Anticipatory Understanding of Adversary Intent: A Signature-Based Knowledge System

DTIC Science & Technology

2009-06-01

concept of logical positivism has been applied more recently to all human knowledge and reflected in current data fusion research, information mining...this work has been successfully translated into useful analytical tools that can provide a rigorous and quantitative basis for predictive analysis

Genetic Diversity of Globally Dispersed Lacustrine Group I Haptophytes: Implications for Quantitative Temperature Reconstructions

NASA Astrophysics Data System (ADS)

Richter, N.; Longo, W. M.; Amaral-Zettler, L. A.; Huang, Y.

2017-12-01

There are significant uncertainties surrounding the forcings that drive terrestrial temperature changes on local and regional scales. Quantitative temperature reconstructions from terrestrial sites, such as lakes, help to unravel the fundamental processes that drive changes in temperature on different temporal and spatial scales. Recent studies at Brown University show that distinct alkenones, long chain ketones produced by haptophytes, are found in many freshwater, alkaline lakes in the Northern Hemisphere, highlighting these systems as targets for quantitative continental temperature reconstructions. These freshwater alkenones are produced by the Group I haptophyte phylotype and are characterized by a distinct signature: the presence of isomeric tri-unsaturated ketones and absence of alkenoates. There are currently no cultured representatives of the "Group I" haptophytes, hence they are only known based on their rRNA gene signatures. Here we present robust evidence that Northern Hemispheric freshwater, alkaline lakes with the characteristic "Group I" alkenone signature all host the same clade of Isochrysidales haptophytes. We employed next generation DNA amplicon sequencing to target haptophyte specific hypervariable regions of the large and small-subunit ribosomal RNA gene from 13 different lakes from three continents (i.e., North America, Europe, and Asia). Combined with previously published sequences, our genetic data show that the Group I haptophyte is genetically diverse on a regional and global scale, and even within the same lake. We present two case studies from a suite of five lakes in Alaska and three in Iceland to assess the impact of various environmental factors affecting Group I diversity and alkenone production. Despite the genetic diversity in this group, the overall ketone signature is conserved. Based on global surface sediment samples and in situ Alaskan lake calibrations, alkenones produced by different operational taxonomic units of the Group I haptophytes appear to display consistent responses to temperature changes, and thus can be used for paleotemperature reconstructions with a universally defined calibration.

Recent advances and remaining challenges for the spectroscopic detection of explosive threats.

PubMed

Fountain, Augustus W; Christesen, Steven D; Moon, Raphael P; Guicheteau, Jason A; Emmons, Erik D

2014-01-01

In 2010, the U.S. Army initiated a program through the Edgewood Chemical Biological Center to identify viable spectroscopic signatures of explosives and initiate environmental persistence, fate, and transport studies for trace residues. These studies were ultimately designed to integrate these signatures into algorithms and experimentally evaluate sensor performance for explosives and precursor materials in existing chemical point and standoff detection systems. Accurate and validated optical cross sections and signatures are critical in benchmarking spectroscopic-based sensors. This program has provided important information for the scientists and engineers currently developing trace-detection solutions to the homemade explosive problem. With this information, the sensitivity of spectroscopic methods for explosives detection can now be quantitatively evaluated before the sensor is deployed and tested.

Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR

PubMed Central

2014-01-01

Background Huanglongbing (HLB) or citrus greening is a devastating disease of citrus. The gram-negative bacterium Candidatus Liberibacter asiaticus (Las) belonging to the α-proteobacteria is responsible for HLB in North America as well as in Asia. Currently, there is no cure for this disease. Early detection and quarantine of Las-infected trees are important management strategies used to prevent HLB from invading HLB-free citrus producing regions. Quantitative real-time PCR (qRT-PCR) based molecular diagnostic assays have been routinely used in the detection and diagnosis of Las. The oligonucleotide primer pairs based on conserved genes or regions, which include 16S rDNA and the β-operon, have been widely employed in the detection of Las by qRT-PCR. The availability of whole genome sequence of Las now allows the design of primers beyond the conserved regions for the detection of Las explicitly. Results We took a complimentary approach by systematically screening the genes in a genome-wide fashion, to identify the unique signatures that are only present in Las by an exhaustive sequence based similarity search against the nucleotide sequence database. Our search resulted in 34 probable unique signatures. Furthermore, by designing the primer pair specific to the identified signatures, we showed that most of our primer sets are able to detect Las from the infected plant and psyllid materials collected from the USA and China by qRT-PCR. Overall, 18 primer pairs of the 34 are found to be highly specific to Las with no cross reactivity to the closely related species Ca. L. americanus (Lam) and Ca. L. africanus (Laf). Conclusions We have designed qRT-PCR primers based on Las specific genes. Among them, 18 are suitable for the detection of Las from Las-infected plant and psyllid samples. The repertoire of primers that we have developed and characterized in this study enhanced the qRT-PCR based molecular diagnosis of HLB. PMID:24533511

Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes.

PubMed

Liu, Ruifeng; AbdulHameed, Mohamed Diwan M; Wallqvist, Anders

2017-09-25

The quantitative structure-activity relationship (QSAR) approach has been used to model a wide range of chemical-induced biological responses. However, it had not been utilized to model chemical-induced genomewide gene expression changes until very recently, owing to the complexity of training and evaluating a very large number of models. To address this issue, we examined the performance of a variable nearest neighbor (v-NN) method that uses information on near neighbors conforming to the principle that similar structures have similar activities. Using a data set of gene expression signatures of 13 150 compounds derived from cell-based measurements in the NIH Library of Integrated Network-based Cellular Signatures program, we were able to make predictions for 62% of the compounds in a 10-fold cross validation test, with a correlation coefficient of 0.61 between the predicted and experimentally derived signatures-a reproducibility rivaling that of high-throughput gene expression measurements. To evaluate the utility of the predicted gene expression signatures, we compared the predicted and experimentally derived signatures in their ability to identify drugs known to cause specific liver, kidney, and heart injuries. Overall, the predicted and experimentally derived signatures had similar receiver operating characteristics, whose areas under the curve ranged from 0.71 to 0.77 and 0.70 to 0.73, respectively, across the three organ injury models. However, detailed analyses of enrichment curves indicate that signatures predicted from multiple near neighbors outperformed those derived from experiments, suggesting that averaging information from near neighbors may help improve the signal from gene expression measurements. Our results demonstrate that the v-NN method can serve as a practical approach for modeling large-scale, genomewide, chemical-induced, gene expression changes.

Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue.

PubMed

Röwer, Claudia; Vissers, Johannes P C; Koy, Cornelia; Kipping, Marc; Hecker, Michael; Reimer, Toralf; Gerber, Bernd; Thiesen, Hans-Jürgen; Glocker, Michael O

2009-12-01

As more and more alternative treatments become available for breast carcinoma, there is a need to stratify patients and individual molecular information seems to be suitable for this purpose. In this study, we applied label-free protein quantitation by nanoscale LC-MS and investigated whether this approach could be used for defining a proteome signature for invasive ductal breast carcinoma. Tissue samples from healthy breast and tumor were collected from three patients. Protein identifications were based on LC-MS peptide fragmentation data which were obtained simultaneously to the quantitative information. Hereby, an invasive ductal breast carcinoma proteome signature was generated which contains 60 protein entries. The on-column concentrations for osteoinductive factor, vimentin, GAP-DH, and NDKA are provided as examples. These proteins represent distinctive gene ontology groups of differentially expressed proteins and are discussed as risk markers for primary tumor pathogenesis. The developed methodology has been found well applicable in a clinical environment in which standard operating procedures can be kept; a prerequisite for the definition of molecular parameter sets that shall be capable for stratification of patients.

Multiscale moment-based technique for object matching and recognition

NASA Astrophysics Data System (ADS)

Thio, HweeLi; Chen, Liya; Teoh, Eam-Khwang

2000-03-01

A new method is proposed to extract features from an object for matching and recognition. The features proposed are a combination of local and global characteristics -- local characteristics from the 1-D signature function that is defined to each pixel on the object boundary, global characteristics from the moments that are generated from the signature function. The boundary of the object is first extracted, then the signature function is generated by computing the angle between two lines from every point on the boundary as a function of position along the boundary. This signature function is position, scale and rotation invariant (PSRI). The shape of the signature function is then described quantitatively by using moments. The moments of the signature function are the global characters of a local feature set. Using moments as the eventual features instead of the signature function reduces the time and complexity of an object matching application. Multiscale moments are implemented to produce several sets of moments that will generate more accurate matching. Basically multiscale technique is a coarse to fine procedure and makes the proposed method more robust to noise. This method is proposed to match and recognize objects under simple transformation, such as translation, scale changes, rotation and skewing. A simple logo indexing system is implemented to illustrate the performance of the proposed method.

Simultaneous quantification of α-lactalbumin and β-casein in human milk using ultra-performance liquid chromatography with tandem mass spectrometry based on their signature peptides and winged isotope internal standards.

PubMed

Chen, Qi; Zhang, Jingshun; Ke, Xing; Lai, Shiyun; Li, Duo; Yang, Jinchuan; Mo, Weimin; Ren, Yiping

2016-09-01

In recent years, there is an increasing need to measure the concentration of individual proteins in human milk, instead of total human milk proteins. Due to lack of human milk protein standards, there are only few quantification methods established. The objective of the present work was to develop a simple and rapid quantification method for simultaneous determination of α-lactalbumin and β-casein in human milk using signature peptides according to a modified quantitative proteomics strategy. The internal standards containing the signature peptide sequences were synthesized with isotope-labeled amino acids. The purity of synthesized peptides as standards was determined by amino acid analysis method and area normalization method. The contents of α-lactalbumin and β-casein in human milk were measured according to the equimolar relationship between the two proteins and their corresponding signature peptides. The method validation results showed a satisfied linearity (R(2)>0.99) and recoveries (97.2-102.5% for α-lactalbumin and 99.5-100.3% for β-casein). The limit of quantification for α-lactalbumin and β-casein was 8.0mg/100g and 1.2mg/100g, respectively. CVs for α-lactalbumin and β-casein in human milk were 5.2% and 3.0%. The contents of α-lactalbumin and β-casein in 147 human milk samples were successfully determined by the established method and their contents were 205.5-578.2mg/100g and 116.4-467.4mg/100g at different lactation stages. The developed method allows simultaneously determination of α-lactalbumin and β-casein in human milk. The quantitative strategy based on signature peptide should be applicable to other endogenous proteins in breast milk and other body fluids. Copyright © 2016 Elsevier B.V. All rights reserved.

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Building gene expression signatures indicative of transcription factor activation to predict AOP modulation

EPA Science Inventory

Building gene expression signatures indicative of transcription factor activation to predict AOP modulation Adverse outcome pathways (AOPs) are a framework for predicting quantitative relationships between molecular initiatin...

Weld radiograph enigmas

NASA Technical Reports Server (NTRS)

Jemian, Wartan A.

1986-01-01

Weld radiograph enigmas are features observed on X-ray radiographs of welds. Some of these features resemble indications of weld defects, although their origin is different. Since they are not understood, they are a source of concern. There is a need to identify their causes and especially to measure their effect on weld mechanical properties. A method is proposed whereby the enigmas can be evaluated and rated, in relation to the full spectrum of weld radiograph indications. Thie method involves a signature and a magnitude that can be used as a quantitive parameter. The signature is generated as the diference between the microdensitometer trace across the radiograph and the computed film intensity derived from a thickness scan along the corresponding region of the sample. The magnitude is the measured difference in intensity between the peak and base line values of the signature. The procedure is demonstated by comparing traces across radiographs of a weld sample before and after the introduction of a hole and by a system based on a MacIntosh mouse used for surface profiling.

Hyperspectral signature analysis of skin parameters

NASA Astrophysics Data System (ADS)

Vyas, Saurabh; Banerjee, Amit; Garza, Luis; Kang, Sewon; Burlina, Philippe

2013-02-01

The temporal analysis of changes in biological skin parameters, including melanosome concentration, collagen concentration and blood oxygenation, may serve as a valuable tool in diagnosing the progression of malignant skin cancers and in understanding the pathophysiology of cancerous tumors. Quantitative knowledge of these parameters can also be useful in applications such as wound assessment, and point-of-care diagnostics, amongst others. We propose an approach to estimate in vivo skin parameters using a forward computational model based on Kubelka-Munk theory and the Fresnel Equations. We use this model to map the skin parameters to their corresponding hyperspectral signature. We then use machine learning based regression to develop an inverse map from hyperspectral signatures to skin parameters. In particular, we employ support vector machine based regression to estimate the in vivo skin parameters given their corresponding hyperspectral signature. We build on our work from SPIE 2012, and validate our methodology on an in vivo dataset. This dataset consists of 241 signatures collected from in vivo hyperspectral imaging of patients of both genders and Caucasian, Asian and African American ethnicities. In addition, we also extend our methodology past the visible region and through the short-wave infrared region of the electromagnetic spectrum. We find promising results when comparing the estimated skin parameters to the ground truth, demonstrating good agreement with well-established physiological precepts. This methodology can have potential use in non-invasive skin anomaly detection and for developing minimally invasive pre-screening tools.

Continual in situ monitoring of pore water stable isotopes in the subsurface

NASA Astrophysics Data System (ADS)

Volkmann, T. H. M.; Weiler, M.

2014-05-01

Stable isotope signatures provide an integral fingerprint of origin, flow paths, transport processes, and residence times of water in the environment. However, the full potential of stable isotopes to quantitatively characterize subsurface water dynamics is yet unfolded due to the difficulty in obtaining extensive, detailed, and repeated measurements of pore water in the unsaturated and saturated zone. This paper presents a functional and cost-efficient system for non-destructive continual in situ monitoring of pore water stable isotope signatures with high resolution. Automatic controllable valve arrays are used to continuously extract diluted water vapor in soil air via a branching network of small microporous probes into a commercial laser-based isotope analyzer. Normalized liquid-phase isotope signatures are then obtained based on a specific on-site calibration approach along with basic corrections for instrument bias and temperature dependent isotopic fractionation. The system was applied to sample depth profiles on three experimental plots with varied vegetation cover in southwest Germany. Two methods (i.e., based on advective versus diffusive vapor extraction) and two modes of sampling (i.e., using multiple permanently installed probes versus a single repeatedly inserted probe) were tested and compared. The results show that the isotope distribution along natural profiles could be resolved with sufficiently high accuracy and precision at sampling intervals of less than four minutes. The presented in situ approaches may thereby be used interchangeably with each other and with concurrent laboratory-based direct equilibration measurements of destructively collected samples. It is thus found that the introduced sampling techniques provide powerful tools towards a detailed quantitative understanding of dynamic and heterogeneous shallow subsurface and vadose zone processes.

Bulk Fermi surface and momentum density in heavily doped La2-xSrxCuO4 using high-resolution Compton scattering and positron annihilation spectroscopies

NASA Astrophysics Data System (ADS)

Al-Sawai, W.; Barbiellini, B.; Sakurai, Y.; Itou, M.; Mijnarends, P. E.; Markiewicz, R. S.; Kaprzyk, S.; Wakimoto, S.; Fujita, M.; Basak, S.; Lin, H.; Wang, Yung Jui; Eijt, S. W. H.; Schut, H.; Yamada, K.; Bansil, A.

2012-03-01

We have observed the bulk Fermi surface (FS) in an overdoped (x=0.3) single crystal of La2-xSrxCuO4 by using Compton scattering. A two-dimensional (2D) momentum density reconstruction from measured Compton profiles yields a clear FS signature in the third Brillouin zone along [100]. The quantitative agreement between density functional theory (DFT) calculations and momentum density experiment suggests that Fermi-liquid physics is restored in the overdoped regime. In particular the predicted FS topology is found to be in good accord with the corresponding experimental data. We find similar quantitative agreement between the measured 2D angular correlation of positron annihilation radiation (2D-ACAR) spectra and the DFT-based computations. However, 2D-ACAR does not give such a clear signature of the FS in the extended momentum space in either the theory or the experiment.

Fatty acid methyl ester (FAME) technology for monitoring biological foaming in activated sludge: full scale plant verification.

PubMed

Lee, J W; Cha, D K; Kim, I; Son, A; Ahn, K H

2008-02-01

Fatty acid methyl ester (FAME) technology was evaluated as a monitoring tool for quantification of Gordonia amarae in activated sludge systems. The fatty acid, 19:1 alcohol, which was identified as a unique fatty acid in G. amarae was not only confirmed to be present in foaming plant samples, but the quantity of the signature peak correlated closely with the degree of foaming. Foaming potential experiment provided a range of critical foaming levels that corresponded to G. amarae population. This range of critical Gordonia levels was correlated to the threshold signature FAME amount. Six full-scale wastewater treatment plants were selected based on a survey to participate in our full-scale study to evaluate the potential application of the FAME technique as the Gordonia monitoring tool. Greater amounts of signature FAME were extracted from the mixed liquor samples obtained from treatment plants experiencing Gordonia foaming problems. The amounts of signature FAME correlated well with the conventional filamentous counting technique. These results demonstrated that the relative abundance of the signature FAMEs can be used to quantitatively monitor the abundance of foam-causing microorganism in activated sludge.

Ventral striatal dopamine reflects behavioral and neural signatures of model-based control during sequential decision making.

PubMed

Deserno, Lorenz; Huys, Quentin J M; Boehme, Rebecca; Buchert, Ralph; Heinze, Hans-Jochen; Grace, Anthony A; Dolan, Raymond J; Heinz, Andreas; Schlagenhauf, Florian

2015-02-03

Dual system theories suggest that behavioral control is parsed between a deliberative "model-based" and a more reflexive "model-free" system. A balance of control exerted by these systems is thought to be related to dopamine neurotransmission. However, in the absence of direct measures of human dopamine, it remains unknown whether this reflects a quantitative relation with dopamine either in the striatum or other brain areas. Using a sequential decision task performed during functional magnetic resonance imaging, combined with striatal measures of dopamine using [(18)F]DOPA positron emission tomography, we show that higher presynaptic ventral striatal dopamine levels were associated with a behavioral bias toward more model-based control. Higher presynaptic dopamine in ventral striatum was associated with greater coding of model-based signatures in lateral prefrontal cortex and diminished coding of model-free prediction errors in ventral striatum. Thus, interindividual variability in ventral striatal presynaptic dopamine reflects a balance in the behavioral expression and the neural signatures of model-free and model-based control. Our data provide a novel perspective on how alterations in presynaptic dopamine levels might be accompanied by a disruption of behavioral control as observed in aging or neuropsychiatric diseases such as schizophrenia and addiction.

Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tholouli, Eleni; MacDermott, Sarah; Hoyland, Judith

2012-08-24

Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection inmore » archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.« less

Quantitative Analysis of {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography Identifies Novel Prognostic Imaging Biomarkers in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Yi; Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo; Song, Jie

Purpose: To identify prognostic biomarkers in pancreatic cancer using high-throughput quantitative image analysis. Methods and Materials: In this institutional review board–approved study, we retrospectively analyzed images and outcomes for 139 locally advanced pancreatic cancer patients treated with stereotactic body radiation therapy (SBRT). The overall population was split into a training cohort (n=90) and a validation cohort (n=49) according to the time of treatment. We extracted quantitative imaging characteristics from pre-SBRT {sup 18}F-fluorodeoxyglucose positron emission tomography, including statistical, morphologic, and texture features. A Cox proportional hazard regression model was built to predict overall survival (OS) in the training cohort using 162more » robust image features. To avoid over-fitting, we applied the elastic net to obtain a sparse set of image features, whose linear combination constitutes a prognostic imaging signature. Univariate and multivariate Cox regression analyses were used to evaluate the association with OS, and concordance index (CI) was used to evaluate the survival prediction accuracy. Results: The prognostic imaging signature included 7 features characterizing different tumor phenotypes, including shape, intensity, and texture. On the validation cohort, univariate analysis showed that this prognostic signature was significantly associated with OS (P=.002, hazard ratio 2.74), which improved upon conventional imaging predictors including tumor volume, maximum standardized uptake value, and total legion glycolysis (P=.018-.028, hazard ratio 1.51-1.57). On multivariate analysis, the proposed signature was the only significant prognostic index (P=.037, hazard ratio 3.72) when adjusted for conventional imaging and clinical factors (P=.123-.870, hazard ratio 0.53-1.30). In terms of CI, the proposed signature scored 0.66 and was significantly better than competing prognostic indices (CI 0.48-0.64, Wilcoxon rank sum test P<1e-6). Conclusion: Quantitative analysis identified novel {sup 18}F-fluorodeoxyglucose positron emission tomography image features that showed improved prognostic value over conventional imaging metrics. If validated in large, prospective cohorts, the new prognostic signature might be used to identify patients for individualized risk-adaptive therapy.« less

Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status

PubMed Central

Li, Qiyuan; Eklund, Aron C.; Juul, Nicolai; Haibe-Kains, Benjamin; Workman, Christopher T.; Richardson, Andrea L.; Szallasi, Zoltan; Swanton, Charles

2010-01-01

Background Expression of the oestrogen receptor (ER) in breast cancer predicts benefit from endocrine therapy. Minimising the frequency of false negative ER status classification is essential to identify all patients with ER positive breast cancers who should be offered endocrine therapies in order to improve clinical outcome. In routine oncological practice ER status is determined by semi-quantitative methods such as immunohistochemistry (IHC) or other immunoassays in which the ER expression level is compared to an empirical threshold[1], [2]. The clinical relevance of gene expression-based ER subtypes as compared to IHC-based determination has not been systematically evaluated. Here we attempt to reduce the frequency of false negative ER status classification using two gene expression approaches and compare these methods to IHC based ER status in terms of predictive and prognostic concordance with clinical outcome. Methodology/Principal Findings Firstly, ER status was discriminated by fitting the bimodal expression of ESR1 to a mixed Gaussian model. The discriminative power of ESR1 suggested bimodal expression as an efficient way to stratify breast cancer; therefore we identified a set of genes whose expression was both strongly bimodal, mimicking ESR expression status, and highly expressed in breast epithelial cell lines, to derive a 23-gene ER expression signature-based classifier. We assessed our classifiers in seven published breast cancer cohorts by comparing the gene expression-based ER status to IHC-based ER status as a predictor of clinical outcome in both untreated and tamoxifen treated cohorts. In untreated breast cancer cohorts, the 23 gene signature-based ER status provided significantly improved prognostic power compared to IHC-based ER status (P = 0.006). In tamoxifen-treated cohorts, the 23 gene ER expression signature predicted clinical outcome (HR = 2.20, P = 0.00035). These complementary ER signature-based strategies estimated that between 15.1% and 21.8% patients of IHC-based negative ER status would be classified with ER positive breast cancer. Conclusion/Significance Expression-based ER status classification may complement IHC to minimise false negative ER status classification and optimise patient stratification for endocrine therapies. PMID:21152022

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

PubMed

Yuan, Yinyin; Failmezger, Henrik; Rueda, Oscar M; Ali, H Raza; Gräf, Stefan; Chin, Suet-Feung; Schwarz, Roland F; Curtis, Christina; Dunning, Mark J; Bardwell, Helen; Johnson, Nicola; Doyle, Sarah; Turashvili, Gulisa; Provenzano, Elena; Aparicio, Sam; Caldas, Carlos; Markowetz, Florian

2012-10-24

Solid tumors are heterogeneous tissues composed of a mixture of cancer and normal cells, which complicates the interpretation of their molecular profiles. Furthermore, tissue architecture is generally not reflected in molecular assays, rendering this rich information underused. To address these challenges, we developed a computational approach based on standard hematoxylin and eosin-stained tissue sections and demonstrated its power in a discovery and validation cohort of 323 and 241 breast tumors, respectively. To deconvolute cellular heterogeneity and detect subtle genomic aberrations, we introduced an algorithm based on tumor cellularity to increase the comparability of copy number profiles between samples. We next devised a predictor for survival in estrogen receptor-negative breast cancer that integrated both image-based and gene expression analyses and significantly outperformed classifiers that use single data types, such as microarray expression signatures. Image processing also allowed us to describe and validate an independent prognostic factor based on quantitative analysis of spatial patterns between stromal cells, which are not detectable by molecular assays. Our quantitative, image-based method could benefit any large-scale cancer study by refining and complementing molecular assays of tumor samples.

Methods for threshold determination in multiplexed assays

DOEpatents

Tammero, Lance F. Bentley; Dzenitis, John M; Hindson, Benjamin J

2014-06-24

Methods for determination of threshold values of signatures comprised in an assay are described. Each signature enables detection of a target. The methods determine a probability density function of negative samples and a corresponding false positive rate curve. A false positive criterion is established and a threshold for that signature is determined as a point at which the false positive rate curve intersects the false positive criterion. A method for quantitative analysis and interpretation of assay results together with a method for determination of a desired limit of detection of a signature in an assay are also described.

Phenotypic signatures arising from unbalanced bacterial growth.

PubMed

Tan, Cheemeng; Smith, Robert Phillip; Tsai, Ming-Chi; Schwartz, Russell; You, Lingchong

2014-08-01

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify "phenotypic signatures" by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains.

Highly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis

PubMed Central

Kim, David M.; Zhang, Hairong; Zhou, Haiying; Du, Tommy; Wu, Qian; Mockler, Todd C.; Berezin, Mikhail Y.

2015-01-01

The optical signature of leaves is an important monitoring and predictive parameter for a variety of biotic and abiotic stresses, including drought. Such signatures derived from spectroscopic measurements provide vegetation indices – a quantitative method for assessing plant health. However, the commonly used metrics suffer from low sensitivity. Relatively small changes in water content in moderately stressed plants demand high-contrast imaging to distinguish affected plants. We present a new approach in deriving sensitive indices using hyperspectral imaging in a short-wave infrared range from 800 nm to 1600 nm. Our method, based on high spectral resolution (1.56 nm) instrumentation and image processing algorithms (quantitative histogram analysis), enables us to distinguish a moderate water stress equivalent of 20% relative water content (RWC). The identified image-derived indices 15XX nm/14XX nm (i.e. 1529 nm/1416 nm) were superior to common vegetation indices, such as WBI, MSI, and NDWI, with significantly better sensitivity, enabling early diagnostics of plant health. PMID:26531782

Discrimination of fungal infections on grape berries via spectral signatures

NASA Astrophysics Data System (ADS)

Molitor, Daniel; Griesser, Michaela; Schütz, Erich; Khuen, Marie-Therese; Schefbeck, Christa; Ronellenfitsch, Franz Kai; Schlerf, Martin; Beyer, Marco; Schoedl-Hummel, Katharina; Anhalt, Ulrike; Forneck, Astrid

2016-04-01

The fungal pathogens Botrytis cinerea and Penicillium expansum are causing economic damages on grapevine worldwide. Especially the simultaneous occurrence of both often results in off-flavours highly threatening wine quality. For the classification of grape quality as well as for the determination of targeted enological treatments, the knowledge of the level of fungal attack is of highest interest. However, visual assessment and pathogen discrimination are cost-intensive. Consequently, a pilot laboratory study aimed at (i) detecting differences in spectral signatures between grape berry lots with different levels of infected berries (B. cinerea and/or P. expansum) and (ii) detecting links between spectral signatures and biochemical as well as quantitative molecular markers for fungal attack. To this end, defined percentages (infection levels) of table grape berries were inoculated with fungal spore suspensions. Spectral measurements were taken using a FieldSpec 3 Max spectroradiometer (ASD Inc., Boulder/Colorado, USA) in regular intervals after inoculation. In addition, fungal attack was determined enzymatically) and quantitatively (real-time PCR). In addition, gluconic acid concentrations (as a potential markers for fungal attack) were determined photometrically. Results indicate that based on spectral signatures, a discrimination of P. expansum and B. cinerea infections as well as of different B. cinerea infection levels is possible. Real-time PCR analyses, detecting DNA levels of both fungi, showed yet a low detection level. Whereas the gluconic acid concentrations turned out to be specific for the two fungi tested (B. cinerea vs. P. expansum) and thus may serve as a differentiating biochemical marker. Correlation analyses between spectral measurements and biological data (gluconic acid concentrations, fungi DNA) as well as further common field and laboratory trials are targeted.

A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy.

PubMed

Farr, Ryan J; Januszewski, Andrzej S; Joglekar, Mugdha V; Liang, Helena; McAulley, Annie K; Hewitt, Alex W; Thomas, Helen E; Loudovaris, Tom; Kay, Thomas W H; Jenkins, Alicia; Hardikar, Anandwardhan A

2015-06-02

MicroRNAs are now increasingly recognized as biomarkers of disease progression. Several quantitative real-time PCR (qPCR) platforms have been developed to determine the relative levels of microRNAs in biological fluids. We systematically compared the detection of cellular and circulating microRNA using a standard 96-well platform, a high-content microfluidics platform and two ultra-high content platforms. We used extensive analytical tools to compute inter- and intra-run variability and concordance measured using fidelity scoring, coefficient of variation and cluster analysis. We carried out unprejudiced next generation sequencing to identify a microRNA signature for Diabetic Retinopathy (DR) and systematically assessed the validation of this signature on clinical samples using each of the above four qPCR platforms. The results indicate that sensitivity to measure low copy number microRNAs is inversely related to qPCR reaction volume and that the choice of platform for microRNA biomarker validation should be made based on the abundance of miRNAs of interest.

Systematic Methodological Evaluation of a Multiplex Bead-Based Flow Cytometry Assay for Detection of Extracellular Vesicle Surface Signatures

PubMed Central

Wiklander, Oscar P. B.; Bostancioglu, R. Beklem; Welsh, Joshua A.; Zickler, Antje M.; Murke, Florian; Corso, Giulia; Felldin, Ulrika; Hagey, Daniel W.; Evertsson, Björn; Liang, Xiu-Ming; Gustafsson, Manuela O.; Mohammad, Dara K.; Wiek, Constanze; Hanenberg, Helmut; Bremer, Michel; Gupta, Dhanu; Björnstedt, Mikael; Giebel, Bernd; Nordin, Joel Z.; Jones, Jennifer C.; EL Andaloussi, Samir; Görgens, André

2018-01-01

Extracellular vesicles (EVs) can be harvested from cell culture supernatants and from all body fluids. EVs can be conceptually classified based on their size and biogenesis as exosomes and microvesicles. Nowadays, it is however commonly accepted in the field that there is a much higher degree of heterogeneity within these two subgroups than previously thought. For instance, the surface marker profile of EVs is likely dependent on the cell source, the cell’s activation status, and multiple other parameters. Within recent years, several new methods and assays to study EV heterogeneity in terms of surface markers have been described; most of them are being based on flow cytometry. Unfortunately, such methods generally require dedicated instrumentation, are time-consuming and demand extensive operator expertise for sample preparation, acquisition, and data analysis. In this study, we have systematically evaluated and explored the use of a multiplex bead-based flow cytometric assay which is compatible with most standard flow cytometers and facilitates a robust semi-quantitative detection of 37 different potential EV surface markers in one sample simultaneously. First, assay variability, sample stability over time, and dynamic range were assessed together with the limitations of this assay in terms of EV input quantity required for detection of differently abundant surface markers. Next, the potential effects of EV origin, sample preparation, and quality of the EV sample on the assay were evaluated. The findings indicate that this multiplex bead-based assay is generally suitable to detect, quantify, and compare EV surface signatures in various sample types, including unprocessed cell culture supernatants, cell culture-derived EVs isolated by different methods, and biological fluids. Furthermore, the use and limitations of this assay to assess heterogeneities in EV surface signatures was explored by combining different sets of detection antibodies in EV samples derived from different cell lines and subsets of rare cells. Taken together, this validated multiplex bead-based flow cytometric assay allows robust, sensitive, and reproducible detection of EV surface marker expression in various sample types in a semi-quantitative way and will be highly valuable for many researchers in the EV field in different experimental contexts.

Systematic Methodological Evaluation of a Multiplex Bead-Based Flow Cytometry Assay for Detection of Extracellular Vesicle Surface Signatures.

PubMed

Wiklander, Oscar P B; Bostancioglu, R Beklem; Welsh, Joshua A; Zickler, Antje M; Murke, Florian; Corso, Giulia; Felldin, Ulrika; Hagey, Daniel W; Evertsson, Björn; Liang, Xiu-Ming; Gustafsson, Manuela O; Mohammad, Dara K; Wiek, Constanze; Hanenberg, Helmut; Bremer, Michel; Gupta, Dhanu; Björnstedt, Mikael; Giebel, Bernd; Nordin, Joel Z; Jones, Jennifer C; El Andaloussi, Samir; Görgens, André

2018-01-01

Extracellular vesicles (EVs) can be harvested from cell culture supernatants and from all body fluids. EVs can be conceptually classified based on their size and biogenesis as exosomes and microvesicles. Nowadays, it is however commonly accepted in the field that there is a much higher degree of heterogeneity within these two subgroups than previously thought. For instance, the surface marker profile of EVs is likely dependent on the cell source, the cell's activation status, and multiple other parameters. Within recent years, several new methods and assays to study EV heterogeneity in terms of surface markers have been described; most of them are being based on flow cytometry. Unfortunately, such methods generally require dedicated instrumentation, are time-consuming and demand extensive operator expertise for sample preparation, acquisition, and data analysis. In this study, we have systematically evaluated and explored the use of a multiplex bead-based flow cytometric assay which is compatible with most standard flow cytometers and facilitates a robust semi-quantitative detection of 37 different potential EV surface markers in one sample simultaneously. First, assay variability, sample stability over time, and dynamic range were assessed together with the limitations of this assay in terms of EV input quantity required for detection of differently abundant surface markers. Next, the potential effects of EV origin, sample preparation, and quality of the EV sample on the assay were evaluated. The findings indicate that this multiplex bead-based assay is generally suitable to detect, quantify, and compare EV surface signatures in various sample types, including unprocessed cell culture supernatants, cell culture-derived EVs isolated by different methods, and biological fluids. Furthermore, the use and limitations of this assay to assess heterogeneities in EV surface signatures was explored by combining different sets of detection antibodies in EV samples derived from different cell lines and subsets of rare cells. Taken together, this validated multiplex bead-based flow cytometric assay allows robust, sensitive, and reproducible detection of EV surface marker expression in various sample types in a semi-quantitative way and will be highly valuable for many researchers in the EV field in different experimental contexts.

Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

PubMed

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-03-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

PubMed Central

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-01-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469

Mass spectrometry in life science research.

PubMed

Lehr, Stefan; Markgraf, Daniel

2016-12-01

Investigating complex signatures of biomolecules by mass spectrometry approaches has become indispensable in molecular life science research. Nowadays, various mass spectrometry-based omics technologies are available to monitor qualitative and quantitative changes within hundreds or thousands of biological active components, including proteins/peptides, lipids and metabolites. These comprehensive investigations have the potential to decipher the pathophysiology of disease development at a molecular level and to monitor the individual response of pharmacological treatment or lifestyle intervention.

Determination of burn patient outcome by large-scale quantitative discovery proteomics

PubMed Central

Finnerty, Celeste C.; Jeschke, Marc G.; Qian, Wei-Jun; Kaushal, Amit; Xiao, Wenzhong; Liu, Tao; Gritsenko, Marina A.; Moore, Ronald J.; Camp, David G.; Moldawer, Lyle L.; Elson, Constance; Schoenfeld, David; Gamelli, Richard; Gibran, Nicole; Klein, Matthew; Arnoldo, Brett; Remick, Daniel; Smith, Richard D.; Davis, Ronald; Tompkins, Ronald G.; Herndon, David N.

2013-01-01

Objective Emerging proteomics techniques can be used to establish proteomic outcome signatures and to identify candidate biomarkers for survival following traumatic injury. We applied high-resolution liquid chromatography-mass spectrometry (LC-MS) and multiplex cytokine analysis to profile the plasma proteome of survivors and non-survivors of massive burn injury to determine the proteomic survival signature following a major burn injury. Design Proteomic discovery study. Setting Five burn hospitals across the U.S. Patients Thirty-two burn patients (16 non-survivors and 16 survivors), 19–89 years of age, were admitted within 96 h of injury to the participating hospitals with burns covering >20% of the total body surface area and required at least one surgical intervention. Interventions None. Measurements and Main Results We found differences in circulating levels of 43 proteins involved in the acute phase response, hepatic signaling, the complement cascade, inflammation, and insulin resistance. Thirty-two of the proteins identified were not previously known to play a role in the response to burn. IL-4, IL-8, GM-CSF, MCP-1, and β2-microglobulin correlated well with survival and may serve as clinical biomarkers. Conclusions These results demonstrate the utility of these techniques for establishing proteomic survival signatures and for use as a discovery tool to identify candidate biomarkers for survival. This is the first clinical application of a high-throughput, large-scale LC-MS-based quantitative plasma proteomic approach for biomarker discovery for the prediction of patient outcome following burn, trauma or critical illness. PMID:23507713

Label-free quantitative proteomic analysis of human plasma-derived microvesicles to find protein signatures of abdominal aortic aneurysms.

PubMed

Martinez-Pinna, Roxana; Gonzalez de Peredo, Anne; Monsarrat, Bernard; Burlet-Schiltz, Odile; Martin-Ventura, Jose Luis

2014-08-01

To find potential biomarkers of abdominal aortic aneurysms (AAA), we performed a differential proteomic study based on human plasma-derived microvesicles. Exosomes and microparticles isolated from plasma of AAA patients and control subjects (n = 10 each group) were analyzed by a label-free quantitative MS-based strategy. Homemade and publicly available software packages have been used for MS data analysis. The application of two kinds of bioinformatic tools allowed us to find differential protein profiles from AAA patients. Some of these proteins found by the two analysis methods belong to main pathological mechanisms of AAA such as oxidative stress, immune-inflammation, and thrombosis. Data analysis from label-free MS-based experiments requires the use of sophisticated bioinformatic approaches to perform quantitative studies from complex protein mixtures. The application of two of these bioinformatic tools provided us a preliminary list of differential proteins found in plasma-derived microvesicles not previously associated to AAA, which could help us to understand the pathological mechanisms related to this disease. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of Flavin-containing Monooxygenases 1, 3, and 5 in Human Liver Microsomes by UPLC-MRM-Based Targeted Quantitative Proteomics and Its Application to the Study of Ontogeny.

PubMed

Chen, Yao; Zane, Nicole R; Thakker, Dhiren R; Wang, Michael Zhuo

2016-07-01

Flavin-containing monooxygenases (FMOs) have a significant role in the metabolism of small molecule pharmaceuticals. Among the five human FMOs, FMO1, FMO3, and FMO5 are the most relevant to hepatic drug metabolism. Although age-dependent hepatic protein expression, based on immunoquantification, has been reported previously for FMO1 and FMO3, there is very little information on hepatic FMO5 protein expression. To overcome the limitations of immunoquantification, an ultra-performance liquid chromatography (UPLC)-multiple reaction monitoring (MRM)-based targeted quantitative proteomic method was developed and optimized for the quantification of FMO1, FMO3, and FMO5 in human liver microsomes (HLM). A post-in silico product ion screening process was incorporated to verify LC-MRM detection of potential signature peptides before their synthesis. The developed method was validated by correlating marker substrate activity and protein expression in a panel of adult individual donor HLM (age 39-67 years). The mean (range) protein expression of FMO3 and FMO5 was 46 (26-65) pmol/mg HLM protein and 27 (11.5-49) pmol/mg HLM protein, respectively. To demonstrate quantification of FMO1, a panel of fetal individual donor HLM (gestational age 14-20 weeks) was analyzed. The mean (range) FMO1 protein expression was 7.0 (4.9-9.7) pmol/mg HLM protein. Furthermore, the ontogenetic protein expression of FMO5 was evaluated in fetal, pediatric, and adult HLM. The quantification of FMO proteins also was compared using two different calibration standards, recombinant proteins versus synthetic signature peptides, to assess the ratio between holoprotein versus total protein. In conclusion, a UPLC-MRM-based targeted quantitative proteomic method has been developed for the quantification of FMO enzymes in HLM. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

Quantification of Flavin-containing Monooxygenases 1, 3, and 5 in Human Liver Microsomes by UPLC-MRM-Based Targeted Quantitative Proteomics and Its Application to the Study of Ontogeny

PubMed Central

Chen, Yao; Zane, Nicole R.; Thakker, Dhiren R.

