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PubMed2005

Effect on survey response rate of hand written versus printed signature on a covering letter: randomised controlled trial [ISRCTN67566265].

BACKGROUND: It is important that response rates to postal surveys are as high as possible to ensure that the results are representative and to maximise statistical power. Previous research has suggested that any personalisation of approach helps to improve the response rate. This experiment tested whether personalising questionnaires by hand signing the covering letter improved the response rate compared with a non-personalised group where the investigator's signature on the covering letter was scanned into the document and printed. METHODS: Randomised controlled trial. Questionnaires about surgical techniques of caesarean section were mailed to 3,799 Members and Fellows of the Royal College of Obstetricians and Gynaecologists resident in the UK. Individuals were randomly allocated to receive a covering letter with either a computer printed signature or a hand written signature. Two reminders were sent to non-respondents. The outcome measures were the proportion of questionnaires returned and their time to return. RESULTS: The response rate was 79.1% (1506/1905) in the hand-signed group and 78.4% (1484/1894) in the scanned and printed signature group. There was no detectable difference between the groups in response rate or time taken to respond. CONCLUSION: No advantage was detected to hand signing the covering letter accompanying a postal questionnaire to health professionals.

Adult↗

PubMed2004

Identification of a three-gene expression signature of poor-prognosis breast carcinoma.

BACKGROUND: The clinical course of breast cancer is difficult to predict on the basis of established clinical and pathological prognostic criteria. Given the genetic complexity of breast carcinomas, it is not surprising that correlations with individual genetic abnormalities have also been disappointing. The use of gene expression profiles could result in more accurate and objective prognostication. RESULTS: To this end, we used real-time quantitative RT-PCR assays to quantify the mRNA expression of a large panel (n = 47) of genes previously identified as candidate prognostic molecular markers in a series of 100 ERalpha-positive breast tumor samples from patients with known long-term follow-up. We identified a three-gene expression signature (BRCA2, DNMT3B and CCNE1) as an independent prognostic marker (P = 0.007 by univariate analysis; P = 0.006 by multivariate analysis). This "poor prognosis" signature was then tested on an independent panel of ERalpha-positive breast tumors from a well-defined cohort of 104 postmenopausal breast cancer patients treated with primary surgery followed by adjuvant tamoxifen alone: although this "poor prognosis" signature was associated with shorter relapse-free survival in univariate analysis (P = 0.029), it did not persist as an independent prognostic factor in multivariate analysis (P = 0.27). CONCLUSION: Our results confirm the value of gene expression signatures in predicting the outcome of breast cancer.

Adult↗

PubMed2006

Identification of tumor-specific molecular signatures in intracranial ependymoma and association with clinical characteristics.

PURPOSE: To delineate clinically relevant molecular signatures of intracranial ependymoma. MATERIALS AND METHODS: We analyzed 24 primary intracranial ependymomas. For genomic profiling, microarray-based comparative genomic hybridization (CGH) was used and results were validated by fluorescent in situ hybridization and loss of heterozygosity mapping. We performed gene expression profiling using microarrays, real-time quantitative reverse transcriptase polymerase chain reaction, and methylation analysis of selected genes. We applied class comparison analyses to compare both genomic and expression profiling data with clinical characteristics. RESULTS: A variable number of genomic imbalances were detected by array CGH, revealing multiple regions of recurrent gain (including 2q23, 7p21, 12p, 13q21.1, and 20p12) and loss (including 5q31, 6q26, 7q36, 15q21.1, 16q24, 17p13.3, 19p13.2, and 22q13.3). An ependymoma-specific gene expression signature was characterized by the concurrent abnormal expression of developmental and differentiation pathways, including NOTCH and sonic hedgehog signaling. We identified specific differentially imbalanced genomic clones and gene expression signatures significantly associated with tumor location, patient age at disease onset, and retrospective risk for relapse. Integrated genomic and expression profiling allowed us to identify genes of which the expression is deregulated in intracranial ependymoma, such as overexpression of the putative proto-oncogene YAP1 (located at 11q22) and downregulation of the SULT4A1 gene (at 22q13.3). CONCLUSION: The present exploratory molecular profiling study allowed us to refine previously reported intervals of genomic imbalance, to identify novel restricted regions of gain and loss, and to identify molecular signatures correlating with various clinical variables. Validation of these results on independent data sets represents the next step before translation into the clinical setting.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Content-based searching of multimedia databases by use of approximate digital signatures.

