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PubMed2006

Shot-noise signatures of 0.7 structure and spin in a quantum point contact.

We report simultaneous measurement of shot noise and dc transport in a quantum point contact as a function of source-drain bias, gate voltage, and in-plane magnetic field. Shot noise at zero field exhibits an asymmetry related to the 0.7 structure in conductance. The asymmetry in noise evolves smoothly into the symmetric signature of spin-resolved electron transmission at high field. Comparison to a phenomenological model with density-dependent level splitting yields good quantitative agreement.

Journal Article↗
PubMed2006

Signatures of the Unruh effect from electrons accelerated by ultrastrong laser fields.

We calculate the radiation resulting from the Unruh effect for strongly accelerated electrons and show that the photons are created in pairs whose polarizations are perfectly correlated. Apart from the photon statistics, this quantum radiation can further be discriminated from the classical (Larmor) radiation via the different spectral and angular distributions. The signatures of the Unruh effect become significant if the external electromagnetic field accelerating the electrons is not too far below the Schwinger limit and might be observable with future facilities. Finally, the corrections due to the birefringent nature of the QED vacuum at such ultrahigh fields are discussed.

Journal Article↗
PubMed2005

Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts.

Improved knowledge of the sorghum transcriptome will enhance basic understanding of how plants respond to stresses and serve as a source of genes of value to agriculture. Toward this goal, Sorghum bicolor L. Moench cDNA libraries were prepared from light- and dark-grown seedlings, drought-stressed plants, Colletotrichum-infected seedlings and plants, ovaries, embryos, and immature panicles. Other libraries were prepared with meristems from Sorghum propinquum (Kunth) Hitchc. that had been photoperiodically induced to flower, and with rhizomes from S. propinquum and johnsongrass (Sorghum halepense L. Pers.). A total of 117,682 expressed sequence tags (ESTs) were obtained representing both 3' and 5' sequences from about half that number of cDNA clones. A total of 16,801 unique transcripts, representing tentative UniScripts (TUs), were identified from 55,783 3' ESTs. Of these TUs, 9,032 are represented by two or more ESTs. Collectively, these libraries were predicted to contain a total of approximately 31,000 TUs. Individual libraries, however, were predicted to contain no more than about 6,000 to 9,000, with the exception of light-grown seedlings, which yielded an estimate of close to 13,000. In addition, each library exhibits about the same level of complexity with respect to both the number of TUs preferentially expressed in that library and the frequency with which two or more ESTs is found in only that library. These results indicate that the sorghum genome is expressed in highly selective fashion in the individual organs and in response to the environmental conditions surveyed here. Close to 2,000 differentially expressed TUs were identified among the cDNA libraries examined, of which 775 were differentially expressed at a confidence level of 98%. From these 775 TUs, signature genes were identified defining drought, Colletotrichum infection, skotomorphogenesis (etiolation), ovary, immature panicle, and embryo.

DNA, Complementary↗
PubMed1996

Cold calcium signaling in Arabidopsis involves two cellular pools and a change in calcium signature after acclimation.

Cold shock elicits an immediate rise in cytosolic free calcium concentration ([Ca2+]cyt) in both chilling-resistant Arabidopsis and chilling-sensitive tobacco (Nicotiana plumbaginifolia). In Arabidopsis, lanthanum or EGTA caused a partial inhibition of both cold shock [Ca2+]cyt elevation and cold-dependent kin1 gene expression. This suggested that calcium influx plays a major role in the cold shock [Ca2+]cyt response and that an intracellular calcium source also might be involved. To investigate whether the vacuole (the major intracellular calcium store in plants) is involved, we targeted the calcium-dependent photoprotein aequorin to the cytosolic face of the vacuolar membrane. Cold shock calcium kinetics in this microdomain were consistent with a cold-induced vacuolar release of calcium. Treatment with neomycin or lithium, which interferes with phosphoinositide cycling, resulted in cold shock [Ca2+]cyt kinetics consistent with the involvement of inositol trisphosphate and inositide phosphate signaling in this response. We also investigated the effects of repeated and prolonged low temperature on cold shock [Ca2+]cyt. Differences were observed between the responses of Arabidopsis and N. plum-baginifolia to repeated cold stimulation. Acclimation of Arabidopsis by pretreatment with cold or hydrogen peroxide caused a modified calcium signature to subsequent cold shock. This suggests that acclimation involves modification of plant calcium signaling to provide a "cold memory."