2016-01-01

Flavin-containing monooxygenases (FMOs) have a significant role in the metabolism of small molecule pharmaceuticals. Among the five human FMOs, FMO1, FMO3, and FMO5 are the most relevant to hepatic drug metabolism. Although age-dependent hepatic protein expression, based on immunoquantification, has been reported previously for FMO1 and FMO3, there is very little information on hepatic FMO5 protein expression. To overcome the limitations of immunoquantification, an ultra-performance liquid chromatography (UPLC)-multiple reaction monitoring (MRM)-based targeted quantitative proteomic method was developed and optimized for the quantification of FMO1, FMO3, and FMO5 in human liver microsomes (HLM). A post-in silico product ion screening process was incorporated to verify LC-MRM detection of potential signature peptides before their synthesis. The developed method was validated by correlating marker substrate activity and protein expression in a panel of adult individual donor HLM (age 39–67 years). The mean (range) protein expression of FMO3 and FMO5 was 46 (26–65) pmol/mg HLM protein and 27 (11.5–49) pmol/mg HLM protein, respectively. To demonstrate quantification of FMO1, a panel of fetal individual donor HLM (gestational age 14–20 weeks) was analyzed. The mean (range) FMO1 protein expression was 7.0 (4.9–9.7) pmol/mg HLM protein. Furthermore, the ontogenetic protein expression of FMO5 was evaluated in fetal, pediatric, and adult HLM. The quantification of FMO proteins also was compared using two different calibration standards, recombinant proteins versus synthetic signature peptides, to assess the ratio between holoprotein versus total protein. In conclusion, a UPLC-MRM-based targeted quantitative proteomic method has been developed for the quantification of FMO enzymes in HLM. PMID:26839369

To elute or not to elute in immunocapture bottom-up LC-MS.

PubMed

Levernæs, Maren Christin Stillesby; Broughton, Marianne Nordlund; Reubsaet, Léon; Halvorsen, Trine Grønhaug

2017-06-15

Immunocapture-based bottom-up LC-MS is a promising technique for the quantification of low abundant proteins. Magnetic immunocapture beads provide efficient enrichment from complex samples through the highly specific interaction between the target protein and its antibody. In this article, we have performed the first thorough comparison between digestion of proteins while bound to antibody coated beads versus after elution from the beads. Two previously validated immunocapture based MS methods for the quantification of pro-gastrin releasing peptide (ProGRP) and human chorionic gonadotropin (hCG) were used as model systems. The tryptic peptide generation was shown to be protein dependent and influenced by protein folding and accessibility towards trypsin both on-beads and in the eluate. The elution of proteins bound to the beads was also shown to be incomplete. In addition, the on-beads digestion suffered from non-specific binding of the trypsin generated peptides. A combination of on-beads digestion and elution may be applied to improve both the quantitative (peak area of the signature peptides) and qualitative yield (number of missed cleavages, total number of identified peptides, coverage, signal intensity and number of zero missed cleavage peptides) of the target proteins. The quantitative yield of signature peptides was shown to be reproducible in all procedures tested. Copyright © 2017 Elsevier B.V. All rights reserved.

Temporal measurement and analysis of high-resolution spectral signatures of plants and relationships to biophysical characteristics

NASA Astrophysics Data System (ADS)

Bostater, Charles R., Jr.; Rebbman, Jan; Hall, Carlton; Provancha, Mark; Vieglais, David

1995-11-01

Measurements of temporal reflectance signatures as a function of growing season for sand live oak (Quercus geminata), myrtle oak (Q. myrtifolia, and saw palmetto (Serenoa repens) were collected during a two year study period. Canopy level spectral reflectance signatures, as a function of 252 channels between 368 and 1115 nm, were collected using near nadir viewing geometry and a consistent sun illumination angle. Leaf level reflectance measurements were made in the laboratory using a halogen light source and an environmental optics chamber with a barium sulfate reflectance coating. Spectral measurements were related to several biophysical measurements utilizing optimal passive ambient correlation spectroscopy (OPACS) technique. Biophysical parameters included percent moisture, water potential (MPa), total chlorophyll, and total Kjeldahl nitrogen. Quantitative data processing techniques were used to determine optimal bands based on the utilization of a second order derivative or inflection estimator. An optical cleanup procedure was then employed that computes the double inflection ratio (DIR) spectra for all possible three band combinations normalized to the previously computed optimal bands. These results demonstrate a unique approach to the analysis of high spectral resolution reflectance signatures for estimation of several biophysical measures of plants at the leaf and canopy level from optimally selected bands or bandwidths.

Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes

PubMed Central

Flechner, Stuart M.; Kurian, Sunil M.; Head, Steven R.; Sharp, Starlette M.; Whisenant, Thomas C.; Zhang, Jie; Chismar, Jeffrey D.; Horvath, Steve; Mondala, Tony; Gilmartin, Timothy; Cook, Daniel J.; Kay, Steven A.; Walker, John R.; Salomon, Daniel R.

2007-01-01

A major challenge for kidney transplantation is balancing the need for immunosuppression to prevent rejection, while minimizing drug-induced toxicities. We used DNA microarrays (HG-U95Av2 GeneChips, Affymetrix) to determine gene expression profiles for kidney biopsies and peripheral blood lymphocytes (PBLs) in transplant patients including normal donor kidneys, well-functioning transplants without rejection, kidneys undergoing acute rejection, and transplants with renal dysfunction without rejection. We developed a data analysis schema based on expression signal determination, class comparison and prediction, hierarchical clustering, statistical power analysis and real-time quantitative PCR validation. We identified distinct gene expression signatures for both biopsies and PBLs that correlated significantly with each of the different classes of transplant patients. This is the most complete report to date using commercial arrays to identify unique expression signatures in transplant biopsies distinguishing acute rejection, acute dysfunction without rejection and well-functioning transplants with no rejection history. We demonstrate for the first time the successful application of high density DNA chip analysis of PBL as a diagnostic tool for transplantation. The significance of these results, if validated in a multicenter prospective trial, would be the establishment of a metric based on gene expression signatures for monitoring the immune status and immunosuppression of transplanted patients. PMID:15307835

Sequence signatures of allosteric proteins towards rational design.

PubMed

Namboodiri, Saritha; Verma, Chandra; Dhar, Pawan K; Giuliani, Alessandro; Nair, Achuthsankar S

2010-12-01

Allostery is the phenomenon of changes in the structure and activity of proteins that appear as a consequence of ligand binding at sites other than the active site. Studying mechanistic basis of allostery leading to protein design with predetermined functional endpoints is an important unmet need of synthetic biology. Here, we screened the amino acid sequence landscape in search of sequence-signatures of allostery using Recurrence Quantitative Analysis (RQA) method. A characteristic vector, comprised of 10 features extracted from RQA was defined for amino acid sequences. Using Principal Component Analysis, four factors were found to be important determinants of allosteric behavior. Our sequence-based predictor method shows 82.6% accuracy, 85.7% sensitivity and 77.9% specificity with the current dataset. Further, we show that Laminarity-Mean-hydrophobicity representing repeated hydrophobic patches is the most crucial indicator of allostery. To our best knowledge this is the first report that describes sequence determinants of allostery based on hydrophobicity. As an outcome of these findings, we plan to explore possibility of inducing allostery in proteins.

A Potential Biofilm Metabolite Signature for Caries Activity - A Pilot Clinical Study

PubMed Central

Zandona, F; Soini, HA; Novotny, MV; Santiago, E; Eckert, GJ; Preisser, JS; Benecha, HK; Arthur, RA; Zero, DT

2016-01-01

Background This study's aim was to compare the dental biofilm metabolite-profile of caries-active (N=11) or caries-free (N=4) children by gas chromatography-mass spectrometry (GC/MS) analyses. Methods Samples collected after overnight fasting, with or without a previous glucose rinse, were combined for each child based on the caries status of the site, re-suspended in ethanol and analyzed by GC/MS. Results Biofilm from caries-active sites exhibited a different chromatographic profile compared to caries-free sites. Qualitative and quantitative analysis suggested a special cluster of branched alcohols and esters present at substantially higher intensity in biofilms of caries-active sites. Conclusions This pilot study indicates that there are metabolites present in the biofilm which have the potential to provide a characteristic metabolomics signature for caries activity. PMID:27885354

Weak fault detection and health degradation monitoring using customized standard multiwavelets

NASA Astrophysics Data System (ADS)

Yuan, Jing; Wang, Yu; Peng, Yizhen; Wei, Chenjun

2017-09-01

Due to the nonobvious symptoms contaminated by a large amount of background noise, it is challenging to beforehand detect and predictively monitor the weak faults for machinery security assurance. Multiwavelets can act as adaptive non-stationary signal processing tools, potentially viable for weak fault diagnosis. However, the signal-based multiwavelets suffer from such problems as the imperfect properties missing the crucial orthogonality, the decomposition distortion impossibly reflecting the relationships between the faults and signatures, the single objective optimization and independence for fault prognostic. Thus, customized standard multiwavelets are proposed for weak fault detection and health degradation monitoring, especially the weak fault signature quantitative identification. First, the flexible standard multiwavelets are designed using the construction method derived from scalar wavelets, seizing the desired properties for accurate detection of weak faults and avoiding the distortion issue for feature quantitative identification. Second, the multi-objective optimization combined three dimensionless indicators of the normalized energy entropy, normalized singular entropy and kurtosis index is introduced to the evaluation criterions, and benefits for selecting the potential best basis functions for weak faults without the influence of the variable working condition. Third, an ensemble health indicator fused by the kurtosis index, impulse index and clearance index of the original signal along with the normalized energy entropy and normalized singular entropy by the customized standard multiwavelets is achieved using Mahalanobis distance to continuously monitor the health condition and track the performance degradation. Finally, three experimental case studies are implemented to demonstrate the feasibility and effectiveness of the proposed method. The results show that the proposed method can quantitatively identify the fault signature of a slight rub on the inner race of a locomotive bearing, effectively detect and locate the potential failure from a complicated epicyclic gear train and successfully reveal the fault development and performance degradation of a test bearing in the lifetime.

Proton radiation-induced miRNA signatures in mouse blood: Characterization and comparison with 56Fe-ion and gamma radiation

PubMed Central

Templin, Thomas; Young, Erik F.; Smilenov, Lubomir B.

2013-01-01

Purpose Previously, we showed that microRNA (miRNA) signatures derived from the peripheral blood of mice are highly specific for both radiation energy (γ-rays or high linear energy transfer [LET] 56Fe ions) and radiation dose. Here, we investigate to what extent miRNA expression signatures derived from mouse blood can be used as biomarkers for exposure to 600 MeV proton radiation. Materials and methods We exposed mice to 600 MeV protons, using doses of 0.5 or 1.0 Gy, isolated total RNA at 6 h or 24 h after irradiation, and used quantitative real-time polymerase chain reaction (PCR) to determine the changes in miRNA expression. Results A total of 26 miRNA were differentially expressed after proton irradiation, in either one (77%) or multiple conditions (23%). Statistical classifiers based on proton, γ, and 56Fe-ion miRNA expression signatures predicted radiation type and proton dose with accuracies of 81% and 88%, respectively. Importantly, gene ontology analysis for proton-irradiated cells shows that genes targeted by radiation-induced miRNA are involved in biological processes and molecular functions similar to those controlled by miRNA in γ ray- and 56Fe-irradiated cells. Conclusions Mouse blood miRNA signatures induced by proton, γ, or 56Fe irradiation are radiation type- and dose-specific. These findings underline the complexity of the miRNA-mediated radiation response. PMID:22551419

27 CFR 73.11 - What are the required components and controls for acceptable electronic signatures?

Code of Federal Regulations, 2014 CFR

2014-04-01

... signatures not based on biometrics. If you use electronic signatures that are not based upon biometrics you...) Electronic signatures based on biometrics. If you use electronic signatures based upon biometrics, they must...

27 CFR 73.11 - What are the required components and controls for acceptable electronic signatures?

Code of Federal Regulations, 2012 CFR

2012-04-01

... signatures not based on biometrics. If you use electronic signatures that are not based upon biometrics you...) Electronic signatures based on biometrics. If you use electronic signatures based upon biometrics, they must...

27 CFR 73.11 - What are the required components and controls for acceptable electronic signatures?

Code of Federal Regulations, 2011 CFR

2011-04-01

... signatures not based on biometrics. If you use electronic signatures that are not based upon biometrics you...) Electronic signatures based on biometrics. If you use electronic signatures based upon biometrics, they must...

27 CFR 73.11 - What are the required components and controls for acceptable electronic signatures?

Code of Federal Regulations, 2013 CFR

2013-04-01

... signatures not based on biometrics. If you use electronic signatures that are not based upon biometrics you...) Electronic signatures based on biometrics. If you use electronic signatures based upon biometrics, they must...

Genotype-based gene signature of glioma risk.

PubMed

Huang, Yen-Tsung; Zhang, Yi; Wu, Zhijin; Michaud, Dominique S

2017-07-01

Glioma accounts for 80% of malignant brain tumors, but its etiologic determinants remain elusive. Despite genetic susceptibility loci identified by genome-wide association study (GWAS), the agnostic approach leaves open the possibility that other susceptibility genes remain to be discovered. Here we conduct a gene-centric integrative GWAS (iGWAS) of glioma risk that combines transcriptomics and genetics. We synthesized a brain transcriptomics dataset (n = 354), a GWAS dataset (n = 4203), and an advanced glioma tumor transcriptomic dataset (n = 483) to conduct an iGWAS. Using the expression quantitative trait loci (eQTL) dataset, we built models to predict gene expression for the GWAS data, based on eQTL genotypes. With the predicted gene expression, iGWAS analyses were performed using a novel statistical method. Gene signature risk score was constructed using a penalized logistic regression model. A total of 30527 transcripts were analyzed using the iGWAS approach. Four novel glioma susceptibility genes were identified with internal and external validation, including DRD5 (P = 3.0 × 10-79), WDR1 (P = 8.4 × 10-77), NOMO1 (P = 1.3 × 10-25), and PDXDC1 (P = 8.3 × 10-24). The genotype-predicted transcription pattern between cases and controls is consistent with that between tumor and its matched normal tissue. The genotype-based 4-gene signature improved the classification between glioma cases and controls based on age, gender, and population stratification, with area under the receiver operating characteristic curve increasing from 0.77 to 0.85 (P = 8.1 × 10-23). A new genotype-based gene signature of glioma was identified using a novel iGWAS approach, which integrates multiplatform genomic data as well as different genetic association studies. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Cancer Imaging Phenomics Toolkit (CaPTk) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CaPTk is a software toolkit to facilitate translation of quantitative image analysis methods that help us obtain rich imaging phenotypic signatures of oncologic images and relate them to precision diagnostics and prediction of clinical outcomes, as well as to underlying molecular characteristics of cancer. The stand-alone graphical user interface of CaPTk brings analysis methods from the realm of medical imaging research to the clinic, and will be extended to use web-based services for computationally-demanding pipelines.

A New Approach to Threshold Attribute Based Signatures

DTIC Science & Technology

2011-01-01

Inspired by developments in attribute based encryption and signatures, there has recently been a spurtof progress in the direction of threshold ...attribute based signatures (t-ABS). In this work we propose anovel approach to construct threshold attribute based signatures inspired by ring signatures...Thresholdattribute based signatures, dened by a (t; n) threshold predicate, ensure that the signer holds atleastt out of a specied set of n attributes

Semi-automated extraction of landslides in Taiwan based on SPOT imagery and DEMs

NASA Astrophysics Data System (ADS)

Eisank, Clemens; Hölbling, Daniel; Friedl, Barbara; Chen, Yi-Chin; Chang, Kang-Tsung

2014-05-01

The vast availability and improved quality of optical satellite data and digital elevation models (DEMs), as well as the need for complete and up-to-date landslide inventories at various spatial scales have fostered the development of semi-automated landslide recognition systems. Among the tested approaches for designing such systems, object-based image analysis (OBIA) stepped out to be a highly promising methodology. OBIA offers a flexible, spatially enabled framework for effective landslide mapping. Most object-based landslide mapping systems, however, have been tailored to specific, mainly small-scale study areas or even to single landslides only. Even though reported mapping accuracies tend to be higher than for pixel-based approaches, accuracy values are still relatively low and depend on the particular study. There is still room to improve the applicability and objectivity of object-based landslide mapping systems. The presented study aims at developing a knowledge-based landslide mapping system implemented in an OBIA environment, i.e. Trimble eCognition. In comparison to previous knowledge-based approaches, the classification of segmentation-derived multi-scale image objects relies on digital landslide signatures. These signatures hold the common operational knowledge on digital landslide mapping, as reported by 25 Taiwanese landslide experts during personal semi-structured interviews. Specifically, the signatures include information on commonly used data layers, spectral and spatial features, and feature thresholds. The signatures guide the selection and implementation of mapping rules that were finally encoded in Cognition Network Language (CNL). Multi-scale image segmentation is optimized by using the improved Estimation of Scale Parameter (ESP) tool. The approach described above is developed and tested for mapping landslides in a sub-region of the Baichi catchment in Northern Taiwan based on SPOT imagery and a high-resolution DEM. An object-based accuracy assessment is conducted by quantitatively comparing extracted landslide objects with landslide polygons that were visually interpreted by local experts. The applicability and transferability of the mapping system are evaluated by comparing initial accuracies with those achieved for the following two tests: first, usage of a SPOT image from the same year, but for a different area within the Baichi catchment; second, usage of SPOT images from multiple years for the same region. The integration of the common knowledge via digital landslide signatures is new in object-based landslide studies. In combination with strategies to optimize image segmentation this may lead to a more objective, transferable and stable knowledge-based system for the mapping of landslides from optical satellite data and DEMs.

Feature-based characterisation of signature topography in laser powder bed fusion of metals

NASA Astrophysics Data System (ADS)

Senin, Nicola; Thompson, Adam; Leach, Richard

2018-04-01

The use of state-of-the-art areal topography measurement instrumentation allows for a high level of detail in the acquisition of topographic information at micrometric scales. The 3D geometric models of surface topography obtained from measured data create new opportunities for the investigation of manufacturing processes through characterisation of the surfaces of manufactured parts. Conventional methods for quantitative assessment of topography usually only involve the computation of texture parameters, summary indicators of topography-related characteristics that are computed over the investigated area. However, further useful information may be obtained through characterisation of signature topographic formations, as more direct indicators of manufacturing process behaviour and performance. In this work, laser powder bed fusion of metals is considered. An original algorithmic method is proposed to isolate relevant topographic formations and to quantify their dimensional and geometric properties, using areal topography data acquired by state-of-the-art areal topography measurement instrumentation.

Wavelet-based multiscale analysis of bioimpedance data measured by electric cell-substrate impedance sensing for classification of cancerous and normal cells.

PubMed

Das, Debanjan; Shiladitya, Kumar; Biswas, Karabi; Dutta, Pranab Kumar; Parekh, Aditya; Mandal, Mahitosh; Das, Soumen

2015-12-01

The paper presents a study to differentiate normal and cancerous cells using label-free bioimpedance signal measured by electric cell-substrate impedance sensing. The real-time-measured bioimpedance data of human breast cancer cells and human epithelial normal cells employs fluctuations of impedance value due to cellular micromotions resulting from dynamic structural rearrangement of membrane protrusions under nonagitated condition. Here, a wavelet-based multiscale quantitative analysis technique has been applied to analyze the fluctuations in bioimpedance. The study demonstrates a method to classify cancerous and normal cells from the signature of their impedance fluctuations. The fluctuations associated with cellular micromotion are quantified in terms of cellular energy, cellular power dissipation, and cellular moments. The cellular energy and power dissipation are found higher for cancerous cells associated with higher micromotions in cancer cells. The initial study suggests that proposed wavelet-based quantitative technique promises to be an effective method to analyze real-time bioimpedance signal for distinguishing cancer and normal cells.

Polarimetric signature imaging of anisotropic bio-medical tissues

NASA Astrophysics Data System (ADS)

Wu, Stewart H.; Yang, De-Ming; Chiou, Arthur; Nee, Soe-Mie F.; Nee, Tsu-Wei

2010-02-01

Polarimetric imaging of Stokes vector (I, Q, U, V) can provide 4 independent signatures showing the linear and circular polarizations of biological tissues and cells. Using a recently developed Stokes digital imaging system, we measured the Stokes vector images of tissue samples from sections of rat livers containing normal portions and hematomas. The derived Mueller matrix elements can quantitatively provide multi-signature data of the bio-sample. This polarimetric optical technology is a new option of biosensing technology to inspect the structures of tissue samples, particularly for discriminating tumor and non-tumor biopsy. This technology is useful for critical disease discrimination and medical diagnostics applications.

High temperature polymer degradation: Rapid IR flow-through method for volatile quantification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giron, Nicholas H.; Celina, Mathew C.

Accelerated aging of polymers at elevated temperatures often involves the generation of volatiles. These can be formed as the products of oxidative degradation reactions or intrinsic pyrolytic decomposition as part of polymer scission reactions. A simple analytical method for the quantification of water, CO 2, and CO as fundamental signatures of degradation kinetics is required. Here, we describe an analytical framework and develops a rapid mid-IR based gas analysis methodology to quantify volatiles that are contained in small ampoules after aging exposures. The approach requires identification of unique spectral signatures, systematic calibration with known concentrations of volatiles, and a rapidmore » acquisition FTIR spectrometer for time resolved successive spectra. Furthermore, the volatiles are flushed out from the ampoule with dry N2 carrier gas and are then quantified through spectral and time integration. This method is sufficiently sensitive to determine absolute yields of ~50 μg water or CO 2, which relates to probing mass losses of less than 0.01% for a 1 g sample, i.e. the early stages in the degradation process. Such quantitative gas analysis is not easily achieved with other approaches. Our approach opens up the possibility of quantitative monitoring of volatile evolution as an avenue to explore polymer degradation kinetics and its dependence on time and temperature.« less

Quantitative Absorption and Kinetic Studies of Transient Species Using Gas Phase Optical Calorimetry

NASA Astrophysics Data System (ADS)

Melnik, Dmitry G.

2014-06-01

Quantitative measurements of the absorption cross-sections and reaction rates constants of free radicals by spectroscopic means requires the knowledge of the absolute concentration of the target species. We have demonstrated earlier that such information can be retrieved from absorption measurements of the well-known ``reporter" molecule, co-produced in radical synthesis. This method is limited to photochemical protocols allowing for production of ``reporters" stochiometrically with the target species. This limitation can be overcome by use of the optical calorimetry (OC) which measures heat signatures of a photochemical protocol. These heat signatures are directly related to the amount of species produced and the thermochemical data of the reactants and stable products whose accuracy is usually substantially higher than that of the absorption data for prospective ``reporters". The implementation of the OC method presented in this talk is based on the measurements of the frequency shift of the resonances due to the change in the optical density of the reactiove sample within a Fabry-Perot cavity caused by deposition of heat from the absorbed photolysis beam and subsequent chemical reactions. Preliminary results will be presented and future development of this experimental technique will be discussed. D. Melnik, R. Chhantyal-Pun and T. A. Miller, J. Phys. Chem. A, 114, 11583, (2010)

High temperature polymer degradation: Rapid IR flow-through method for volatile quantification

DOE PAGES

Giron, Nicholas H.; Celina, Mathew C.

2017-05-19

Accelerated aging of polymers at elevated temperatures often involves the generation of volatiles. These can be formed as the products of oxidative degradation reactions or intrinsic pyrolytic decomposition as part of polymer scission reactions. A simple analytical method for the quantification of water, CO 2, and CO as fundamental signatures of degradation kinetics is required. Here, we describe an analytical framework and develops a rapid mid-IR based gas analysis methodology to quantify volatiles that are contained in small ampoules after aging exposures. The approach requires identification of unique spectral signatures, systematic calibration with known concentrations of volatiles, and a rapidmore » acquisition FTIR spectrometer for time resolved successive spectra. Furthermore, the volatiles are flushed out from the ampoule with dry N2 carrier gas and are then quantified through spectral and time integration. This method is sufficiently sensitive to determine absolute yields of ~50 μg water or CO 2, which relates to probing mass losses of less than 0.01% for a 1 g sample, i.e. the early stages in the degradation process. Such quantitative gas analysis is not easily achieved with other approaches. Our approach opens up the possibility of quantitative monitoring of volatile evolution as an avenue to explore polymer degradation kinetics and its dependence on time and temperature.« less

Propagation of Dipolarization Signatures Observed by the Van Allen Probes in the Inner Magnetosphere

NASA Astrophysics Data System (ADS)

Ohtani, S.; Motoba, T.; Gkioulidou, M.; Takahashi, K.; Kletzing, C.

2017-12-01

Dipolarization, the change of the local magnetic field from a stretched to a more dipolar configuration, is one of the most fundamental processes of magnetospheric physics. It is especially critical for the dynamics of the inner magnetosphere. The associated electric field accelerates ions and electrons and transports them closer to Earth. Such injected ions intensify the ring current, and electrons constitute the seed population of the radiation belt. Those ions and electrons may also excite various waves that play important roles in the enhancement and loss of the radiation belt electrons. Despite such critical consequences, the general characteristics of dipolarization in the inner magnetosphere still remain to be understood. The Van Allen Probes mission, which consists of two probes that orbit through the equatorial region of the inner magnetosphere, provides an ideal opportunity to examine dipolarization signatures in the core of the ring current. In the present study we investigate the spatial expansion of the dipolarization region by examining the correlation and time delay of dipolarization signatures observed by the two probes. Whereas in general it requires three-point measurements to deduce the propagation of a signal on a certain plane, we statically examined the observed time delays and found that dipolarization signatures tend to propagate radially inward as well as away from midnight. In this paper we address the propagation of dipolarization signatures quantitatively and compare with the propagation velocities reported previously based on observations made farther away from Earth. We also discuss how often and under what conditions the dipolarization region expands.

Gene signature based on degradome-related genes can predict distal metastasis in cervical cancer patients.

PubMed

Fernandez-Retana, Jorge; Zamudio-Meza, Horacio; Rodriguez-Morales, Miguel; Pedroza-Torres, Abraham; Isla-Ortiz, David; Herrera, Luis; Jacobo-Herrera, Nadia; Peralta-Zaragoza, Oscar; López-Camarillo, César; Morales-Gonzalez, Fermin; Cantu de Leon, David; Pérez-Plasencia, Carlos

2017-06-01

Cervical cancer is one of the leading causes of death in women worldwide, which mainly affects developing countries. The patients who suffer a recurrence and/or progression disease have a higher risk of developing distal metastases. Proteases comprising the degradome given its ability to promote cell growth, migration, and invasion of tissues play an important role during tumor development and progression. In this study, we used high-density microarrays and quantitative reverse transcriptase polymerase chain reaction to evaluate the degradome profile and their inhibitors in 112 samples of patients diagnosed with locally advanced cervical cancer. Clinical follow-up was done during a period of 3 years. Using a correlation analysis between the response to treatment and the development of metastasis, we established a molecular signature comprising eight degradome-related genes (FAM111B, FAM111A, CFB, PSMB8, PSMB9, CASP7, PRSS16, and CD74) with the ability to discriminate patients at risk of distal metastases. In conclusion, present results show that molecular signature obtained from degradome genes can predict the possibility of metastasis in patients with locally advanced cervical cancer.

Medical imaging and computers in the diagnosis of breast cancer

NASA Astrophysics Data System (ADS)

Giger, Maryellen L.

2014-09-01

Computer-aided diagnosis (CAD) and quantitative image analysis (QIA) methods (i.e., computerized methods of analyzing digital breast images: mammograms, ultrasound, and magnetic resonance images) can yield novel image-based tumor and parenchyma characteristics (i.e., signatures that may ultimately contribute to the design of patient-specific breast cancer management plans). The role of QIA/CAD has been expanding beyond screening programs towards applications in risk assessment, diagnosis, prognosis, and response to therapy as well as in data mining to discover relationships of image-based lesion characteristics with genomics and other phenotypes; thus, as they apply to disease states. These various computer-based applications are demonstrated through research examples from the Giger Lab.

*K-means and cluster models for cancer signatures.

PubMed

Kakushadze, Zura; Yu, Willie

2017-09-01

We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means' computational cost is a fraction of NMF's. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have especially high within-cluster correlations with 11 other cancers indicating common underlying structures. Our approach opens a novel avenue for studying such structures. *K-means is universal and can be applied in other fields. We discuss some potential applications in quantitative finance.

Quantitative mapping of suspended solids in wastewater sludge plumes in the New York Bight apex

NASA Technical Reports Server (NTRS)

Johnson, R. W.; Duedall, I. W.; Glasgow, R. M.; Proni, J. R.; Nelsen, T. A.

1977-01-01

The purpose of this investigation was to apply the previously reported methodology to remotely sensed data that were collected over wastewater sludge plumes in the New York Bight apex on September 22, 1975. Spectral signatures were also determined during this study. These signatures may be useful in the specific identification of sludge plumes, as opposed to other plumes such as those created by the disposal of industrial acid wastes.

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

PubMed

Arntzen, Magnus Ø; Koehler, Christian J; Barsnes, Harald; Berven, Frode S; Treumann, Achim; Thiede, Bernd

2011-02-04

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing

PubMed Central

Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; Martínez de la Vega, Octavio; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C.; Vielle-Calzada, Jean-Philippe

2012-01-01

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies. PMID:22442422

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing.

PubMed

Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; de la Vega, Octavio Martínez; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C; Vielle-Calzada, Jean-Philippe

2012-06-01

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts.

PubMed

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2013-06-01

To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values≤false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 post-anakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts

PubMed Central

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2014-01-01

Objective To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. Methods We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values ≤ false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Results Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 postanakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. Conclusions We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra. PMID:23223423

Pilot study for supervised target detection applied to spatially registered multiparametric MRI in order to non-invasively score prostate cancer.

PubMed

Mayer, Rulon; Simone, Charles B; Skinner, William; Turkbey, Baris; Choykey, Peter

2018-03-01

Gleason Score (GS) is a validated predictor of prostate cancer (PCa) disease progression and outcomes. GS from invasive needle biopsies suffers from significant inter-observer variability and possible sampling error, leading to underestimating disease severity ("underscoring") and can result in possible complications. A robust non-invasive image-based approach is, therefore, needed. Use spatially registered multi-parametric MRI (MP-MRI), signatures, and supervised target detection algorithms (STDA) to non-invasively GS PCa at the voxel level. This study retrospectively analyzed 26 MP-MRI from The Cancer Imaging Archive. The MP-MRI (T2, Diffusion Weighted, Dynamic Contrast Enhanced) were spatially registered to each other, combined into stacks, and stitched together to form hypercubes. Multi-parametric (or multi-spectral) signatures derived from a training set of registered MP-MRI were transformed using statistics-based Whitening-Dewhitening (WD). Transformed signatures were inserted into STDA (having conical decision surfaces) applied to registered MP-MRI determined the tumor GS. The MRI-derived GS was quantitatively compared to the pathologist's assessment of the histology of sectioned whole mount prostates from patients who underwent radical prostatectomy. In addition, a meta-analysis of 17 studies of needle biopsy determined GS with confusion matrices and was compared to the MRI-determined GS. STDA and histology determined GS are highly correlated (R = 0.86, p < 0.02). STDA more accurately determined GS and reduced GS underscoring of PCa relative to needle biopsy as summarized by meta-analysis (p < 0.05). This pilot study found registered MP-MRI, STDA, and WD transforms of signatures shows promise in non-invasively GS PCa and reducing underscoring with high spatial resolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative evaluation of hidden defects in cast iron components using ultrasound activated lock-in vibrothermography.

PubMed

Montanini, R; Freni, F; Rossi, G L

2012-09-01

This paper reports one of the first experimental results on the application of ultrasound activated lock-in vibrothermography for quantitative assessment of buried flaws in complex cast parts. The use of amplitude modulated ultrasonic heat generation allowed selective response of defective areas within the part, as the defect itself is turned into a local thermal wave emitter. Quantitative evaluation of hidden damages was accomplished by estimating independently both the area and the depth extension of the buried flaws, while x-ray 3D computed tomography was used as reference for sizing accuracy assessment. To retrieve flaw's area, a simple yet effective histogram-based phase image segmentation algorithm with automatic pixels classification has been developed. A clear correlation was found between the thermal (phase) signature measured by the infrared camera on the target surface and the actual mean cross-section area of the flaw. Due to the very fast cycle time (<30 s/part), the method could potentially be applied for 100% quality control of casting components.

[Investigation of quantitative detection of water quality using spectral fluorescence signature].

PubMed

He, Jun-hua; Cheng, Yong-jin; Han, Yan-ling; Zhang, Hao; Yang, Tao

2008-08-01

A method of spectral analysis, which can simultaneously detect dissolved organic matter (DOM) and chlorophyll a (Chl-a) in natural water, was developed in the present paper with the intention of monitoring water quality fast and quantitatively. Firstly, the total luminescence spectra (TLS) of water sample from East Lake in Wuhan city were measured by the use of laser (532 nm) induced fluorescence (LIF). There were obvious peaks of relative intensity at the wavelength value of 580, 651 and 687 nm in the TLS of the sample, which correspond respectively to spectra of DOM, and the Raman scattering of water and Chl-a in the water. Then the spectral fluorescence signature (SFS) technique was adopted to analyze and distinguish spectral characteristics of DOM and Chl-a in natural water. The calibration curves and function expressions, which indicate the relation between the normalized fluorescence intensities of DOM and Chl-a in water and their concentrations, were obtained respectively under the condition of low concentration(< 40 mg x L(-1))by using normalization of Raman scattering spectrum of water. The curves have a high linearity. When the concentration of the solution with humic acid is large (> 40 mg x L(-1)), the Raman scattering signal is totally absorbed by the molecules of humic acid being on the ground state, so the normalization technique can not be adopted. However the function expression between the concentration of the solution with humic acid and its relative fluorescence peak intensity can be acquired directly with the aid of experiment of fluorescence spectrum. It is concluded that although the expression is non-linearity as a whole, there is a excellent linear relation between the fluorescence intensity and concentration of DOM when the concentration is less than 200 mg x L(-1). The method of measurement based on spectral fluorescence signature technique and the calibration curves gained will have prospects of broad application. It can recognize fast what pollutants are and detect quantitatively their contents in water. It is realizable to monitor the quality of natural water with real time, dynamics and inlarge area.

Identification of host response signatures of infection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branda, Steven S.; Sinha, Anupama; Bent, Zachary

2013-02-01

Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to themore » pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for large-scale, highly-efficient efforts to identify and verify infection-specific host NA signatures in human populations.« less

Proteomics assisted profiling of antimicrobial peptide signatures from black pepper (Piper nigrum L.).

PubMed

Umadevi, P; Soumya, M; George, Johnson K; Anandaraj, M

2018-05-01

Plant antimicrobial peptides are the interesting source of studies in defense response as they are essential components of innate immunity which exert rapid defense response. In spite of abundant reports on the isolation of antimicrobial peptides (AMPs) from many sources, the profile of AMPs expressed/identified from single crop species under certain stress/physiological condition is still unknown. This work describes the AMP signature profile of black pepper and their expression upon Phytophthora infection using label-free quantitative proteomics strategy. The differential expression of 24 AMPs suggests that a combinatorial strategy is working in the defense network. The 24 AMP signatures belonged to the cationic, anionic, cysteine-rich and cysteine-free group. As the first report on the possible involvement of AMP signature in Phytophthora infection, our results offer a platform for further study on regulation, evolutionary importance and exploitation of theses AMPs as next generation molecules against pathogens.

Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity.

PubMed

Kaufman, Alon; Dror, Gideon; Meilijson, Isaac; Ruppin, Eytan

2006-12-08

The claim that genetic properties of neurons significantly influence their synaptic network structure is a common notion in neuroscience. The nematode Caenorhabditis elegans provides an exciting opportunity to approach this question in a large-scale quantitative manner. Its synaptic connectivity network has been identified, and, combined with cellular studies, we currently have characteristic connectivity and gene expression signatures for most of its neurons. By using two complementary analysis assays we show that the expression signature of a neuron carries significant information about its synaptic connectivity signature, and identify a list of putative genes predicting neural connectivity. The current study rigorously quantifies the relation between gene expression and synaptic connectivity signatures in the C. elegans nervous system and identifies subsets of neurons where this relation is highly marked. The results presented and the genes identified provide a promising starting point for further, more detailed computational and experimental investigations.

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

PubMed Central

Tan, Cheemeng; Smith, Robert Phillip; Tsai, Ming-Chi; Schwartz, Russell; You, Lingchong

2014-01-01

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains. PMID:25101949

Signature Verification Based on Handwritten Text Recognition

NASA Astrophysics Data System (ADS)

Viriri, Serestina; Tapamo, Jules-R.

Signatures continue to be an important biometric trait because it remains widely used primarily for authenticating the identity of human beings. This paper presents an efficient text-based directional signature recognition algorithm which verifies signatures, even when they are composed of special unconstrained cursive characters which are superimposed and embellished. This algorithm extends the character-based signature verification technique. The experiments carried out on the GPDS signature database and an additional database created from signatures captured using the ePadInk tablet, show that the approach is effective and efficient, with a positive verification rate of 94.95%.

Genetic parameters and signatures of selection in two divergent laying hen lines selected for feather pecking behaviour.

PubMed

Grams, Vanessa; Wellmann, Robin; Preuß, Siegfried; Grashorn, Michael A; Kjaer, Jörgen B; Bessei, Werner; Bennewitz, Jörn

2015-09-30

Feather pecking (FP) in laying hens is a well-known and multi-factorial behaviour with a genetic background. In a selection experiment, two lines were developed for 11 generations for high (HFP) and low (LFP) feather pecking, respectively. Starting with the second generation of selection, there was a constant difference in mean number of FP bouts between both lines. We used the data from this experiment to perform a quantitative genetic analysis and to map selection signatures. Pedigree and phenotypic data were available for the last six generations of both lines. Univariate quantitative genetic analyses were conducted using mixed linear and generalized mixed linear models assuming a Poisson distribution. Selection signatures were mapped using 33,228 single nucleotide polymorphisms (SNPs) genotyped on 41 HFP and 34 LFP individuals of generation 11. For each SNP, we estimated Wright's fixation index (FST). We tested the null hypothesis that FST is driven purely by genetic drift against the alternative hypothesis that it is driven by genetic drift and selection. The mixed linear model failed to analyze the LFP data because of the large number of 0s in the observation vector. The Poisson model fitted the data well and revealed a small but continuous genetic trend in both lines. Most of the 17 genome-wide significant SNPs were located on chromosomes 3 and 4. Thirteen clusters with at least two significant SNPs within an interval of 3 Mb maximum were identified. Two clusters were mapped on chromosomes 3, 4, 8 and 19. Of the 17 genome-wide significant SNPs, 12 were located within the identified clusters. This indicates a non-random distribution of significant SNPs and points to the presence of selection sweeps. Data on FP should be analysed using generalised linear mixed models assuming a Poisson distribution, especially if the number of FP bouts is small and the distribution is heavily peaked at 0. The FST-based approach was suitable to map selection signatures that need to be confirmed by linkage or association mapping.