We propose the use of approximate digital signatures of selected multimedia feature vectors for fast content-based retrieval in large multimedia databases. We adapt and extend the approximate message authentication code (AMAC), introduced by some of the authors recently in the area of message authentication, to the multimedia searching problem. An AMAC is a binary signature with the ability to reflect changes in the message it represents. The Hamming distance between two AMACs is used to measure the degree of the similarity between multimedia objects. We develop a method to compress AMAC signatures to create a direct look-up table that allows for fast searching of a database. The color histogram is used as the example feature space to show how the signature is applied. Experimental results show that the performance of the proposed method is comparable with existing methods based on other popular metrics, but it significantly decreases search time.

Journal Article↗

PubMed2004

Thermal signature characteristics of vehicle/terrain interaction disturbances: implications for battlefield vehicle classification.

Thermal emissivity spectra (8-14 microm) of track impressions/background were determined in conjunction with operation of six military vehicle types, T-72 and M1 Tanks, an M2 Bradley Fighting Vehicle, a 5-ton truck, a D7 tractor, and a High Mobility Multipurpose Wheeled Vehicle (HMMWV), over diverse soil surfaces to determine if vehicle type could be related to track thermal signatures. Results suggest soil compaction and fragmentation/pulverization are primary parameters affecting track signatures and that soil and vehicle/terrain-contact type determine which parameter dominates. Steel-tracked vehicles exert relatively low ground-contact pressure but tend to fragment/pulverize soil more so than do rubber-tired vehicles, which tend mainly to compact. In quartz-rich, lean clay soil tracked vehicles produced impressions with spectral contrast of the quartz reststrahlen features decreased from that of the background. At the same time, 5-ton truck tracks exhibited increased contrast on the same surface, suggesting that steel tracks fragmented soil while rubber tires mainly produced compaction. The structure of materials such as sand and moist clay-rich river sediment makes them less subject to further fragmentation/pulverization; thus, compaction was the main factor affecting signatures in these media, and both tracked and wheeled vehicles created impressions with increased spectral contrast on these surfaces. These results suggest that remotely sensed thermal signatures could differentiate tracked and wheeled vehicles on terrain in many areas of the world of strategic interest. Significant applications include distinguishing visually/spectrally identical lightweight decoys from actual threat vehicles.

Journal Article↗

PubMed2025

Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom.

Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Silencing mechanisms targeting TEs at the epigenetic or transcript level have independently evolved in many lineages. In fungi, repeat-induced point mutation (RIP) targets TEs by recognizing repetitive sequences and inducing mutagenesis. However, the prevalence of RIP across the fungal kingdom and the fidelity of the canonical C-to-T mutation signatures remain unclear. In this study, we address these gaps by tracking shifts in genome architecture across the fungal kingdom. We find that a striking approximately 30-fold increase in genome size within a clade of leotiomycetes is associated with the absence of several RIP-related genes, suggesting a relaxation of genome defense mechanisms during this expansion. To track the impact of genome defenses, we designed a quantitative screen for RIP-like mutation signatures. The phylum of ascomycetes was unique in showing enrichment in mutation signatures in non-coding and repetitive sequences, consistent with a phylogenetically restricted occurrence of RIP-like genome defense systems. Then, we performed a phylogeny-aware association study to identify gene functions associated with RIP-like mutation signatures. We identified a zinc-finger protein as the strongest candidate underpinning a novel mechanism of genome defenses. Our findings reveal the multifaceted drivers of genome defense systems and their close ties to genome size evolution in fungi, particularly in lineages with evidence for recent RIP activity, highlighting how proximate molecular mechanisms can shape genome evolution on deep phylogenetic scales.

