS AND METHODS: Using custom-designed DNA chips we analyzed the expression of the 76 genes in RNA of frozen tumor samples from 180 LNN patients who did not receive adjuvant systemic treatment. RESULTS: In this independent validation, the 76-gene signature was highly informative in identifying patients with distant metastasis within 5 years (hazard ratio, [HR], 7.41; 95% CI, 2.63 to 20.9), even when corrected for traditional prognostic factors in multivariate analysis (HR, 11.36; 95% CI, 2.67 to 48.4). The actuarial 5- and 10-year distant metastasis-free survival were 96% (95% CI, 89% to 99%) and 94% (95% CI, 83% to 98%), respectively, for the good profile group and 74% (95% CI, 64% to 81%) and 65% (53% to 74%), respectively for the poor profile group. The sensitivity for 5-yr distant metastasis-free survival was 90%, and the specificity was 50%. The positive and negative predictive values were 38% (95% CI, 29% to 47%) and 94% (95% CI, 86% to 97%), respectively. The 76-gene signature was confirmed as a strong prognostic factor in subgroups of estrogen receptor-positive patients, pre- and postmenopausal patients, and patients with tumor sizes 20 mm or smaller. The subgroup of patients with estrogen receptor-negative tumors was considered too small to perform a separate analysis. CONCLUSION: Our data provide a strong methodologic and clinical multicenter validation of the predefined prognostic 76-gene signature in LNN breast cancer patients.

Adult↗
PubMed2006

Gene expression signature predicting pathologic complete response with gemcitabine, epirubicin, and docetaxel in primary breast cancer.

PURPOSE: Primary systemic therapy (PST) with gemcitabine (G), epirubicin (E), and docetaxel (Doc) has resulted in a pathologic complete response (pCR) in 26% of primary breast cancer patients. This study was aimed at the identification of a gene expression signature in diagnostic core biopsy tissue samples that predicts pCR. PATIENTS AND METHODS: Core biopsy samples from patients with operable primary breast cancer, T2-4N0-2M0, enrolled onto two phase I and II trials evaluating GEDoc (n = 48) and GE sequentially followed by Doc (GEsDoc; n = 52) as PST were snap frozen and subjected to RNA expression profiling. A signature predicting pCR was discovered in the training set (GEsDoc) applying a support vector machine algorithm, and performance of this classifier was validated on the independent test set (GEDoc) by receiver operator characteristics analysis. RESULTS: We identified a signature consisting of 512 genes, which was enriched in genes involved in transforming growth factor beta and RAS-mediated signaling pathways, that predicts pCR with a sensitivity of 78%, a specificity of 90%, and an overall accuracy of 88% (95% CI, 75% to 95%). Apart from our signature, only HER2 overexpression was an independent predictor of pCR in multivariate analysis. CONCLUSION: In conclusion, our gene expression signature allows prediction of pCR to PST containing G, E, and Doc with unprecedented high overall accuracy and robustness.

Adult↗
PubMed1997

Psychophysical signatures associated with magnocellular and parvocellular pathway contrast gain.

Physiological data have revealed characteristic contrast gain and temporal integration signatures of the magnocellular (MC) and the parvocellular (PC) pathways. The goal in this study was to find psychophysical correlates of these signatures. Psychophysical forced-choice, luminance pedestal discrimination data were collected with a stimulus-surround display. A 2.05 degrees four-square stimulus array was varied from 73 to 182 trolands (Td) in a larger 115-Td surround. When the stimulus array was pulsed briefly, discrimination thresholds showed a minimum at the surround retinal illuminance, increasing in a V shape when the stimulus array was incremental or decremental to the surround. When the stimulus array was presented continuously as a steady pedestal within the constant 115-Td surround, discrimination thresholds increased monotonically with stimulus array retinal illuminance, obeying a slope of unity. Exposure duration variation showed temporal summation to extend to longer durations for the pulse increments and decrements than for the steady pedestal condition. Discrimination thresholds for pulsed medium-sized contrast steps showed the contrast pedestal paradigm showed the temporal signature of the MC pathway. Discrimination thresholds for small pedestal steps of the stimulus array from a steady pedestal showed the contrast gain signature of the MC pathway. The data suggested a difference in the spatiotemporal control of adaptation of the two pathways: The MC pathway adapted locally to the stimulus array, while the PC pathways showed little evidence of local adaptation. The experiments show that characteristic signatures of MC- and PC-pathway processing can be demonstrated by use of psychophysical procedures.