Magnetoresistive biosensors for quantitative proteomics

NASA Astrophysics Data System (ADS)

Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

2017-08-01

Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

Multiple-Line Inference of Selection on Quantitative Traits

PubMed Central

Riedel, Nico; Khatri, Bhavin S.; Lässig, Michael; Berg, Johannes

2015-01-01

Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population genetics test for selection acting on a quantitative trait that is based on multiple-line crosses. We show that using multiple lines increases both the power and the scope of selection inferences. First, a test based on three or more lines detects selection with strongly increased statistical significance, and we show explicitly how the sensitivity of the test depends on the number of lines. Second, a multiple-line test can distinguish between different lineage-specific selection scenarios. Our analytical results are complemented by extensive numerical simulations. We then apply the multiple-line test to QTL data on floral character traits in plant species of the Mimulus genus and on photoperiodic traits in different maize strains, where we find a signature of lineage-specific selection not seen in two-line tests. PMID:26139839

Nest signature changes throughout colony cycle and after social parasite invasion in social wasps

PubMed Central

Blancato, Giuliano; Picchi, Laura; Lucas, Christophe

2017-01-01

Social insects recognize their nestmates by means of a cuticular hydrocarbon signature shared by colony members, but how nest signature changes across time has been rarely tested in longitudinal studies and in the field. In social wasps, the chemical signature is also deposited on the nest surface, where it is used by newly emerged wasps as a reference to learn their colony odor. Here, we investigate the temporal variations of the chemical signature that wasps have deposited on their nests. We followed the fate of the colonies of the social paper wasp Polistes biglumis in their natural environment from colony foundation to decline. Because some colonies were invaded by the social parasite Polistes atrimandibularis, we also tested the effects of social parasites on the nest signature. We observed that, as the season progresses, the nest signature changed; the overall abundance of hydrocarbons as well as the proportion of longer-chain and branched hydrocarbons increased. Where present, social parasites altered the host-nest signature qualitatively (adding parasite-specific alkenes) and quantitatively (by interfering with the increase in overall hydrocarbon abundance). Our results show that 1) colony odor is highly dynamic both in colonies controlled by legitimate foundresses and in those controlled by social parasites; 2) emerged offspring contribute little to colony signature, if at all, in comparison to foundresses; and 3) social parasites, that later mimic host signature, initially mark host nests with species-specific hydrocarbons. This study implies that important updating of the neural template used in nestmate recognition should occur in social insects. PMID:29261775

From High-Throughput Microarray-Based Screening to Clinical Application: The Development of a Second Generation Multigene Test for Breast Cancer Prognosis

PubMed Central

Brase, Jan C.; Kronenwett, Ralf; Petry, Christoph; Denkert, Carsten; Schmidt, Marcus

2013-01-01

Several multigene tests have been developed for breast cancer patients to predict the individual risk of recurrence. Most of the first generation tests rely on proliferation-associated genes and are commonly carried out in central reference laboratories. Here, we describe the development of a second generation multigene assay, the EndoPredict test, a prognostic multigene expression test for estrogen receptor (ER) positive, human epidermal growth factor receptor (HER2) negative (ER+/HER2−) breast cancer patients. The EndoPredict gene signature was initially established in a large high-throughput microarray-based screening study. The key steps for biomarker identification are discussed in detail, in comparison to the establishment of other multigene signatures. After biomarker selection, genes and algorithms were transferred to a diagnostic platform (reverse transcription quantitative PCR (RT-qPCR)) to allow for assaying formalin-fixed, paraffin-embedded (FFPE) samples. A comprehensive analytical validation was performed and a prospective proficiency testing study with seven pathological laboratories finally proved that EndoPredict can be reliably used in the decentralized setting. Three independent large clinical validation studies (n = 2,257) demonstrated that EndoPredict offers independent prognostic information beyond current clinicopathological parameters and clinical guidelines. The review article summarizes several important steps that should be considered for the development process of a second generation multigene test and offers a means for transferring a microarray signature from the research laboratory to clinical practice. PMID:27605191

New insights into the diets of harbor seals in the Salish Sea revealed by quantitative fatty acid signature analysis

USGS Publications Warehouse

Bromaghin, Jeffrey F.; Lance, Monique M.; Elliott, Elizabeth W.; Jeffries, Steven J.; Acevedo-Gutiérrez, Alejandro; Kennish, John M.

2013-01-01

Harbor seals (Phoca vitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available information on harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

Hair sterol signatures coupled to multivariate data analysis reveal an increased 7β-hydroxycholesterol production in cognitive impairment.

PubMed

Son, Hyun-Hwa; Lee, Do-Yup; Seo, Hong Seog; Jeong, Jihyeon; Moon, Ju-Yeon; Lee, Jung-Eun; Chung, Bong Chul; Kim, Eosu; Choi, Man Ho

2016-01-01

Altered cholesterol metabolism could be associated with cognitive impairment. The quantitative profiling of 19 hair sterols was developed using gas chromatography-mass spectrometry coupled to multivariate data analysis. The limit of quantification of all sterols ranged from 5 to 20 ng/g, while the calibration linearity was higher than 0.98. The precision (% CV) and accuracy (% bias) ranged from 3.2% to 9.8% and from 83.2% to 119.4%, respectively. Among the sterols examined, 8 were quantitatively detected from two strands of 3-cm-long scalp hair samples of female participants, including mild cognitive impairment (MCI, n=15), Alzheimer's disease (AD, n=31), and healthy controls (HC, n=36). The cognitive impairment (MCI or AD) was correlated with a higher metabolic rate than that of HCs based on 7β-hydroxycholesterol (P<0.005). Significant negative correlations (r=-0.822) were detected between Mini-Mental State Examination (MMSE) scores and hair sample metabolic ratios of 7β-hydroxycholesterol to cholesterol, which is an accepted, sensitive, and specific tool for discriminating HCs from individuals with MCI or AD. In conclusion, improved diagnostic values can be obtained using hair sterol signatures coupled with MMSE scores. This method may prove useful for predictive diagnosis in population screening of cognitive impairment. Copyright © 2015 Elsevier Ltd. All rights reserved.

21 CFR 11.200 - Electronic signature components and controls.

Code of Federal Regulations, 2011 CFR

2011-04-01

... signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1... signatures based upon biometrics shall be designed to ensure that they cannot be used by anyone other than...

21 CFR 11.200 - Electronic signature components and controls.

Code of Federal Regulations, 2013 CFR

2013-04-01

... signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1... signatures based upon biometrics shall be designed to ensure that they cannot be used by anyone other than...

21 CFR 11.200 - Electronic signature components and controls.

Code of Federal Regulations, 2012 CFR

2012-04-01

... signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1... signatures based upon biometrics shall be designed to ensure that they cannot be used by anyone other than...

21 CFR 11.200 - Electronic signature components and controls.

Code of Federal Regulations, 2014 CFR

2014-04-01

... signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1... signatures based upon biometrics shall be designed to ensure that they cannot be used by anyone other than...

Quantum dot nanoprobe-based quantitative analysis for prostate cancer (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kang, Benedict J.; Jang, Gun Hyuk; Park, Sungwook; Lee, Kwan Hyi

2016-09-01

Prostate cancer causes one of the leading cancer-related deaths among the Caucasian adult males in Europe and the United State of America. However, it has a high recovery rate indicating when a proper treatment is delivered to a patient. There are cases of over- or under-treatments which exacerbate the disease states indicating the importance of proper therapeutic approach depending on stage of the disease. Recognition of the unmet needs has raised a need for stratification of the disease. There have been attempts to stratify based on biomarker expression patterns in the course of disease progression. To closely observe the biomarker expression patterns, we propose the use of quantitative imaging method by using fabricated quantum dot-based nanoprobe to quantify biomarker expression on the surface of prostate cancer cells. To characterize the cell line and analyze the biomarker levels, cluster of differentiation 44 (CD 44), prostate specific membrane antigen (PSMA), and epithelial cell adhesion molecule (EpCAM) are used. Each selected biomarker per cell line has been quantified from which we established a signature of biomarkers of a prostate cancer cell line.

Identity-Based Verifiably Encrypted Signatures without Random Oracles

NASA Astrophysics Data System (ADS)

Zhang, Lei; Wu, Qianhong; Qin, Bo

Fair exchange protocol plays an important role in electronic commerce in the case of exchanging digital contracts. Verifiably encrypted signatures provide an optimistic solution to these scenarios with an off-line trusted third party. In this paper, we propose an identity-based verifiably encrypted signature scheme. The scheme is non-interactive to generate verifiably encrypted signatures and the resulting encrypted signature consists of only four group elements. Based on the computational Diffie-Hellman assumption, our scheme is proven secure without using random oracles. To the best of our knowledge, this is the first identity-based verifiably encrypted signature scheme provably secure in the standard model.

Quantifying uncertainties in streamflow predictions through signature based inference of hydrological model parameters

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Reichert, Peter; Kavetski, Dmitri; Albert, Calro

2016-04-01

The calibration of hydrological models based on signatures (e.g. Flow Duration Curves - FDCs) is often advocated as an alternative to model calibration based on the full time series of system responses (e.g. hydrographs). Signature based calibration is motivated by various arguments. From a conceptual perspective, calibration on signatures is a way to filter out errors that are difficult to represent when calibrating on the full time series. Such errors may for example occur when observed and simulated hydrographs are shifted, either on the "time" axis (i.e. left or right), or on the "streamflow" axis (i.e. above or below). These shifts may be due to errors in the precipitation input (time or amount), and if not properly accounted in the likelihood function, may cause biased parameter estimates (e.g. estimated model parameters that do not reproduce the recession characteristics of a hydrograph). From a practical perspective, signature based calibration is seen as a possible solution for making predictions in ungauged basins. Where streamflow data are not available, it may in fact be possible to reliably estimate streamflow signatures. Previous research has for example shown how FDCs can be reliably estimated at ungauged locations based on climatic and physiographic influence factors. Typically, the goal of signature based calibration is not the prediction of the signatures themselves, but the prediction of the system responses. Ideally, the prediction of system responses should be accompanied by a reliable quantification of the associated uncertainties. Previous approaches for signature based calibration, however, do not allow reliable estimates of streamflow predictive distributions. Here, we illustrate how the Bayesian approach can be employed to obtain reliable streamflow predictive distributions based on signatures. A case study is presented, where a hydrological model is calibrated on FDCs and additional signatures. We propose an approach where the likelihood function for the signatures is derived from the likelihood for streamflow (rather than using an "ad-hoc" likelihood for the signatures as done in previous approaches). This likelihood is not easily tractable analytically and we therefore cannot apply "simple" MCMC methods. This numerical problem is solved using Approximate Bayesian Computation (ABC). Our result indicate that the proposed approach is suitable for producing reliable streamflow predictive distributions based on calibration to signature data. Moreover, our results provide indications on which signatures are more appropriate to represent the information content of the hydrograph.

Quantitative use of multiincidence-angle SAR for geologic mapping

NASA Technical Reports Server (NTRS)

Farr, T. G.; Albee, A. L.; Evans, D. L.; Solomon, J. E.; Daily, M. I.; Labotka, T. C.; Smith, M. O.

1984-01-01

It is proposed that techniques be developed and used for quantitative interpretation of shuttle imaging radar-B (SIR-B) data for lithologic identification and mapping. The use of backscatter versus incidence angle signatures derived from SIR-B images is to be investigated. The use of SIR-B with other sensors for geologic mapping is also to be considered. Anticipated results are discussed in terms of geologic mapping.

Quantitative imaging of disease signatures through radioactive decay signal conversion

PubMed Central

Thorek, Daniel LJ; Ogirala, Anuja; Beattie, Bradley J; Grimm, Jan

2013-01-01

In the era of personalized medicine there is an urgent need for in vivo techniques able to sensitively detect and quantify molecular activities. Sensitive imaging of gamma rays is widely used, but radioactive decay is a physical constant and signal is independent of biological interactions. Here we introduce a framework of novel targeted and activatable probes excited by a nuclear decay-derived signal to identify and measure molecular signatures of disease. This was accomplished utilizing Cerenkov luminescence (CL), the light produced by β-emitting radionuclides such as clinical positron emission tomography (PET) tracers. Disease markers were detected using nanoparticles to produce secondary Cerenkov-induced fluorescence. This approach reduces background signal compared to conventional fluorescence imaging. In addition to information from a PET scan, we demonstrate novel medical utility by quantitatively determining prognostically relevant enzymatic activity. This technique can be applied to monitor other markers and facilitates a shift towards activatable nuclear medicine agents. PMID:24013701

New approaches to investigating social gestures in autism spectrum disorder

PubMed Central

2012-01-01

The combination of economic games and human neuroimaging presents the possibility of using economic probes to identify biomarkers for quantitative features of healthy and diseased cognition. These probes span a range of important cognitive functions, but one new use is in the domain of reciprocating social exchange with other humans - a capacity perturbed in a number of psychopathologies. We summarize the use of a reciprocating exchange game to elicit neural and behavioral signatures for subjects diagnosed with autism spectrum disorder (ASD). Furthermore, we outline early efforts to capture features of social exchange in computational models and use these to identify quantitative behavioral differences between subjects with ASD and matched controls. Lastly, we summarize a number of subsequent studies inspired by the modeling results, which suggest new neural and behavioral signatures that could be used to characterize subtle deficits in information processing during interactions with other humans. PMID:22958572

A Quantitative ADME-base Tool for Exploring Human ...

EPA Pesticide Factsheets

Exposure to a wide range of chemicals through our daily habits and routines is ubiquitous and largely unavoidable within modern society. The potential for human exposure, however, has not been quantified for the vast majority of chemicals with wide commercial use. Creative advances in exposure science are needed to support efficient and effective evaluation and management of chemical risks, particularly for chemicals in consumer products. The U.S. Environmental Protection Agency Office of Research and Development is developing, or collaborating in the development of, scientifically-defensible methods for making quantitative or semi-quantitative exposure predictions. The Exposure Prioritization (Ex Priori) model is a simplified, quantitative visual dashboard that provides a rank-ordered internalized dose metric to simultaneously explore exposures across chemical space (not chemical by chemical). Diverse data streams are integrated within the interface such that different exposure scenarios for “individual,” “population,” or “professional” time-use profiles can be interchanged to tailor exposure and quantitatively explore multi-chemical signatures of exposure, internalized dose (uptake), body burden, and elimination. Ex Priori has been designed as an adaptable systems framework that synthesizes knowledge from various domains and is amenable to new knowledge/information. As such, it algorithmically captures the totality of exposure across pathways. It

Detecting of transient vibration signatures using an improved fast spatial-spectral ensemble kurtosis kurtogram and its applications to mechanical signature analysis of short duration data from rotating machinery

NASA Astrophysics Data System (ADS)

Chen, BinQiang; Zhang, ZhouSuo; Zi, YanYang; He, ZhengJia; Sun, Chuang

2013-10-01

Detecting transient vibration signatures is of vital importance for vibration-based condition monitoring and fault detection of the rotating machinery. However, raw mechanical signals collected by vibration sensors are generally mixtures of physical vibrations of the multiple mechanical components installed in the examined machinery. Fault-generated incipient vibration signatures masked by interfering contents are difficult to be identified. The fast kurtogram (FK) is a concise and smart gadget for characterizing these vibration features. The multi-rate filter-bank (MRFB) and the spectral kurtosis (SK) indicator of the FK are less powerful when strong interfering vibration contents exist, especially when the FK are applied to vibration signals of short duration. It is encountered that the impulsive interfering contents not authentically induced by mechanical faults complicate the optimal analyzing process and lead to incorrect choosing of the optimal analysis subband, therefore the original FK may leave out the essential fault signatures. To enhance the analyzing performance of FK for industrial applications, an improved version of fast kurtogram, named as "fast spatial-spectral ensemble kurtosis kurtogram", is presented. In the proposed technique, discrete quasi-analytic wavelet tight frame (QAWTF) expansion methods are incorporated as the detection filters. The QAWTF, constructed based on dual tree complex wavelet transform, possesses better vibration transient signature extracting ability and enhanced time-frequency localizability compared with conventional wavelet packet transforms (WPTs). Moreover, in the constructed QAWTF, a non-dyadic ensemble wavelet subband generating strategy is put forward to produce extra wavelet subbands that are capable of identifying fault features located in transition-band of WPT. On the other hand, an enhanced signal impulsiveness evaluating indicator, named "spatial-spectral ensemble kurtosis" (SSEK), is put forward and utilized as the quantitative measure to select optimal analyzing parameters. The SSEK indicator is robuster in evaluating the impulsiveness intensity of vibration signals due to its better suppressing ability of Gaussian noise, harmonics and sporadic impulsive shocks. Numerical validations, an experimental test and two engineering applications were used to verify the effectiveness of the proposed technique. The analyzing results of the numerical validations, experimental tests and engineering applications demonstrate that the proposed technique possesses robuster transient vibration content detecting performance in comparison with the original FK and the WPT-based FK method, especially when they are applied to the processing of vibration signals of relative limited duration.

Research on Signature Verification Method Based on Discrete Fréchet Distance

NASA Astrophysics Data System (ADS)

Fang, J. L.; Wu, W.

2018-05-01

This paper proposes a multi-feature signature template based on discrete Fréchet distance, which breaks through the limitation of traditional signature authentication using a single signature feature. It solves the online handwritten signature authentication signature global feature template extraction calculation workload, signature feature selection unreasonable problem. In this experiment, the false recognition rate (FAR) and false rejection rate (FRR) of the statistical signature are calculated and the average equal error rate (AEER) is calculated. The feasibility of the combined template scheme is verified by comparing the average equal error rate of the combination template and the original template.

Effect of baking and fermentation on the stable carbon and nitrogen isotope ratios of grain-based food.

PubMed

Bostic, Joshua N; Palafox, Sherilyn J; Rottmueller, Marina E; Jahren, A Hope

2015-05-30

Isotope ratio mass spectrometry (IRMS) is used extensively to reconstruct general attributes of prehistoric and modern diets in both humans and animals. In order to apply these methods to the accurate determination of specific intakes of foods/nutrients of interest, the isotopic signature of individually consumed foods must be constrained. For example, 86% of the calories consumed in the USA are derived from processed and prepared foods, but the relationship between the stable isotope composition of raw ingredients and the resulting products has not been characterized. To examine the effect of common cooking techniques on the stable isotope composition of grain-based food items, we prepared yeast buns and sugar cookies from standardized recipes and measured bulk δ(13) C and δ(15) N values of samples collected throughout a 75 min fermentation process (buns) and before and after baking at 190°C (buns and cookies). Simple isotope mixing models were used to determine if the isotopic signatures of 13 multi-ingredient foods could be estimated from the isotopic signatures of their constituent raw ingredients. No variations in δ(13) C or δ(15) N values were detected between pre- and post-baked yeast buns (pre: -24.78‰/2.61‰, post: -24.75‰/2.74‰), beet-sugar cookies (pre: -24.48‰/3.84‰, post: -24.47‰/3.57‰), and cane-sugar cookies (pre: -19.07‰/2.97‰, post: -19.02‰/3.21‰), or throughout a 75 min fermentation process in yeast buns. Using isotopic mass balance equations, the δ(13) C/δ(15) N values of multi-ingredient foods were estimated from the isotopic composition of constituent raw ingredients to within 0.14 ± 0.13‰/0.24 ± 0.17‰ for gravimetrically measured recipes and 0.40 ± 0.38‰/0.58 ± 0.53‰ for volumetrically measured recipes. Two common food preparation techniques, baking and fermentation, do not substantially affect the carbon or nitrogen isotopic signature of grain-based foods. Mass-balance equations can be used to accurately estimate the isotopic signature of multi-ingredient food items for which quantitative ingredient information is available. Copyright © 2015 John Wiley & Sons, Ltd.

Quantitative proteome analysis using isobaric peptide termini labeling (IPTL).

PubMed

Arntzen, Magnus O; Koehler, Christian J; Treumann, Achim; Thiede, Bernd

2011-01-01

The quantitative comparison of proteome level changes across biological samples has become an essential feature in proteomics that remains challenging. We have recently introduced isobaric peptide termini labeling (IPTL), a novel strategy for isobaric quantification based on the derivatization of peptide termini with complementary isotopically labeled reagents. Unlike non-isobaric quantification methods, sample complexity at the MS level is not increased, providing improved sensitivity and protein coverage. The distinguishing feature of IPTL when comparing it to more established isobaric labeling methods (iTRAQ and TMT) is the presence of quantification signatures in all sequence-determining ions in MS/MS spectra, not only in the low mass reporter ion region. This makes IPTL a quantification method that is accessible to mass spectrometers with limited capabilities in the low mass range. Also, the presence of several quantification points in each MS/MS spectrum increases the robustness of the quantification procedure.

Induced Polarization Signature of Biofilms in Porous Media: From Laboratory Experiments to Theoretical Developments and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atekwana, Estella; Patrauchan, Marianna; Revil, Andre

2016-10-04

Bioremediation strategies for mitigating the transport of heavy metals and radionuclides in subsurface sediments have largely targeted the use of dissimilatory metal and sulfate-reducing bacteria. Growth and metabolic activities from these organisms can significantly influence biogeochemical processes, including mineral dissolution/precipitation, fluctuating pH and redox potential (Eh) values, development of biofilms, and decreasing hydraulic conductivity. The Spectral Induced Polarization (SIP) technique has emerged as the technique most sensitive to the presence of microbial cells and biofilms in porous media; yet it is often difficult to unambiguously distinguish the impact of multiple and often competing processes that occur during in-situ biostimulation activitiesmore » on the SIP signatures. The main goal of our project is to quantitatively characterize major components within bacterial biofilms (cells, DNA, metals, metabolites etc.) contributing to detectable SIP signatures. We specifically: (i) evaluated the contribution of biofilm components to SIP signatures, (ii) determined the contribution of biogenic minerals commonly found in biofilms to SIP signatures, (iii) determined if the SIP signatures can be used to quantify the rates of biofilm formation, (iv) developed models and a fundamental understanding of potential underlying polarization mechanisms at low frequencies (<40 kHz) resulting from the presence of microbial cells and biofilms« less

Glove-based approach to online signature verification.

PubMed

Kamel, Nidal S; Sayeed, Shohel; Ellis, Grant A

2008-06-01

Utilizing the multiple degrees of freedom offered by the data glove for each finger and the hand, a novel on-line signature verification system using the Singular Value Decomposition (SVD) numerical tool for signature classification and verification is presented. The proposed technique is based on the Singular Value Decomposition in finding r singular vectors sensing the maximal energy of glove data matrix A, called principal subspace, so the effective dimensionality of A can be reduced. Having modeled the data glove signature through its r-principal subspace, signature authentication is performed by finding the angles between the different subspaces. A demonstration of the data glove is presented as an effective high-bandwidth data entry device for signature verification. This SVD-based signature verification technique is tested and its performance is shown to be able to recognize forgery signatures with a false acceptance rate of less than 1.2%.

Lightning charge moment changes estimated by high speed photometric observations from ISS

NASA Astrophysics Data System (ADS)

Hobara, Y.; Kono, S.; Suzuki, K.; Sato, M.; Takahashi, Y.; Adachi, T.; Ushio, T.; Suzuki, M.

2017-12-01

Optical observations by the CCD camera using the orbiting satellite is generally used to derive the spatio-temporal global distributions of the CGs and ICs. However electrical properties of the lightning such as peak current and lightning charge are difficult to obtain from the space. In particular, CGs with considerably large lightning charge moment changes (CMC) and peak currents are crucial parameters to generate red sprites and elves, respectively, and so it must be useful to obtain these parameters from space. In this paper, we obtained the lightning optical signatures by using high speed photometric observations from the International Space Station GLIMS (Global Lightning and Sprit MeasurementS JEM-EF) mission. These optical signatures were compared quantitatively with radio signatures recognized as truth values derived from ELF electromagnetic wave observations on the ground to verify the accuracy of the optically derived values. High correlation (R > 0.9) was obtained between lightning optical irradiance and current moment, and quantitative relational expression between these two parameters was derived. Rather high correlation (R > 0.7) was also obtained between the integrated irradiance and the lightning CMC. Our results indicate the possibility to derive lightning electrical properties (current moment and CMC) from optical measurement from space. Moreover, we hope that these results will also contribute to forthcoming French microsatellite mission TARANIS.

Profiling In Situ Microbial Community Structure with an Amplification Microarray

PubMed Central

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

21 CFR 11.200 - Electronic signature components and controls.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Electronic signature components and controls. 11... SERVICES GENERAL ELECTRONIC RECORDS; ELECTRONIC SIGNATURES Electronic Signatures § 11.200 Electronic signature components and controls. (a) Electronic signatures that are not based upon biometrics shall: (1...

Uncovering the genetic signature of quantitative trait evolution with replicated time series data.

PubMed

Franssen, S U; Kofler, R; Schlötterer, C

2017-01-01

The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis.

PubMed

Sethi, Manveen K; Thaysen-Andersen, Morten; Kim, Hoguen; Park, Cheol Keun; Baker, Mark S; Packer, Nicolle H; Paik, Young-Ki; Hancock, William S; Fanayan, Susan

2015-08-03

Modern proteomics has proven instrumental in our understanding of the molecular deregulations associated with the development and progression of cancer. Herein, we profile membrane-enriched proteome of tumor and adjacent normal tissues from eight CRC patients using label-free nanoLC-MS/MS-based quantitative proteomics and advanced pathway analysis. Of the 948 identified proteins, 184 proteins were differentially expressed (P<0.05, fold change>1.5) between the tumor and non-tumor tissue (69 up-regulated and 115 down-regulated in tumor tissues). The CRC tumor and non-tumor tissues clustered tightly in separate groups using hierarchical cluster analysis of the differentially expressed proteins, indicating a strong CRC-association of this proteome subset. Specifically, cancer associated proteins such as FN1, TNC, DEFA1, ITGB2, MLEC, CDH17, EZR and pathways including actin cytoskeleton and RhoGDI signaling were deregulated. Stage-specific proteome signatures were identified including up-regulated ribosomal proteins and down-regulated annexin proteins in early stage CRC. Finally, EGFR(+) CRC tissues showed an EGFR-dependent down-regulation of cell adhesion molecules, relative to EGFR(-) tissues. Taken together, this study provides a detailed map of the altered proteome and associated protein pathways in CRC, which enhances our mechanistic understanding of CRC biology and opens avenues for a knowledge-driven search for candidate CRC protein markers. Copyright © 2015 Elsevier B.V. All rights reserved.

Detectable Changes in The Blood Transcriptome Are Present after Two Weeks of Antituberculosis Therapy

PubMed Central

Bloom, Chloe I.; Graham, Christine M.; Berry, Matthew P. R.; Wilkinson, Katalin A.; Oni, Tolu; Rozakeas, Fotini; Xu, Zhaohui; Rossello-Urgell, Jose; Chaussabel, Damien; Banchereau, Jacques; Pascual, Virginia; Lipman, Marc; Wilkinson, Robert J.; O’Garra, Anne

2012-01-01

Rationale Globally there are approximately 9 million new active tuberculosis cases and 1.4 million deaths annually. Effective antituberculosis treatment monitoring is difficult as there are no existing biomarkers of poor adherence or inadequate treatment earlier than 2 months after treatment initiation. Inadequate treatment leads to worsening disease, disease transmission and drug resistance. Objectives To determine if blood transcriptional signatures change in response to antituberculosis treatment and could act as early biomarkers of a successful response. Methods Blood transcriptional profiles of untreated active tuberculosis patients in South Africa were analysed before, during (2 weeks and 2 months), at the end of (6 months) and after (12 months) antituberculosis treatment, and compared to individuals with latent tuberculosis. An active-tuberculosis transcriptional signature and a specific treatment-response transcriptional signature were derived. The specific treatment response transcriptional signature was tested in two independent cohorts. Two quantitative scoring algorithms were applied to measure the changes in the transcriptional response. The most significantly represented pathways were determined using Ingenuity Pathway Analysis. Results An active tuberculosis 664-transcript signature and a treatment specific 320-transcript signature significantly diminished after 2 weeks of treatment in all cohorts, and continued to diminish until 6 months. The transcriptional response to treatment could be individually measured in each patient. Conclusions Significant changes in the transcriptional signatures measured by blood tests were readily detectable just 2 weeks after treatment initiation. These findings suggest that blood transcriptional signatures could be used as early surrogate biomarkers of successful treatment response. PMID:23056259

Multiparty Quantum Blind Signature Scheme Based on Graph States

NASA Astrophysics Data System (ADS)

Jian-Wu, Liang; Xiao-Shu, Liu; Jin-Jing, Shi; Ying, Guo

2018-05-01

A multiparty quantum blind signature scheme is proposed based on the principle of graph state, in which the unitary operations of graph state particles can be applied to generate the quantum blind signature and achieve verification. Different from the classical blind signature based on the mathematical difficulty, the scheme could guarantee not only the anonymity but also the unconditionally security. The analysis shows that the length of the signature generated in our scheme does not become longer as the number of signers increases, and it is easy to increase or decrease the number of signers.

Infrared and radar signatures of lunar craters - Implications about crater evolution

NASA Technical Reports Server (NTRS)

Thompson, T. W.; Cutts, J. A.; Shorthill, R. W.; Zisk, S. H.

1980-01-01

Geological models accounting for the strongly crater size-dependent IR and radar signatures of lunar crater floors are examined. The simplest model involves the formation and subsequent 'gardening' of an impact melt layer on the crater floor, but while adequate in accounting for the gradual fading of IR temperatures and echo strengths in craters larger than 30 km in diameter, it is inadequate for smaller ones. It is concluded that quantitative models of the evolution of rock populations in regoliths and of the interaction of microwaves with regoliths are needed in order to understand crater evolutionary processes.

Tractography optimization using quantitative T1 mapping in the human optic radiation.

PubMed

Schurr, Roey; Duan, Yiran; Norcia, Anthony M; Ogawa, Shumpei; Yeatman, Jason D; Mezer, Aviv A

2018-06-21

Diffusion MRI tractography is essential for reconstructing white-matter projections in the living human brain. Yet tractography results miss some projections and falsely identify others. A challenging example is the optic radiation (OR) that connects the thalamus and the primary visual cortex. Here, we tested whether OR tractography can be optimized using quantitative T1 mapping. Based on histology, we proposed that myelin-sensitive T1 values along the OR should remain consistently low compared with adjacent white matter. We found that complementary information from the T1 map allows for increasing the specificity of the reconstructed OR tract by eliminating falsely identified projections. This T1-filtering outperforms other, diffusion-based tractography filters. These results provide evidence that the smooth microstructural signature along the tract can be used as constructive input for tractography. Finally, we demonstrate that this approach can be generalized to the HCP-available MRI measurements. We conclude that multimodal MRI microstructural information can be used to eliminate spurious tractography results in the case of the OR. Copyright © 2018. Published by Elsevier Inc.

Structure and evolution of a European Parliament via a network and correlation analysis

NASA Astrophysics Data System (ADS)

Puccio, Elena; Pajala, Antti; Piilo, Jyrki; Tumminello, Michele

2016-11-01

We present a study of the network of relationships among elected members of the Finnish parliament, based on a quantitative analysis of initiative co-signatures, and its evolution over 16 years. To understand the structure of the parliament, we constructed a statistically validated network of members, based on the similarity between the patterns of initiatives they signed. We looked for communities within the network and characterized them in terms of members' attributes, such as electoral district and party. To gain insight on the nested structure of communities, we constructed a hierarchical tree of members from the correlation matrix. Afterwards, we studied parliament dynamics yearly, with a focus on correlations within and between parties, by also distinguishing between government and opposition. Finally, we investigated the role played by specific individuals, at a local level. In particular, whether they act as proponents who gather consensus, or as signers. Our results provide a quantitative background to current theories in political science. From a methodological point of view, our network approach has proven able to highlight both local and global features of a complex social system.

Mesures spectroscopiques de constituants et de polluants atmosphériques par techniques in situ et à distance, au sol ou embarquéesSpectroscopic measurements of atmospheric constituents and pollutants by in situ and remote techniques from the ground and in flight

NASA Astrophysics Data System (ADS)

Camy-Peyret, Claude; Payan, Sébastien; Jeseck, Pascal; Té, Yao

2001-09-01

Infrared spectroscopy is a powerful tool for precise measurements of atmospheric trace species concentrations through the use of characteristic spectral signatures of the different molecular species and their associated vibration-rotation bands in the mid- or near-infrared. Different methods based on quantitative spectroscopy permit tropospheric or stratospheric measurements: in situ long path absorption, atmospheric absorption/emission by Fourier transform spectroscopy with high spectral resolution instruments on the ground, airborne, balloon-borne or satellite-borne.

In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The φ-Index.

PubMed

Bakas, Spyridon; Akbari, Hamed; Pisapia, Jared; Martinez-Lage, Maria; Rozycki, Martin; Rathore, Saima; Dahmane, Nadia; O'Rourke, Donald M; Davatzikos, Christos

2017-08-15

Purpose: The epidermal growth factor receptor variant III ( EGFRvIII ) mutation has been considered a driver mutation and therapeutic target in glioblastoma, the most common and aggressive brain cancer. Currently, detecting EGFRvIII requires postoperative tissue analyses, which are ex vivo and unable to capture the tumor's spatial heterogeneity. Considering the increasing evidence of in vivo imaging signatures capturing molecular characteristics of cancer, this study aims to detect EGFRvIII in primary glioblastoma noninvasively, using routine clinically acquired imaging. Experimental Design: We found peritumoral infiltration and vascularization patterns being related to EGFRvIII status. We therefore constructed a quantitative within-patient peritumoral heterogeneity index (PHI/φ-index), by contrasting perfusion patterns of immediate and distant peritumoral edema. Application of φ-index in preoperative perfusion scans of independent discovery ( n = 64) and validation ( n = 78) cohorts, revealed the generalizability of this EGFRvIII imaging signature. Results: Analysis in both cohorts demonstrated that the obtained signature is highly accurate (89.92%), specific (92.35%), and sensitive (83.77%), with significantly distinctive ability ( P = 4.0033 × 10 -10 , AUC = 0.8869). Findings indicated a highly infiltrative-migratory phenotype for EGFRvIII + tumors, which displayed similar perfusion patterns throughout peritumoral edema. Contrarily, EGFRvIII - tumors displayed perfusion dynamics consistent with peritumorally confined vascularization, suggesting potential benefit from extensive peritumoral resection/radiation. Conclusions: This EGFRvIII signature is potentially suitable for clinical translation, since obtained from analysis of clinically acquired images. Use of within-patient heterogeneity measures, rather than population-based associations, renders φ-index potentially resistant to inter-scanner variations. Overall, our findings enable noninvasive evaluation of EGFRvIII for patient selection for targeted therapy, stratification into clinical trials, personalized treatment planning, and potentially treatment-response evaluation. Clin Cancer Res; 23(16); 4724-34. ©2017 AACR . ©2017 American Association for Cancer Research.

Scenario drafting to anticipate future developments in technology assessment.

PubMed

Retèl, Valesca P; Joore, Manuela A; Linn, Sabine C; Rutgers, Emiel J T; van Harten, Wim H

2012-08-16

Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers.

Scenario drafting to anticipate future developments in technology assessment

PubMed Central

2012-01-01

Background Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. Methods To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). Results In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. Conclusions When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers. PMID:22894140

Public-key quantum digital signature scheme with one-time pad private-key

NASA Astrophysics Data System (ADS)

Chen, Feng-Lin; Liu, Wan-Fang; Chen, Su-Gen; Wang, Zhi-Hua

2018-01-01

A quantum digital signature scheme is firstly proposed based on public-key quantum cryptosystem. In the scheme, the verification public-key is derived from the signer's identity information (such as e-mail) on the foundation of identity-based encryption, and the signature private-key is generated by one-time pad (OTP) protocol. The public-key and private-key pair belongs to classical bits, but the signature cipher belongs to quantum qubits. After the signer announces the public-key and generates the final quantum signature, each verifier can verify publicly whether the signature is valid or not with the public-key and quantum digital digest. Analysis results show that the proposed scheme satisfies non-repudiation and unforgeability. Information-theoretic security of the scheme is ensured by quantum indistinguishability mechanics and OTP protocol. Based on the public-key cryptosystem, the proposed scheme is easier to be realized compared with other quantum signature schemes under current technical conditions.

Genes Required for Free Phage Production are Essential for Pseudomonas aeruginosa Chronic Lung Infections.

PubMed

Lemieux, Andrée-Ann; Jeukens, Julie; Kukavica-Ibrulj, Irena; Fothergill, Joanne L; Boyle, Brian; Laroche, Jérôme; Tucker, Nicholas P; Winstanley, Craig; Levesque, Roger C

2016-02-01

The opportunistic pathogen Pseudomonas aeruginosa causes chronic lung infection in patients with cystic fibrosis. The Liverpool Epidemic Strain LESB58 is highly resistant to antibiotics, transmissible, and associated with increased morbidity and mortality. Its genome contains 6 prophages and 5 genomic islands. We constructed a polymerase chain reaction (PCR)-based signature-tagged mutagenesis library of 9216 LESB58 mutants and screened the mutants in a rat model of chronic lung infection. A total of 162 mutants were identified as defective for in vivo maintenance, with 11 signature-tagged mutagenesis mutants having insertions in prophage and genomic island genes. Many of these mutants showed both diminished virulence and reduced phage production. Transcription profiling by quantitative PCR and RNA-Seq suggested that disruption of these prophages had a widespread trans-acting effect on the transcriptome. This study demonstrates that temperate phages play a pivotal role in the establishment of infection through modulation of bacterial host gene expression. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Heart energy signature spectrogram for cardiovascular diagnosis

PubMed Central

Kudriavtsev, Vladimir; Polyshchuk, Vladimir; Roy, Douglas L

2007-01-01

A new method and application is proposed to characterize intensity and pitch of human heart sounds and murmurs. Using recorded heart sounds from the library of one of the authors, a visual map of heart sound energy was established. Both normal and abnormal heart sound recordings were studied. Representation is based on Wigner-Ville joint time-frequency transformations. The proposed methodology separates acoustic contributions of cardiac events simultaneously in pitch, time and energy. The resolution accuracy is superior to any other existing spectrogram method. The characteristic energy signature of the innocent heart murmur in a child with the S3 sound is presented. It allows clear detection of S1, S2 and S3 sounds, S2 split, systolic murmur, and intensity of these components. The original signal, heart sound power change with time, time-averaged frequency, energy density spectra and instantaneous variations of power and frequency/pitch with time, are presented. These data allow full quantitative characterization of heart sounds and murmurs. High accuracy in both time and pitch resolution is demonstrated. Resulting visual images have self-referencing quality, whereby individual features and their changes become immediately obvious. PMID:17480232

Ferromagnetism and spin-dependent transport at a complex oxide interface

NASA Astrophysics Data System (ADS)

Ayino, Yilikal; Xu, Peng; Tigre-Lazo, Juan; Yue, Jin; Jalan, Bharat; Pribiag, Vlad S.