Acclimatization↗
PubMed2006

Velocity-image model for online signature verification.

In general, online signature capturing devices provide outputs in the form of shape and velocity signals. In the past, strokes have been extracted while tracking velocity signal minimas. However, the resulting strokes are larger and complicated in shape and thus make the subsequent job of generating a discriminative template difficult. We propose a new stroke-based algorithm that splits velocity signal into various bands. Based on these bands, strokes are extracted which are smaller and more simpler in nature. Training of our proposed system revealed that low- and high-velocity bands of the signal are unstable, whereas the medium-velocity band can be used for discrimination purposes. Euclidean distances of strokes extracted on the basis of medium velocity band are used for verification purpose. The experiments conducted show improvement in discriminative capability of the proposed stroke-based system.

Algorithms↗
PubMed2006

Adaptive AR and neurofuzzy approaches: access to cerebral particle signatures.

In recent years, a relationship has been suggested between the occurrence of cerebral embolism and stroke. Ultrasound has therefore become essential in the detection of emboli when monitoring cerebral vascular disorders and forms part of ultrasound brain-imaging techniques. Such detection is based on investigating the middle cerebral artery using a TransCranial Doppler (TCD) system, and analyzing the Doppler signal of the embolism. Most of the emboli detected in practical experiments are large emboli because their signatures are easy to recognize in the TCD signal. However, detection of small emboli remains a challenge. Various approaches have been proposed to solve the problem, ranging from the exclusive use of expert human knowledge to automated collection of signal parameters. Many studies have recently been performed using time-frequency distributions and classical parameter modeling for automatic detection of emboli. It has been shown that autoregressive (AR) modeling associated with an abrupt change detection technique is one of the best methods for detection of microemboli. One alternative to this is a technique based on taking expert knowledge into account. This paper aims to unite these two approaches using AR modeling and expert knowledge through a neurofuzzy approach. The originality of this approach lies in combining these two techniques and then proposing a parameter referred to as score ranging from 0 to 1. Unlike classical techniques, this score is not only a measure of confidence of detection but also a tool enabling the final detection of the presence or absence of microemboli to be performed by the practitioner. Finally, this paper provides performance evaluation and comparison with an automated technique, i.e., AR modeling used in vitro.

Algorithms↗
PubMed2004

Determining correspondence in 3-D MR brain images using attribute vectors as morphological signatures of voxels.

Finding point correspondence in anatomical images is a key step in shape analysis and deformable registration. This paper proposes an automatic correspondence detection algorithm for intramodality MR brain images of different subjects using wavelet-based attribute vectors (WAVs) defined on every image voxel. The attribute vector (AV) is extracted from the wavelet subimages and reflects the image structure in a large neighborhood around the respective voxel in a multiscale fashion. It plays the role of a morphological signature for each voxel, and our goal is, therefore, to make it distinctive of the respective voxel. Correspondence is then determined from similarities of AVs. By incorporating the prior knowledge of the spatial relationship among voxels, the ability of the proposed algorithm to find anatomical correspondence is further improved. Experiments with MR images of human brains show that the algorithm performs similarly to experts, even for complex cortical structures.

Aged↗
PubMed2006

Rapid object indexing using locality sensitive hashing and joint 3D-signature space estimation.

We propose a new method for rapid 3D object indexing that combines feature-based methods with coarse alignment-based matching techniques. Our approach achieves a sublinear complexity on the number of models, maintaining at the same time a high degree of performance for real 3D sensed data that is acquired in largely uncontrolled settings. The key component of our method is to first index surface descriptors computed at salient locations from the scene into the whole model database using the Locality Sensitive Hashing (LSH), a probabilistic approximate nearest neighbor method. Progressively complex geometric constraints are subsequently enforced to further prune the initial candidates and eliminate false correspondences due to inaccuracies in the surface descriptors and the errors of the LSH algorithm. The indexed models are selected based on the MAP rule using posterior probability of the models estimated in the joint 3D-signature space. Experiments with real 3D data employing a large database of vehicles, most of them very similar in shape, containing 1,000,000 features from more than 365 models demonstrate a high degree of performance in the presence of occlusion and obscuration, unmodeled vehicle interiors and part articulations, with an average processing time between 50 and 100 seconds per query.