Adaptation, Physiological↗
PubMedDate not supplied

A robust and accurate method for calculating the fractal signature of texture in macroradiographs of osteoarthritic knees.

In osteoarthritis of the knee, horizontal trabeculae in the tibia thicken, leading to the appearance of horizontal striations on radiographs. Any attempt to understand and monitor the disease process must examine these changes. We have previously described a method of analysing the texture in these images that uses the mathematical morphology operations of dilation and erosion to calculate how image fractal dimension varies with resolution. This variation with resolution is the fractal signature. Calculation of fractal dimension should be independent of linear transformations in image values, and it is shown that careful choice of morphological structuring element is required for this. In this paper we describe the dependence of our method of calculating the fractal signature on image acquisition and digitization parameters. Errors due to variations in pixel size, X-ray exposure, and patient repositioning are small compared to the changes seen in the signature due to osteoarthritic change. Using pairs of orthogonal structuring elements, one tuned to calculate the signature due to horizontal image structure and the other for vertical image structure, texture directionality is examined. The difference between the two resulting signatures in individual knees is shown to be a measure of the change in texture seen in osteoarthritis.

Algorithms↗
PubMed2004

Implementation framework for digital signatures for electronic data interchange in healthcare.

This paper aims to propose an action plan for the deployment of the use of digital signatures in Belgian healthcare. This action plan is the result of a number of technical, legal and organisational requirements. It starts by establishing the functional components that are needed to set up a framework for the deployment of digital signatures. The main components should implement an infrastructure for: --the creation of digital signatures; --the verification of digital signatures; --the certification of signature keys; --the certification of attributes; --the handling of revocation. The tasks in the action plan are the logical consequence of all the functions that need to be addressed. The objective of this report is to list what has to be done and how it can be done in the context of healthcare, rather to state who will perform the functions required.

Belgium↗
PubMedDate not supplied

Legibility of doctor's signatures: novel approaches to improving an age-old problem.

UNLABELLED: In today's medico-legal environment, the importance of identification of the authors of notes in patient medical charts cannot be overemphasized. We evaluated three different techniques of signing patient notes, over a one month period, in order to determine which technique was the most effective in identifying the author of the note. Surgical NCHDs in our hospital were divided into three groups. Group 1 was asked to sign the notes as they normally would. Group 2 was asked to print their name in block capitals after their signature and Group 3 was given pens with a personal self inking stamp to be used in addition to signing the notes. The number of signatures in all the charts, compliance with the assigned technique and the legibility of signatures were calculated. RESULTS: in Group 1, all NCHDs signed their name when writing notes (100% compliance), however the NCHD's signature was identified only 37% of the time. In Groups 2 (who signed in block capitals) and Group 3 (who used the pen with personalised stamp) the author was identifiable 100% of the time when the respective signing method was used. Using the pen with personalised self inking stamp was significantly more popular (77% compliance) compared to signing in block capitals (46% compliance). In conclusion the pen, with personalised self inking stamp, provides a fast and effective means to clarify signatures of NCHD's documentation, which is not only important in a day to day patient management, but is essential from a medico-legal stand point.

Handwriting↗
PubMed1996

Amino acid signatures in the primate retina.

Pattern recognition of amino acid signals partitions virtually all of the macaque retina into 16 separable biochemical theme classes, some further divisible by additional criteria. The photoreceptor-->bipolar cell-->ganglion cell pathway is composed of six separable theme classes, each possessing a characteristic glutamate signature. Neuronal aspartate and glutamine levels are always positively correlated with glutamate signals, implying that they largely represent glutamate precursor pools. Amacrine cells may be parsed into four glycine-dominated (including one glycine/GABA immunoreactive population) and four GABA-dominated populations. Horizontal cells in central retina possess a distinctive GABA signature, although their GABA content is constitutively lower than that of amacrine cells and shows both regional and sample variability. Finally, a taurine-glutamine signature defines Müller's cells. We thus have established the fundamental biochemical signatures of the primate retina along with multiple metabolic subtypes for each neurochemical class and demonstrated that virtually all neuronal space can be accounted for by cells bearing characteristic glutamate, GABA, or glycine signatures.

Amino Acids↗