2018-03-01

Complex oxide interfaces are a promising platform for studying a wide array of correlated electron phenomena in low dimensions, including magnetism and superconductivity. The microscopic origin of these phenomena in complex oxide interfaces remains an open question. Here we investigate the magnetic properties of semi-insulating NdTi O3/SrTi O3 (NTO/STO) interfaces and present the first millikelvin study of NTO/STO. The magnetoresistance (MR) reveals signatures of local ferromagnetic order and of spin-dependent thermally activated transport, which are described quantitatively by a simple phenomenological model. We discuss possible origins of the interfacial ferromagnetism. In addition, the MR also shows transient hysteretic features on a time scale of ˜10 -100 s . We demonstrate that these are consistent with an extrinsic magnetothermal origin, which may have been misinterpreted in previous reports of magnetism in STO-based oxide interfaces. The existence of these two MR regimes (steady-state and transient) highlights the importance of time-dependent measurements for distinguishing signatures of ferromagnetism from other effects that can produce hysteresis at low temperatures.

Operation Sun Beam, Shot Small Boy. Project Officer's report - Project 6. 9. Correlation of present and previous electric-field measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reno; Fowles, H.M.

On most previous nuclear detonations, signatures and quantitative measurements of the electric-field signals associated with the detonations was obtained at distances such that normal radiation field characteristics apply. On Small Boy, measurements were made from stations located much closer in, such as to be inside, on the boundary of and just outside the limits of the ionized sphere created by the nuclear burst. The electric-field characteristics in these regions were unknown. In the hope of providing continuity from the region of the unknown into the reasonably well-understood region of the radiation field, this project was requested to make the typicalmore » radiation-field type of measurement that had been made on previous detonations. This report covers the signature characteristics and quantitative measurements of the electric-field signal from Small Boy as seen from outside the immediate region of theoretical generating mechanism.« less

RxnSim: a tool to compare biochemical reactions.

PubMed

Giri, Varun; Sivakumar, Tadi Venkata; Cho, Kwang Myung; Kim, Tae Yong; Bhaduri, Anirban

2015-11-15

: Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patterns. We describe a tool, RxnSim, which computes reaction similarity based on the molecular signatures of participating molecules. The tool is able to compare reactions based on similarities of substrates and products in addition to their transformation. It allows masking of user-defined chemical moieties for weighted similarity computations. RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http://cran.r-project.org/web/packages/RxnSim/). anirban.b@samsung.com or ty76.kim@samsung.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A New Gene Expression Signature for Triple-Negative Breast Cancer Using Frozen Fresh Tissue before Neoadjuvant Chemotherapy

PubMed Central

Santuario-Facio, Sandra K; Cardona-Huerta, Servando; Perez-Paramo, Yadira X; Trevino, Victor; Hernandez-Cabrera, Francisco; Rojas-Martinez, Augusto; Uscanga-Perales, Grecia; Martinez-Rodriguez, Jorge L; Martinez-Jacobo, Lizeth; Padilla-Rivas, Gerardo; Muñoz-Maldonado, Gerardo; Gonzalez-Guerrero, Juan Francisco; Valero-Gomez, Javier; Vazquez-Guerrero, Ana L; Martinez-Rodriguez, Herminia G; Barboza-Quintana, Alvaro; Barboza-Quintana, Oralia; Garza-Guajardo, Raquel; Ortiz-Lopez, Rocio

2017-01-01

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer tumors. Comparisons between TNBC and non–triple-negative breast cancer (nTNBC) may help to differentiate key components involved in TNBC neoplasms. The purpose of the study was to analyze the expression profile of TNBC versus nTNBC tumors in a homogeneous population from northeastern Mexico. A prospective study of 50 patients (25 TNBC and 25 nTNBC) was conducted. Clinic parameters were equally distributed for TNBC and nTNBC: age at diagnosis (51 versus 47 years, p = 0.1), glucose level (107 mg/dl versus 104 mg/dl, p = 0.64), and body mass index (28 versus 29, p = 0.14). Core biopsies were collected for histopathological diagnosis and gene expression analysis. Total RNA was isolated and expression profiling was performed. Forty genes showed differential expression pattern in TNBC tumors. Among these, nine overexpressed genes (PRKX/PRKY, UGT8, HMGA1, LPIN1, HAPLN3, FAM171A1, BCL141A, FOXC1, and ANKRD11), and one underexpressed gene (ANX9) are involved in general metabolism. Based on this biochemical peculiarity and the overexpression of BCL11A and FOXC1 (involved in tumor growth and metastasis, respectively), we validated by quantitative polymerase chain reaction the expression profiles of seven genes out of the signature. In this report, a new gene signature for TNBC is proposed. To our knowledge, this is the first TNBC signature that describes genes involved in general metabolism. The findings may be pertinent for Mexican patients and require evaluation in other ethnic groups and populations. PMID:28474731

Cities through the Prism of People’s Spending Behavior

PubMed Central

Hawelka, Bartosz; Murillo Arias, Juan; Ratti, Carlo

2016-01-01

Scientific studies of society increasingly rely on digital traces produced by various aspects of human activity. In this paper, we exploit a relatively unexplored source of data–anonymized records of bank card transactions collected in Spain by a big European bank, and propose a new classification scheme of cities based on the economic behavior of their residents. First, we study how individual spending behavior is qualitatively and quantitatively affected by various factors such as customer’s age, gender, and size of his/her home city. We show that, similar to other socioeconomic urban quantities, individual spending activity exhibits a statistically significant superlinear scaling with city size. With respect to the general trends, we quantify the distinctive signature of each city in terms of residents’ spending behavior, independently from the effects of scale and demographic heterogeneity. Based on the comparison of city signatures, we build a novel classification of cities across Spain in three categories. That classification exhibits a substantial stability over different city definitions and connects with a meaningful socioeconomic interpretation. Furthermore, it corresponds with the ability of cities to attract foreign visitors, which is a particularly remarkable finding given that the classification was based exclusively on the behavioral patterns of city residents. This highlights the far-reaching applicability of the presented classification approach and its ability to discover patterns that go beyond the quantities directly involved in it. PMID:26849218

Cities through the Prism of People's Spending Behavior.

PubMed

Sobolevsky, Stanislav; Sitko, Izabela; Tachet des Combes, Remi; Hawelka, Bartosz; Murillo Arias, Juan; Ratti, Carlo

2016-01-01

Scientific studies of society increasingly rely on digital traces produced by various aspects of human activity. In this paper, we exploit a relatively unexplored source of data-anonymized records of bank card transactions collected in Spain by a big European bank, and propose a new classification scheme of cities based on the economic behavior of their residents. First, we study how individual spending behavior is qualitatively and quantitatively affected by various factors such as customer's age, gender, and size of his/her home city. We show that, similar to other socioeconomic urban quantities, individual spending activity exhibits a statistically significant superlinear scaling with city size. With respect to the general trends, we quantify the distinctive signature of each city in terms of residents' spending behavior, independently from the effects of scale and demographic heterogeneity. Based on the comparison of city signatures, we build a novel classification of cities across Spain in three categories. That classification exhibits a substantial stability over different city definitions and connects with a meaningful socioeconomic interpretation. Furthermore, it corresponds with the ability of cities to attract foreign visitors, which is a particularly remarkable finding given that the classification was based exclusively on the behavioral patterns of city residents. This highlights the far-reaching applicability of the presented classification approach and its ability to discover patterns that go beyond the quantities directly involved in it.

A Quantum Multi-Proxy Weak Blind Signature Scheme Based on Entanglement Swapping

NASA Astrophysics Data System (ADS)

Yan, LiLi; Chang, Yan; Zhang, ShiBin; Han, GuiHua; Sheng, ZhiWei

2017-02-01

In this paper, we present a multi-proxy weak blind signature scheme based on quantum entanglement swapping of Bell states. In the scheme, proxy signers can finish the signature instead of original singer with his/her authority. It can be applied to the electronic voting system, electronic paying system, etc. The scheme uses the physical characteristics of quantum mechanics to implement delegation, signature and verification. It could guarantee not only the unconditionally security but also the anonymity of the message owner. The security analysis shows the scheme satisfies the security features of multi-proxy weak signature, singers cannot disavowal his/her signature while the signature cannot be forged by others, and the message owner can be traced.

Model-based development of a fault signature matrix to improve solid oxide fuel cell systems on-site diagnosis

NASA Astrophysics Data System (ADS)

Polverino, Pierpaolo; Pianese, Cesare; Sorrentino, Marco; Marra, Dario

2015-04-01

The paper focuses on the design of a procedure for the development of an on-field diagnostic algorithm for solid oxide fuel cell (SOFC) systems. The diagnosis design phase relies on an in-deep analysis of the mutual interactions among all system components by exploiting the physical knowledge of the SOFC system as a whole. This phase consists of the Fault Tree Analysis (FTA), which identifies the correlations among possible faults and their corresponding symptoms at system components level. The main outcome of the FTA is an inferential isolation tool (Fault Signature Matrix - FSM), which univocally links the faults to the symptoms detected during the system monitoring. In this work the FTA is considered as a starting point to develop an improved FSM. Making use of a model-based investigation, a fault-to-symptoms dependency study is performed. To this purpose a dynamic model, previously developed by the authors, is exploited to simulate the system under faulty conditions. Five faults are simulated, one for the stack and four occurring at BOP level. Moreover, the robustness of the FSM design is increased by exploiting symptom thresholds defined for the investigation of the quantitative effects of the simulated faults on the affected variables.

Keystroke dynamics in the pre-touchscreen era

PubMed Central

Ahmad, Nasir; Szymkowiak, Andrea; Campbell, Paul A.

2013-01-01

Biometric authentication seeks to measure an individual’s unique physiological attributes for the purpose of identity verification. Conventionally, this task has been realized via analyses of fingerprints or signature iris patterns. However, whilst such methods effectively offer a superior security protocol compared with password-based approaches for example, their substantial infrastructure costs, and intrusive nature, make them undesirable and indeed impractical for many scenarios. An alternative approach seeks to develop similarly robust screening protocols through analysis of typing patterns, formally known as keystroke dynamics. Here, keystroke analysis methodologies can utilize multiple variables, and a range of mathematical techniques, in order to extract individuals’ typing signatures. Such variables may include measurement of the period between key presses, and/or releases, or even key-strike pressures. Statistical methods, neural networks, and fuzzy logic have often formed the basis for quantitative analysis on the data gathered, typically from conventional computer keyboards. Extension to more recent technologies such as numerical keypads and touch-screen devices is in its infancy, but obviously important as such devices grow in popularity. Here, we review the state of knowledge pertaining to authentication via conventional keyboards with a view toward indicating how this platform of knowledge can be exploited and extended into the newly emergent type-based technological contexts. PMID:24391568

Keystroke dynamics in the pre-touchscreen era.

PubMed

Ahmad, Nasir; Szymkowiak, Andrea; Campbell, Paul A

2013-12-19

Biometric authentication seeks to measure an individual's unique physiological attributes for the purpose of identity verification. Conventionally, this task has been realized via analyses of fingerprints or signature iris patterns. However, whilst such methods effectively offer a superior security protocol compared with password-based approaches for example, their substantial infrastructure costs, and intrusive nature, make them undesirable and indeed impractical for many scenarios. An alternative approach seeks to develop similarly robust screening protocols through analysis of typing patterns, formally known as keystroke dynamics. Here, keystroke analysis methodologies can utilize multiple variables, and a range of mathematical techniques, in order to extract individuals' typing signatures. Such variables may include measurement of the period between key presses, and/or releases, or even key-strike pressures. Statistical methods, neural networks, and fuzzy logic have often formed the basis for quantitative analysis on the data gathered, typically from conventional computer keyboards. Extension to more recent technologies such as numerical keypads and touch-screen devices is in its infancy, but obviously important as such devices grow in popularity. Here, we review the state of knowledge pertaining to authentication via conventional keyboards with a view toward indicating how this platform of knowledge can be exploited and extended into the newly emergent type-based technological contexts.

A unified theory of impact crises and mass extinctions: quantitative tests.

PubMed

Rampino, M R; Haggerty, B M; Pagano, T C

1997-05-30

Several quantitative tests of a general hypothesis linking impacts of large asteroids and comets with mass extinctions of life are possible based on astronomical data, impact dynamics, and geological information. The waiting times of large-body impacts on the Earth derived from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing, large-scale environmental disasters, predict the impacts of objects > or = 5 km in diameter (> or = 10(7) Mt TNT equivalent) could be sufficient to explain the record of approximately 25 extinction pulses in the last 540 Myr, with the 5 recorded major mass extinctions related to impacts of the largest objects of > or = 10 km in diameter (> or = 10(8) Mt events). Smaller impacts (approximately 10(6) Mt), with significant regional environmental effects, could be responsible for the lesser boundaries in the geologic record. Tests of the "kill curve" relationship for impact-induced extinctions based on new data on extinction intensities, and several well-dated large impact craters, also suggest that major mass extinctions require large impacts, and that a step in the kill curve may exist at impacts that produce craters of approximately 100 km diameter, smaller impacts being capable of only relatively weak extinction pulses. Single impact craters less than approximately 60 km in diameter should not be associated with detectable global extinction pulses (although they may explain stage and zone boundaries marked by lesser faunal turnover), but multiple impacts in that size range may produce significant stepped extinction pulses. Statistical tests of the last occurrences of species at mass-extinction boundaries are generally consistent with predictions for abrupt or stepped extinctions, and several boundaries are known to show "catastrophic" signatures of environmental disasters and biomass crash, impoverished postextinction fauna and flora dominated by stress-tolerant and opportunistic species, and gradual ecological recovery and radiation of new taxa. Isotopic and other geochemical signatures are also generally consistent with the expected after-effects of catastrophic impacts. Seven of the recognized extinction pulses seem to be associated with concurrent (in some cases multiple) stratigraphic impact markers (e.g., layers with high iridium, shocked minerals, microtektites), and/or large, dated impact craters. Other less well-studied crisis intervals show elevated iridium, but well below that of the K/T spike, which might be explained by low-Ir impactors, ejecta blowoff, or sedimentary reworking and dilution of impact signatures. The best explanation for a possible periodic component of approximately 30 Myr in mass extinctions and clusters of impacts is the pulselike modulation of the comet flux associated with the solar system's periodic passage through the plane of the Milky Way Galaxy. The quantitative agreement between paleontologic and astronomical data suggests an important underlying unification of the processes involved.

A Quantum Multi-proxy Blind Signature Scheme Based on Genuine Four-Qubit Entangled State

NASA Astrophysics Data System (ADS)

Tian, Juan-Hong; Zhang, Jian-Zhong; Li, Yan-Ping

2016-02-01

In this paper, we propose a multi-proxy blind signature scheme based on controlled teleportation. Genuine four-qubit entangled state functions as quantum channel. The scheme uses the physical characteristics of quantum mechanics to implement delegation, signature and verification. The security analysis shows the scheme satisfies the security features of multi-proxy signature, unforgeability, undeniability, blindness and unconditional security.

Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis

PubMed Central

Dinalankara, Wikum; Bravo, Héctor Corrada

2015-01-01

Gene expression signatures are commonly used to create cancer prognosis and diagnosis methods, yet only a small number of them are successfully deployed in the clinic since many fail to replicate performance on subsequent validation. A primary reason for this lack of reproducibility is the fact that these signatures attempt to model the highly variable and unstable genomic behavior of cancer. Our group recently introduced gene expression anti-profiles as a robust methodology to derive gene expression signatures based on the observation that while gene expression measurements are highly heterogeneous across tumors of a specific cancer type relative to the normal tissue, their degree of deviation from normal tissue expression in specific genes involved in tissue differentiation is a stable tumor mark that is reproducible across experiments and cancer types. Here we show that constructing gene expression signatures based on variability and the anti-profile approach yields classifiers capable of successfully distinguishing benign growths from cancerous growths based on deviation from normal expression. We then show that this same approach generates stable and reproducible signatures that predict probability of relapse and survival based on tumor gene expression. These results suggest that using the anti-profile framework for the discovery of genomic signatures is an avenue leading to the development of reproducible signatures suitable for adoption in clinical settings. PMID:26078586

Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer

PubMed Central

Kim, Yunee; Jeon, Jouhyun; Mejia, Salvador; Yao, Cindy Q; Ignatchenko, Vladimir; Nyalwidhe, Julius O; Gramolini, Anthony O; Lance, Raymond S; Troyer, Dean A; Drake, Richard R; Boutros, Paul C; Semmes, O. John; Kislinger, Thomas

2016-01-01

Biomarkers are rapidly gaining importance in personalized medicine. Although numerous molecular signatures have been developed over the past decade, there is a lack of overlap and many biomarkers fail to validate in independent patient cohorts and hence are not useful for clinical application. For these reasons, identification of novel and robust biomarkers remains a formidable challenge. We combine targeted proteomics with computational biology to discover robust proteomic signatures for prostate cancer. Quantitative proteomics conducted in expressed prostatic secretions from men with extraprostatic and organ-confined prostate cancers identified 133 differentially expressed proteins. Using synthetic peptides, we evaluate them by targeted proteomics in a 74-patient cohort of expressed prostatic secretions in urine. We quantify a panel of 34 candidates in an independent 207-patient cohort. We apply machine-learning approaches to develop clinical predictive models for prostate cancer diagnosis and prognosis. Our results demonstrate that computationally guided proteomics can discover highly accurate non-invasive biomarkers. PMID:27350604

Can specific transcriptional regulators assemble a universal cancer signature?

NASA Astrophysics Data System (ADS)

Roy, Janine; Isik, Zerrin; Pilarsky, Christian; Schroeder, Michael

2013-10-01

Recently, there is a lot of interest in using biomarker signatures derived from gene expression data to predict cancer progression. We assembled signatures of 25 published datasets covering 13 types of cancers. How do these signatures compare with each other? On one hand signatures answering the same biological question should overlap, whereas signatures predicting different cancer types should differ. On the other hand, there could also be a Universal Cancer Signature that is predictive independently of the cancer type. Initially, we generate signatures for all datasets using classical approaches such as t-test and fold change and then, we explore signatures resulting from a network-based method, that applies the random surfer model of Google's PageRank algorithm. We show that the signatures as published by the authors and the signatures generated with classical methods do not overlap - not even for the same cancer type - whereas the network-based signatures strongly overlap. Selecting 10 out of 37 universal cancer genes gives the optimal prediction for all cancers thus taking a first step towards a Universal Cancer Signature. We furthermore analyze and discuss the involved genes in terms of the Hallmarks of cancer and in particular single out SP1, JUN/FOS and NFKB1 and examine their specific role in cancer progression.

A miRNA Signature for Cognitive Deficits and Alcohol Use Disorder in Persons Living with HIV/AIDS

PubMed Central

Wyczechowska, Dorota; Lin, Hui-Yi; LaPlante, Andrea; Jeansonne, Duane; Lassak, Adam; Parsons, Christopher H.; Molina, Patricia E.; Peruzzi, Francesca

2017-01-01

HIV-associated neurocognitive disorders (HAND) affects more than half of persons living with HIV-1/AIDS (PLWHA). Identification of biomarkers representing the cognitive status of PLWHA is a critical step for implementation of successful cognitive, behavioral and pharmacological strategies to prevent onset and progression of HAND. However, the presence of co-morbidity factors in PLWHA, the most common being substance abuse, can prevent the identification of such biomarkers. We have optimized a protocol to profile plasma miRNAs using quantitative RT-qPCR and found a miRNA signature with very good discriminatory ability to distinguish PLWHA with cognitive impairment from those without cognitive impairment. Here, we have evaluated this miRNA signature in PLWHA with alcohol use disorder (AUD) at LSU Health Sciences Center (LSUHSC). The results show that AUD is a potential confounding factor for the miRNAs associated with cognitive impairment in PLWHA. Furthermore, we have investigated the miRNA signature associated with cognitive impairment in an independent cohort of PLWHA using plasma samples from the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) program. Despite differences between the two cohorts in socioeconomic status, AUD, and likely misuse of illicit or prescription drugs, we validated a miRNA signature for cognitive deficits found at LSUHSC in the CHARTER samples. PMID:29187813

A quantum proxy group signature scheme based on an entangled five-qubit state

NASA Astrophysics Data System (ADS)

Wang, Meiling; Ma, Wenping; Wang, Lili; Yin, Xunru

2015-09-01

A quantum proxy group signature (QPGS) scheme based on controlled teleportation is presented, by using the entangled five-qubit quantum state functions as quantum channel. The scheme uses the physical characteristics of quantum mechanics to implement delegation, signature and verification. The security of the scheme is guaranteed by the entanglement correlations of the entangled five-qubit state, the secret keys based on the quantum key distribution (QKD) and the one-time pad algorithm, all of which have been proven to be unconditionally secure and the signature anonymity.

Virtual Liver: Quantitative Dose-Response Using Systems Biology

EPA Science Inventory

The U.S. EPA’s ToxCast™ program uses hundreds of high-throughput, in vitro assays to screen chemicals in order to rapidly identify signatures of toxicity. These assays measure the in vitro concentrations at which cellular pathways are perturbed by chemicals. The U.S. EPA’s Virtu...

A correlative and quantitative imaging approach enabling characterization of primary cell-cell communication: Case of human CD4+ T cell-macrophage immunological synapses.

PubMed

Kasprowicz, Richard; Rand, Emma; O'Toole, Peter J; Signoret, Nathalie

2018-05-22

Cell-to-cell communication engages signaling and spatiotemporal reorganization events driven by highly context-dependent and dynamic intercellular interactions, which are difficult to capture within heterogeneous primary cell cultures. Here, we present a straightforward correlative imaging approach utilizing commonly available instrumentation to sample large numbers of cell-cell interaction events, allowing qualitative and quantitative characterization of rare functioning cell-conjugates based on calcium signals. We applied this approach to examine a previously uncharacterized immunological synapse, investigating autologous human blood CD4 + T cells and monocyte-derived macrophages (MDMs) forming functional conjugates in vitro. Populations of signaling conjugates were visualized, tracked and analyzed by combining live imaging, calcium recording and multivariate statistical analysis. Correlative immunofluorescence was added to quantify endogenous molecular recruitments at the cell-cell junction. By analyzing a large number of rare conjugates, we were able to define calcium signatures associated with different states of CD4 + T cell-MDM interactions. Quantitative image analysis of immunostained conjugates detected the propensity of endogenous T cell surface markers and intracellular organelles to polarize towards cell-cell junctions with high and sustained calcium signaling profiles, hence defining immunological synapses. Overall, we developed a broadly applicable approach enabling detailed single cell- and population-based investigations of rare cell-cell communication events with primary cells.

Instant Integrated Ultradeep Quantitative-structural Membrane Proteomics Discovered Post-translational Modification Signatures for Human Cys-loop Receptor Subunit Bias*

PubMed Central

Zhang, Xi

2016-01-01

Neurotransmitter ligand-gated ion channels (LGICs) are widespread and pivotal in brain functions. Unveiling their structure-function mechanisms is crucial to drive drug discovery, and demands robust proteomic quantitation of expression, post-translational modifications (PTMs) and dynamic structures. Yet unbiased digestion of these modified transmembrane proteins—at high efficiency and peptide reproducibility—poses the obstacle. Targeting both enzyme-substrate contacts and PTMs for peptide formation and detection, we devised flow-and-detergent-facilitated protease and de-PTM digestions for deep sequencing (FDD) method that combined omni-compatible detergent, tandem immobilized protease/PNGase columns, and Cys-selective reduction/alkylation, to achieve streamlined ultradeep peptide preparation within minutes not days, at high peptide reproducibility and low abundance-bias. FDD transformed enzyme-protein contacts into equal catalytic travel paths through enzyme-excessive columns regardless of protein abundance, removed products instantly preventing inhibition, tackled intricate structures via sequential multiple micro-digestions along the flow, and precisely controlled peptide formation by flow rate. Peptide-stage reactions reduced steric bias; low contamination deepened MS/MS scan; distinguishing disulfide from M oxidation and avoiding gain/loss artifacts unmasked protein-endogenous oxidation states. Using a recent interactome of 285-kDa human GABA type A receptor, this pilot study validated FDD platform's applicability to deep sequencing (up to 99% coverage), H/D-exchange and TMT-based structural mapping. FDD discovered novel subunit-specific PTM signatures, including unusual nontop-surface N-glycosylations, that may drive subunit biases in human Cys-loop LGIC assembly and pharmacology, by redefining subunit/ligand interfaces and connecting function domains. PMID:27073180

MicroRNA-150 Is up-regulated in extranodal marginal zone lymphoma of MALT type.

PubMed

Gebauer, Niklas; Kuba, Johannes; Senft, Andrea; Schillert, Arne; Bernard, Veronica; Thorns, Christoph

2014-01-01

The mechanisms promoting malignant transformation from chronic Helicobacter pylori-gastritis to gastric extranodal marginal zone lymphoma (MALT lymphoma) are insufficiently characterized. This follow-up study aimed to validate candidate microRNAs (miRs) in the process of neoplastic transformation. MicroRNA expression signatures (n=20) were generated for a total of 60 cases of gastric lesions ranging from Wotherspoon 0-5 employing a quantitative real-time polymerase chain reaction (PCR) approach. Morphological and immunohistochemical characterization of the cohort was supplemented by PCR-based immunoglobulin heavy chain recombination studies. Quantitative expression of miR-150, miR-142.3p, miR-375 and miR-494 was significantly de-regulated in samples from MALT lymphoma compared to those from gastritis. The previously reported up-regulation of miR-150 in marginal zone lymphoma of MALT type was verified in an independent cohort of lymphoma samples employing a modified methodology. This further substantiates the role of miR-150 as a potential oncomiR in MALT lymphoma.

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

PubMed Central

Munoz, Javier; Low, Teck Y; Kok, Yee J; Chin, Angela; Frese, Christian K; Ding, Vanessa; Choo, Andre; Heck, Albert J R

2011-01-01

Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of hESCs and hiPSCS at the proteome level as 97.8% of the proteins were found unchanged. Nevertheless, a small group of 58 proteins, mainly related to metabolism, antigen processing and cell adhesion, was found significantly differentially expressed between hiPSCs and hESCs. A comparison of the regulated proteins with previously published transcriptomic studies showed a low overlap, highlighting the emerging notion that differences between both pluripotent cell lines rather reflect experimental conditions than a recurrent molecular signature. PMID:22108792

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montanini, R.; Freni, F.; Rossi, G. L.

This paper reports one of the first experimental results on the application of ultrasound activated lock-in vibrothermography for quantitative assessment of buried flaws in complex cast parts. The use of amplitude modulated ultrasonic heat generation allowed selective response of defective areas within the part, as the defect itself is turned into a local thermal wave emitter. Quantitative evaluation of hidden damages was accomplished by estimating independently both the area and the depth extension of the buried flaws, while x-ray 3D computed tomography was used as reference for sizing accuracy assessment. To retrieve flaw's area, a simple yet effective histogram-based phasemore » image segmentation algorithm with automatic pixels classification has been developed. A clear correlation was found between the thermal (phase) signature measured by the infrared camera on the target surface and the actual mean cross-section area of the flaw. Due to the very fast cycle time (<30 s/part), the method could potentially be applied for 100% quality control of casting components.« less

A quantitative visual dashboard to explore exposures to ...

EPA Pesticide Factsheets

The Exposure Prioritization (Ex Priori) model features a simplified, quantitative visual dashboard to explore exposures across chemical space. Diverse data streams are integrated within the interface such that different exposure scenarios for “individual,” “population,” or “professional” time-use profiles can be interchanged to tailor exposure and quantitatively explore multi-chemical signatures of exposure, internalized dose (uptake), body burden, and elimination. Ex Priori will quantitatively extrapolate single-point estimates of both exposure and internal dose for multiple exposure scenarios, factors, products, and pathways. Currently, EPA is investigating its usefulness in life cycle analysis, insofar as its ability to enhance exposure factors used in calculating characterization factors for human health. Presented at 2016 Annual ISES Meeting held in Utrecht, The Netherlands, from 9-13 October 2016.

WO{sub 3} thin film based multiple sensor array for electronic nose application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramgir, Niranjan S., E-mail: niranjanpr@yahoo.com, E-mail: deepakcct1991@gmail.com; Goyal, C. P.; Datta, N.

2015-06-24

Multiple sensor array comprising 16 x 2 sensing elements were realized using RF sputtered WO{sub 3} thin films. The sensor films were modified with a thin layer of sensitizers namely Au, Ni, Cu, Al, Pd, Ti, Pt. The resulting sensor array were tested for their response towards different gases namely H{sub 2}S, NH{sub 3}, NO and C{sub 2}H{sub 5}OH. The sensor response values measured from the response curves indicates that the sensor array generates a unique signature pattern (bar chart) for the gases. The sensor response values can be used to get both qualitative and quantitative information about the gas.

Determination of lunar ilmentite abundances from remotely sensed data

NASA Technical Reports Server (NTRS)

Johnson, J. R.; Larson, S. M.; Singer, Robert B.

1990-01-01

The mapping of ilmenite on the surface of the moon is a necessary precursor to the investigation of prospective lunar base sites. Telescopic observations of the moon using a variety of narrow bandpass optical interference filters are being performed as a preliminary means of achieving this goal. Specifically, ratios of images obtained using filters centered at 0.40 and 0.56 microns provide quantitative estimates of TiO2 abundances. Analysis of preliminary distribution maps of TiO2 concentrations allows identification of specific high-Ti areas. Investigations of these areas using slit spectra in the range 0.03 to 0.85 microns are underway to search for discrete spectral signatures attributable to ilmenite.

Provably secure identity-based identification and signature schemes from code assumptions

PubMed Central

Zhao, Yiming

2017-01-01

Code-based cryptography is one of few alternatives supposed to be secure in a post-quantum world. Meanwhile, identity-based identification and signature (IBI/IBS) schemes are two of the most fundamental cryptographic primitives, so several code-based IBI/IBS schemes have been proposed. However, with increasingly profound researches on coding theory, the security reduction and efficiency of such schemes have been invalidated and challenged. In this paper, we construct provably secure IBI/IBS schemes from code assumptions against impersonation under active and concurrent attacks through a provably secure code-based signature technique proposed by Preetha, Vasant and Rangan (PVR signature), and a security enhancement Or-proof technique. We also present the parallel-PVR technique to decrease parameter values while maintaining the standard security level. Compared to other code-based IBI/IBS schemes, our schemes achieve not only preferable public parameter size, private key size, communication cost and signature length due to better parameter choices, but also provably secure. PMID:28809940

Provably secure identity-based identification and signature schemes from code assumptions.

PubMed

Song, Bo; Zhao, Yiming

2017-01-01

Code-based cryptography is one of few alternatives supposed to be secure in a post-quantum world. Meanwhile, identity-based identification and signature (IBI/IBS) schemes are two of the most fundamental cryptographic primitives, so several code-based IBI/IBS schemes have been proposed. However, with increasingly profound researches on coding theory, the security reduction and efficiency of such schemes have been invalidated and challenged. In this paper, we construct provably secure IBI/IBS schemes from code assumptions against impersonation under active and concurrent attacks through a provably secure code-based signature technique proposed by Preetha, Vasant and Rangan (PVR signature), and a security enhancement Or-proof technique. We also present the parallel-PVR technique to decrease parameter values while maintaining the standard security level. Compared to other code-based IBI/IBS schemes, our schemes achieve not only preferable public parameter size, private key size, communication cost and signature length due to better parameter choices, but also provably secure.

Global Metabolomic Identification of Long-Term Dose-Dependent Urinary Biomarkers in Nonhuman Primates Exposed to Ionizing Radiation.

PubMed

Pannkuk, Evan L; Laiakis, Evagelia C; Authier, Simon; Wong, Karen; Fornace, Albert J

2015-08-01

Due to concerns surrounding potential large-scale radiological events, there is a need to determine robust radiation signatures for the rapid identification of exposed individuals, which can then be used to guide the development of compact field deployable instruments to assess individual dose. Metabolomics provides a technology to process easily accessible biofluids and determine rigorous quantitative radiation biomarkers with mass spectrometry (MS) platforms. While multiple studies have utilized murine models to determine radiation biomarkers, limited studies have profiled nonhuman primate (NHP) metabolic radiation signatures. In addition, these studies have concentrated on short-term biomarkers (i.e., <72 h). The current study addresses the need for biomarkers beyond 72 h using a NHP model. Urine samples were collected at 7 days postirradiation (2, 4, 6, 7 and 10 Gy) and processed with ultra-performance liquid chromatography (UPLC) quadrupole time-of-flight (QTOF) MS, acquiring global metabolomic radiation signatures. Multivariate data analysis revealed clear separation between control and irradiated groups. Thirteen biomarkers exhibiting a dose response were validated with tandem MS. There was significantly higher excretion of l-carnitine, l-acetylcarnitine, xanthine and xanthosine in males versus females. Metabolites validated in this study suggest perturbation of several pathways including fatty acid β oxidation, tryptophan metabolism, purine catabolism, taurine metabolism and steroid hormone biosynthesis. In this novel study we detected long-term biomarkers in a NHP model after exposure to radiation and demonstrate differences between sexes using UPLC-QTOF-MS-based metabolomics technology.

Simultaneous estimation of diet composition and calibration coefficients with fatty acid signature data

USGS Publications Warehouse

Bromaghin, Jeffrey F.; Budge, Suzanne M.; Thiemann, Gregory W.; Rode, Karyn D.

2017-01-01

Knowledge of animal diets provides essential insights into their life history and ecology, although diet estimation is challenging and remains an active area of research. Quantitative fatty acid signature analysis (QFASA) has become a popular method of estimating diet composition, especially for marine species. A primary assumption of QFASA is that constants called calibration coefficients, which account for the differential metabolism of individual fatty acids, are known. In practice, however, calibration coefficients are not known, but rather have been estimated in feeding trials with captive animals of a limited number of model species. The impossibility of verifying the accuracy of feeding trial derived calibration coefficients to estimate the diets of wild animals is a foundational problem with QFASA that has generated considerable criticism. We present a new model that allows simultaneous estimation of diet composition and calibration coefficients based only on fatty acid signature samples from wild predators and potential prey. Our model performed almost flawlessly in four tests with constructed examples, estimating both diet proportions and calibration coefficients with essentially no error. We also applied the model to data from Chukchi Sea polar bears, obtaining diet estimates that were more diverse than estimates conditioned on feeding trial calibration coefficients. Our model avoids bias in diet estimates caused by conditioning on inaccurate calibration coefficients, invalidates the primary criticism of QFASA, eliminates the need to conduct feeding trials solely for diet estimation, and consequently expands the utility of fatty acid data to investigate aspects of ecology linked to animal diets.

Signature Pedagogy: A Literature Review of Social Studies and Technology Research

ERIC Educational Resources Information Center

Beck, Dennis; Eno, Jenni

2012-01-01

A literature review of 121 peer-reviewed articles, books, and conference proceedings was conducted to determine the signature pedagogies of social studies education and technology integration. The authors found that the signature social studies pedagogy is based on two primary instructional models: direct-instruction and inquiry-based,…

Flag-based detection of weak gas signatures in long-wave infrared hyperspectral image sequences

NASA Astrophysics Data System (ADS)

Marrinan, Timothy; Beveridge, J. Ross; Draper, Bruce; Kirby, Michael; Peterson, Chris

2016-05-01

We present a flag manifold based method for detecting chemical plumes in long-wave infrared hyperspectral movies. The method encodes temporal and spatial information related to a hyperspectral pixel into a flag, or nested sequence of linear subspaces. The technique used to create the flags pushes information about the background clutter, ambient conditions, and potential chemical agents into the leading elements of the flags. Exploiting this temporal information allows for a detection algorithm that is sensitive to the presence of weak signals. This method is compared to existing techniques qualitatively on real data and quantitatively on synthetic data to show that the flag-based algorithm consistently performs better on data when the SINRdB is low, and beats the ACE and MF algorithms in probability of detection for low probabilities of false alarm even when the SINRdB is high.

A Quantum Proxy Blind Signature Scheme Based on Genuine Five-Qubit Entangled State

NASA Astrophysics Data System (ADS)

Zeng, Chuan; Zhang, Jian-Zhong; Xie, Shu-Cui

2017-06-01

In this paper, a quantum proxy blind signature scheme based on controlled quantum teleportation is proposed. This scheme uses a genuine five-qubit entangled state as quantum channel and adopts the classical Vernam algorithm to blind message. We use the physical characteristics of quantum mechanics to implement delegation, signature and verification. Security analysis shows that our scheme is valid and satisfy the properties of a proxy blind signature, such as blindness, verifiability, unforgeability, undeniability.

Authentication Based on Pole-zero Models of Signature Velocity

PubMed Central

Rashidi, Saeid; Fallah, Ali; Towhidkhah, Farzad

2013-01-01

With the increase of communication and financial transaction through internet, on-line signature verification is an accepted biometric technology for access control and plays a significant role in authenticity and authorization in modernized society. Therefore, fast and precise algorithms for the signature verification are very attractive. The goal of this paper is modeling of velocity signal that pattern and properties is stable for persons. With using pole-zero models based on discrete cosine transform, precise method is proposed for modeling and then features is founded from strokes. With using linear, parzen window and support vector machine classifiers, the signature verification technique was tested with a large number of authentic and forgery signatures and has demonstrated the good potential of this technique. The signatures are collected from three different database include a proprietary database, the SVC2004 and the Sabanci University signature database benchmark databases. Experimental results based on Persian, SVC2004 and SUSIG databases show that our method achieves an equal error rate of 5.91%, 5.62% and 3.91% in the skilled forgeries, respectively. PMID:24696797

A security and privacy preserving e-prescription system based on smart cards.

PubMed

Hsu, Chien-Lung; Lu, Chung-Fu

2012-12-01

In 2002, Ateniese and Medeiros proposed an e-prescription system, in which the patient can store e-prescription and related information using smart card. Latter, Yang et al. proposed a novel smart-card based e-prescription system based on Ateniese and Medeiros's system in 2004. Yang et al. considered the privacy issues of prescription data and adopted the concept of a group signature to provide patient's privacy protection. To make the e-prescription system more realistic, they further applied a proxy signature to allow a patient to delegate his signing capability to other people. This paper proposed a novel security and privacy preserving e-prescription system model based on smart cards. A new role, chemist, is included in the system model for settling the medicine dispute. We further presented a concrete identity-based (ID-based) group signature scheme and an ID-based proxy signature scheme to realize the proposed model. Main property of an ID-based system is that public key is simple user's identity and can be verified without extra public key certificates. Our ID-based group signature scheme can allow doctors to sign e-prescription anonymously. In a case of a medical dispute, identities of the doctors can be identified. The proposed ID-based proxy signature scheme can improve signing delegation and allows a delegation chain. The proposed e-prescription system based on our proposed two cryptographic schemes is more practical and efficient than Yang et al.'s system in terms of security, communication overheads, computational costs, practical considerations.

Security of a sessional blind signature based on quantum cryptograph

NASA Astrophysics Data System (ADS)

Wang, Tian-Yin; Cai, Xiao-Qiu; Zhang, Rui-Ling

2014-08-01

We analyze the security of a sessional blind signature protocol based on quantum cryptograph and show that there are two security leaks in this protocol. One is that the legal user Alice can change the signed message after she gets a valid blind signature from the signatory Bob, and the other is that an external opponent Eve also can forge a valid blind message by a special attack, which are not permitted for blind signature. Therefore, this protocol is not secure in the sense that it does not satisfy the non-forgeability of blind signatures. We also discuss the methods to prevent the attack strategies in the end.