Genome, Fungal↗

PubMed2006

A gene expression signature predicts survival of patients with stage I non-small cell lung cancer.

BACKGROUND: Lung cancer is the leading cause of cancer-related death in the United States. Nearly 50% of patients with stages I and II non-small cell lung cancer (NSCLC) will die from recurrent disease despite surgical resection. No reliable clinical or molecular predictors are currently available for identifying those at high risk for developing recurrent disease. As a consequence, it is not possible to select those high-risk patients for more aggressive therapies and assign less aggressive treatments to patients at low risk for recurrence. METHODS AND FINDINGS: In this study, we applied a meta-analysis of datasets from seven different microarray studies on NSCLC for differentially expressed genes related to survival time (under 2 y and over 5 y). A consensus set of 4,905 genes from these studies was selected, and systematic bias adjustment in the datasets was performed by distance-weighted discrimination (DWD). We identified a gene expression signature consisting of 64 genes that is highly predictive of which stage I lung cancer patients may benefit from more aggressive therapy. Kaplan-Meier analysis of the overall survival of stage I NSCLC patients with the 64-gene expression signature demonstrated that the high- and low-risk groups are significantly different in their overall survival. Of the 64 genes, 11 are related to cancer metastasis (APC, CDH8, IL8RB, LY6D, PCDHGA12, DSP, NID, ENPP2, CCR2, CASP8, and CASP10) and eight are involved in apoptosis (CASP8, CASP10, PIK3R1, BCL2, SON, INHA, PSEN1, and BIK). CONCLUSIONS: Our results indicate that gene expression signatures from several datasets can be reconciled. The resulting signature is useful in predicting survival of stage I NSCLC and might be useful in informing treatment decisions.

Algorithms↗

PubMed2024

Genome-wide scan for selection signatures in Mexican Sardo Negro Zebu cattle.

The Sardo Negro cattle (SN) is the only zebu cattle breed developed in Mexico. Since its development, the selection could have led to an increase in the homozygosity level in some regions of the genome and made differentiation with other cattle populations. We aimed to identify and characterize selection signatures in SN using medium-density SNP data using four approaches: 1) Runs of homozygosity (ROH) 2) Nucleotide Diversity 3) Tajima's D and 4) the Wright's fixation index (FST). A sample of 555 SN animals genotyped for 65k SNPs was used to obtain ROH segments considered regions under selection. The FST values were estimated by comparing the sample of genotyped SN animals with samples of genotyped animals from the Gir, Brahman, and Ongole breeds. Only one region mapped to 35.78-42.51 Mb on BTA6 was considered a selection signature by the ROH method. This selection signature overlapped with the lowest diversity, negative values of Tajima's D and a diversification region between SN and the other Zebu breeds by FST. We found several candidate genes (LCORL, NCAPG, and SLIT2) related to growth and other economically important productive traits in this common region. Using the FST method, different regions, such as regions on BTA8 (8:93.4-93.9 Mb), BTA11 (11:99.2-99.7), and BTA14 (14: 26.1-26.8) related to growth and milk traits also were defined as candidate selection signatures. The selective signals identified in this study reflected the direction of the selection pressure that primarily involves the increase of live weight traits in the Sardo Negro cattle breeding program.

Animals↗

PubMed2025

Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.

Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have a close interrelationship with intestinal microbiota. Recently, we have utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenome sequencing. The gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (P < 0.001). No differences in the microbial composition were observed between midgut NET patients with and without CS (P > 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsiella, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristics (AUROC) curve 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). Thus, this study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.

Aged↗

PubMed2026

Identification of a novel signature for prognostic stratification and integrative analyses in lung adenocarcinoma.