Algorithms↗
PubMed2006

Symbolic signatures for deformable shapes.

Recognizing classes of objects from their shape is an unsolved problem in machine vision that entails the ability of a computer system to represent and generalize complex geometrical information on the basis of a finite amount of prior data. A practical approach to this problem is particularly difficult to implement, not only because the shape variability of relevant object classes is generally large, but also because standard sensing devices used to capture the real world only provide a partial view of a scene, so there is partial information pertaining to the objects of interest. In this work, we develop an algorithmic framework for recognizing classes of deformable shapes from range data. The basic idea of our component-based approach is to generalize existing surface representations that have proven effective in recognizing specific 3D objects to the problem of object classes using our newly introduced symbolic-signature representation that is robust to deformations, as opposed to a numeric representation that is often tied to a specific shape. Based on this approach, we present a system that is capable of recognizing and classifying a variety of object shape classes from range data. We demonstrate our system in a series of large-scale experiments that were motivated by specific applications in scene analysis and medical diagnosis.

Algorithms↗
PubMed2007

Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.

Lysosomal DNase IIalpha is essential for DNA waste removal and auxiliary apoptotic DNA fragmentation in higher eukaryotes. Despite the key role of this enzyme, little is known about its structure-function relationships. Here, mutational and biochemical analyses were used to characterize human DNase IIalpha variants expressed in mammalian cells. The resulting data strongly support the hypothesis that the enzyme is a monomeric phospholipase D-family member with a pseudodimeric protein fold. According to our results, DNase IIalpha contains two requisite PLD-signature motifs ((113)HTK(115) and (295)HSK(297)) in the N- and C-terminal subdomains, respectively, that together form a single active site. Based on these data, we present an experimentally validated structural model of DNase IIalpha.

Amino Acid Motifs↗
PubMed2026

Molecular Signature of Prediabetes With High-Risk of Diabetes Revealed by Deep Plasma Proteome.

AIMS: Prediabetes is biologically heterogeneous, but molecular subtypes linked to diabetes progression remain poorly defined. We aimed to identify plasma proteome-based subtypes of impaired fasting glucose (IFG), characterise their molecular features and assess their association with future diabetes risk. MATERIALS AND METHODS: We quantified 2584 plasma proteins using liquid chromatography-mass spectrometry in 538 IFG participants from a prospective discovery cohort (Nutrition and Health of Aging Population in China, NHAPC). Proteomic subtypes were defined by consensus clustering, linked to longitudinal changes in insulin sensitivity and incident type 2 diabetes mellitus (T2DM), which were further validated in an independent Shanghai Brain Aging Study (SBAS) cohort. RESULTS: Two reproducible IFG molecular subtypes based on plasma proteomics were identified. The high-risk subtype showed higher incident diabetes and a greater 6-year decline in insulin sensitivity and was characterised by enrichment of glycolysis/gluconeogenesis, insulin signalling and neutrophil degranulation, together with a dyslipidemic lipidomic profile indicating co-dysregulation of glucose and lipid homeostasis. The low-risk subtype demonstrated a higher complement cascade and high-density lipoprotein particle remodelling signature. In the high-risk subtype, key proteins and lipids showed stronger associations with longitudinal declines in insulin sensitivity, including PPBP, PGK1 and ALDOA, as well as PE-P 18:0/20:3 and PE-P 18:1/20:3. CONCLUSIONS: Proteome-based molecular subtyping stratifies IFG individuals with similar fasting glucose levels but distinct biology and future diabetes risk, supporting earlier and more targeted prevention.

Humans↗
PubMed2004

Bayesian variable selection in multinomial probit models to identify molecular signatures of disease stage.