Using Association Mapping in Teosinte (Zea Mays ssp Parviglumis) to Investigate the Function of Selection-Candidate Genes

USDA-ARS?s Scientific Manuscript database

Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its proge...

Methods for analyzing optical observations of tsunami-induced signatures in airglow emissions from ground-based and space-based platforms

NASA Astrophysics Data System (ADS)

Grawe, M.; Makela, J. J.

2016-12-01

Airglow imaging of the 630.0-nm redline emission has emerged as a useful tool for studying the properties of tsunami-ionospheric coupling in recent years, offering spatially continuous coverage of the sky with a single instrument. Past studies have shown that airglow signatures induced by tsunamis are inherently anisotropic due to the observation geometry and effects from the geomagnetic field. Here, we present details behind the techniques used to determine the parameters of the signature (orientation, wavelength, etc) with potential extensions to real or quasi-real time and a tool for interpreting the location and strength of the signatures in the field of view. We demonstrate application of the techniques to ground-based optical measurements of several tsunami-induced signatures taking place over the past five years from an imaging system in Hawaii. Additionally, these methods are extended for use on space-based observation platforms, offering advantages over ground-based installations.

Quantitative Evaluation of Serum Proteins Uncovers a Protein Signature Related to Maturity-Onset Diabetes of the Young (MODY).

PubMed

Tuerxunyiming, Muhadasi; Xian, Feng; Zi, Jin; Yimamu, Yilihamujiang; Abuduwayite, Reshalaiti; Ren, Yan; Li, Qidan; Abudula, Abulizi; Liu, SiQi; Mohemaiti, Patamu

2018-01-05

Maturity-onset diabetes of the young (MODY) is an inherited monogenic type of diabetes. Genetic mutations in MODY often cause nonsynonymous changes that directly lead to the functional distortion of proteins and the pathological consequences. Herein, we proposed that the inherited mutations found in a MODY family could cause a disturbance of protein abundance, specifically in serum. The serum samples were collected from a Uyghur MODY family through three generations, and the serum proteins after depletion treatment were examined by quantitative proteomics to characterize the MODY-related serum proteins followed by verification using target quantification of proteomics. A total of 32 serum proteins were preliminarily identified as the MODY-related. Further verification test toward the individual samples demonstrated the 12 candidates with the significantly different abundance in the MODY patients. A comparison of the 12 proteins among the sera of type 1 diabetes, type 2 diabetes, MODY, and healthy subjects was conducted and revealed a protein signature related with MODY composed of the serum proteins such as SERPINA7, APOC4, LPA, C6, and F5.

Direct observation of bulk Fermi surface at higher Brillouin zones in a heavily hole-doped cuprate

NASA Astrophysics Data System (ADS)

Al-Sawai, W.; Sakurai, Y.; Itou, M.; Barbiellini, B.; Mijnarends, P. E.; Markiewicz, R. S.; Kaprzyk, S.; Gillet, J.-M.; Wakimoto, S.; Fujita, M.; Basak, S.; Lin, H.; Bansil, A.; Yamada, K.

2010-03-01

We have observed the bulk Fermi surface (FS) in an overdoped (x=0.3) single crystal of La2-xSrxCuO4 by using Compton scattering. A 2-D momentum density reconstruction [1] from measured Compton profiles, yields a clear FS signature in a higher Brillouin zone centered at p=(1.5,1.5) a.u. The quantitative agreement with density functional theory (DFT) calculations [2] and momentum density experiment suggests that Fermi-liquid physics is restored in the overdoped regime. We have also measured the 2-D angular correlation of positron annihilation radiation (2D-ACAR) [3] and noticed a similar quantitative agreement with the DFT simulations. However, 2D-ACAR does not give a clear signature of the FS in the extended momentum space in both theory and experiment. Work supported in part by the US DOE.[1] Y. Tanaka et al., Phys. Rev. B 63, 045120 (2001).[2] S. Sahrakorpi et al., Phys. Rev. Lett. 95, 157601 (2005).[3] L. C. Smedskjaer et al., J. Phys. Chem. Solids 52, 1541 (1991).

Coupling of oceanic carbon and nitrogen: A window to spatially resolved quantitative reconstruction of nitrate inventories

NASA Astrophysics Data System (ADS)

Glock, N.; Liebetrau, V.; Gorb, S.; Wallmann, K. J. G.; Erdem, Z.; Schönfeld, J.; Eisenhauer, A.

2017-12-01

Anthropogenic impact has led to a severe acceleration of the global nitrogen cycle. Every second nitrogen atom in the biosphere may now originate from anthropogenic sources such as chemical fertilizers and the burning of fossil fuels. A quantitative reconstruction of past reactive nitrogen inventories is invaluable to facilitate projections for future scenarios and calibrations for such paleoproxies should be done as long the natural signature is still visible. Here we present a first quantitative reconstruction of nitrate concentrations in intermediate water depths of the Peruvian oxygen minimum zone over the last deglaciation using the pore density in the benthic foraminiferal species Bolivina spissa. A comparison of the nitrate reconstruction to the stable carbon isotope (δ13C) record reveals a strong coupling between the carbon and nitrogen cycles. The linear correlation between δ13C and nitrate availability remained stable over the last 22,000 years, facilitating the use of δ13C records as a quantitative nitrate proxy. The combination of the pore density record with δ13C records shows an elevated oceanic nitrate inventory during the Last Glacial Maximum as compared to the Holocene. Our novel proxy approach is consistent with the results of previous δ15N-based biogeochemical modeling studies, and thus provides sound estimates of the nitrate inventory in the glacial and deglacial ocean.

Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability.

PubMed

Alvarez, Sophie; Roy Choudhury, Swarup; Pandey, Sona

2014-03-07

Wheat is one of the most highly cultivated cereals in the world. Like other cultivated crops, wheat production is significantly affected by abiotic stresses such as drought. Multiple wheat varieties suitable for different geographical regions of the world have been developed that are adapted to different environmental conditions; however, the molecular basis of such adaptations remains unknown in most cases. We have compared the quantitative proteomics profile of the roots of two different wheat varieties, Nesser (drought-tolerant) and Opata (drought-sensitive), in the absence and presence of abscisic acid (ABA, as a proxy for drought). A labeling LC-based quantitative proteomics approach using iTRAQ was applied to elucidate the changes in protein abundance levels. Quantitative differences in protein levels were analyzed for the evaluation of inherent differences between the two varieties as well as the overall and variety-specific effect of ABA on the root proteome. This study reveals the most elaborate ABA-responsive root proteome identified to date in wheat. A large number of proteins exhibited inherently different expression levels between Nesser and Opata. Additionally, significantly higher numbers of proteins were ABA-responsive in Nesser roots compared with Opata roots. Furthermore, several proteins showed variety-specific regulation by ABA, suggesting their role in drought adaptation.

Algorithms for Hyperspectral Endmember Extraction and Signature Classification with Morphological Dendritic Networks

NASA Astrophysics Data System (ADS)

Schmalz, M.; Ritter, G.

Accurate multispectral or hyperspectral signature classification is key to the nonimaging detection and recognition of space objects. Additionally, signature classification accuracy depends on accurate spectral endmember determination [1]. Previous approaches to endmember computation and signature classification were based on linear operators or neural networks (NNs) expressed in terms of the algebra (R, +, x) [1,2]. Unfortunately, class separation in these methods tends to be suboptimal, and the number of signatures that can be accurately classified often depends linearly on the number of NN inputs. This can lead to poor endmember distinction, as well as potentially significant classification errors in the presence of noise or densely interleaved signatures. In contrast to traditional CNNs, autoassociative morphological memories (AMM) are a construct similar to Hopfield autoassociatived memories defined on the (R, +, ?,?) lattice algebra [3]. Unlimited storage and perfect recall of noiseless real valued patterns has been proven for AMMs [4]. However, AMMs suffer from sensitivity to specific noise models, that can be characterized as erosive and dilative noise. On the other hand, the prior definition of a set of endmembers corresponds to material spectra lying on vertices of the minimum convex region covering the image data. These vertices can be characterized as morphologically independent patterns. It has further been shown that AMMs can be based on dendritic computation [3,6]. These techniques yield improved accuracy and class segmentation/separation ability in the presence of highly interleaved signature data. In this paper, we present a procedure for endmember determination based on AMM noise sensitivity, which employs morphological dendritic computation. We show that detected endmembers can be exploited by AMM based classification techniques, to achieve accurate signature classification in the presence of noise, closely spaced or interleaved signatures, and simulated camera optical distortions. In particular, we examine two critical cases: (1) classification of multiple closely spaced signatures that are difficult to separate using distance measures, and (2) classification of materials in simulated hyperspectral images of spaceborne satellites. In each case, test data are derived from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to classical NN based techniques.

An individual and a sex odor signature in kittiwakes? Study of the semiochemical composition of preen secretion and preen down feathers

NASA Astrophysics Data System (ADS)

Leclaire, Sarah; Merkling, Thomas; Raynaud, Christine; Giacinti, Géraldine; Bessière, Jean-Marie; Hatch, Scott A.; Danchin, Étienne

2011-07-01

The importance of olfaction in birds' social behavior has long been denied. Avian chemical signaling has thus been relatively unexplored. The black-legged kittiwake provides a particularly appropriate model for investigating this topic. Kittiwakes preferentially mate with genetically dissimilar individuals, but the cues used to assess genetic characteristics remain unknown. As in other vertebrates, their body odors may carry individual and sexual signatures thus potentially reliably signaling individual genetic makeup. Here, we test whether body odors in preen gland secretion and preen down feathers in kittiwakes may provide a sex and an individual signature. Using gas chromatography and mass spectrometry, we found that male and female odors differ quantitatively, suggesting that scent may be one of the multiple cues used by birds to discriminate between sexes. We further detected an individual signature in the volatile and nonvolatile fractions of preen secretion and preen down feathers. These results suggest that kittiwake body odor may function as a signal associated with mate recognition. It further suggests that preen odor might broadcast the genetic makeup of individuals, and could be used in mate choice to assess the genetic compatibility of potential mates.

Radiation Gene-expression Signatures in Primary Breast Cancer Cells.

PubMed

Minafra, Luigi; Bravatà, Valentina; Cammarata, Francesco P; Russo, Giorgio; Gilardi, Maria C; Forte, Giusi I

2018-05-01

In breast cancer (BC) care, radiation therapy (RT) is an efficient treatment to control localized tumor. Radiobiological research is needed to understand molecular differences that affect radiosensitivity of different tumor subtypes and the response variability. The aim of this study was to analyze gene expression profiling (GEP) in primary BC cells following irradiation with doses of 9 Gy and 23 Gy delivered by intraoperative electron radiation therapy (IOERT) in order to define gene signatures of response to high doses of ionizing radiation. We performed GEP by cDNA microarrays and evaluated cell survival after IOERT treatment in primary BC cell cultures. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate candidate genes. We showed, for the first time, a 4-gene and a 6-gene signature, as new molecular biomarkers, in two primary BC cell cultures after exposure at 9 Gy and 23 Gy respectively, for which we observed a significantly high survival rate. Gene signatures activated by different doses of ionizing radiation may predict response to RT and contribute to defining a personalized biological-driven treatment plan. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

MiR-204 down-regulation elicited perturbation of a gene target signature common to human cholangiocarcinoma and gastric cancer.

PubMed

Canu, Valeria; Sacconi, Andrea; Lorenzon, Laura; Biagioni, Francesca; Lo Sardo, Federica; Diodoro, Maria Grazia; Muti, Paola; Garofalo, Alfredo; Strano, Sabrina; D'Errico, Antonietta; Grazi, Gian Luca; Cioce, Mario; Blandino, Giovanni

2017-05-02

There is high need of novel diagnostic and prognostic tools for tumors of the digestive system, such as gastric cancer and cholangiocarcinoma. We recently found that miR-204 was deeply downregulated in gastric cancer tissues. Here we investigated whether this was common to other tumors of the digestive system and whether this elicited a miR-204-dependent gene target signature, diagnostically and therapeutically relevant. Finally, we assessed the contribution of the identified target genes to the cell cycle progression and clonogenicity of gastric cancer and cholangiocarcinoma cell lines. We employed quantitative PCR and Affymetrix profiling for gene expression studies. In silico analysis aided us to identifying a miR-204 target signature in publicly available databases (TGCA). We employed transient transfection experiments, clonogenic assays and cell cycle profiling to evaluate the biological consequences of miR-204 perturbation. We identified a novel miR-204 gene target signature perturbed in gastric cancer and in cholangiocarcinoma specimens. We validated its prognostic relevance and mechanistically addressed its biological relevance in GC and CC cell lines. We suggest that restoring the physiological levels of miR-204 in some gastrointestinal cancers might be exploited therapeutically.

An individual and a sex odor signature in kittiwakes? Study of the semiochemical composition of preen secretion and preen down feathers

USGS Publications Warehouse

Leclaire, Sarah; Merkling, Thomas; Raynaud, C.; Giacinti, Géraldine; Bessiere, J.-M.; Hatch, Scott A.; Danchin, Etienne

2011-01-01

The importance of olfaction in birds' social behavior has long been denied. Avian chemical signaling has thus been relatively unexplored. The black-legged kittiwake provides a particularly appropriate model for investigating this topic. Kittiwakes preferentially mate with genetically dissimilar individuals, but the cues used to assess genetic characteristics remain unknown. As in other vertebrates, their body odors may carry individual and sexual signatures thus potentially reliably signaling individual genetic makeup. Here, we test whether body odors in preen gland secretion and preen down feathers in kittiwakes may provide a sex and an individual signature. Using gas chromatography and mass spectrometry, we found that male and female odors differ quantitatively, suggesting that scent may be one of the multiple cues used by birds to discriminate between sexes. We further detected an individual signature in the volatile and nonvolatile fractions of preen secretion and preen down feathers. These results suggest that kittiwake body odor may function as a signal associated with mate recognition. It further suggests that preen odor might broadcast the genetic makeup of individuals, and could be used in mate choice to assess the genetic compatibility of potential mates.

Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes

PubMed Central

Li, Jing-Woei; Lee, Heung-Man; Wang, Ying; Tong, Amy Hin-Yan; Yip, Kevin Y.; Tsui, Stephen Kwok-Wing; Lok, Si; Ozaki, Risa; Luk, Andrea O; Kong, Alice P. S.; So, Wing-Yee; Ma, Ronald C. W.; Chan, Juliana C. N.; Chan, Ting-Fung

2016-01-01

Protein interactions play significant roles in complex diseases. We analyzed peripheral blood mononuclear cells (PBMC) transcriptome using a multi-method strategy. We constructed a tissue-specific interactome (T2Di) and identified 420 molecular signatures associated with T2D-related comorbidity and symptoms, mainly implicated in inflammation, adipogenesis, protein phosphorylation and hormonal secretion. Apart from explaining the residual associations within the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) study, the T2Di signatures were enriched in pathogenic cell type-specific regulatory elements related to fetal development, immunity and expression quantitative trait loci (eQTL). The T2Di revealed a novel locus near a well-established GWAS loci AChE, in which SRRT interacts with JAZF1, a T2D-GWAS gene implicated in pancreatic function. The T2Di also included known anti-diabetic drug targets (e.g. PPARD, MAOB) and identified possible druggable targets (e.g. NCOR2, PDGFR). These T2Di signatures were validated by an independent computational method, and by expression data of pancreatic islet, muscle and liver with some of the signatures (CEBPB, SREBF1, MLST8, SRF, SRRT and SLC12A9) confirmed in PBMC from an independent cohort of 66 T2D and 66 control subjects. By combining prior knowledge and transcriptome analysis, we have constructed an interactome to explain the multi-layered regulatory pathways in T2D. PMID:27752041

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances.

PubMed

Li, X; Yang, S; Dong, K; Tang, Z; Li, K; Fan, B; Wang, Z; Liu, B

2017-10-01

Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.

Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes.

PubMed

Lee, Kang-Hoon; Shin, Kyung-Seop; Lim, Debora; Kim, Woo-Chan; Chung, Byung Chang; Han, Gyu-Bum; Roh, Jeongkyu; Cho, Dong-Ho; Cho, Kiho

2015-07-01

The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme. An algorithm for computing distances among GSIs was formulated using the GSIs' variables (word identity, frequency, and frequency order). The utility of the GSI-distance computation system was demonstrated with control genomes. GSI-based computation of genome-relatedness among 1766 microbes (117 archaea and 1649 bacteria) identified their clustering patterns; although the majority paralleled the established classification, some did not. The Genome Signature Imaging system, with its visualization and distance computation functions, enables genome-scale evolutionary studies involving numerous genomes with varying sizes. Copyright © 2015 Elsevier Inc. All rights reserved.

SMOS reveals the signature of Indian Ocean Dipole events

NASA Astrophysics Data System (ADS)

Durand, Fabien; Alory, Gaël; Dussin, Raphaël; Reul, Nicolas

2013-12-01

The tropical Indian Ocean experiences an interannual mode of climatic variability, known as the Indian Ocean Dipole (IOD). The signature of this variability in ocean salinity is hypothesized based on modeling and assimilation studies, on account of scanty observations. Soil Moisture and Ocean Salinity (SMOS) satellite has been designed to take up the challenge of sea surface salinity remote sensing. We show that SMOS data can be used to infer the pattern of salinity variability linked with the IOD events. The core of maximum variability is located in the central tropical basin, south of the equator. This region is anomalously salty during the 2010 negative IOD event, and anomalously fresh during the 2011 positive IOD event. The peak-to-peak anomaly exceeds one salinity unit, between late 2010 and late 2011. In conjunction with other observational datasets, SMOS data allow us to draw the salt budget of the area. It turns out that the horizontal advection is the main driver of salinity anomalies. This finding is confirmed by the analysis of the outputs of a numerical model. This study shows that the advent of SMOS makes it feasible the quantitative assessment of the mechanisms of ocean surface salinity variability in the tropical basins, at interannual timescales.

Analysis of pressure blips in aft-finocyl solid rocket motor

NASA Astrophysics Data System (ADS)

Di Giacinto, M.; Favini, B.; Cavallini, E.

2016-07-01

Ballistic anomalies have frequently occurred during the firing of several solid rocket motors (SRMs) (Inertial Upper Stage, Space Shuttle Redesigned SRM (RSRM) and Titan IV SRM Upgrade (SRMU)), producing even relevant and unexpected variations of the SRM pressure trace from its nominal profile. This paper has the purpose to provide a numerical analysis of the following possible causes of ballistic anomalies in SRMs: an inert object discharge, a slag ejection, and an unexpected increase in the propellant burning rate or in the combustion surface. The SRM configuration under investigation is an aft-finocyl SRM with a first-stage/small booster design. The numerical simulations are performed with a quasi-one-dimensional (Q1D) unsteady model of the SRM internal ballistics, properly tailored to model each possible cause of the ballistic anomalies. The results have shown that a classification based on the head-end pressure (HEP) signature, relating each other the HEP shape and the ballistic anomaly cause, can be made. For each cause of ballistic anomalies, a deepened discussion of the parameters driving the HEP signatures is provided, as well as qualitative and quantitative assessments of the resultant pressure signals.

Real-time detection of deoxyribonucleic acid bases via their negative differential conductance signature.

PubMed

Dragoman, D; Dragoman, M

2009-08-01

In this Brief Report, we present a method for the real-time detection of the bases of the deoxyribonucleic acid using their signatures in negative differential conductance measurements. The present methods of electronic detection of deoxyribonucleic acid bases are based on a statistical analysis because the electrical currents of the four bases are weak and do not differ significantly from one base to another. In contrast, we analyze a device that combines the accumulated knowledge in nanopore and scanning tunneling detection and which is able to provide very distinctive electronic signatures for the four bases.

Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes.

PubMed

Higdon, Roger; Kala, Jessie; Wilkins, Devan; Yan, Julia Fangfei; Sethi, Manveen K; Lin, Liang; Liu, Siqi; Montague, Elizabeth; Janko, Imre; Choiniere, John; Kolker, Natali; Hancock, William S; Kolker, Eugene; Fanayan, Susan

2017-02-03

Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled the total transcriptome and proteome of two established MB cell lines, Daoy and UW228, using high-throughput RNA sequencing (RNA-Seq) and label-free nano-LC-MS/MS-based quantitative proteomics, coupled with advanced pathway analysis. While Daoy has been suggested to belong to the sonic hedgehog (SHH) subtype, the exact UW228 subtype is not yet clearly established. Thus, a goal of this study was to identify protein markers and pathways that would help elucidate their subtype classification. A number of differentially expressed genes and proteins, including a number of adhesion, cytoskeletal and signaling molecules, were observed between the two cell lines. While several cancer-associated genes/proteins exhibited similar expression across the two cell lines, upregulation of a number of signature proteins and enrichment of key components of SHH and WNT signaling pathways were uniquely observed in Daoy and UW228, respectively. The novel information on differentially expressed genes/proteins and enriched pathways provide insights into the biology of MB, which could help elucidate their subtype classification.

Metabolic fate of polyphenols in the human superorganism

PubMed Central

van Duynhoven, John; Vaughan, Elaine E.; Jacobs, Doris M.; Kemperman, Robèr A.; van Velzen, Ewoud J. J.; Gross, Gabriele; Roger, Laure C.; Possemiers, Sam; Smilde, Age K.; Doré, Joël; Westerhuis, Johan A.; Van de Wiele, Tom

2011-01-01

Dietary polyphenols are components of many foods such as tea, fruit, and vegetables and are associated with several beneficial health effects although, so far, largely based on epidemiological studies. The intact forms of complex dietary polyphenols have limited bioavailability, with low circulating levels in plasma. A major part of the polyphenols persists in the colon, where the resident microbiota produce metabolites that can undergo further metabolism upon entering systemic circulation. Unraveling the complex metabolic fate of polyphenols in this human superorganism requires joint deployment of in vitro and humanized mouse models and human intervention trials. Within these systems, the variation in diversity and functionality of the colonic microbiota can increasingly be captured by rapidly developing microbiomics and metabolomics technologies. Furthermore, metabolomics is coming to grips with the large biological variation superimposed on relatively subtle effects of dietary interventions. In particular when metabolomics is deployed in conjunction with a longitudinal study design, quantitative nutrikinetic signatures can be obtained. These signatures can be used to define nutritional phenotypes with different kinetic characteristics for the bioconversion capacity for polyphenols. Bottom-up as well as top-down approaches need to be pursued to link gut microbial diversity to functionality in nutritional phenotypes and, ultimately, to bioactivity of polyphenols. This approach will pave the way for personalization of nutrition based on gut microbial functionality of individuals or populations. PMID:20615997

A genome-wide scan for signatures of directional selection in domesticated pigs.

PubMed

Moon, Sunjin; Kim, Tae-Hun; Lee, Kyung-Tai; Kwak, Woori; Lee, Taeheon; Lee, Si-Woo; Kim, Myung-Jick; Cho, Kyuho; Kim, Namshin; Chung, Won-Hyong; Sung, Samsun; Park, Taesung; Cho, Seoae; Groenen, Martien Am; Nielsen, Rasmus; Kim, Yuseob; Kim, Heebal

2015-02-25

Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Classification of multiple sclerosis patients by latent class analysis of magnetic resonance imaging characteristics.

PubMed

Zwemmer, J N P; Berkhof, J; Castelijns, J A; Barkhof, F; Polman, C H; Uitdehaag, B M J

2006-10-01

Disease heterogeneity is a major issue in multiple sclerosis (MS). Classification of MS patients is usually based on clinical characteristics. More recently, a pathological classification has been presented. While clinical subtypes differ by magnetic resonance imaging (MRI) signature on a group level, a classification of individual MS patients based purely on MRI characteristics has not been presented so far. To investigate whether a restricted classification of MS patients can be made based on a combination of quantitative and qualitative MRI characteristics and to test whether the resulting subgroups are associated with clinical and laboratory characteristics. MRI examinations of the brain and spinal cord of 50 patients were scored for 21 quantitative and qualitative characteristics. Using latent class analysis, subgroups were identified, for whom disease characteristics and laboratory measures were compared. Latent class analysis revealed two subgroups that mainly differed in the extent of lesion confluency and MRI correlates of neuronal loss in the brain. Demographics and disease characteristics were comparable except for cognitive deficits. No correlations with laboratory measures were found. Latent class analysis offers a feasible approach for classifying subgroups of MS patients based on the presence of MRI characteristics. The reproducibility, longitudinal evolution and further clinical or prognostic relevance of the observed classification will have to be explored in a larger and independent sample of patients.

Memory, executive, and multidomain subtle cognitive impairment: clinical and biomarker findings.

PubMed

Toledo, Jon B; Bjerke, Maria; Chen, Kewei; Rozycki, Martin; Jack, Clifford R; Weiner, Michael W; Arnold, Steven E; Reiman, Eric M; Davatzikos, Christos; Shaw, Leslie M; Trojanowski, John Q

2015-07-14

We studied the biomarker signatures and prognoses of 3 different subtle cognitive impairment (SCI) groups (executive, memory, and multidomain) as well as the subjective memory complaints (SMC) group. We studied 522 healthy controls in the Alzheimer's Disease Neuroimaging Initiative (ADNI). Cutoffs for executive, memory, and multidomain SCI were defined using participants who remained cognitively normal (CN) for 7 years. CSF Alzheimer disease (AD) biomarkers, composite and region-of-interest (ROI) MRI, and fluorodeoxyglucose-PET measures were compared in these participants. Using a stringent cutoff (fifth percentile), 27.6% of the ADNI participants were classified as SCI. Most single ROI or global-based measures were not sensitive to detect differences between groups. Only MRI-SPARE-AD (Spatial Pattern of Abnormalities for Recognition of Early AD), a quantitative MRI pattern-based global index, showed differences between all groups, excluding the executive SCI group. Atrophy patterns differed in memory SCI and SMC. The CN and the SMC groups presented a similar distribution of preclinical dementia stages. Fifty percent of the participants with executive, memory, and multidomain SCI progressed to mild cognitive impairment or dementia at 7, 5, and 2 years, respectively. Our results indicate that (1) the different SCI categories have different clinical prognoses and biomarker signatures, (2) longitudinally followed CN subjects are needed to establish clinical cutoffs, (3) subjects with SMC show a frontal pattern of brain atrophy, and (4) pattern-based analyses outperform commonly used single ROI-based neuroimaging biomarkers and are needed to detect initial stages of cognitive impairment. © 2015 American Academy of Neurology.

Feasibility of Autonomous Monitoring of CO2 Leakage in Aquifers: Results From Controlled Laboratory Experiments

NASA Astrophysics Data System (ADS)

Versteeg, R.; Leger, E.; Dafflon, B.

2016-12-01

Geologic sequestration of CO2 is one of the primary proposed approaches for reducing total atmospheric CO2 concentrations. MVAA (Monitoring, Verification, Accounting and Assessment) of CO2 sequestration is an essential part of the geologic CO2 sequestration cycle. MVAA activities need to meet multiple operational, regulatory and environmental objectives, including ensuring the protection of underground sources of drinking water. Anticipated negative consequences of CO2 leakage into groundwater, besides possible brine contamination and release of gaseous CO2, include a significant increase of dissolved CO2 into shallow groundwater systems, which will decrease groundwater pH and can potentially mobilize naturally occurring trace metals and ions that are commonly absorbed to or contained in sediments. Autonomous electrical geophysical monitoring in aquifers has the potential of allowing for rapid and automated detection of CO2 leakage. However, while the feasibility of such monitoring has been demonstrated by a number of different field experiments, automated interpretation of complex electrical resistivity data requires the development of quantitative relationships between complex electrical resistivity signatures and dissolved CO2 in the aquifer resulting from leakage Under a DOE SBIR funded effort we performed multiple tank scale experiments in which we investigated complex electrical resistivity signatures associated with dissolved CO2 plumes in saturated sediments. We also investigated the feasibility of distinguishing CO2 leakage signatures from signatures associated with other processes such as salt water movement, temperature variations and other variations in chemical or physical conditions. In addition to these experiments we also numerically modeled the tank experiments. These experiments showed that (a) we can distinguish CO2 leakage signatures from other signatures, (b) CO2 leakage signatures have a consistent characteristic, (c) laboratory experiments are in agreement with field results, and (d) we can numerically simulate the main characteristics of CO2 leakage and associated electrical geophysical signatures.

Content Based Image Retrieval based on Wavelet Transform coefficients distribution

PubMed Central

Lamard, Mathieu; Cazuguel, Guy; Quellec, Gwénolé; Bekri, Lynda; Roux, Christian; Cochener, Béatrice

2007-01-01

In this paper we propose a content based image retrieval method for diagnosis aid in medical fields. We characterize images without extracting significant features by using distribution of coefficients obtained by building signatures from the distribution of wavelet transform. The research is carried out by computing signature distances between the query and database images. Several signatures are proposed; they use a model of wavelet coefficient distribution. To enhance results, a weighted distance between signatures is used and an adapted wavelet base is proposed. Retrieval efficiency is given for different databases including a diabetic retinopathy, a mammography and a face database. Results are promising: the retrieval efficiency is higher than 95% for some cases using an optimization process. PMID:18003013

Revocable identity-based proxy re-signature against signing key exposure.

PubMed

Yang, Xiaodong; Chen, Chunlin; Ma, Tingchun; Wang, Jinli; Wang, Caifen

2018-01-01

Identity-based proxy re-signature (IDPRS) is a novel cryptographic primitive that allows a semi-trusted proxy to convert a signature under one identity into another signature under another identity on the same message by using a re-signature key. Due to this transformation function, IDPRS is very useful in constructing privacy-preserving schemes for various information systems. Key revocation functionality is important in practical IDPRS for managing users dynamically; however, the existing IDPRS schemes do not provide revocation mechanisms that allow the removal of misbehaving or compromised users from the system. In this paper, we first introduce a notion called revocable identity-based proxy re-signature (RIDPRS) to achieve the revocation functionality. We provide a formal definition of RIDPRS as well as its security model. Then, we present a concrete RIDPRS scheme that can resist signing key exposure and prove that the proposed scheme is existentially unforgeable against adaptive chosen identity and message attacks in the standard model. To further improve the performance of signature verification in RIDPRS, we introduce a notion called server-aided revocable identity-based proxy re-signature (SA-RIDPRS). Moreover, we extend the proposed RIDPRS scheme to the SA-RIDPRS scheme and prove that this extended scheme is secure against adaptive chosen message and collusion attacks. The analysis results show that our two schemes remain efficient in terms of computational complexity when implementing user revocation procedures. In particular, in the SA-RIDPRS scheme, the verifier needs to perform only a bilinear pairing and four exponentiation operations to verify the validity of the signature. Compared with other IDPRS schemes in the standard model, our SA-RIDPRS scheme greatly reduces the computation overhead of verification.

Revocable identity-based proxy re-signature against signing key exposure

PubMed Central

Ma, Tingchun; Wang, Jinli; Wang, Caifen

2018-01-01

Identity-based proxy re-signature (IDPRS) is a novel cryptographic primitive that allows a semi-trusted proxy to convert a signature under one identity into another signature under another identity on the same message by using a re-signature key. Due to this transformation function, IDPRS is very useful in constructing privacy-preserving schemes for various information systems. Key revocation functionality is important in practical IDPRS for managing users dynamically; however, the existing IDPRS schemes do not provide revocation mechanisms that allow the removal of misbehaving or compromised users from the system. In this paper, we first introduce a notion called revocable identity-based proxy re-signature (RIDPRS) to achieve the revocation functionality. We provide a formal definition of RIDPRS as well as its security model. Then, we present a concrete RIDPRS scheme that can resist signing key exposure and prove that the proposed scheme is existentially unforgeable against adaptive chosen identity and message attacks in the standard model. To further improve the performance of signature verification in RIDPRS, we introduce a notion called server-aided revocable identity-based proxy re-signature (SA-RIDPRS). Moreover, we extend the proposed RIDPRS scheme to the SA-RIDPRS scheme and prove that this extended scheme is secure against adaptive chosen message and collusion attacks. The analysis results show that our two schemes remain efficient in terms of computational complexity when implementing user revocation procedures. In particular, in the SA-RIDPRS scheme, the verifier needs to perform only a bilinear pairing and four exponentiation operations to verify the validity of the signature. Compared with other IDPRS schemes in the standard model, our SA-RIDPRS scheme greatly reduces the computation overhead of verification. PMID:29579125

Signature-based store checking buffer

DOEpatents

Sridharan, Vilas; Gurumurthi, Sudhanva

2015-06-02

A system and method for optimizing redundant output verification, are provided. A hardware-based store fingerprint buffer receives multiple instances of output from multiple instances of computation. The store fingerprint buffer generates a signature from the content included in the multiple instances of output. When a barrier is reached, the store fingerprint buffer uses the signature to verify the content is error-free.

Signature scheme based on bilinear pairs

NASA Astrophysics Data System (ADS)

Tong, Rui Y.; Geng, Yong J.

2013-03-01

An identity-based signature scheme is proposed by using bilinear pairs technology. The scheme uses user's identity information as public key such as email address, IP address, telephone number so that it erases the cost of forming and managing public key infrastructure and avoids the problem of user private generating center generating forgery signature by using CL-PKC framework to generate user's private key.

Characterization of palmprints by wavelet signatures via directional context modeling.

PubMed

Zhang, Lei; Zhang, David

2004-06-01

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.

DEVELOPMENT OF AN IN SITU THERMAL EXTRACTION DETECTION SYSTEM (TEDS) FOR RAPID, ACCURATE, QUANTITATIVE ANALYSIS OF ENVIRONMENTAL POLLUTANTS IN THE SUBSURFACE - PHASE I

EPA Science Inventory

Ion Signature Technology, Inc. (IST) will develop and market a collection and analysis system that will retrieve soil-bound pollutants as well as soluble and non-soluble contaminants from groundwater as the probe is pushed by cone penetrometry of Geoprobe into the subsurface. ...

Bifurcation and Hysteresis Effects in Student Performance: The Signature of Complexity and Chaos in Educational Research

ERIC Educational Resources Information Center

Stamovlasis, Dimitrios

2014-01-01

This paper addresses some methodological issues concerning traditional linear approaches and shows the need for a paradigm shift in education research towards the Complexity and Nonlinear Dynamical Systems (NDS) framework. It presents a quantitative piece of research aiming to test the nonlinear dynamical hypothesis in education. It applies…

Instant Integrated Ultradeep Quantitative-structural Membrane Proteomics Discovered Post-translational Modification Signatures for Human Cys-loop Receptor Subunit Bias.

PubMed

Zhang, Xi

2016-12-01

Neurotransmitter ligand-gated ion channels (LGICs) are widespread and pivotal in brain functions. Unveiling their structure-function mechanisms is crucial to drive drug discovery, and demands robust proteomic quantitation of expression, post-translational modifications (PTMs) and dynamic structures. Yet unbiased digestion of these modified transmembrane proteins-at high efficiency and peptide reproducibility-poses the obstacle. Targeting both enzyme-substrate contacts and PTMs for peptide formation and detection, we devised flow-and-detergent-facilitated protease and de-PTM digestions for deep sequencing (FDD) method that combined omni-compatible detergent, tandem immobilized protease/PNGase columns, and Cys-selective reduction/alkylation, to achieve streamlined ultradeep peptide preparation within minutes not days, at high peptide reproducibility and low abundance-bias. FDD transformed enzyme-protein contacts into equal catalytic travel paths through enzyme-excessive columns regardless of protein abundance, removed products instantly preventing inhibition, tackled intricate structures via sequential multiple micro-digestions along the flow, and precisely controlled peptide formation by flow rate. Peptide-stage reactions reduced steric bias; low contamination deepened MS/MS scan; distinguishing disulfide from M oxidation and avoiding gain/loss artifacts unmasked protein-endogenous oxidation states. Using a recent interactome of 285-kDa human GABA type A receptor, this pilot study validated FDD platform's applicability to deep sequencing (up to 99% coverage), H/D-exchange and TMT-based structural mapping. FDD discovered novel subunit-specific PTM signatures, including unusual nontop-surface N-glycosylations, that may drive subunit biases in human Cys-loop LGIC assembly and pharmacology, by redefining subunit/ligand interfaces and connecting function domains. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Overexpression of the Cytokine BAFF and Autoimmunity Risk.

PubMed

Steri, Maristella; Orrù, Valeria; Idda, M Laura; Pitzalis, Maristella; Pala, Mauro; Zara, Ilenia; Sidore, Carlo; Faà, Valeria; Floris, Matteo; Deiana, Manila; Asunis, Isadora; Porcu, Eleonora; Mulas, Antonella; Piras, Maria G; Lobina, Monia; Lai, Sandra; Marongiu, Mara; Serra, Valentina; Marongiu, Michele; Sole, Gabriella; Busonero, Fabio; Maschio, Andrea; Cusano, Roberto; Cuccuru, Gianmauro; Deidda, Francesca; Poddie, Fausto; Farina, Gabriele; Dei, Mariano; Virdis, Francesca; Olla, Stefania; Satta, Maria A; Pani, Mario; Delitala, Alessandro; Cocco, Eleonora; Frau, Jessica; Coghe, Giancarlo; Lorefice, Lorena; Fenu, Giuseppe; Ferrigno, Paola; Ban, Maria; Barizzone, Nadia; Leone, Maurizio; Guerini, Franca R; Piga, Matteo; Firinu, Davide; Kockum, Ingrid; Lima Bomfim, Izaura; Olsson, Tomas; Alfredsson, Lars; Suarez, Ana; Carreira, Patricia E; Castillo-Palma, Maria J; Marcus, Joseph H; Congia, Mauro; Angius, Andrea; Melis, Maurizio; Gonzalez, Antonio; Alarcón Riquelme, Marta E; da Silva, Berta M; Marchini, Maurizio; Danieli, Maria G; Del Giacco, Stefano; Mathieu, Alessandro; Pani, Antonello; Montgomery, Stephen B; Rosati, Giulio; Hillert, Jan; Sawcer, Stephen; D'Alfonso, Sandra; Todd, John A; Novembre, John; Abecasis, Gonçalo R; Whalen, Michael B; Marrosu, Maria G; Meloni, Alessandra; Sanna, Serena; Gorospe, Myriam; Schlessinger, David; Fiorillo, Edoardo; Zoledziewska, Magdalena; Cucca, Francesco

2017-04-27

Genomewide association studies of autoimmune diseases have mapped hundreds of susceptibility regions in the genome. However, only for a few association signals has the causal gene been identified, and for even fewer have the causal variant and underlying mechanism been defined. Coincident associations of DNA variants affecting both the risk of autoimmune disease and quantitative immune variables provide an informative route to explore disease mechanisms and drug-targetable pathways. Using case-control samples from Sardinia, Italy, we performed a genomewide association study in multiple sclerosis followed by TNFSF13B locus-specific association testing in systemic lupus erythematosus (SLE). Extensive phenotyping of quantitative immune variables, sequence-based fine mapping, cross-population and cross-phenotype analyses, and gene-expression studies were used to identify the causal variant and elucidate its mechanism of action. Signatures of positive selection were also investigated. A variant in TNFSF13B, encoding the cytokine and drug target B-cell activating factor (BAFF), was associated with multiple sclerosis as well as SLE. The disease-risk allele was also associated with up-regulated humoral immunity through increased levels of soluble BAFF, B lymphocytes, and immunoglobulins. The causal variant was identified: an insertion-deletion variant, GCTGT→A (in which A is the risk allele), yielded a shorter transcript that escaped microRNA inhibition and increased production of soluble BAFF, which in turn up-regulated humoral immunity. Population genetic signatures indicated that this autoimmunity variant has been evolutionarily advantageous, most likely by augmenting resistance to malaria. A TNFSF13B variant was associated with multiple sclerosis and SLE, and its effects were clarified at the population, cellular, and molecular levels. (Funded by the Italian Foundation for Multiple Sclerosis and others.).