BACKGROUND: Recently, research has revealed that the Golgi apparatus is involved in the development process of cancer; however, the specific effect of Golgi apparatus-related genes (GAGs) in lung adenocarcinoma (LUAD) remains unclear. This study aims to construct a more concise and practical risk model in LUAD using GAG. METHODS: The gene expression profiles of patients with LUAD were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and GAGs were downloaded from the Gene Set Enrichment Analysis (GSEA) database. Univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses were performed to identify the prognostic GAG signature. Kaplan-Meier and receiver operating characteristic (ROC) curves were plotted to validate the predictive effect of the prognostic signatures. The correlation between the risk model and the immune landscape was examined using CIBERSORT and TIDE analyses. Also, the genes in the signature were assessed by single-cell RNA sequencing (scRNA-seq). RESULTS: A prognostic signature comprising 5 GAG genes (GNPNAT1, RGS20, CAV3, NTSR1, and FURIN) was established after LASSO and multi-Cox analyses. Both the Kaplan-Meier analysis and the ROC curves supported the strong predictive utility of the risk model. Specifically, the former yielded significant stratification in all three validation datasets (P=1.2001e-05, P=0.006, and P=0.04), while the latter provided further evidence of its predictive precision through the area under the curve. In addition, we found that the low-risk group responded better to immunotherapy than the high-risk group (P<0.0001). scRNA-seq analysis revealed the distribution patterns of the 5 GAG genes in cells. Finally, we assessed the situation of tumor mutation burden (TMB) and performed functional analysis based on the risk model of GAGs. CONCLUSIONS: The risk model based on GAGs can effectively stratify the prognosis of patients and predict immunotherapy responses in LUAD.

Golgi apparatus↗

PubMed1977

Effects of self-esteem and status on size of signature.

142 second year university students from both Memorial University of Newfoundland (n = 81) and Laurentian University (n = 61) wrote their own signatures as they imagined the following people would do: (a) faculty member (high status) with high self-esteem, (b) faculty member (high status) with low self-esteem, (c) student (low status) with high self-esteem, and (d) student (low status) with low self-esteem. The areas of the signatures were calculated in square centimeters, and there was a significant positive relationship between size of signature and the conditions of high and low self-esteem for both "faculty" and "student" role-playing conditions. There was however no significant relationship between size of signature and status. The results held for both groups of subjects.

Faculty↗

PubMed1995

Electronic signature thrives in different environments.

Implementing electronic signature has been a positive experience for both our organizations. The benefits we sought were there, and unforeseen benefits surfaced. Five activities that facilitated the success of electronic signature at our two facilities were (1) flowcharting the electronic signature process prior to purchase and installation; (2) becoming familiar with legal requirements for electronic signature, and assuring that products under consideration meet these requirements; (3) gaining the support of medical staff leadership; (4) using a written agreement of password confidentiality and document responsibility with physicians; and (5) thoroughly training medical records staff, then establishing a positive one-on-one training procedure for physicians with a high degree of staff attention.

Authorship↗

PubMed1999

Differential signatures of bacterial and mammalian IMP dehydrogenase enzymes.

IMP dehydrogenase (IMPDH) is an essential enzyme of de novo guanine nucleotide synthesis. IMPDH inhibitors have clinical utility as antiviral, anticancer or immunosuppressive agents. The essential nature of this enzyme suggests its therapeutic applications may be extended to the development of antimicrobial agents. Bacterial IMPDH enzymes show biochemical and kinetic characteristics that are different than the mammalian IMPDH enzymes, suggesting IMPDH may be an attractive target for the development of antimicrobial agents. We suggest that the biochemical and kinetic differences between bacterial and mammalian enzymes are a consequence of the variance of specific, identifiable amino acid residues. Identification of these residues or combination of residues that impart this mammalian or bacterial enzyme signature is a prerequisite for the rational identification of agents that specifically target the bacterial enzyme. We used sequence alignments of IMPDH proteins to identify sequence signatures associated with bacterial or eukaryotic IMPDH enzymes. These selections were further refined to discern those likely to have a role in catalysis using information derived from the bacterial and mammalian IMPDH crystal structures and site-specific mutagenesis. Candidate bacterial sequence signatures identified by this process include regions involved in subunit interactions, the active site flap and the NAD binding region. Analysis of sequence alignments in these regions indicates a pattern of catalytic residues conserved in all enzymes and a secondary pattern of amino acid conservation associated with the major phylogenetic groups. Elucidation of the basis for this mammalian/bacterial IMPDH signature will provide insight into the catalytic mechanism of this enzyme and the foundation for the development of highly specific inhibitors.