Here we focus on discrimination problems where the number of predictors substantially exceeds the sample size and we propose a Bayesian variable selection approach to multinomial probit models. Our method makes use of mixture priors and Markov chain Monte Carlo techniques to select sets of variables that differ among the classes. We apply our methodology to a problem in functional genomics using gene expression profiling data. The aim of the analysis is to identify molecular signatures that characterize two different stages of rheumatoid arthritis.

Arthritis, Rheumatoid↗
PubMed2006

Functional signatures of protective antiviral T-cell immunity in human virus infections.

The most common human viruses have different abilities to establish persistent chronic infection. Virus-specific T-cell responses are critical in the control of virus replication and in the prevention of disease in chronic infection. A large number of phenotypic markers and a series of functions have been used to characterize virus-specific CD4+ and CD8+ T-cell responses, and these studies have shown great phenotypic and functional heterogeneity of the T-cell responses against different viruses. The heterogeneity of the T-cell response has been proposed to be specific to each virus. However, over the past 2 years, several studies have provided evidence that the phenotypic and functional heterogeneity of CD4+ and CD8+ T-cell responses is predominantly regulated by the levels of antigen load. The levels of antigen load modulate the phenotypic and functional patterns of the T-cell response within the same virus infection. Furthermore, the functional characterization of virus-specific CD4+ and CD8+ T-cell responses has identified signatures of protective antiviral immunity. Polyfunctional, i.e. interleukin-2 and interferon-gamma (IFN-gamma) secretion and proliferation, and not monofunctional, i.e. IFN-gamma secretion, CD4+ and CD8+ T-cell responses represent correlates of protective antiviral immunity in chronic virus infections.

Acute Disease↗
PubMed2006

Genome-wide transcriptional profiling in human squamous cell carcinoma of the skin identifies unique tumor-associated signatures.

The elucidation of specific genetic changes associated with human cancer pathogenesis has focused efforts to relate such changes to the neoplastic phenotype. To further our understanding of the genetic basis of human squamous cell carcinoma (SCC) of the skin, this study used a genome-wide (12 627 sequences) approach to determine transcriptional signatures in lesional and nonlesional sites from five SCC patients. Several novel genes involving the p53 pathway, anti-apoptotic pathways, signal transduction, structural loss and DNA replication, including BCL2A1, MUC4, PTPN11 (SHP2) and FGF9, are upregulated in SCC and could warrant further study regarding their role in disease pathogenesis. SCC pathology is likely combinatorial in nature involving the compounded changes from several cellular processes.

Aged↗
PubMed1994

Bacterial binding protein-dependent permeases: characterization of distinctive signatures for functionally related integral cytoplasmic membrane proteins.

Bacterial binding protein-dependent transport systems belong to the superfamily of ABC transporters, which is widely distributed among living organisms. Their hydrophobic membrane proteins are the least characterized components. The primary structures of 61 integral membrane proteins from 35 uptake systems were compared in order to characterize a short conserved hydrophilic segment, with a consensus EAA---G---------I-LP, located approximately 100 residues from the C-terminus. Secondary structure predictions indicated that this conserved region might be formed by two amphipathic alpha-helices connected by a loop containing the invariant G residue. We classified the conserved motifs and found that membrane proteins from systems transporting structurally related substrates specifically display a greater number of identical residues in the conserved region. We determined a consensus for each class of membrane protein and showed that these can be considered as signatures.

ATP-Binding Cassette Transporters↗
PubMed2004

Characterization of C-terminal domains of Arabidopsis heat stress transcription factors (Hsfs) and identification of a new signature combination of plant class A Hsfs with AHA and NES motifs essential for activator function and intracellular localization.