Seismic signature analysis for discrimination of people from animals

NASA Astrophysics Data System (ADS)

Damarla, Thyagaraju; Mehmood, Asif; Sabatier, James M.

2013-05-01

Cadence analysis has been the main focus for discriminating between the seismic signatures of people and animals. However, cadence analysis fails when multiple targets are generating the signatures. We analyze the mechanism of human walking and the signature generated by a human walker, and compare it with the signature generated by a quadruped. We develop Fourier-based analysis to differentiate the human signatures from the animal signatures. We extract a set of basis vectors to represent the human and animal signatures using non-negative matrix factorization, and use them to separate and classify both the targets. Grazing animals such as deer, cows, etc., often produce sporadic signals as they move around from patch to patch of grass and one must characterize them so as to differentiate their signatures from signatures generated by a horse steadily walking along a path. These differences in the signatures are used in developing a robust algorithm to distinguish the signatures of animals from humans. The algorithm is tested on real data collected in a remote area.

Quality of signatures. [spectral signatures of winter wheat grown in Texas

NASA Technical Reports Server (NTRS)

Kan, E. P. F.

1974-01-01

Three conclusions are drawn on the usability, inherent variations, and noise aspects of the spectral signatures processed from data collected by the Field Signature Acquisition System (FSAS). Conclusions are based on the spectral data collected from winter wheat of the 1972/73 season, grown at Texas A and M University, College Station, Texas.

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

PubMed

Qian, Lunwen; Hickey, Lee T; Stahl, Andreas; Werner, Christian R; Hayes, Ben; Snowdon, Rod J; Voss-Fels, Kai P

2017-01-01

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

Whole mouse blood microRNA as biomarkers for exposure to γ-rays and 56Fe ions

PubMed Central

Templin, Thomas; Amundson, Sally A.; Brenner, David J.; Smilenov, Lubomir B.

2013-01-01

Purpose Biomarkers of ionising radiation exposure are useful in a variety of scenarios, such as medical diagnostic imaging, occupational exposures, and spaceflight. This study investigates to what extent microRNA (miRNA) expression signatures in mouse peripheral blood can be used as biomarkers for exposures to radiation with low and high linear energy transfers. Materials and methods Mice were irradiated with doses of 0.5, 1.5, or 5.0 Gy γ-rays (dose rate of 0.0136 Gy/s) or with doses of 0.1 or 0.5 Gy 56Fe ions (dose rate of 0.00208 Gy/s). Total RNA was isolated from whole blood at 6 h or 24 h after irradiation. Three animals per irradiation condition were used. Differentially expressed miRNA were determined by means of quantitative real-time polymerase chain reaction. Results miRNA expression signatures were radiation type-specific and dose- and time-dependent. The differentially expressed miRNA were expressed in either one condition (71%) or multiple conditions (29%). Classifiers based on the differentially expressed miRNA predicted radiation type or dose with accuracies between 75% and 100%. Gene-ontology analyses show that miRNA induced by irradiation are involved in the control of several biological processes, such as mRNA transcription regulation, nucleic-acid metabolism, and development. Conclusion miRNA signatures induced by ionising radiation in mouse blood are radiation type- and radiation dose-specific. These findings underline the complexity of the radiation response and the importance of miRNA in it. PMID:21271940

AdaBoost-based on-line signature verifier

NASA Astrophysics Data System (ADS)

Hongo, Yasunori; Muramatsu, Daigo; Matsumoto, Takashi

2005-03-01

Authentication of individuals is rapidly becoming an important issue. The authors previously proposed a Pen-input online signature verification algorithm. The algorithm considers a writer"s signature as a trajectory of pen position, pen pressure, pen azimuth, and pen altitude that evolve over time, so that it is dynamic and biometric. Many algorithms have been proposed and reported to achieve accuracy for on-line signature verification, but setting the threshold value for these algorithms is a problem. In this paper, we introduce a user-generic model generated by AdaBoost, which resolves this problem. When user- specific models (one model for each user) are used for signature verification problems, we need to generate the models using only genuine signatures. Forged signatures are not available because imposters do not give forged signatures for training in advance. However, we can make use of another's forged signature in addition to the genuine signatures for learning by introducing a user generic model. And Adaboost is a well-known classification algorithm, making final decisions depending on the sign of the output value. Therefore, it is not necessary to set the threshold value. A preliminary experiment is performed on a database consisting of data from 50 individuals. This set consists of western-alphabet-based signatures provide by a European research group. In this experiment, our algorithm gives an FRR of 1.88% and an FAR of 1.60%. Since no fine-tuning was done, this preliminary result looks very promising.

Pose-oblivious shape signature.

PubMed

Gal, Ran; Shamir, Ariel; Cohen-Or, Daniel

2007-01-01

A 3D shape signature is a compact representation for some essence of a shape. Shape signatures are commonly utilized as a fast indexing mechanism for shape retrieval. Effective shape signatures capture some global geometric properties which are scale, translation, and rotation invariant. In this paper, we introduce an effective shape signature which is also pose-oblivious. This means that the signature is also insensitive to transformations which change the pose of a 3D shape such as skeletal articulations. Although some topology-based matching methods can be considered pose-oblivious as well, our new signature retains the simplicity and speed of signature indexing. Moreover, contrary to topology-based methods, the new signature is also insensitive to the topology change of the shape, allowing us to match similar shapes with different genus. Our shape signature is a 2D histogram which is a combination of the distribution of two scalar functions defined on the boundary surface of the 3D shape. The first is a definition of a novel function called the local-diameter function. This function measures the diameter of the 3D shape in the neighborhood of each vertex. The histogram of this function is an informative measure of the shape which is insensitive to pose changes. The second is the centricity function that measures the average geodesic distance from one vertex to all other vertices on the mesh. We evaluate and compare a number of methods for measuring the similarity between two signatures, and demonstrate the effectiveness of our pose-oblivious shape signature within a 3D search engine application for different databases containing hundreds of models.

Label-free visualization of collagen in submucosa as a potential diagnostic marker for early detection of colorectal cancer

NASA Astrophysics Data System (ADS)

Qiu, Jingting; Yang, Yinghong; Jiang, Weizhong; Feng, Changyin; Chen, Zhifen; Guan, Guoxian; Zhu, Xiaoqin; Zhuo, Shuangmu; Chen, Jianxin

2014-09-01

The collagen signature in colorectal submucosa is changed due to remodeling of the extracellular matrix during the malignant process and plays an important role in noninvasive early detection of human colorectal cancer. In this work, multiphoton microscopy (MPM) was used to monitor the changes of collagen in normal colorectal submucosa (NCS) and cancerous colorectal submucosa (CCS). What's more, the collagen content was quantitatively measured. It was found that in CCS the morphology of collagen becomes much looser and the collagen content is significantly reduced compared to NCS. These results suggest that MPM has the ability to provide collagen signature as a potential diagnostic marker for early detection of colorectal cancer.

Proposal for chiral-boson search at LHC via their unique new signature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chizhov, M. V.; Bednyakov, V. A.; Budagov, J. A.

The resonance production of new chiral spin-1 bosons and their detection through the Drell-Yan process at the CERN LHC is considered. Quantitative evaluations of various differential cross sections of the chiral-boson production are made within the CalcHEP package. The new neutral chiral bosons can be observed as a Breit-Wigner resonance peak in the invariant-dilepton-mass distribution, as usual. However, unique new signatures of the chiral bosons exist. First, there is no Jacobian peak in the lepton transverse-momentum distribution. Second, the lepton angular distribution in the Collins-Soper frame for the high on-peak invariant masses of the lepton pairs has a peculiar 'swallowtail'more » shape.« less

The signature-based radiation-scanning approach to standoff detection of improvised explosive devices.

PubMed

Brewer, R L; Dunn, W L; Heider, S; Matthew, C; Yang, X

2012-07-01

The signature-based radiation-scanning technique for detection of improvised explosive devices is described. The technique seeks to detect nitrogen-rich chemical explosives present in a target. The technology compares a set of "signatures" obtained from a test target to a collection of "templates", sets of signatures for a target that contain an explosive in a specific configuration. Interrogation of nitrogen-rich fertilizer samples, which serve as surrogates for explosives, is shown experimentally to be able to discriminate samples of 3.8L and larger. Copyright © 2011 Elsevier Ltd. All rights reserved.

Arbitrated Quantum Signature with Hamiltonian Algorithm Based on Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Shi, Ronghua; Ding, Wanting; Shi, Jinjing

2018-03-01

A novel arbitrated quantum signature (AQS) scheme is proposed motivated by the Hamiltonian algorithm (HA) and blind quantum computation (BQC). The generation and verification of signature algorithm is designed based on HA, which enables the scheme to rely less on computational complexity. It is unnecessary to recover original messages when verifying signatures since the blind quantum computation is applied, which can improve the simplicity and operability of our scheme. It is proved that the scheme can be deployed securely, and the extended AQS has some extensive applications in E-payment system, E-government, E-business, etc.

Arbitrated Quantum Signature with Hamiltonian Algorithm Based on Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Shi, Ronghua; Ding, Wanting; Shi, Jinjing

2018-07-01

A novel arbitrated quantum signature (AQS) scheme is proposed motivated by the Hamiltonian algorithm (HA) and blind quantum computation (BQC). The generation and verification of signature algorithm is designed based on HA, which enables the scheme to rely less on computational complexity. It is unnecessary to recover original messages when verifying signatures since the blind quantum computation is applied, which can improve the simplicity and operability of our scheme. It is proved that the scheme can be deployed securely, and the extended AQS has some extensive applications in E-payment system, E-government, E-business, etc.

A quantitative investigation of the fracture pump-in/flowback test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plahn, S.V.; Nolte, K.G.; Miska, S.

1995-12-31

Fracture closure pressure is an important parameter for fracture treatment design and evaluation. The pump-in/flowback (PIFB) test is frequently used to estimate its magnitude. The test is attractive because bottomhole pressures during flowback develop a distinct and repeatable signature. This is in contrast to the pump-in/shut-in test where strong indications of fracture closure are rarely seen. Various techniques exist for extracting closure pressure from the flowback pressure response. Unfortunately, these procedures give different estimates for closure pressure and their theoretical bases are not well established. We present results that place the PIFB test on a more solid foundation. A numericalmore » model is used to simulate the PIFB test and glean physical mechanisms contributing to the response. Based on our simulation results, we propose an interpretation procedure which gives better estimates for closure pressure than existing techniques.« less

Performance characterization of material identification systems

NASA Astrophysics Data System (ADS)

Brown, Christopher D.; Green, Robert L.

2006-10-01

In recent years a number of analytical devices have been proposed and marketed specifically to enable field-based material identification. Technologies reliant on mass, near- and mid-infrared, and Raman spectroscopies are available today, and other platforms are imminent. These systems tend to perform material recognition based on an on-board library of material signatures. While figures of merit for traditional quantitative analytical sensors are broadly established (e.g., SNR, selectivity, sensitivity, limit of detection/decision), measures of performance for material identification systems have not been systematically discussed. In this paper we present an approach to performance characterization similar in spirit to ROC curves, but including elements of precision-recall curves and specialized for the intended-use of material identification systems. Important experimental considerations are discussed, including study design, sources of bias, uncertainty estimation, and cross-validation and the approach as a whole is illustrated using a commercially available handheld Raman material identification system.

Carbon Monoxide Stable Isotopes: Extraction Technique Development and Urban Atmospheric Analysis

NASA Astrophysics Data System (ADS)

Vimont, Isaac Josef

We have developed an extraction system to analyze isotopes of carbon monoxide (CO). We then analyzed CO isotopes for two years at Indianapolis, IN, USA. These measurements were done at three towers, one of which measured incoming, background air into the city. We quantitatively removed the background signal and determined the urban CO mole fraction and isotopic enhancements. During the winter months, we constrained the isotopic signature and concluded that the majority of CO produced during the winter was produced by fossil fuel combustion. We found that the Indianapolis fossil fuel signature differed from that of studies done in Europe. Further, we performed a limited traffic study to look at CO isotopes from traffic. While this was not conclusive, it did support our hypothesis that a larger fraction of the Indianapolis vehicle fleet may have malfunctioning catalytic systems, which biases the isotopic results, particularly for delta18O. We used the wintertime fossil fuel isotopic signature to help constrain the summertime budget. It was hypothesized that a second source of CO was significant during the summer months. Oxidation of biogenically produced volatile organic compounds (BVOC's) was one possible source. Oxidized BVOC's were consistent with the changes between our winter and summer isotopic source signatures. We then used the isotopic signatures to determine that between zero and sixty percent of the summertime CO budget was produced from oxidized VOC's. This provided the first direct evidence of a larger percentage of urban CO being produced by oxidized VOC's.

MicroRNA Based Liquid Biopsy: The Experience of the Plasma miRNA Signature Classifier (MSC) for Lung Cancer Screening.

PubMed

Mensah, Mavis; Borzi, Cristina; Verri, Carla; Suatoni, Paola; Conte, Davide; Pastorino, Ugo; Orazio, Fortunato; Sozzi, Gabriella; Boeri, Mattia

2017-10-26

The development of a minimally invasive test, such as liquid biopsy, for early lung cancer detection in its preclinical phase is crucial to improve the outcome of this deadly disease. MicroRNAs (miRNAs) are tissue specific, small, non-coding RNAs regulating gene expression, which may act as extracellular messengers of biological signals derived from the cross-talk between the tumor and its surrounding microenvironment. They could thus represent ideal candidates for early detection of lung cancer. In this work, a methodological workflow for the prospective validation of a circulating miRNA test using custom made microfluidic cards and quantitative Real-Time PCR in plasma samples of volunteers enrolled in a lung cancer screening trial is proposed. In addition, since the release of hemolysis-related miRNAs and more general technical issues may affect the analysis, the quality control steps included in the standard operating procedures are also presented. The protocol is reproducible and gives reliable quantitative results; however, when using large clinical series, both pre-analytical and analytical features should be cautiously evaluated.

Passive thermal infrared hyperspectral imaging for quantitative imaging of shale gas leaks

NASA Astrophysics Data System (ADS)

Gagnon, Marc-André; Tremblay, Pierre; Savary, Simon; Farley, Vincent; Guyot, Éric; Lagueux, Philippe; Morton, Vince; Giroux, Jean; Chamberland, Martin

2017-10-01

There are many types of natural gas fields including shale formations that are common especially in the St-Lawrence Valley (Canada). Since methane (CH4), the major component of shale gas, is odorless, colorless and highly flammable, in addition to being a greenhouse gas, methane emanations and/or leaks are important to consider for both safety and environmental reasons. Telops recently launched on the market the Hyper-Cam Methane, a field-deployable thermal infrared hyperspectral camera specially tuned for detecting methane infrared spectral features under ambient conditions and over large distances. In order to illustrate the benefits of this novel research instrument for natural gas imaging, the instrument was brought on a site where shale gas leaks unexpectedly happened during a geological survey near the Enfant-Jesus hospital in Quebec City, Canada, during December 2014. Quantitative methane imaging was carried out based on methane's unique infrared spectral signature. Optical flow analysis was also carried out on the data to estimate the methane mass flow rate. The results show how this novel technique could be used for advanced research on shale gases.

Individuality and togetherness in joint improvised motion.

PubMed

Hart, Yuval; Noy, Lior; Feniger-Schaal, Rinat; Mayo, Avraham E; Alon, Uri

2014-01-01

Actors, dancers and musicians that improvise together report special moments of togetherness: high performance and synchrony, seemingly without a leader and a follower. Togetherness seems to conflict with individuality- the idiosyncratic character of each person's performance. To understand the relation of individuality and togetherness, we employed the mirror game paradigm in which two players are asked to mirror each other and create interesting synchronized motion, with and without a designated leader. The mirror game enables quantitative characterization of moments of togetherness in which complex motion is generated with high synchrony. We find that each person as a leader does basic strokes of motion with a characteristic signature, in terms of the shape of their velocity profile between two stopping events. In moments of togetherness both players change their signature to a universal stroke shape. This universal velocity profile resembles a half-period of a sine wave, and is therefore symmetric and maximally smooth. Thus, instead of converging to an intermediate motion signature, or having one player dominate, players seem to shift their basic motion signatures to a shape that is altogether different from their individually preferred shapes; the resulting motion may be easier to predict and to agree on. The players then build complex motion by using such smooth elementary strokes.

Individuality and Togetherness in Joint Improvised Motion

PubMed Central

Feniger-Schaal, Rinat; Mayo, Avraham E.; Alon, Uri

2014-01-01

Actors, dancers and musicians that improvise together report special moments of togetherness: high performance and synchrony, seemingly without a leader and a follower. Togetherness seems to conflict with individuality- the idiosyncratic character of each person's performance. To understand the relation of individuality and togetherness, we employed the mirror game paradigm in which two players are asked to mirror each other and create interesting synchronized motion, with and without a designated leader. The mirror game enables quantitative characterization of moments of togetherness in which complex motion is generated with high synchrony. We find that each person as a leader does basic strokes of motion with a characteristic signature, in terms of the shape of their velocity profile between two stopping events. In moments of togetherness both players change their signature to a universal stroke shape. This universal velocity profile resembles a half-period of a sine wave, and is therefore symmetric and maximally smooth. Thus, instead of converging to an intermediate motion signature, or having one player dominate, players seem to shift their basic motion signatures to a shape that is altogether different from their individually preferred shapes; the resulting motion may be easier to predict and to agree on. The players then build complex motion by using such smooth elementary strokes. PMID:24533054

Detecting and visualizing weak signatures in hyperspectral data

NASA Astrophysics Data System (ADS)

MacPherson, Duncan James

This thesis evaluates existing techniques for detecting weak spectral signatures from remotely sensed hyperspectral data. Algorithms are presented that successfully detect hard-to-find 'mystery' signatures in unknown cluttered backgrounds. The term 'mystery' is used to describe a scenario where the spectral target and background endmembers are unknown. Sub-Pixel analysis and background suppression are used to find deeply embedded signatures which can be less than 10% of the total signal strength. Existing 'mystery target' detection algorithms are derived and compared. Several techniques are shown to be superior both visually and quantitatively. Detection performance is evaluated using confidence metrics that are developed. A multiple algorithm approach is shown to improve detection confidence significantly. Although the research focuses on remote sensing applications, the algorithms presented can be applied to a wide variety of diverse fields such as medicine, law enforcement, manufacturing, earth science, food production, and astrophysics. The algorithms are shown to be general and can be applied to both the reflective and emissive parts of the electromagnetic spectrum. The application scope is a broad one and the final results open new opportunities for many specific applications including: land mine detection, pollution and hazardous waste detection, crop abundance calculations, volcanic activity monitoring, detecting diseases in food, automobile or airplane target recognition, cancer detection, mining operations, extracting galactic gas emissions, etc.

Digital Signature Management.

ERIC Educational Resources Information Center

Hassler, Vesna; Biely, Helmut

1999-01-01

Describes the Digital Signature Project that was developed in Austria to establish an infrastructure for applying smart card-based digital signatures in banking and electronic-commerce applications. Discusses the need to conform to international standards, an international certification infrastructure, and security features for a public directory…

System and method of detecting cavitation in pumps

DOEpatents

Lu, Bin; Sharma, Santosh Kumar; Yan, Ting; Dimino, Steven A.

2017-10-03

A system and method for detecting cavitation in pumps for fixed and variable supply frequency applications is disclosed. The system includes a controller having a processor programmed to repeatedly receive real-time operating current data from a motor driving a pump, generate a current frequency spectrum from the current data, and analyze current data within a pair of signature frequency bands of the current frequency spectrum. The processor is further programmed to repeatedly determine fault signatures as a function of the current data within the pair of signature frequency bands, repeatedly determine fault indices based on the fault signatures and a dynamic reference signature, compare the fault indices to a reference index, and identify a cavitation condition in a pump based on a comparison between the reference index and a current fault index.

Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays

USDA-ARS?s Scientific Manuscript database

To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and ...

Rydberg Atoms in Strong Fields: a Testing Ground for Quantum Chaos.

NASA Astrophysics Data System (ADS)

Courtney, Michael

1995-01-01

Rydberg atoms in strong static electric and magnetic fields provide experimentally accessible systems for studying the connections between classical chaos and quantum mechanics in the semiclassical limit. This experimental accessibility has motivated the development of reliable quantum mechanical solutions. This thesis uses both experimental and computed quantum spectra to test the central approaches to quantum chaos. These central approaches consist mainly of developing methods to compute the spectra of quantum systems in non -perturbative regimes, correlating statistical descriptions of eigenvalues with the classical behavior of the same Hamiltonian, and the development of semiclassical methods such as periodic-orbit theory. Particular emphasis is given to identifying the spectral signature of recurrences --quantum wave packets which follow classical orbits. The new findings include: the breakdown of the connection between energy-level statistics and classical chaos in odd-parity diamagnetic lithium, the discovery of the signature of very long period orbits in atomic spectra, quantitative evidence for the scattering of recurrences by the alkali -metal core, quantitative description of the behavior of recurrences near bifurcations, and a semiclassical interpretation of the evolution of continuum Stark spectra. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.).

Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients.

PubMed

Tan, Tuan Zea; Miow, Qing Hao; Miki, Yoshio; Noda, Tetsuo; Mori, Seiichi; Huang, Ruby Yun-Ju; Thiery, Jean Paul

2014-10-01

Epithelial-mesenchymal transition (EMT) is a reversible and dynamic process hypothesized to be co-opted by carcinoma during invasion and metastasis. Yet, there is still no quantitative measure to assess the interplay between EMT and cancer progression. Here, we derived a method for universal EMT scoring from cancer-specific transcriptomic EMT signatures of ovarian, breast, bladder, lung, colorectal and gastric cancers. We show that EMT scoring exhibits good correlation with previously published, cancer-specific EMT signatures. This universal and quantitative EMT scoring was used to establish an EMT spectrum across various cancers, with good correlation noted between cell lines and tumours. We show correlations between EMT and poorer disease-free survival in ovarian and colorectal, but not breast, carcinomas, despite previous notions. Importantly, we found distinct responses between epithelial- and mesenchymal-like ovarian cancers to therapeutic regimes administered with or without paclitaxel in vivo and demonstrated that mesenchymal-like tumours do not always show resistance to chemotherapy. EMT scoring is thus a promising, versatile tool for the objective and systematic investigation of EMT roles and dynamics in cancer progression, treatment response and survival. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

The diversity of methoxyphenols released by pyrolysis-gas chromatography as predictor of soil carbon storage.

PubMed

Jiménez-González, Marco A; Álvarez, Ana M; Carral, Pilar; González-Vila, Francisco J; Almendros, Gonzalo

2017-07-28

The variable extent to which environmental factors are involved in soil carbon storage is currently a subject of controversy. In fact, justifying why some soils accumulate more organic matter than others is not trivial. Some abiotic factors such as organo-mineral associations have classically been invoked as the main drivers for soil C stabilization. However, in this research indirect evidences based on correlations between soil C storage and compositional descriptors of the soil organic matter are presented. It is assumed that the intrinsic structure of soil organic matter should have a bearing in the soil carbon storage. This is examined here by focusing on the methoxyphenols released by direct pyrolysis from a wide variety of topsoil samples from continental Mediterranean ecosystems from Spain with different properties and carbon content. Methoxyphenols are typical signature compounds presumptively informing on the occurrence and degree of alteration of lignin in soils. The methoxyphenol assemblages (12 major guaiacyl- and syringyl-type compounds) were analyzed by pyrolysis-gas chromatography-mass spectrometry. The Shannon-Wiener diversity index was chosen to describe the complexity of this phenolic signature. A series of exploratory statistical analyses (simple regression, partial least squares regression, multidimensional scaling) were applied to analyze the relationships existing between chemical and spectroscopic characteristics and the carbon content in the soils. These treatments coincided in pointing out that significant correlations exist between the progressive molecular diversity of the methoxyphenol assemblages and the concentration of organic carbon stored in the corresponding soils. This potential of the diversity in the phenolic signature as a surrogate index of the carbon storage in soils is tentatively interpreted as the accumulation of plant macromolecules altered into microbially reworked structures not readily recognized by soil enzymes. From a quantitative viewpoint, the partial least squares regression models exclusively based on total abundances of the 12 major methoxyphenols were especially successful in forecasting soil carbon storage. Copyright © 2017 Elsevier B.V. All rights reserved.

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

PubMed Central

Shiraishi, Yuichi; Tremmel, Georg; Miyano, Satoru; Stephens, Matthew

2015-01-01

Recent advances in sequencing technologies have enabled the production of massive amounts of data on somatic mutations from cancer genomes. These data have led to the detection of characteristic patterns of somatic mutations or “mutation signatures” at an unprecedented resolution, with the potential for new insights into the causes and mechanisms of tumorigenesis. Here we present new methods for modelling, identifying and visualizing such mutation signatures. Our methods greatly simplify mutation signature models compared with existing approaches, reducing the number of parameters by orders of magnitude even while increasing the contextual factors (e.g. the number of flanking bases) that are accounted for. This improves both sensitivity and robustness of inferred signatures. We also provide a new intuitive way to visualize the signatures, analogous to the use of sequence logos to visualize transcription factor binding sites. We illustrate our new method on somatic mutation data from urothelial carcinoma of the upper urinary tract, and a larger dataset from 30 diverse cancer types. The results illustrate several important features of our methods, including the ability of our new visualization tool to clearly highlight the key features of each signature, the improved robustness of signature inferences from small sample sizes, and more detailed inference of signature characteristics such as strand biases and sequence context effects at the base two positions 5′ to the mutated site. The overall framework of our work is based on probabilistic models that are closely connected with “mixed-membership models” which are widely used in population genetic admixture analysis, and in machine learning for document clustering. We argue that recognizing these relationships should help improve understanding of mutation signature extraction problems, and suggests ways to further improve the statistical methods. Our methods are implemented in an R package pmsignature (https://github.com/friend1ws/pmsignature) and a web application available at https://friend1ws.shinyapps.io/pmsignature_shiny/. PMID:26630308

Prevalence of interferon type I signature in CD14 monocytes of patients with Sjögren's syndrome and association with disease activity and BAFF gene expression

PubMed Central

Brkic, Zana; Maria, Naomi I; van Helden-Meeuwsen, Cornelia G; van de Merwe, Joop P; van Daele, Paul L; Dalm, Virgil A; Wildenberg, Manon E; Beumer, Wouter; Drexhage, Hemmo A; Versnel, Marjan A

2013-01-01

Objective To determine the prevalence of upregulation of interferon (IFN) type I inducible genes, the so called ‘IFN type I signature’, in CD14 monocytes in 69 patients with primary Sjögren's syndrome (pSS) and 44 healthy controls (HC) and correlate it with disease manifestations and expression of B cell activating factor (BAFF). Methods Expression of IFI44L, IFI44, IFIT3, LY6E and MX1 was measured using real time quantitative PCR in monocytes. Expression values were used to calculate IFN type I scores for each subject. pSS patients positive for the IFN type I signature (IFN score≥10) and patients negative for the signature (IFN score<10) were then compared for clinical disease manifestations and BAFF expression. A bioassay using a monocytic cell line was performed to study whether BAFF mRNA expression was inducible by IFN type I activity in serum of patients with pSS. Results An IFN type I signature was present in 55% of patients with pSS compared with 4.5% of HC. Patients with the IFN type I signature showed: (a) higher EULAR Sjögren's Syndrome Disease Activity Index scores; higher anti-Ro52, anti-Ro60 and anti-La autoantibodies; higher rheumatoid factor; higher serum IgG; lower C3, lower absolute lymphocyte and neutrophil counts; (b)higher BAFF gene expression in monocytes. In addition, serum of signature-positive patients induced BAFF gene expression in monocytes. Conclusions The monocyte IFN type I signature identifies a subgroup of patients with pSS with a higher clinical disease activity together with higher BAFF mRNA expression. Such patients might benefit from treatment blocking IFN type I production or activity. PMID:22736090

Texture-Based Automated Lithological Classification Using Aeromagenetic Anomaly Images

USGS Publications Warehouse

Shankar, Vivek

2009-01-01

This report consists of a thesis submitted to the faculty of the Department of Electrical and Computer Engineering, in partial fulfillment of the requirements for the degree of Master of Science, Graduate College, The University of Arizona, 2004 Aeromagnetic anomaly images are geophysical prospecting tools frequently used in the exploration of metalliferous minerals and hydrocarbons. The amplitude and texture content of these images provide a wealth of information to geophysicists who attempt to delineate the nature of the Earth's upper crust. These images prove to be extremely useful in remote areas and locations where the minerals of interest are concealed by basin fill. Typically, geophysicists compile a suite of aeromagnetic anomaly images, derived from amplitude and texture measurement operations, in order to obtain a qualitative interpretation of the lithological (rock) structure. Texture measures have proven to be especially capable of capturing the magnetic anomaly signature of unique lithological units. We performed a quantitative study to explore the possibility of using texture measures as input to a machine vision system in order to achieve automated classification of lithological units. This work demonstrated a significant improvement in classification accuracy over random guessing based on a priori probabilities. Additionally, a quantitative comparison between the performances of five classes of texture measures in their ability to discriminate lithological units was achieved.

Quantitation of 47 human tear proteins using high resolution multiple reaction monitoring (HR-MRM) based-mass spectrometry.

PubMed

Tong, Louis; Zhou, Xi Yuan; Jylha, Antti; Aapola, Ulla; Liu, Dan Ning; Koh, Siew Kwan; Tian, Dechao; Quah, Joanne; Uusitalo, Hannu; Beuerman, Roger W; Zhou, Lei

2015-02-06

Tear proteins are intimately related to the pathophysiology of the ocular surface. Many recent studies have demonstrated that the tear is an accessible fluid for studying eye diseases and biomarker discovery. This study describes a high resolution multiple reaction monitoring (HR-MRM) approach for developing assays for quantification of biologically important tear proteins. Human tear samples were collected from 1000 subjects with no eye complaints (411 male, 589 female, average age: 55.5±14.5years) after obtaining informed consent. Tear samples were collected using Schirmer's strips and pooled into a single global control sample. Quantification of proteins was carried out by selecting "signature" peptides derived by trypsin digestion. A 1-h nanoLC-MS/MS run was used to quantify the tear proteins in HR-MRM mode. Good reproducibility of signal intensity (using peak areas) was demonstrated for all 47 HR-MRM assays with an average coefficient of variation (CV%) of 4.82% (range: 1.52-10.30%). All assays showed consistent retention time with a CV of less than 0.80% (average: 0.57%). HR-MRM absolute quantitation of eight tear proteins was demonstrated using stable isotope-labeled peptides. In this study, we demonstrated for the first time the technique to quantify 47 human tear proteins in HR-MRM mode using approximately 1μl of human tear sample. These multiplexed HR-MRM-based assays show great promise of further development for biomarker validation in human tear samples. Both discovery-based and targeted quantitative proteomics can be achieved in a single quadrupole time-of-flight mass spectrometer platform (TripleTOF 5600 system). Copyright © 2015 Elsevier B.V. All rights reserved.

An Improved Quantum Proxy Blind Signature Scheme Based on Genuine Seven-Qubit Entangled State

NASA Astrophysics Data System (ADS)

Yang, Yuan-Yuan; Xie, Shu-Cui; Zhang, Jian-Zhong

2017-07-01

An improved quantum proxy blind signature scheme based on controlled teleportation is proposed in this paper. Genuine seven-qubit entangled state functions as quantum channel. We use the physical characteristics of quantum mechanics to implement delegation, signature and verification. Security analysis shows that our scheme is unforgeability, undeniability, blind and unconditionally secure. Meanwhile, we propose a trust party to provide higher security, the trust party is costless.

A New Adaptive Structural Signature for Symbol Recognition by Using a Galois Lattice as a Classifier.

PubMed

Coustaty, M; Bertet, K; Visani, M; Ogier, J

2011-08-01

In this paper, we propose a new approach for symbol recognition using structural signatures and a Galois lattice as a classifier. The structural signatures are based on topological graphs computed from segments which are extracted from the symbol images by using an adapted Hough transform. These structural signatures-that can be seen as dynamic paths which carry high-level information-are robust toward various transformations. They are classified by using a Galois lattice as a classifier. The performance of the proposed approach is evaluated based on the GREC'03 symbol database, and the experimental results we obtain are encouraging.

Validation of the Lung Subtyping Panel in Multiple Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Lung Tumor Gene Expression Data Sets.

PubMed

Faruki, Hawazin; Mayhew, Gregory M; Fan, Cheng; Wilkerson, Matthew D; Parker, Scott; Kam-Morgan, Lauren; Eisenberg, Marcia; Horten, Bruce; Hayes, D Neil; Perou, Charles M; Lai-Goldman, Myla

2016-06-01

Context .- A histologic classification of lung cancer subtypes is essential in guiding therapeutic management. Objective .- To complement morphology-based classification of lung tumors, a previously developed lung subtyping panel (LSP) of 57 genes was tested using multiple public fresh-frozen gene-expression data sets and a prospectively collected set of formalin-fixed, paraffin-embedded lung tumor samples. Design .- The LSP gene-expression signature was evaluated in multiple lung cancer gene-expression data sets totaling 2177 patients collected from 4 platforms: Illumina RNAseq (San Diego, California), Agilent (Santa Clara, California) and Affymetrix (Santa Clara) microarrays, and quantitative reverse transcription-polymerase chain reaction. Gene centroids were calculated for each of 3 genomic-defined subtypes: adenocarcinoma, squamous cell carcinoma, and neuroendocrine, the latter of which encompassed both small cell carcinoma and carcinoid. Classification by LSP into 3 subtypes was evaluated in both fresh-frozen and formalin-fixed, paraffin-embedded tumor samples, and agreement with the original morphology-based diagnosis was determined. Results .- The LSP-based classifications demonstrated overall agreement with the original clinical diagnosis ranging from 78% (251 of 322) to 91% (492 of 538 and 869 of 951) in the fresh-frozen public data sets and 84% (65 of 77) in the formalin-fixed, paraffin-embedded data set. The LSP performance was independent of tissue-preservation method and gene-expression platform. Secondary, blinded pathology review of formalin-fixed, paraffin-embedded samples demonstrated concordance of 82% (63 of 77) with the original morphology diagnosis. Conclusions .- The LSP gene-expression signature is a reproducible and objective method for classifying lung tumors and demonstrates good concordance with morphology-based classification across multiple data sets. The LSP panel can supplement morphologic assessment of lung cancers, particularly when classification by standard methods is challenging.

Secure and Efficient Signature Scheme Based on NTRU for Mobile Payment

NASA Astrophysics Data System (ADS)

Xia, Yunhao; You, Lirong; Sun, Zhe; Sun, Zhixin

2017-10-01

Mobile payment becomes more and more popular, however the traditional public-key encryption algorithm has higher requirements for hardware which is not suitable for mobile terminals of limited computing resources. In addition, these public-key encryption algorithms do not have the ability of anti-quantum computing. This paper researches public-key encryption algorithm NTRU for quantum computation through analyzing the influence of parameter q and k on the probability of generating reasonable signature value. Two methods are proposed to improve the probability of generating reasonable signature value. Firstly, increase the value of parameter q. Secondly, add the authentication condition that meet the reasonable signature requirements during the signature phase. Experimental results show that the proposed signature scheme can realize the zero leakage of the private key information of the signature value, and increase the probability of generating the reasonable signature value. It also improve rate of the signature, and avoid the invalid signature propagation in the network, but the scheme for parameter selection has certain restrictions.

Detection of illegal transfer of videos over the Internet

NASA Astrophysics Data System (ADS)

Chaisorn, Lekha; Sainui, Janya; Manders, Corey

2010-07-01

In this paper, a method for detecting infringements or modifications of a video in real-time is proposed. The method first segments a video stream into shots, after which it extracts some reference frames as keyframes. This process is performed employing a Singular Value Decomposition (SVD) technique developed in this work. Next, for each input video (represented by its keyframes), ordinal-based signature and SIFT (Scale Invariant Feature Transform) descriptors are generated. The ordinal-based method employs a two-level bitmap indexing scheme to construct the index for each video signature. The first level clusters all input keyframes into k clusters while the second level converts the ordinal-based signatures into bitmap vectors. On the other hand, the SIFT-based method directly uses the descriptors as the index. Given a suspect video (being streamed or transferred on the Internet), we generate the signature (ordinal and SIFT descriptors) then we compute similarity between its signature and those signatures in the database based on ordinal signature and SIFT descriptors separately. For similarity measure, besides the Euclidean distance, Boolean operators are also utilized during the matching process. We have tested our system by performing several experiments on 50 videos (each about 1/2 hour in duration) obtained from the TRECVID 2006 data set. For experiments set up, we refer to the conditions provided by TRECVID 2009 on "Content-based copy detection" task. In addition, we also refer to the requirements issued in the call for proposals by MPEG standard on the similar task. Initial result shows that our framework is effective and robust. As compared to our previous work, on top of the achievement we obtained by reducing the storage space and time taken in the ordinal based method, by introducing the SIFT features, we could achieve an overall accuracy in F1 measure of about 96% (improved about 8%).

Interpreting stream sediment fingerprints against primary and secondary source signatures in agricultural catchments

NASA Astrophysics Data System (ADS)

Blake, Will H.; Haley, Steve; Smith, Hugh G.; Taylor, Alex; Goddard, Rupert; Lewin, Sean; Fraser, David

2013-04-01

Many sediment fingerprinting studies adopt a black box approach to source apportionment whereby the properties of downstream sediment are compared quantitatively to the geochemical fingerprints of potential catchment sources without consideration of potential signature development or modification during transit. Working within a source-pathway-receptor framework, this study aimed to undertake sediment source apportionment within 6 subcatchments of an agricultural river basin with specific attention to the potential role of contaminants (vehicle emissions and mine waste) in development of stream sediment signatures. Fallout radionuclide (FRN) and geochemical fingerprinting methods were adopted independently to establish source signatures for primary sediment sources of surface and subsurface soil materials under various land uses plus reworked mine and 'secondary' soil material deposited, in transit, along road networks. FRN data demonstrated expected variability between surface soil (137Cs = 14 ± 3 Bq kg-1; 210Pbxs = 40 ± 7 Bq kg-1) and channel bank materials (137Cs = 3 ± 1 Bq kg-1; 210Pbxs = 24 ± 5 Bq kg-1) but road transported soil material was considerably elevated in 210Pbxs (up to 673 ± 51 Bq kg-1) due to sediment interaction with pluvial surface water within the road network. Geochemical discrimination between surface and subsurface soil materials was dominated by alkaline earth and alkali metals e.g. Ba, Rb, Ca, K, Mg which are sensitive to weathering processes in soil. Magnetic susceptibility and heavy metals were important discriminators of road transported material which demonstrated transformation of the signatures of material transported via the road network. Numerical unmixing of stream sediment indicated that alongside channel bank erosion, road transported material was an important component in some systems in accord with FRN evidence. While mining spoil also ranked as a significant source in an affected catchment, perhaps related to legacy sediment, the potential role of dissolved metal leaching and subsequent sediment-water interaction within the channel on signature modification remained unclear. Consideration of sediment signature modification en route from primary source to stream elucidated important information regarding sediment transfer pathways and dynamics relevant to sediment management decisions. Further work on sediment-water interactions and potential for signature transformation in the channel environment is required.