Amino Acid Sequence↗

PubMed2003

The molecular signature of mantle cell lymphoma reveals multiple signals favoring cell survival.

Mantle cell lymphoma (MCL) is a prototypical neoplastic disease in which a common cytogenetic alteration, t11;14, leading to cyclin D1 overexpression, is associated with other changes that need to be considered in an explanation of the clinical, morphological, and molecular variability of this disease. Using a cDNA microarray (Oncochip-CNIO) containing clones for 6386 cancer-related genes, we have analyzed the expression profiles of a series of 38 cases. After normalization with the expression profiling of sorted mantle zone lymphocytes, we have related the findings to conventional clinical and molecular variables, including immunoglobulin variable heavy chain somatic mutation, blastoid cytology, increased proliferation, and long-term survival. MCL signature (446 genes) includes genes involved in apoptosis, cell cycle, signal transduction, and cell structure. Especially striking was the presence of multiple concurrent alterations in the tumor necrosis factor and nuclear factor kappaB pathway, and the overexpression of IL10R and SPARC genes. We also identified a molecular signature for the presence of immunoglobulin variable heavy chain somatic mutation, which includes a number of genes potentially relevant in cancer (CDC14A, ras, and others). Signatures for proliferation and blastoid cytology were also found. An integrated analysis of these data yields a gene-expression based survival predictor (26 genes grouped into two clusters), which distinguishes half of the patients with a survival probability of 52% at 5 years. The predictive model has been confirmed by cross-validation. In conclusion, MCL seems to combine a disease-specific signature and different sets of genes of which the expression is associated with key clinical, molecular, and immunophenotypical events.

Adult↗

PubMed2006

River capture, range expansion, and cladogenesis: the genetic signature of freshwater vicariance.

River capture is potentially a key geomorphological driver of range expansion and cladogenesis in freshwater-limited taxa. While previous studies of freshwater fish, in particular, have indicated strong relationships between historical river connections and phylogeographic pattern, their analyses have been restricted to single taxa and geological hypotheses were typically constructed a posteriori. Here we assess the broader significance of river capture among taxa by testing multiple species for the genetic signature of a recent river capture event in New Zealand. During the Quaternary an upper tributary of the Clarence River system was diverted into the headwaters of the Wairau River catchment. Mitochondrial DNA (control region and cytochrome b) sequencing of two native galaxiid fishes (Galaxias vulgaris and Galaxias divergens) supports headwater exchange: populations from the Clarence and Wairau Rivers are closely related sister-groups, whereas samples from the geographically intermediate Awatere River are genetically divergent. The upland bully Gobiomorphus breviceps (Eleotridae), in contrast, lacks a genetic signature of the capture event. We hypothesize that there is an increased likelihood of observing genetic signatures from river capture events when they facilitate range expansion, as is inferred for the two galaxiid taxa studied here. When river capture merely translocates genetic lineages among established populations, by contrast, we suggest that the genetic signature of capture is less likely to be retained, as might be inferred for G. breviceps. Rates of molecular evolution calibrated against this recent event were elevated relative to traditional estimates, consistent with the contribution of polymorphisms to branch lengths at shallow phylogenetic levels prior to fixation by purifying selection and drift.

Animals↗

PubMedDate not supplied

Visual receptive fields of cat cortical neurons lack the distinctive geniculate Y cell signature.