Heat stress transcription factors (Hsfs) are the major regulators of the plant heat stress (hs) response. Sequencing of the Arabidopsis genome revealed the existence of 21 open-reading frames (ORFs) encoding putative Hsfs assigned to classes A-C. Here we present results of a functional genomics approach to the Arabidopsis Hsf family focused on the analysis of their C-terminal domains (CTDs) harboring conserved modules for their function as transcription factors and their intracellular localization. Using reporter assays in tobacco protoplasts and yeast as well as glutathione-S-transferase (GST) pull-down assays, we demonstrate that short peptide motifs enriched with aromatic and large hydrophobic amino acid (aa) residues embedded in an acidic surrounding (AHA motifs) are essential for transcriptional activity of class A Hsfs. In contrast to this, class B and C Hsfs lack AHA motifs and have no activator function on their own. We also provide evidence for the function of a leucine (Leu)-rich region centered around a conserved QMGPhiL motif at the very C-terminus as a nuclear export signal (NES) of class A Hsfs. Sequence comparison indicates that the combination of a C-terminal AHA motif with the consensus sequence FWxxF/L,F/I/L as well as the adjacent NES represents a signature domain for plant class A Hsfs, which allowed to identify more than 60 new Hsfs from the expressed sequence tag (EST) database.

Amino Acid Motifs↗
PubMed2006

Molecular signature of mice T lymphocytes following tolerance induction by allogeneic BMT and CD40-CD40L costimulation blockade.

Tolerance induction by mixed chimerism and costimulation blockade is a promising approach to avoid immunosuppression, but the molecular basis of tolerant T lymphocytes remains elusive. We investigated the genome-wide gene expression profile of murine T lymphocytes after tolerance induction by allogeneic bone marrow transplantation (BMT) and costimulatory blockade using the anti-CD40L antibody MR1. Molecular functions, biological processes, cellular locations, and coregulation of identified genes were determined. A total of 113 unique genes exhibited a significant differential expression between the lymphocytes of MR1-treated Tolerance (TOL) and untreated recipients Control (CTRL). The majority of genes upregulated in the TOL group are involved in several signal transduction cascades such as members of the MAPKKK cascade (IL6, Tob2, Stk39, and Dusp24). Other genes involved in lymphocyte differentiation and highly expressed in the TOL group are lymphotactin, the estrogen receptors (ERs) and the suppressor of cytokine signaling 7. Common transcription factors such as ER 1 alpha, GATA-binding protein 1, insulin promoter factor 1, and paired-related homeobox 2 could be identified in the promoter regions of upregulated genes in the TOL group. These data suggest that T lymphoctes of tolerant mice exhibit a distinct molecular expression profile, which needs to be evaluated in other experimental tolerance models to determine whether it is a universal signature of tolerance.

Animals↗
PubMed2007

Impact of carbon metabolism on 13C signatures of cyanobacteria and green non-sulfur-like bacteria inhabiting a microbial mat from an alkaline siliceous hot spring in Yellowstone National Park (USA).

Alkaline siliceous hot spring microbial mats in Yellowstone National Park are composed of two dominant phototropic groups, cyanobacteria and green non-sulfur-like bacteria (GNSLB). While cyanobacteria are thought to cross-feed low-molecular-weight organic compounds to support photoheterotrophic metabolism in GNSLB, it is unclear how this could lead to the heavier stable carbon isotopic signatures in GNSLB lipids compared with cyanobacterial lipids found in previous studies. The two groups of phototrophs were separated using percoll density gradient centrifugation and subsequent lipid and stable carbon isotopic analysis revealed that we obtained fractions with a approximately 60-fold enrichment in cyanobacterial and an approximately twofold enrichment in GNSLB biomass, respectively, compared with the mat itself. This technique was used to study the diel cycling and 13C content of the glucose pools in and the uptake of 13C-bicarbonate by the cyanobacteria and GNSLB, as well as the transfer of incorporated 13C from cyanobacteria to GNSLB. The results show that cyanobacteria have the highest bicarbonate uptake rates and accumulate glucose during the afternoon in full light conditions. In contrast, GNSLB have relatively higher bicarbonate uptake rates compared with cyanobacteria in the morning at low light levels. During the night GNSLB take up carbon that is likely derived through fermentation of cyanobacterial glucose enriched in 13C. The assimilation of 13C-enriched cyanobacterial carbon may thus lead to enriched 13C-contents of GNSLB cell components.

Bicarbonates↗