In-Flight Technique for Acquiring Mid- And Far-Field Sonic Boom Signatures

NASA Technical Reports Server (NTRS)

Stansbery, Eugene G.; Baize, Daniel G.; Maglieri, Domenic, J.

1999-01-01

Flight test experiments have been conducted to establish the feasibility of obtaining sonic boom signature measurements below a supersonic aircraft using the NASA Portable Automatic Triggering System (PATS) mounted in the USMC Pioneer Unmanned Aerial Vehicle (UAV). This study forms a part of the NASA sonic boom minimization activities, specifically the demonstration of persistence of modified boom signatures to very large distances in a real atmosphere. The basic objective of the measurement effort was to obtain a qualitative view of the sonic boom signature in terms of its shape, number of shocks, their locations, and their relative strength. Results suggest that the technique may very well provide quantitative information relative to mid-field and far-field boom signatures. The purpose of this presentation is to describe the arrangement and operation of this in-flight system and to present the resulting sonic boom measurements. Adaption and modification of two PATS to the UAV payload section are described and include transducer location, mounting arrangement and recording system isolation. Ground static runup, takeoff and landing, and cruise flight checkouts regarding UAV propeller and flow noise on the PATS automated triggering system and recording mode are discussed. For the proof-of-concept tests, the PATS instrumented UAV was flown under radar control in steady-level flight at the altitude of 8700 feet MSL and at a cruise speed of about 60 knots. The USN F-4N sonic boom generating aircraft was vectored over the UAV on reciprocal headings at altitudes of about 1 1,000 feet MSL and 13,000 feet MSL at about Mach 1. 15. Sonic boom signatures were acquired on both PATS for all six supersonic passes. Although the UAV propeller noise is clearly evident in all the measurements, the F-4 boom signature is clearly distinguishable and is typically N-wave in character with sharply rising shock fronts and with a mid-shock associated with the inlet-wing juncture. Consideration is being given to adapting the PATS/TJAV measurements technique to the NASA Learjet to determine feasibility of acquiring in-flight boom signatures in the altitude range of 10,000 feet to 40,000 feet.

Quantitative understanding of Forbush decrease drivers based on shock-only and CME-only models using global signature of February 14, 1978 event

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raghav, Anil; Lotekar, Ajay; Bhaskar, Ankush

We have studied the Forbush decrease (FD) event that occurred on February 14, 1978 using 43 neutron monitor observatories to understand the global signature of FD. We have studied rigidity dependence of shock amplitude and total FD amplitude. We have found almost the same power law index for both shock phase amplitude and total FD amplitude. Local time variation of shock phase amplitude and maximum depression time of FD have been investigated which indicate possible effect of shock/CME orientation. We have analyzed rigidity dependence of time constants of two phase recovery. Time constants of slow component of recovery phase showmore » rigidity dependence and imply possible effect of diffusion. Solar wind speed was observed to be well correlated with slow component of FD recovery phase. This indicates solar wind speed as possible driver of recovery phase. To investigate the contribution of interplanetary drivers, shock and CME in FD, we have used shock-only and CME-only models. We have applied these models separately to shock phase and main phase amplitudes respectively. This confirms presently accepted physical scenario that the first step of FD is due to propagating shock barrier and second step is due to flux rope of CME/magnetic cloud.« less

Establishment of quantitative hydrological indexes for studies of hydro-biogeochemical interactions at the subsurface.

NASA Astrophysics Data System (ADS)

Alves Meira Neto, A.; Sengupta, A.; Wang, Y.; Volkmann, T.; Chorover, J.; Troch, P. A. A.

2017-12-01

Advances in the understanding of processes in the critical zone (CZ) are dependent on studies coupling the fields of hydrology, microbiology, geochemistry and soil development. At the same time, better insights are needed to integrate hydrologic information into biogeochemical analysis of subsurface environments. This study investigated potential hydrological indexes that help explaining spatiotemporal biogeochemical patterns. The miniLEO is a 2 m3, 10 degree sloping lysimeter located at Biosphere 2 - University of Arizona. The lysimeter was initially filled with pristine basaltic soil and subject to intermittent rainfall applications throughout the period of 18 months followed by its excavation, resulting in a grid-based sample collection at 324 locations. As a result, spatially distributed microbiological and geochemical patterns as well as soil physical properties were obtained. A hydrologic model was then developed in order to simulate the history of the system until the excavation. After being calibrated against sensor data to match its observed input-state-output behavior, the resulting distributed fields of flow velocities and moisture states were retrieved. These results were translated into several hydrological indexes to be used in with distributed microbiological and geochemical signatures. Our study attempts at conciliating sound hydrological modelling with an investigation of the subsurface biological signatures, thus providing a unique opportunity for understanding of fine-scale hydro-biological interactions.

Sound waves and resonances in electron-hole plasma

NASA Astrophysics Data System (ADS)

Lucas, Andrew

2016-06-01

Inspired by the recent experimental signatures of relativistic hydrodynamics in graphene, we investigate theoretically the behavior of hydrodynamic sound modes in such quasirelativistic fluids near charge neutrality, within linear response. Locally driving an electron fluid at a resonant frequency to such a sound mode can lead to large increases in the electrical response at the edges of the sample, a signature, which cannot be explained using diffusive models of transport. We discuss the robustness of this signal to various effects, including electron-acoustic phonon coupling, disorder, and long-range Coulomb interactions. These long-range interactions convert the sound mode into a collective plasmonic mode at low frequencies unless the fluid is charge neutral. At the smallest frequencies, the response in a disordered fluid is quantitatively what is predicted by a "momentum relaxation time" approximation. However, this approximation fails at higher frequencies (which can be parametrically small), where the classical localization of sound waves cannot be neglected. Experimental observation of such resonances is a clear signature of relativistic hydrodynamics, and provides an upper bound on the viscosity of the electron-hole plasma.

Unsupervised color normalisation for H and E stained histopathology image analysis

NASA Astrophysics Data System (ADS)

Celis, Raúl; Romero, Eduardo

2015-12-01

In histology, each dye component attempts to specifically characterise different microscopic structures. In the case of the Hematoxylin-Eosin (H&E) stain, universally used for routine examination, quantitative analysis may often require the inspection of different morphological signatures related mainly to nuclei patterns, but also to stroma distribution. Nevertheless, computer systems for automatic diagnosis are often fraught by color variations ranging from the capturing device to the laboratory specific staining protocol and stains. This paper presents a novel colour normalisation method for H&E stained histopathology images. This method is based upon the opponent process theory and blindly estimates the best color basis for the Hematoxylin and Eosin stains without relying on prior knowledge. Stain Normalisation and Color Separation are transversal to any Framework of Histopathology Image Analysis.

Recent advances in targeted endoscopic imaging: Early detection of gastrointestinal neoplasms

PubMed Central

Kwon, Yong-Soo; Cho, Young-Seok; Yoon, Tae-Jong; Kim, Ho-Shik; Choi, Myung-Gyu

2012-01-01

Molecular imaging has emerged as a new discipline in gastrointestinal endoscopy. This technology encompasses modalities that can visualize disease-specific morphological or functional tissue changes based on the molecular signature of individual cells. Molecular imaging has several advantages including minimal damage to tissues, repetitive visualization, and utility for conducting quantitative analyses. Advancements in basic science coupled with endoscopy have made early detection of gastrointestinal cancer possible. Molecular imaging during gastrointestinal endoscopy requires the development of safe biomarkers and exogenous probes to detect molecular changes in cells with high specificity anda high signal-to-background ratio. Additionally, a high-resolution endoscope with an accurate wide-field viewing capability must be developed. Targeted endoscopic imaging is expected to improve early diagnosis and individual therapy of gastrointestinal cancer. PMID:22442742

Genomic analyses provide insights into the history of tomato breeding.

PubMed

Lin, Tao; Zhu, Guangtao; Zhang, Junhong; Xu, Xiangyang; Yu, Qinghui; Zheng, Zheng; Zhang, Zhonghua; Lun, Yaoyao; Li, Shuai; Wang, Xiaoxuan; Huang, Zejun; Li, Junming; Zhang, Chunzhi; Wang, Taotao; Zhang, Yuyang; Wang, Aoxue; Zhang, Yancong; Lin, Kui; Li, Chuanyou; Xiong, Guosheng; Xue, Yongbiao; Mazzucato, Andrea; Causse, Mathilde; Fei, Zhangjun; Giovannoni, James J; Chetelat, Roger T; Zamir, Dani; Städler, Thomas; Li, Jingfu; Ye, Zhibiao; Du, Yongchen; Huang, Sanwen

2014-11-01

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

A Quantum Proxy Signature Scheme Based on Genuine Five-qubit Entangled State

NASA Astrophysics Data System (ADS)

Cao, Hai-Jing; Huang, Jun; Yu, Yao-Feng; Jiang, Xiu-Li

2014-09-01

In this paper a very efficient and secure proxy signature scheme is proposed. It is based on controlled quantum teleportation. Genuine five-qubit entangled state functions as quantum channel. The scheme uses the physical characteristics of quantum mechanics to implement delegation, signature and verification. Quantum key distribution and one-time pad are adopted in our scheme, which could guarantee not only the unconditional security of the scheme but also the anonymity of the messages owner.

Lattice enumeration for inverse molecular design using the signature descriptor.

PubMed

Martin, Shawn

2012-07-23

We describe an inverse quantitative structure-activity relationship (QSAR) framework developed for the design of molecular structures with desired properties. This framework uses chemical fragments encoded with a molecular descriptor known as a signature. It solves a system of linear constrained Diophantine equations to reorganize the fragments into novel molecular structures. The method has been previously applied to problems in drug and materials design but has inherent computational limitations due to the necessity of solving the Diophantine constraints. We propose a new approach to overcome these limitations using the Fincke-Pohst algorithm for lattice enumeration. We benchmark the new approach against previous results on LFA-1/ICAM-1 inhibitory peptides, linear homopolymers, and hydrofluoroether foam blowing agents. Software implementing the new approach is available at www.cs.otago.ac.nz/homepages/smartin.

A signature inferred from Drosophila mitotic genes predicts survival of breast cancer patients.

PubMed

Damasco, Christian; Lembo, Antonio; Somma, Maria Patrizia; Gatti, Maurizio; Di Cunto, Ferdinando; Provero, Paolo

2011-02-28

The classification of breast cancer patients into risk groups provides a powerful tool for the identification of patients who will benefit from aggressive systemic therapy. The analysis of microarray data has generated several gene expression signatures that improve diagnosis and allow risk assessment. There is also evidence that cell proliferation-related genes have a high predictive power within these signatures. We thus constructed a gene expression signature (the DM signature) using the human orthologues of 108 Drosophila melanogaster genes required for either the maintenance of chromosome integrity (36 genes) or mitotic division (72 genes). The DM signature has minimal overlap with the extant signatures and is highly predictive of survival in 5 large breast cancer datasets. In addition, we show that the DM signature outperforms many widely used breast cancer signatures in predictive power, and performs comparably to other proliferation-based signatures. For most genes of the DM signature, an increased expression is negatively correlated with patient survival. The genes that provide the highest contribution to the predictive power of the DM signature are those involved in cytokinesis. This finding highlights cytokinesis as an important marker in breast cancer prognosis and as a possible target for antimitotic therapies.

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data

PubMed Central

Fortney, Kristen; Griesman, Joshua; Kotlyar, Max; Pastrello, Chiara; Angeli, Marc; Sound-Tsao, Ming; Jurisica, Igor

2015-01-01

Repurposing FDA-approved drugs with the aid of gene signatures of disease can accelerate the development of new therapeutics. A major challenge to developing reliable drug predictions is heterogeneity. Different gene signatures of the same disease or drug treatment often show poor overlap across studies, as a consequence of both biological and technical variability, and this can affect the quality and reproducibility of computational drug predictions. Existing algorithms for signature-based drug repurposing use only individual signatures as input. But for many diseases, there are dozens of signatures in the public domain. Methods that exploit all available transcriptional knowledge on a disease should produce improved drug predictions. Here, we adapt an established meta-analysis framework to address the problem of drug repurposing using an ensemble of disease signatures. Our computational pipeline takes as input a collection of disease signatures, and outputs a list of drugs predicted to consistently reverse pathological gene changes. We apply our method to conduct the largest and most systematic repurposing study on lung cancer transcriptomes, using 21 signatures. We show that scaling up transcriptional knowledge significantly increases the reproducibility of top drug hits, from 44% to 78%. We extensively characterize drug hits in silico, demonstrating that they slow growth significantly in nine lung cancer cell lines from the NCI-60 collection, and identify CALM1 and PLA2G4A as promising drug targets for lung cancer. Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain. PMID:25786242

Atmospheric chemical transport based on high-resolution model-derived winds: A case study

NASA Astrophysics Data System (ADS)

Hannan, John R.; Fuelberg, Henry E.; Thompson, Anne M.; Bieberbach, George; Knabb, Richard D.; Kondo, Yutaka; Anderson, Bruce E.; Browell, Edward V.; Gregory, Gerald L.; Sachse, Glen W.; Singh, Hanwant B.

2000-02-01

Flight 10 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) extended southwest of Lajes, Azores. A variety of chemical signatures was encountered. These signatures are examined in detail, relating them to meteorological data from a high-resolution numerical model having a horizontal grid spacing of 30 and 90 km with 26 vertical levels. The meteorological output at hourly intervals is used to create backward trajectories from the locations of the chemical signatures. Four major categories of chemical signatures are discussed: stratospheric, lightning, continental pollution, and a mixed chemical layer. The strong stratospheric signal is encountered just south of the Azores in a region of depressed tropopause height. Three chemical signatures at different altitudes in the upper troposphere are attributed to lightning. Backward trajectories from these signatures extend to locations of cloud-to-ground lightning. Specifically, results show that the trajectories pass over regions of lightning 1-2 days earlier over the eastern Gulf of Mexico and off the southeast coast of the United States. The lowest leg of the flight exhibits a chemical signature consistent with continental pollution. Trajectories from this signature are found to pass over the highly populated Northeast Corridor of the United States. Surface-based pollution apparently is lofted to the altitudes of the trajectories by convective clouds along the East Coast that did not contain lightning. Finally, a mixed layer is described. Its chemical signature is intermediate to those of lightning and continental pollution. Backward trajectories from this layer pass between the trajectories of the lightning and pollution signatures. Thus they likely are impacted by both sources.

Photonic quantum digital signatures operating over kilometer ranges in installed optical fiber

NASA Astrophysics Data System (ADS)

Collins, Robert J.; Fujiwara, Mikio; Amiri, Ryan; Honjo, Toshimori; Shimizu, Kaoru; Tamaki, Kiyoshi; Takeoka, Masahiro; Andersson, Erika; Buller, Gerald S.; Sasaki, Masahide

2016-10-01

The security of electronic communications is a topic that has gained noteworthy public interest in recent years. As a result, there is an increasing public recognition of the existence and importance of mathematically based approaches to digital security. Many of these implement digital signatures to ensure that a malicious party has not tampered with the message in transit, that a legitimate receiver can validate the identity of the signer and that messages are transferable. The security of most digital signature schemes relies on the assumed computational difficulty of solving certain mathematical problems. However, reports in the media have shown that certain implementations of such signature schemes are vulnerable to algorithmic breakthroughs and emerging quantum processing technologies. Indeed, even without quantum processors, the possibility remains that classical algorithmic breakthroughs will render these schemes insecure. There is ongoing research into information-theoretically secure signature schemes, where the security is guaranteed against an attacker with arbitrary computational resources. One such approach is quantum digital signatures. Quantum signature schemes can be made information-theoretically secure based on the laws of quantum mechanics while comparable classical protocols require additional resources such as anonymous broadcast and/or a trusted authority. Previously, most early demonstrations of quantum digital signatures required dedicated single-purpose hardware and operated over restricted ranges in a laboratory environment. Here, for the first time, we present a demonstration of quantum digital signatures conducted over several kilometers of installed optical fiber. The system reported here operates at a higher signature generation rate than previous fiber systems.

Carbon and nitrogen isotopic signatures and nitrogen profile to identify adulteration in organic fertilizers.

PubMed

Verenitch, Sergei; Mazumder, Asit

2012-08-29

Recently it has been shown that stable isotopes of nitrogen can be used to discriminate between organic and synthetic fertilizers, but the robustness of the approach is questionable. This work developed a comprehensive method that is far more robust in identifying an adulteration of organic nitrogen fertilizers. Organic fertilizers of various types (manures, composts, blood meal, bone meal, fish meal, products of poultry and plant productions, molasses and seaweed based, and others) available on the North American market were analyzed to reveal the most sensitive criteria as well as their quantitative ranges, which can be used in their authentication. Organic nitrogen fertilizers of known origins with a wide δ(15)N range between -0.55 and 28.85‰ (n = 1258) were characterized for C and N content, δ(13)C, δ(15)N, viscosity, pH, and nitrogen profile (urea, ammonia, organic N, water insoluble N, and NO3). A statistically significant data set of characterized unique organic nitrogen fertilizers (n = 335) of various known origins has been assembled. Deliberately adulterated samples of different types of organic fertilizers mixed with synthetic fertilizers at a wide range of proportions have been used to develop the quantitative critical characteristics of organic fertilizers as the key indicators of their adulteration. Statistical analysis based on the discriminant functions of the quantitative critical characteristics of organic nitrogen fertilizers from 14 different source materials revealed a very high average rate of correct classification. The developed methodology has been successfully used as a source identification tool for numerous commercial nitrogen fertilizers available on the North American market.

E-learning platform for automated testing of electronic circuits using signature analysis method

NASA Astrophysics Data System (ADS)

Gherghina, Cǎtǎlina; Bacivarov, Angelica; Bacivarov, Ioan C.; Petricǎ, Gabriel

2016-12-01

Dependability of electronic circuits can be ensured only through testing of circuit modules. This is done by generating test vectors and their application to the circuit. Testability should be viewed as a concerted effort to ensure maximum efficiency throughout the product life cycle, from conception and design stage, through production to repairs during products operating. In this paper, is presented the platform developed by authors for training for testability in electronics, in general and in using signature analysis method, in particular. The platform allows highlighting the two approaches in the field namely analog and digital signature of circuits. As a part of this e-learning platform, it has been developed a database for signatures of different electronic components meant to put into the spotlight different techniques implying fault detection, and from this there were also self-repairing techniques of the systems with this kind of components. An approach for realizing self-testing circuits based on MATLAB environment and using signature analysis method is proposed. This paper analyses the benefits of signature analysis method and simulates signature analyzer performance based on the use of pseudo-random sequences, too.

Identification of crops in Central Arkansas using visual and infrared spectral reflectance signatures

NASA Technical Reports Server (NTRS)

1977-01-01

The spectral reflectance signatures of principle crops of central Arkansas were calibrated. Data were collected by conducting ground based reflectance signatures at well controlled test sites. Data collected were primarily for soybeans, therefore, additional measurements are essential to the acquisition of significant results.

Source-to-Sink Methods by Hyperspectral Imaging: a Case Study of the Laminated Sediments of Lake Linné (Svalbard).

NASA Astrophysics Data System (ADS)

Van Exem, A.; Debret, M.; Copard, Y.; Verpoorter, C.; Sorrel, P.; de Wet, G.; Werner, A.; Roof, S.; Laignel, B.; Retelle, M.

2016-12-01

Laminated sediments contained valuable information recorded on a micrometric scale. Information about sediments flux and origins require high-resolution source tracking analysis. Quick and non-destructive, hyperspectral imaging provides contiguous reflectance datasets into 2 dimensions with a spatial resolution of 0.02 mm. Located on the west of the Spitzbergen, Lake Linné is the largest lake in the region. Erosion is mainly driven by glacier fluctuations and three different bedrocks are potential sediment sources. Organic matter (coal) is only found in some carboniferous rocks. Four cores recovered from different parts of the lake contain millimeter scale laminae. Two approaches were compared: (i) measurement of statistical correlations between the sediments and source samples, (ii) extraction of extreme spectral signatures from the VNIR hyperspectral images. Total Organic Carbon (TOC) values of all samples were also given by bulk geochemistry (RE6 ® pyrolyzer). Consequently, the measured similarity between the hyperspectral image and the field samples illustrates the sources contribution within the core. Three sample clusters and three equivalent spectral signatures were found. TOC values from the archive show good correlation (r=0.86, p<0.001, n=73) with the hyperspectral signature relative to TOC content. A least-squares regression (r²=0.74) was used to extrapolate TOC values in order to represent their distribution at 0.02 mm resolution. This is the first source-to-sink study based on imaging spectroscopy. Our results indicate that hyperspectral imagery is a useful tool to (i) identify sediment sources, (ii) perform continuous paleo-environmental reconstruction at high resolution, and (iii) can provide quantitative results (TOC values) validated by destructive analyses.

Mapping the Natchez Trace Parkway

USGS Publications Warehouse

Rangoonwala, Amina; Bannister, Terri; Ramsey, Elijah W.

2011-01-01

Based on a National Park Service (NPS) landcover classification, a landcover map of the 715-km (444-mile) NPS Natchez Trace Parkway (hereafter referred to as the "Parkway") was created. The NPS landcover classification followed National Vegetation Classification (NVC) protocols. The landcover map, which extended the initial landcover classification to the entire Parkway, was based on color-infrared photography converted to 1-m raster-based digital orthophoto quarter quadrangles, according to U.S. Geological Survey mapping standards. Our goal was to include as many alliance classes as possible in the Parkway landcover map. To reach this goal while maintaining a consistent and quantifiable map product throughout the Parkway extent, a mapping strategy was implemented based on the migration of class-based spectral textural signatures and the congruent progressive refinement of those class signatures along the Parkway. Progressive refinement provided consistent mapping by evaluating the spectral textural distinctiveness of the alliance-association classes, and where necessary, introducing new map classes along the Parkway. By following this mapping strategy, the use of raster-based image processing and geographic information system analyses for the map production provided a quantitative and reproducible product. Although field-site classification data were severely limited, the combination of spectral migration of class membership along the Parkway and the progressive classification strategy produced an organization of alliances that was internally highly consistent. The organization resulted from the natural patterns or alignments of spectral variance and the determination of those spectral patterns that were compositionally similar in the dominant species as NVC alliances. Overall, the mapped landcovers represented the existent spectral textural patterns that defined and encompassed the complex variety of compositional alliances and associations of the Parkway. Based on that mapped representation, forests dominate the Parkway landscape. Grass is the second largest Parkway land cover, followed by scrub-shrub and shrubland classes and pine plantations. The map provides a good representation of the landcover patterns and their changes over the extent of the Parkway, south to north.

Place recognition using batlike sonar.

PubMed

Vanderelst, Dieter; Steckel, Jan; Boen, Andre; Peremans, Herbert; Holderied, Marc W

2016-08-02

Echolocating bats have excellent spatial memory and are able to navigate to salient locations using bio-sonar. Navigating and route-following require animals to recognize places. Currently, it is mostly unknown how bats recognize places using echolocation. In this paper, we propose template based place recognition might underlie sonar-based navigation in bats. Under this hypothesis, bats recognize places by remembering their echo signature - rather than their 3D layout. Using a large body of ensonification data collected in three different habitats, we test the viability of this hypothesis assessing two critical properties of the proposed echo signatures: (1) they can be uniquely classified and (2) they vary continuously across space. Based on the results presented, we conclude that the proposed echo signatures satisfy both criteria. We discuss how these two properties of the echo signatures can support navigation and building a cognitive map.

A Third-Party E-Payment Protocol Based on Quantum Group Blind Signature

NASA Astrophysics Data System (ADS)

Zhang, Jian-Zhong; Yang, Yuan-Yuan; Xie, Shu-Cui

2017-09-01

A third-party E-payment protocol based on quantum group blind signature is proposed in this paper. Our E-payment protocol could protect user's anonymity as the traditional E-payment systems do, and also have unconditional security which the classical E-payment systems can not provide. To achieve that, quantum key distribution, one-time pad and quantum group blind signature are adopted in our scheme. Furthermore, if there were a dispute, the manager Trent can identify who tells a lie.

Improved Group Signature Scheme Based on Quantum Teleportation

NASA Astrophysics Data System (ADS)

Su, Qi; Li, Wen-Min

2014-04-01

Recently, Wen et al. proposed a group signature scheme based on quantum teleportation (Wen et al. 81(5):055001, 2010). In this paper, we find that it is vulnerable to the inside attack, by which all other legal members of the group can forge the signature utilizing the anti-commutative relationship between the Pauli operation Y and the encryption operation H, and the public board. Then we present an improved scheme where the eavesdropping process after the transmission is involved to increase the security.

A Quantum Proxy Weak Blind Signature Scheme Based on Controlled Quantum Teleportation

NASA Astrophysics Data System (ADS)

Cao, Hai-Jing; Yu, Yao-Feng; Song, Qin; Gao, Lan-Xiang

2015-04-01

Proxy blind signature is applied to the electronic paying system, electronic voting system, mobile agent system, security of internet, etc. A quantum proxy weak blind signature scheme is proposed in this paper. It is based on controlled quantum teleportation. Five-qubit entangled state functions as quantum channel. The scheme uses the physical characteristics of quantum mechanics to implement message blinding, so it could guarantee not only the unconditional security of the scheme but also the anonymity of the messages owner.

Spectral signatures for RDX-based explosives in the 3 micron region

NASA Astrophysics Data System (ADS)

Osborn, Tabetha; Kaimal, Sindhu; Reeve, Scott W.; Burns, William

2008-04-01

Explosive compounds such as RDX, and HMX present significant challenges to optically based sensors. This difficulty is due in part to the low vapor pressures these compounds possess. One approach for sensing explosives that circumvents the low explosive vapor pressure problem, involves focusing on the trace amounts of relatively high vapor pressure impurities that will be present in the vapor signature. In order to effectively detect these volatile impurities, the spectral signature databases must be readily available. One of our goals therefore, is the generation of a database of high resolution spectral signatures for these volatile organic impurities. Some rather formidable spectroscopic measurement challenges have been encountered while working to extend the spectral signature effort to the 3 micron region. Here we will outline progress to date, with a focus on the volatile organic compounds formaldehyde, acetaldehyde, nitromethane, acetone, isobutene, and cyclohexanone.

Prediction of sonic boom from experimental near-field overpressure data. Volume 2: Data base construction

NASA Technical Reports Server (NTRS)

Glatt, C. R.; Reiners, S. J.; Hague, D. S.

1975-01-01

A computerized method for storing, updating and augmenting experimentally determined overpressure signatures has been developed. A data base of pressure signatures for a shuttle type vehicle has been stored. The data base has been used for the prediction of sonic boom with the program described in Volume I.

Development of Asset Fault Signatures for Prognostic and Health Management in the Nuclear Industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vivek Agarwal; Nancy J. Lybeck; Randall Bickford

2014-06-01

Proactive online monitoring in the nuclear industry is being explored using the Electric Power Research Institute’s Fleet-Wide Prognostic and Health Management (FW-PHM) Suite software. The FW-PHM Suite is a set of web-based diagnostic and prognostic tools and databases that serves as an integrated health monitoring architecture. The FW-PHM Suite has four main modules: Diagnostic Advisor, Asset Fault Signature (AFS) Database, Remaining Useful Life Advisor, and Remaining Useful Life Database. This paper focuses on development of asset fault signatures to assess the health status of generator step-up generators and emergency diesel generators in nuclear power plants. Asset fault signatures describe themore » distinctive features based on technical examinations that can be used to detect a specific fault type. At the most basic level, fault signatures are comprised of an asset type, a fault type, and a set of one or more fault features (symptoms) that are indicative of the specified fault. The AFS Database is populated with asset fault signatures via a content development exercise that is based on the results of intensive technical research and on the knowledge and experience of technical experts. The developed fault signatures capture this knowledge and implement it in a standardized approach, thereby streamlining the diagnostic and prognostic process. This will support the automation of proactive online monitoring techniques in nuclear power plants to diagnose incipient faults, perform proactive maintenance, and estimate the remaining useful life of assets.« less

Efficient Fair Exchange from Identity-Based Signature

NASA Astrophysics Data System (ADS)

Yum, Dae Hyun; Lee, Pil Joong

A fair exchange scheme is a protocol by which two parties Alice and Bob exchange items or services without allowing either party to gain advantages by quitting prematurely or otherwise misbehaving. To this end, modern cryptographic solutions use a semi-trusted arbitrator who involves only in cases where one party attempts to cheat or simply crashes. We call such a fair exchange scheme optimistic. When no registration is required between the signer and the arbitrator, we say that the fair exchange scheme is setup free. To date, the setup-free optimist fair exchange scheme under the standard RSA assumption was only possible from the generic construction of [12], which uses ring signatures. In this paper, we introduce a new setup-free optimistic fair exchange scheme under the standard RSA assumption. Our scheme uses the GQ identity-based signature and is more efficient than [12]. The construction can also be generalized by using various identity-based signature schemes. Our main technique is to allow each user to choose his (or her) own “random” public key in the identitybased signature scheme.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine.

PubMed

Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma'ayan, Avi

2016-01-01

The library of integrated network-based cellular signatures (LINCS) L1000 data set currently comprises of over a million gene expression profiles of chemically perturbed human cell lines. Through unique several intrinsic and extrinsic benchmarking schemes, we demonstrate that processing the L1000 data with the characteristic direction (CD) method significantly improves signal to noise compared with the MODZ method currently used to compute L1000 signatures. The CD processed L1000 signatures are served through a state-of-the-art web-based search engine application called L1000CDS 2 . The L1000CDS 2 search engine provides prioritization of thousands of small-molecule signatures, and their pairwise combinations, predicted to either mimic or reverse an input gene expression signature using two methods. The L1000CDS 2 search engine also predicts drug targets for all the small molecules profiled by the L1000 assay that we processed. Targets are predicted by computing the cosine similarity between the L1000 small-molecule signatures and a large collection of signatures extracted from the gene expression omnibus (GEO) for single-gene perturbations in mammalian cells. We applied L1000CDS 2 to prioritize small molecules that are predicted to reverse expression in 670 disease signatures also extracted from GEO, and prioritized small molecules that can mimic expression of 22 endogenous ligand signatures profiled by the L1000 assay. As a case study, to further demonstrate the utility of L1000CDS 2 , we collected expression signatures from human cells infected with Ebola virus at 30, 60 and 120 min. Querying these signatures with L1000CDS 2 we identified kenpaullone, a GSK3B/CDK2 inhibitor that we show, in subsequent experiments, has a dose-dependent efficacy in inhibiting Ebola infection in vitro without causing cellular toxicity in human cell lines. In summary, the L1000CDS 2 tool can be applied in many biological and biomedical settings, while improving the extraction of knowledge from the LINCS L1000 resource.

Identification and Characteristics of Signature Whistles in Wild Bottlenose Dolphins (Tursiops truncatus) from Namibia

PubMed Central

Elwen, Simon Harvey; Nastasi, Aurora

2014-01-01

A signature whistle type is a learned, individually distinctive whistle type in a dolphin's acoustic repertoire that broadcasts the identity of the whistle owner. The acquisition and use of signature whistles indicates complex cognitive functioning that requires wider investigation in wild dolphin populations. Here we identify signature whistle types from a population of approximately 100 wild common bottlenose dolphins (Tursiops truncatus) inhabiting Walvis Bay, and describe signature whistle occurrence, acoustic parameters and temporal production. A catalogue of 43 repeatedly emitted whistle types (REWTs) was generated by analysing 79 hrs of acoustic recordings. From this, 28 signature whistle types were identified using a method based on the temporal patterns in whistle sequences. A visual classification task conducted by 5 naïve judges showed high levels of agreement in classification of whistles (Fleiss-Kappa statistic, κ = 0.848, Z = 55.3, P<0.001) and supported our categorisation. Signature whistle structure remained stable over time and location, with most types (82%) recorded in 2 or more years, and 4 identified at Walvis Bay and a second field site approximately 450 km away. Whistle acoustic parameters were consistent with those of signature whistles documented in Sarasota Bay (Florida, USA). We provide evidence of possible two-voice signature whistle production by a common bottlenose dolphin. Although signature whistle types have potential use as a marker for studying individual habitat use, we only identified approximately 28% of those from the Walvis Bay population, despite considerable recording effort. We found that signature whistle type diversity was higher in larger dolphin groups and groups with calves present. This is the first study describing signature whistles in a wild free-ranging T. truncatus population inhabiting African waters and it provides a baseline on which more in depth behavioural studies can be based. PMID:25203814

Signatures of pairing in the magnetic excitation spectrum of strongly correlated two-leg ladders [Signatures of pairing in the magnetic excitation spectrum of strongly correlated ladders

DOE PAGES

Nocera, Alberto; Patel, Niravkumar D.; Dagotto, Elbio R.; ...

2017-11-13

Magnetic interactions are widely believed to play a crucial role in the microscopic mechanism leading to high critical temperature superconductivity. It is therefore important to study the signatures of pairing in the magnetic excitation spectrum of simple models known to show unconventional superconducting tendencies. Using the density matrix renormalization group technique, we calculate the dynamical spin structure factor S(k,ω) of a generalized t–U–J Hubbard model away from half filling in a two-leg ladder geometry. The addition of J enhances pairing tendencies. We analyze quantitatively the signatures of pairing in the magnetic excitation spectra. We found that the superconducting pair-correlation strength,more » that can be estimated independently from ground state properties, is closely correlated with the integrated low-energy magnetic spectral weight in the vicinity of (π,π). In this wave-vector region, robust spin incommensurate features develop with increasing doping. The branch of the spectrum with rung direction wave vector k rung=0 does not change substantially with doping where pairing dominates and thus plays a minor role. As a result, we discuss the implications of our results for neutron scattering experiments, where the spin excitation dynamics of hole-doped quasi-one-dimensional magnetic materials can be measured and also address implications for recent resonant inelastic x-ray scattering experiments.« less

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

PubMed

Forslund, Kristoffer; Hildebrand, Falk; Nielsen, Trine; Falony, Gwen; Le Chatelier, Emmanuelle; Sunagawa, Shinichi; Prifti, Edi; Vieira-Silva, Sara; Gudmundsdottir, Valborg; Pedersen, Helle K; Arumugam, Manimozhiyan; Kristiansen, Karsten; Voigt, Anita Yvonne; Vestergaard, Henrik; Hercog, Rajna; Costea, Paul Igor; Kultima, Jens Roat; Li, Junhua; Jørgensen, Torben; Levenez, Florence; Dore, Joël; Nielsen, H Bjørn; Brunak, Søren; Raes, Jeroen; Hansen, Torben; Wang, Jun; Ehrlich, S Dusko; Bork, Peer; Pedersen, Oluf

2015-12-10

In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.

Signatures of pairing in the magnetic excitation spectrum of strongly correlated two-leg ladders [Signatures of pairing in the magnetic excitation spectrum of strongly correlated ladders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nocera, Alberto; Patel, Niravkumar D.; Dagotto, Elbio R.

Magnetic interactions are widely believed to play a crucial role in the microscopic mechanism leading to high critical temperature superconductivity. It is therefore important to study the signatures of pairing in the magnetic excitation spectrum of simple models known to show unconventional superconducting tendencies. Using the density matrix renormalization group technique, we calculate the dynamical spin structure factor S(k,ω) of a generalized t–U–J Hubbard model away from half filling in a two-leg ladder geometry. The addition of J enhances pairing tendencies. We analyze quantitatively the signatures of pairing in the magnetic excitation spectra. We found that the superconducting pair-correlation strength,more » that can be estimated independently from ground state properties, is closely correlated with the integrated low-energy magnetic spectral weight in the vicinity of (π,π). In this wave-vector region, robust spin incommensurate features develop with increasing doping. The branch of the spectrum with rung direction wave vector k rung=0 does not change substantially with doping where pairing dominates and thus plays a minor role. As a result, we discuss the implications of our results for neutron scattering experiments, where the spin excitation dynamics of hole-doped quasi-one-dimensional magnetic materials can be measured and also address implications for recent resonant inelastic x-ray scattering experiments.« less

matK-QR classifier: a patterns based approach for plant species identification.

PubMed

More, Ravi Prabhakar; Mane, Rupali Chandrashekhar; Purohit, Hemant J

2016-01-01

DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK ( matK ) and ribulose-1, 5-bisphosphate carboxylase ( rbcL ) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification. In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. Due to the higher discrimination success obtained with the matK as compared to the rbcL , we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK -QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species. This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK -QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species.

Mammographic evidence of microenvironment changes in tumorous breasts.

PubMed

Marin, Zach; Batchelder, Kendra A; Toner, Brian C; Guimond, Lyne; Gerasimova-Chechkina, Evgeniya; Harrow, Amy R; Arneodo, Alain; Khalil, Andre

2017-04-01

The microenvironment of breast tumors plays a critical role in tumorigenesis. As long as the structural integrity of the microenvironment is upheld, the tumor is suppressed. If tissue structure is lost through disruptions in the normal cell cycle, the microenvironment may act as a tumor promoter. Therefore, the properties that distinguish between healthy and tumorous tissues may not be solely in the tumor characteristics but rather in surrounding non-tumor tissue. The goal of this paper was to show preliminary evidence that tissue disruption and loss of homeostasis in breast tissue microenvironment and breast bilateral asymmetry can be quantitatively and objectively assessed from mammography via a localized, wavelet-based analysis of the whole breast. A wavelet-based multifractal formalism called the 2D Wavelet Transform Modulus Maxima (WTMM) method was used to quantitate density fluctuations from mammographic breast tissue via the Hurst exponent (H). Each entire mammogram was cut in hundreds of 360 × 360 pixel subregions in a gridding scheme of overlapping sliding windows, with each window boundary separated by 32 pixels. The 2D WTMM method was applied to each subregion individually. A data mining approach was set up to determine which metrics best discriminated between normal vs. cancer cases. These same metrics were then used, without modification, to discriminate between normal vs. benign and benign vs. cancer cases. The density fluctuations in healthy mammographic breast tissue are either monofractal anti-correlated (H < 1/2) for fatty tissue or monofractal long-range correlated (H>1/2) for dense tissue. However, tissue regions with H~1/2, as well as left vs. right breast asymetries, were found preferably in tumorous (benign or cancer) breasts vs. normal breasts, as quantified via a combination metric yielding a P-value ~ 0.0006. No metric considered showed significant differences between cancer vs. benign breasts. Since mammographic tissue regions associated with uncorrelated (H~1/2) density fluctuations were predominantly in tumorous breasts, and since the underlying physical processes associated with a H~1/2 signature are those of randomness, lack of spatial correlation, and free diffusion, it is hypothesized that this signature is also associated with tissue disruption and loss of tissue homeostasis. © 2017 American Association of Physicists in Medicine.

Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures.