Retinal ganglion and lateral geniculate cells of the primary visual pathway may be categorized as X or Y according to their spatial linearity summation properties. In particular, Y cell spatial-frequency transfer functions have a distinctive spatial--linearity signature. Their receptive fields comprise a temporally and spatially linear mechanism (center plus antagonistic surround) that responds to relatively low spatial frequency stimuli, and a temporally nonlinear mechanism, coextensive with the linear mechanism, that--though broad in extent--responds best to high spatial-frequency stimuli. This component exhibits spatially nonlinear properties. We looked for this Y cell signature in cat visual cortical cells. If the predominant excitatory input to a certain type of cortical cell were from lateral geniculate nucleus (LGN) Y cells, we would expect to find the Y cell signature underlying the cortical cell transfer function. However, we have not found this Y cell signature in any of the cortical cell studied, and in particular not in the nonlinear complex cells. This would suggest that cortical spatial summation nonlinearities are not functionally derived from input Y cell nonlinearities.

Animals↗

PubMed1996

Kinetoplast DNA signatures of Trypanosoma cruzi strains obtained directly from infected tissues.

We report here a polymerase chain reaction (PCR)-based DNA profiling technique that permits Trypanosoma cruzi strain characterization by direct study of infected tissues. This is based on application of a recently developed method of DNA fragment identification, called low-stringency single specific primer PCR (LSSP-PCR), to the study of the variable region of kinetoplast DNA (kDNA) minicircles from T. cruzi Thus, we can translate the intraspecific polymorphism in the nucleotide sequence of kDNA minicircles into a specific and highly reproducible kDNA signature. Comparison with the phenogram obtained by DNA fingerprinting analysis of a set of T. cruzi strains showed good qualitative correlation between the degree of divergence of the LSSP-PCR profiles and the genetic distance between the strains. kDNA signatures of heart tissue from acutely or chronically infected animals revealed perfect concordance with the patterns obtained from cultured parasites for the CL and Colombiana strains but not for the Y strain, which is known to be multiclonal. However, the match was perfect for studies with two clones of the Y strain. We take this as evidence that in some multiclonal strains there is heterogeneity among the clones in the degree of tropism for the heart tissue. Finally, we showed that it is possible to obtain a T. cruzi kDNA signature from the heart of a human patient with chronic Chagasic myocardiopathy. kDNA signatures obtained by LSSP-PCR of sequences amplified from infected tissues constitute a new tool to study the molecular epidemiology of Chagas' disease.

Animals↗

PubMed2026

Integrated Genome-Wide Association Studies and Selection Signature Analysis Reveal the Genetic Architecture of the Wattle Trait in Goats.

Wattles are finger-like appendages on the ventral neck of goats, serving as a distinctive morphological marker for breed identification that serves potential implications for production performance. However, their genetic basis remains incompletely characterized. Here, we integrated a genome-wide association study (GWAS) and selection signature analysis to identify candidate genes and genomic regions associated with the wattle trait in goats. Using a linear mixed model, GWAS on 463 goats (23 wattled and 440 non-wattled) identified 385 quantitative trait loci (QTLs) at a 5% false discovery rate, yielding 346 candidate genes. The most significant association signal was observed on chromosome 10 (72.61-73.48 Mb), where the lead SNP (rs636481767) is located within a region containing GJD2, GREM1, and FMN1, showing strong linkage disequilibrium (r2 > 0.6) with surrounding loci. Subsequent selection signature analysis (23 wattled and 23 non-wattled) identified 83 genomic regions harboring 119 candidate genes. The strongest signals were detected at MFSD14B on chromosome 8 (FST = 0.154, log2π-ratio = 2.611) and PDLIM7 on chromosome 7 (FST = 0.144, log2π-ratio = 0.806). KEGG pathway enrichment analysis revealed that GWAS-associated genes were involved in glycosylation and immune responses, whereas selection-signature genes were enriched in DNA repair and the Hippo, Notch, and Wnt pathways. Furthermore, cross-species PheWAS revealed that human FMN1 is associated with dermatological, skeletal, and metabolic phenotypes, while porcine FMN1 is associated with backfat thickness and loin muscle depth. Overall, this study provides molecular markers of potential value for goat breeding and pinpoints key candidate genes for future functional validation of wattle development.

Animals↗