PubMed

Iandolino, Alberto; Nobuta, Kan; da Silva, Francisco Goes; Cook, Douglas R; Meyers, Blake C

2008-05-12

Vitis vinifera (V. vinifera) is the primary grape species cultivated for wine production, with an industry valued annually in the billions of dollars worldwide. In order to sustain and increase grape production, it is necessary to understand the genetic makeup of grape species. Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry. The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). A total of 2,635,293 17-base and 2,259,286 20-base signatures were obtained, representing at least 30,737 and 26,878 distinct sequences. The average normalized abundance per signature was approximately 49 TPM (Transcripts Per Million). Comparisons of the MPSS signatures with available Vitis species' ESTs and a unigene set demonstrated that 6,430 distinct contigs and 2,190 singletons have a perfect match to at least one MPSS signature. Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera. The MPSS data presented here not only achieved a higher level of saturation than previous EST based analyses, but in doing so, expand the known set of transcripts of grape berries during the unique stage in development that immediately precedes the onset of ripening. The MPSS dataset also revealed evidence of antisense expression not previously reported in grapes but comparable to that reported in other plant species. Finally, we developed a novel web-based, public resource for utilization of the grape MPSS data [1].

An integrated mRNA and microRNA expression signature for glioblastoma multiforme prognosis.

PubMed

Xiong, Jie; Bing, Zhitong; Su, Yanlin; Deng, Defeng; Peng, Xiaoning

2014-01-01

Although patients with Glioblastoma multiforme (GBM) have grave prognosis, significant variability in patient outcome is observed. The objective of this study is to identify a molecular signature for GBM prognosis. We subjected 355 mRNA and microRNA expression profiles to elastic net-regulated Cox regression for identification of an integrated RNA signature for GBM prognosis. A prognostic index (PI) was generated for patient stratification. Survival comparison was conducted by Kaplan-Meier method and a general multivariate Cox regression procedure was applied to evaluate the independence of the PI. The abilities and efficiencies of signatures to predict GBM patient outcome was assessed and compared by the area under the curve (AUC) of the receiver-operator characteristic (ROC). An integrated RNA prognostic signature consisted by 4 protective mRNAs, 12 risky mRNAs, and 1 risky microRNA was identified. Decreased survival was associated with being in the high-risk group (hazard ratio = 2.864, P<0.0001). The prognostic value of the integrated signature was validated in five independent GBM expression datasets (n = 201, hazard ratio = 2.453, P<0.0001). The PI outperformed the known clinical factors, mRNA-only, and miRNA-only prognostic signatures for GBM prognosis (area under the ROC curve for the integrated RNA, mRNA-only, and miRNA-only signatures were 0.828, 0.742, and 0.757 at 3 years of overall survival, respectively, P<0.0001 by permutation test). We describe the first, to our knowledge, robust transcriptome-based integrated RNA signature that improves the current GBM prognosis based on clinical variables, mRNA-only, and miRNA-only signatures.

An Integrated mRNA and microRNA Expression Signature for Glioblastoma Multiforme Prognosis

PubMed Central

Xiong, Jie; Bing, Zhitong; Su, Yanlin; Deng, Defeng; Peng, Xiaoning

2014-01-01

Although patients with Glioblastoma multiforme (GBM) have grave prognosis, significant variability in patient outcome is observed. The objective of this study is to identify a molecular signature for GBM prognosis. We subjected 355 mRNA and microRNA expression profiles to elastic net-regulated Cox regression for identification of an integrated RNA signature for GBM prognosis. A prognostic index (PI) was generated for patient stratification. Survival comparison was conducted by Kaplan-Meier method and a general multivariate Cox regression procedure was applied to evaluate the independence of the PI. The abilities and efficiencies of signatures to predict GBM patient outcome was assessed and compared by the area under the curve (AUC) of the receiver-operator characteristic (ROC). An integrated RNA prognostic signature consisted by 4 protective mRNAs, 12 risky mRNAs, and 1 risky microRNA was identified. Decreased survival was associated with being in the high-risk group (hazard ratio = 2.864, P<0.0001). The prognostic value of the integrated signature was validated in five independent GBM expression datasets (n = 201, hazard ratio = 2.453, P<0.0001). The PI outperformed the known clinical factors, mRNA-only, and miRNA-only prognostic signatures for GBM prognosis (area under the ROC curve for the integrated RNA, mRNA-only, and miRNA-only signatures were 0.828, 0.742, and 0.757 at 3 years of overall survival, respectively, P<0.0001 by permutation test). We describe the first, to our knowledge, robust transcriptome-based integrated RNA signature that improves the current GBM prognosis based on clinical variables, mRNA-only, and miRNA-only signatures. PMID:24871302

Atmospheric Chemical Transport Based on High Resolution Model- Derived Winds: A Case Study

NASA Technical Reports Server (NTRS)

Hannan, John R.; Fuelberg, Henry E.; Thompson, Anne M.; Bieberbach, George, Jr.; Knabb, Richard D.; Kondo, Yutaka; Anderson, Bruce E.; Browell, Edward V.; Gregory, Gerald L.; Sachse, Glen;

Age and gender-invariant features of handwritten signatures for verification systems

NASA Astrophysics Data System (ADS)

AbdAli, Sura; Putz-Leszczynska, Joanna

2014-11-01

Handwritten signature is one of the most natural biometrics, the study of human physiological and behavioral patterns. Behavioral biometrics includes signatures that may be different due to its owner gender or age because of intrinsic or extrinsic factors. This paper presents the results of the author's research on age and gender influence on verification factors. The experiments in this research were conducted using a database that contains signatures and their associated metadata. The used algorithm is based on the universal forgery feature idea, where the global classifier is able to classify a signature as a genuine one or, as a forgery, without the actual knowledge of the signature template and its owner. Additionally, the reduction of the dimensionality with the MRMR method is discussed.

Place recognition using batlike sonar

PubMed Central

Vanderelst, Dieter; Steckel, Jan; Boen, Andre; Peremans, Herbert; Holderied, Marc W

2016-01-01

Echolocating bats have excellent spatial memory and are able to navigate to salient locations using bio-sonar. Navigating and route-following require animals to recognize places. Currently, it is mostly unknown how bats recognize places using echolocation. In this paper, we propose template based place recognition might underlie sonar-based navigation in bats. Under this hypothesis, bats recognize places by remembering their echo signature - rather than their 3D layout. Using a large body of ensonification data collected in three different habitats, we test the viability of this hypothesis assessing two critical properties of the proposed echo signatures: (1) they can be uniquely classified and (2) they vary continuously across space. Based on the results presented, we conclude that the proposed echo signatures satisfy both criteria. We discuss how these two properties of the echo signatures can support navigation and building a cognitive map. DOI: http://dx.doi.org/10.7554/eLife.14188.001 PMID:27481189

Shell Buckling Design Criteria Based on Manufacturing Imperfection Signatures

NASA Technical Reports Server (NTRS)

Hilburger, Mark W.; Nemeth, Michael P.; Starnes, James H., Jr.

2004-01-01

An analysis-based approach .for developing shell-buckling design criteria for laminated-composite cylindrical shells that accurately accounts for the effects of initial geometric imperfections is presented. With this approach, measured initial geometric imperfection data from six graphite-epoxy shells are used to determine a manufacturing-process-specific imperfection signature for these shells. This imperfection signature is then used as input into nonlinear finite-element analyses. The imperfection signature represents a "first-approximation" mean imperfection shape that is suitable for developing preliminary-design data. Comparisons of test data and analytical results obtained by using several different imperfection shapes are presented for selected shells. Overall, the results indicate that the analysis-based approach presented for developing reliable preliminary-design criteria has the potential to provide improved, less conservative buckling-load estimates, and to reduce the weight and cost of developing buckling-resistant shell structures.

Joint Estimation of Time-Frequency Signature and DOA Based on STFD for Multicomponent Chirp Signals

PubMed Central

Zhao, Ziyue; Liu, Congfeng

2014-01-01

In the study of the joint estimation of time-frequency signature and direction of arrival (DOA) for multicomponent chirp signals, an estimation method based on spatial time-frequency distributions (STFDs) is proposed in this paper. Firstly, array signal model for multicomponent chirp signals is presented and then array processing is applied in time-frequency analysis to mitigate cross-terms. According to the results of the array processing, Hough transform is performed and the estimation of time-frequency signature is obtained. Subsequently, subspace method for DOA estimation based on STFD matrix is achieved. Simulation results demonstrate the validity of the proposed method. PMID:27382610

Joint Estimation of Time-Frequency Signature and DOA Based on STFD for Multicomponent Chirp Signals.

PubMed

Zhao, Ziyue; Liu, Congfeng

2014-01-01

In the study of the joint estimation of time-frequency signature and direction of arrival (DOA) for multicomponent chirp signals, an estimation method based on spatial time-frequency distributions (STFDs) is proposed in this paper. Firstly, array signal model for multicomponent chirp signals is presented and then array processing is applied in time-frequency analysis to mitigate cross-terms. According to the results of the array processing, Hough transform is performed and the estimation of time-frequency signature is obtained. Subsequently, subspace method for DOA estimation based on STFD matrix is achieved. Simulation results demonstrate the validity of the proposed method.

Developing a global model of magnetospheric substorms

NASA Astrophysics Data System (ADS)

Kan, J. R.

1990-09-01

Competing models of magnetospheric substorms are discussed. The definitions of the three substorm phases are presented, and the advantages and drawbacks of the near-earth X-line model, magnetosphere-ionosphere coupling model, low-latitude boundary layer model, and thermal catastrophe model are examined. It is shown that the main challenge to achieving a quantitative understanding of the magnetospheric signatures of substorms is to understand the anomalous dissipation processes in collisionless plasmas.

Invited Article: Quantitative imaging of explosions with high-speed cameras

DOE PAGES

McNesby, Kevin L.; Homan, Barrie E.; Benjamin, Richard A.; ...

2016-05-31

Here, the techniques presented in this paper allow for mapping of temperature, pressure, chemical species, and energy deposition during and following detonations of explosives, using high speed cameras as the main diagnostic tool. Additionally, this work provides measurement in the explosive near to far-field (0-500 charge diameters) of surface temperatures, peak air-shock pressures, some chemical species signatures, shock energy deposition, and air shock formation.

An in fiber experimental approach to photonic quantum digital signatures that does not require quantum memory

NASA Astrophysics Data System (ADS)

Collins, Robert J.; Donaldon, Ross J.; Dunjko, Vedran; Wallden, Petros; Clarke, Patrick J.; Andersson, Erika; Jeffers, John; Buller, Gerald S.

2014-10-01

Classical digital signatures are commonly used in e-mail, electronic financial transactions and other forms of electronic communications to ensure that messages have not been tampered with in transit, and that messages are transferrable. The security of commonly used classical digital signature schemes relies on the computational difficulty of inverting certain mathematical functions. However, at present, there are no such one-way functions which have been proven to be hard to invert. With enough computational resources certain implementations of classical public key cryptosystems can be, and have been, broken with current technology. It is nevertheless possible to construct information-theoretically secure signature schemes, including quantum digital signature schemes. Quantum signature schemes can be made information theoretically secure based on the laws of quantum mechanics, while classical comparable protocols require additional resources such as secret communication and a trusted authority. Early demonstrations of quantum digital signatures required quantum memory, rendering them impractical at present. Our present implementation is based on a protocol that does not require quantum memory. It also uses the new technique of unambiguous quantum state elimination, Here we report experimental results for a test-bed system, recorded with a variety of different operating parameters, along with a discussion of aspects of the system security.

Genomic and transcriptomic predictors of triglyceride response to regular exercise

PubMed Central

Sarzynski, Mark A; Davidsen, Peter K; Sung, Yun Ju; Hesselink, Matthijs K C; Schrauwen, Patrick; Rice, Treva K; Rao, D C; Falciani, Francesco; Bouchard, Claude

2015-01-01

Aim We performed genome-wide and transcriptome-wide profiling to identify genes and single nucleotide polymorphisms (SNPs) associated with the response of triglycerides (TG) to exercise training. Methods Plasma TG levels were measured before and after a 20-week endurance training programme in 478 white participants from the HERITAGE Family Study. Illumina HumanCNV370-Quad v3.0 BeadChips were genotyped using the Illumina BeadStation 500GX platform. Affymetrix HG-U133+2 arrays were used to quantitate gene expression levels from baseline muscle biopsies of a subset of participants (N=52). Genome-wide association study (GWAS) analysis was performed using MERLIN, while transcriptomic predictor models were developed using the R-package GALGO. Results The GWAS results showed that eight SNPs were associated with TG training-response (ΔTG) at p<9.9×10−6, while another 31 SNPs showed p values <1×10−4. In multivariate regression models, the top 10 SNPs explained 32.0% of the variance in ΔTG, while conditional heritability analysis showed that four SNPs statistically accounted for all of the heritability of ΔTG. A molecular signature based on the baseline expression of 11 genes predicted 27% of ΔTG in HERITAGE, which was validated in an independent study. A composite SNP score based on the top four SNPs, each from the genomic and transcriptomic analyses, was the strongest predictor of ΔTG (R2=0.14, p=3.0×10−68). Conclusions Our results indicate that skeletal muscle transcript abundance at 11 genes and SNPs at a number of loci contribute to TG response to exercise training. Combining data from genomics and transcriptomics analyses identified a SNP-based gene signature that should be further tested in independent samples. PMID:26491034

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

PubMed Central

Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

2013-01-01

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

A cytoarchitecture-driven myelin model reveals area-specific signatures in human primary and secondary areas using ultra-high resolution in-vivo brain MRI.

PubMed

Dinse, J; Härtwich, N; Waehnert, M D; Tardif, C L; Schäfer, A; Geyer, S; Preim, B; Turner, R; Bazin, P-L

2015-07-01

This work presents a novel approach for modelling laminar myelin patterns in the human cortex in brain MR images on the basis of known cytoarchitecture. For the first time, it is possible to estimate intracortical contrast visible in quantitative ultra-high resolution MR images in specific primary and secondary cytoarchitectonic areas. The presented technique reveals different area-specific signatures which may help to study the spatial distribution of cortical T1 values and the distribution of cortical myelin in general. It may lead to a new discussion on the concordance of cyto- and myeloarchitectonic boundaries, given the absence of such concordance atlases. The modelled myelin patterns are quantitatively compared with data from human ultra-high resolution in-vivo 7T brain MR images (9 subjects). In the validation, the results are compared to one post-mortem brain sample and its ex-vivo MRI and histological data. Details of the analysis pipeline are provided. In the context of the increasing interest in advanced methods in brain segmentation and cortical architectural studies, the presented model helps to bridge the gap between the microanatomy revealed by classical histology and the macroanatomy visible in MRI. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites.

PubMed

Routtu, J; Ebert, D

2015-02-01

Understanding the genetic architecture of host resistance is key for understanding the evolution of host-parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host-parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host-parasite systems. Only the Pasteuria-Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium-Daphnia system remains unclear.

Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites

PubMed Central

Routtu, J; Ebert, D

2015-01-01

Understanding the genetic architecture of host resistance is key for understanding the evolution of host–parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host–parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host–parasite systems. Only the Pasteuria–Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium–Daphnia system remains unclear. PMID:25335558

Endogenous Versus Exogenous Shocks in Complex Networks: An Empirical Test Using Book Sale Rankings

NASA Astrophysics Data System (ADS)

Sornette, D.; Deschâtres, F.; Gilbert, T.; Ageon, Y.

2004-11-01

We study the precursory and recovery signatures accompanying shocks in complex networks, that we test on a unique database of the Amazon.com ranking of book sales. We find clear distinguishing signatures classifying two types of sales peaks. Exogenous peaks occur abruptly and are followed by a power law relaxation, while endogenous peaks occur after a progressively accelerating power law growth followed by an approximately symmetrical power law relaxation which is slower than for exogenous peaks. These results are rationalized quantitatively by a simple model of epidemic propagation of interactions with long memory within a network of acquaintances. The observed relaxation of sales implies that the sales dynamics is dominated by cascades rather than by the direct effects of news or advertisements, indicating that the social network is close to critical.

Endogenous versus exogenous shocks in complex networks: an empirical test using book sale rankings.

PubMed

Sornette, D; Deschâtres, F; Gilbert, T; Ageon, Y

2004-11-26

We study the precursory and recovery signatures accompanying shocks in complex networks, that we test on a unique database of the Amazon.com ranking of book sales. We find clear distinguishing signatures classifying two types of sales peaks. Exogenous peaks occur abruptly and are followed by a power law relaxation, while endogenous peaks occur after a progressively accelerating power law growth followed by an approximately symmetrical power law relaxation which is slower than for exogenous peaks. These results are rationalized quantitatively by a simple model of epidemic propagation of interactions with long memory within a network of acquaintances. The observed relaxation of sales implies that the sales dynamics is dominated by cascades rather than by the direct effects of news or advertisements, indicating that the social network is close to critical.

Endogenous versus Exogenous Origins of Crises

NASA Astrophysics Data System (ADS)

Sornette, Didier

Are large biological extinctions such as the Cretaceous/Tertiary KT boundary due to a meteorite, extreme volcanic activity or self-organized critical extinction cascades? Are commercial successes due to a progressive reputation cascade or the result of a well orchestrated advertisement? Determining the chain of causality for Xevents in complex systems requires disentangling interwoven exogenous and endogenous contributions with either no clear signature or too many signatures. Here, I review several efforts carried out with collaborators which suggest a general strategy for understanding the organizations of several complex systems under the dual effect of endogenous and exogenous fluctuations. The studied examples are: internet download shocks, book sale shocks, social shocks, financial volatility shocks, and financial crashes. Simple models are offered to quantitatively relate the endogenous organization to the exogenous response of the system. Suggestions for applications of these ideas to many other systems are offered.

Non-invasive, Contrast-enhanced Spectral Imaging of Breast Cancer Signatures in Preclinical Animal Models In vivo

PubMed Central

Ramanujan, V Krishnan; Ren, Songyang; Park, Sangyong; Farkas, Daniel L

2011-01-01

We report here a non-invasive multispectral imaging platform for monitoring spectral reflectance and fluorescence images from primary breast carcinoma and metastatic lymph nodes in preclinical rat model in vivo. The system is built around a monochromator light source and an acousto-optic tunable filter (AOTF) for spectral selection. Quantitative analysis of the measured reflectance profiles in the presence of a widely-used lymphazurin dye clearly demonstrates the capability of the proposed imaging platform to detect tumor-associated spectral signatures in the primary tumors as well as metastatic lymphatics. Tumor-associated changes in vascular oxygenation and interstitial fluid pressure are reasoned to be the physiological sources of the measured reflectance profiles. We also discuss the translational potential of our imaging platform in intra-operative clinical setting. PMID:21572915

A Third-Party E-payment Protocol Based on Quantum Multi-proxy Blind Signature

NASA Astrophysics Data System (ADS)

Niu, Xu-Feng; Zhang, Jian-Zhong; Xie, Shu-Cui; Chen, Bu-Qing

2018-05-01

A third-party E-payment protocol is presented in this paper. It is based on quantum multi-proxy blind signature. Adopting the techniques of quantum key distribution, one-time pad and quantum multi-proxy blind signature, our third-party E-payment system could protect user's anonymity as the traditional E-payment systems do, and also have unconditional security which the classical E-payment systems can not provide. Furthermore, compared with the existing quantum E-payment systems, the proposed system could support the E-payment which using the third-party platforms.

An E-payment system based on quantum group signature

NASA Astrophysics Data System (ADS)

Xiaojun, Wen

2010-12-01

Security and anonymity are essential to E-payment systems. However, existing E-payment systems will easily be broken into soon with the emergence of quantum computers. In this paper, we propose an E-payment system based on quantum group signature. In contrast to classical E-payment systems, our quantum E-payment system can protect not only the users' anonymity but also the inner structure of customer groups. Because of adopting the two techniques of quantum key distribution, a one-time pad and quantum group signature, unconditional security of our E-payment system is guaranteed.

Observation of a 27-day solar signature in noctilucent cloud altitude

NASA Astrophysics Data System (ADS)

Köhnke, Merlin C.; von Savigny, Christian; Robert, Charles E.

2018-05-01

Previous studies have identified solar 27-day signatures in several parameters in the Mesosphere/Lower thermosphere region, including temperature and Noctilucent cloud (NLC) occurrence frequency. In this study we report on a solar 27-day signature in NLC altitude with peak-to-peak variations of about 400 m. We use SCIAMACHY limb-scatter observations from 2002 to 2012 to detect NLCs. The superposed epoch analysis method is applied to extract solar 27-day signatures. A 27-day signature in NLC altitude can be identified in both hemispheres in the SCIAMACHY dataset, but the signature is more pronounced in the northern hemisphere. The solar signature in NLC altitude is found to be in phase with solar activity and temperature for latitudes ≳ 70 ° N. We provide a qualitative explanation for the positive correlation between solar activity and NLC altitude based on published model simulations.

Realization of Quantum Digital Signatures without the Requirement of Quantum Memory

NASA Astrophysics Data System (ADS)

Collins, Robert J.; Donaldson, Ross J.; Dunjko, Vedran; Wallden, Petros; Clarke, Patrick J.; Andersson, Erika; Jeffers, John; Buller, Gerald S.

2014-07-01

Digital signatures are widely used to provide security for electronic communications, for example, in financial transactions and electronic mail. Currently used classical digital signature schemes, however, only offer security relying on unproven computational assumptions. In contrast, quantum digital signatures offer information-theoretic security based on laws of quantum mechanics. Here, security against forging relies on the impossibility of perfectly distinguishing between nonorthogonal quantum states. A serious drawback of previous quantum digital signature schemes is that they require long-term quantum memory, making them impractical at present. We present the first realization of a scheme that does not need quantum memory and which also uses only standard linear optical components and photodetectors. In our realization, the recipients measure the distributed quantum signature states using a new type of quantum measurement, quantum state elimination. This significantly advances quantum digital signatures as a quantum technology with potential for real applications.

Realization of quantum digital signatures without the requirement of quantum memory.

PubMed

Collins, Robert J; Donaldson, Ross J; Dunjko, Vedran; Wallden, Petros; Clarke, Patrick J; Andersson, Erika; Jeffers, John; Buller, Gerald S

2014-07-25

Digital signatures are widely used to provide security for electronic communications, for example, in financial transactions and electronic mail. Currently used classical digital signature schemes, however, only offer security relying on unproven computational assumptions. In contrast, quantum digital signatures offer information-theoretic security based on laws of quantum mechanics. Here, security against forging relies on the impossibility of perfectly distinguishing between nonorthogonal quantum states. A serious drawback of previous quantum digital signature schemes is that they require long-term quantum memory, making them impractical at present. We present the first realization of a scheme that does not need quantum memory and which also uses only standard linear optical components and photodetectors. In our realization, the recipients measure the distributed quantum signature states using a new type of quantum measurement, quantum state elimination. This significantly advances quantum digital signatures as a quantum technology with potential for real applications.

Modeling magnetic field and TEC signatures of large-amplitude acoustic and gravity waves generated by natural hazard events

NASA Astrophysics Data System (ADS)

Zettergren, M. D.; Snively, J. B.; Inchin, P.; Komjathy, A.; Verkhoglyadova, O. P.

2017-12-01

Ocean and solid earth responses during earthquakes are a significant source of large amplitude acoustic and gravity waves (AGWs) that perturb the overlying ionosphere-thermosphere (IT) system. IT disturbances are routinely detected following large earthquakes (M > 7.0) via GPS total electron content (TEC) observations, which often show acoustic wave ( 3-4 min periods) and gravity wave ( 10-15 min) signatures with amplitudes of 0.05-2 TECU. In cases of very large earthquakes (M > 8.0) the persisting acoustic waves are estimated to have 100-200 m/s compressional velocities in the conducting ionospheric E and F-regions and should generate significant dynamo currents and magnetic field signatures. Indeed, some recent reports (e.g. Hao et al, 2013, JGR, 118, 6) show evidence for magnetic fluctuations, which appear to be related to AGWs, following recent large earthquakes. However, very little quantitative information is available on: (1) the detailed spatial and temporal dependence of these magnetic fluctuations, which are usually observed at a small number of irregularly arranged stations, and (2) the relation of these signatures to TEC perturbations in terms of relative amplitudes, frequency, and timing for different events. This work investigates space- and time-dependent behavior of both TEC and magnetic fluctuations following recent large earthquakes, with the aim to improve physical understanding of these perturbations via detailed, high-resolution, two- and three-dimensional modeling case studies with a coupled neutral atmospheric and ionospheric model, MAGIC-GEMINI (Zettergren and Snively, 2015, JGR, 120, 9). We focus on cases inspired by the large Chilean earthquakes from the past decade (viz., the M > 8.0 earthquakes from 2010 and 2015) to constrain the sources for the model, i.e. size, frequency, amplitude, and timing, based on available information from ocean buoy and seismometer data. TEC data are used to validate source amplitudes and to constrain background ionospheric conditions. Preliminary comparisons against available magnetic field and TEC data from these events provide evidence, albeit limited and localized, that support the validity of the spatially-resolved simulation results.

Analysis of blood-based gene expression in idiopathic Parkinson disease.

PubMed

Shamir, Ron; Klein, Christine; Amar, David; Vollstedt, Eva-Juliane; Bonin, Michael; Usenovic, Marija; Wong, Yvette C; Maver, Ales; Poths, Sven; Safer, Hershel; Corvol, Jean-Christophe; Lesage, Suzanne; Lavi, Ofer; Deuschl, Günther; Kuhlenbaeumer, Gregor; Pawlack, Heike; Ulitsky, Igor; Kasten, Meike; Riess, Olaf; Brice, Alexis; Peterlin, Borut; Krainc, Dimitri

2017-10-17

To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples). Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks. A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E-6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E-4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1 , ATP5A1 , and VDAC3 . We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers. © 2017 American Academy of Neurology.

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy.

PubMed

Shashilov, Victor A; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K

2010-09-01

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Project-Based Learning in International Financial Management

ERIC Educational Resources Information Center

Young, John H.; Legister, Allison P.

2018-01-01

This exploratory study measures the effectiveness of the signature project-based learning model to assess the enhancement of student engagement. The goal of the signature project is to prepare students to apply critical thinking and collaborative skills; making connections between global financial issues and textbook concepts in application to a…

A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.

PubMed

Lee, Unjin; Frankenberger, Casey; Yun, Jieun; Bevilacqua, Elena; Caldas, Carlos; Chin, Suet-Feung; Rueda, Oscar M; Reinitz, John; Rosner, Marsha Rich

2013-01-01

Although triple negative breast cancers (TNBC) are the most aggressive subtype of breast cancer, they currently lack targeted therapies. Because this classification still includes a heterogeneous collection of tumors, new tools to classify TNBCs are urgently required in order to improve our prognostic capability for high risk patients and predict response to therapy. We previously defined a gene expression signature, RKIP Pathway Metastasis Signature (RPMS), based upon a metastasis-suppressive signaling pathway initiated by Raf Kinase Inhibitory Protein (RKIP). We have now generated a new BACH1 Pathway Metastasis gene signature (BPMS) that utilizes targets of the metastasis regulator BACH1. Specifically, we substituted experimentally validated target genes to generate a new BACH1 metagene, developed an approach to optimize patient tumor stratification, and reduced the number of signature genes to 30. The BPMS significantly and selectively stratified metastasis-free survival in basal-like and, in particular, TNBC patients. In addition, the BPMS further stratified patients identified as having a good or poor prognosis by other signatures including the Mammaprint® and Oncotype® clinical tests. The BPMS is thus complementary to existing signatures and is a prognostic tool for high risk ER-HER2- patients. We also demonstrate the potential clinical applicability of the BPMS as a single sample predictor. Together, these results reveal the potential of this pathway-based BPMS gene signature to identify high risk TNBC patients that can respond effectively to targeted therapy, and highlight BPMS genes as novel drug targets for therapeutic development.

A Psychoacoustic Evaluation of Noise Signatures from Advanced Civil Transport Aircraft

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Christian, Andrew

2016-01-01

The NASA Environmentally Responsible Aviation project has been successful in developing and demonstrating technologies for integrated aircraft systems that can simultaneously meet aggressive goals for fuel burn, noise and emissions. Some of the resulting systems substantially differ from the familiar tube and wing designs constituting the current civil transport fleet. This study attempts to explore whether or not the effective perceived noise level metric used in the NASA noise goal accurately reflects human subject response across the range of vehicles considered. Further, it seeks to determine, in a quantitative manner, if the sounds associated with the advanced aircraft are more or less preferable to the reference vehicles beyond any differences revealed by the metric. These explorations are made through psychoacoustic tests in a controlled laboratory environment using simulated stimuli developed from auralizations of selected vehicles based on systems noise assessments.

Border Forces and Friction Control Epithelial Closure Dynamics

PubMed Central

Cochet-Escartin, Olivier; Ranft, Jonas; Silberzan, Pascal; Marcq, Philippe

2014-01-01

We study the closure dynamics of a large number of well-controlled circular apertures within an epithelial monolayer, where the collective cell migration responsible for epithelization is triggered by the removal of a spatial constraint rather than by scratching. Based on experimental observations, we propose a physical model that takes into account border forces, friction with the substrate, and tissue rheology. Border protrusive activity drives epithelization despite the presence of a contractile actomyosin cable at the periphery of the wound. The closure dynamics is quantified by an epithelization coefficient, defined as the ratio of protrusive stress to tissue-substrate friction, that allows classification of different phenotypes. The same analysis demonstrates a distinct signature for human cells bearing the oncogenic RasV12 mutation, demonstrating the potential of the approach to quantitatively characterize metastatic transformations. PMID:24411238

Subsurface Noble Gas Sampling Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carrigan, C. R.; Sun, Y.

2017-09-18

The intent of this document is to provide information about best available approaches for performing subsurface soil gas sampling during an On Site Inspection or OSI. This information is based on field sampling experiments, computer simulations and data from the NA-22 Noble Gas Signature Experiment Test Bed at the Nevada Nuclear Security Site (NNSS). The approaches should optimize the gas concentration from the subsurface cavity or chimney regime while simultaneously minimizing the potential for atmospheric radioxenon and near-surface Argon-37 contamination. Where possible, we quantitatively assess differences in sampling practices for the same sets of environmental conditions. We recognize that allmore » sampling scenarios cannot be addressed. However, if this document helps to inform the intuition of the reader about addressing the challenges resulting from the inevitable deviations from the scenario assumed here, it will have achieved its goal.« less

Sources and dispersal of land-based runoff from small Hawaiian drainages to a coral reef: Insights from geochemical signatures

NASA Astrophysics Data System (ADS)

Takesue, Renee K.; Storlazzi, Curt D.

2017-03-01

Land-based sediment and contaminant runoff is a major threat to coral reefs, and runoff reduction efforts would benefit from knowledge of specific runoff sources. Geochemical signatures of small drainage basins were determined in the fine fraction of soil and sediment, then used in the nearshore region of a coral reef-fringed urban embayment on southeast Oahu, Hawaii, to describe sources and dispersal of land-based runoff. The sedimentary rare earth element ratio (La/Yb)N showed a clear distinction between the two main rock types in the overall contributing area, tholeiitic and alkalic olivine basalt. Based on this geochemical signature it was apparent that the majority of terrigenous sediment on the reef flat originated from geologically old tholeiitic drainages. Sediment from one of five tholeiitic drainages had a distinct geochemical signature, and sediment with this signature was dispersed on the reef flat 2 km west and 150 m offshore of the contributing basin. Sediment and the anthropogenic metals Cd, Pb, and Zn were entrained in runoff from the most heavily urbanized region of the watershed. Although anthropogenic Cd and Zn had localized distributions close to shore, anthropogenic Pb was found associated with fine sediment on the westernmost part of the reef flat and 400 m offshore, illustrating how trade-wind-driven sediment transport can increase the scale of runoff impacts to nearshore communities. Our findings show that sediment geochemical signatures can provide insights about the source and dispersal of land-based runoff in shallow coastal environments. The application of such knowledge to watershed management and habitat remediation efforts can aid in the protection and restoration of runoff-impacted coastal ecosystems worldwide.

Sources and dispersal of land-based runoff from small Hawaiian drainages to a coral reef: Insights from geochemical signatures

USGS Publications Warehouse

Takesue, Renee K.; Storlazzi, Curt

2017-01-01

Land-based sediment and contaminant runoff is a major threat to coral reefs, and runoff reduction efforts would benefit from knowledge of specific runoff sources. Geochemical signatures of small drainage basins were determined in the fine fraction of soil and sediment, then used in the nearshore region of a coral reef-fringed urban embayment on southeast Oahu, Hawaii, to describe sources and dispersal of land-based runoff. The sedimentary rare earth element ratio (La/Yb)N showed a clear distinction between the two main rock types in the overall contributing area, tholeiitic and alkalic olivine basalt. Based on this geochemical signature it was apparent that the majority of terrigenous sediment on the reef flat originated from geologically old tholeiitic drainages. Sediment from one of five tholeiitic drainages had a distinct geochemical signature, and sediment with this signature was dispersed on the reef flat 2 km west and 150 m offshore of the contributing basin. Sediment and the anthropogenic metals Cd, Pb, and Zn were entrained in runoff from the most heavily urbanized region of the watershed. Although anthropogenic Cd and Zn had localized distributions close to shore, anthropogenic Pb was found associated with fine sediment on the westernmost part of the reef flat and 400 m offshore, illustrating how trade-wind-driven sediment transport can increase the scale of runoff impacts to nearshore communities. Our findings show that sediment geochemical signatures can provide insights about the source and dispersal of land-based runoff in shallow coastal environments. The application of such knowledge to watershed management and habitat remediation efforts can aid in the protection and restoration of runoff-impacted coastal ecosystems worldwide.

Quantitative Proteomic Profiling the Molecular Signatures of Annexin A5 in Lung Squamous Carcinoma Cells.

PubMed

Sun, Bing; Bai, Yuxin; Zhang, Liyuan; Gong, Linlin; Qi, Xiaoyu; Li, Huizhen; Wang, Faming; Chi, Xinming; Jiang, Yulin; Shao, Shujuan

Lung cancer remains the leading cancer killer around the world. It's crucial to identify newer mechanism-based targets to effectively manage lung cancer. Annexin A5 (ANXA5) is a protein kinase C inhibitory protein and calcium dependent phospholipid-binding protein, which may act as an endogenous regulator of various pathophysiological processes. However, its molecular mechanism in lung cancer remains poorly understood. This study was designed to determine the mechanism of ANXA5 in lung cancer with a hope to obtain useful information to provide a new therapeutic target. We used a stable isotope dimethyl labeling based quantitative proteomic method to identify differentially expressed proteins in NSCLC cell lines after ANXA5 transfection. Out of 314 proteins, we identified 26 and 44 proteins that were down- and up-regulated upon ANXA5 modulation, respectively. The IPA analysis revealed that glycolysis and gluconeogenesis were the predominant pathways modulated by ANXA5. Multiple central nodes, namely HSPA5, FN1, PDIA6, ENO1, ALDOA, JUP and KRT6A appeared to occupy regulatory nodes in the protein-protein networks upon ANXA5 modulation. Taken together, ANXA5 appears to have pleotropic effects, as it modulates multiple key signaling pathways, supporting the potential usefulness of ANXA5 as a potential target in lung cancer. This study might provide a new insight into the mechanism of ANXA5 in lung cancer.

Absolute quantification of prion protein (90-231) using stable isotope-labeled chymotryptic peptide standards in a LC-MRM AQUA workflow.

PubMed

Sturm, Robert; Sheynkman, Gloria; Booth, Clarissa; Smith, Lloyd M; Pedersen, Joel A; Li, Lingjun

2012-09-01

Substantial evidence indicates that the disease-associated conformer of the prion protein (PrP(TSE)) constitutes the etiologic agent in prion diseases. These diseases affect multiple mammalian species. PrP(TSE) has the ability to convert the conformation of the normal prion protein (PrP(C)) into a β-sheet rich form resistant to proteinase K digestion. Common immunological techniques lack the sensitivity to detect PrP(TSE) at subfemtomole levels, whereas animal bioassays, cell culture, and in vitro conversion assays offer higher sensitivity but lack the high-throughput the immunological assays offer. Mass spectrometry is an attractive alternative to the above assays as it offers high-throughput, direct measurement of a protein's signature peptide, often with subfemtomole sensitivities. Although a liquid chromatography-multiple reaction monitoring (LC-MRM) method has been reported for PrP(TSE), the chemical composition and lack of amino acid sequence conservation of the signature peptide may compromise its accuracy and make it difficult to apply to multiple species. Here, we demonstrate that an alternative protease (chymotrypsin) can produce signature peptides suitable for a LC-MRM absolute quantification (AQUA) experiment. The new method offers several advantages, including: (1) a chymotryptic signature peptide lacking chemically active residues (Cys, Met) that can confound assay accuracy; (2) low attomole limits of detection and quantitation (LOD and LOQ); and (3) a signature peptide retaining the same amino acid sequence across most mammals naturally susceptible to prion infection as well as important laboratory models. To the authors' knowledge, this is the first report on the use of a non-tryptic peptide in a LC-MRM AQUA workflow.

Absolute quantification of prion protein (90-231) using stable isotope-labeled chymotryptic peptide standards in a LC-MRM AQUA workflow

PubMed Central

Sturm, Robert; Kreitinger, Gloria; Booth, Clarissa; Smith, Lloyd; Pedersen, Joel; Li, Lingjun

2012-01-01

Substantial evidence indicates that the disease-associated conformer of the prion protein (PrPTSE) constitutes the etiological agent in prion diseases. These diseases affect multiple mammalian species. PrPTSE has the ability to convert the conformation of the normal prion protein (PrPC) into a β-sheet rich form resistant to proteinase K digestion. Common immunological techniques lack the sensitivity to detect PrPTSE at sub-femtomole levels while animal bioassays, cell culture, and in vitro conversion assays offer ultrasensitivity but lack the high-throughput the immunological assays offer. Mass spectrometry is an attractive alternative to the above assays as it offers high-throughput, direct measurement of a protein’s signature peptide, often with sub-femtomole sensitivities. Although a liquid chromatography-multiple reaction monitoring (LC-MRM) method has been reported for PrPTSE, the chemical composition and lack of amino acid sequence conservation of the signature peptide may compromise its accuracy and make it difficult to apply to multiple species. Here, we demonstrate that an alternative protease (chymotrypsin) can produce signature peptides suitable for a LC-MRM absolute quantification (AQUA) experiment. The new method offers several advantages, including: (1) a chymotryptic signature peptide lacking chemically active residues (Cys, Met) that can confound assay accuracy; (2) low attomole limits of detection and quantitation (LOD and LOQ); and (3) a signature peptide retaining the same amino acid sequence across most mammals naturally susceptible to prion infection as well as important laboratory models. To the authors’ knowledge, this is the first report of the use of a non-tryptic peptide in a LC-MRM AQUA workflow. PMID:22714949

Absolute Quantification of Prion Protein (90-231) Using Stable Isotope-Labeled Chymotryptic Peptide Standards in a LC-MRM AQUA Workflow

NASA Astrophysics Data System (ADS)

Sturm, Robert; Sheynkman, Gloria; Booth, Clarissa; Smith, Lloyd M.; Pedersen, Joel A.; Li, Lingjun

2012-09-01

Substantial evidence indicates that the disease-associated conformer of the prion protein (PrPTSE) constitutes the etiologic agent in prion diseases. These diseases affect multiple mammalian species. PrPTSE has the ability to convert the conformation of the normal prion protein (PrPC) into a β-sheet rich form resistant to proteinase K digestion. Common immunological techniques lack the sensitivity to detect PrPTSE at subfemtomole levels, whereas animal bioassays, cell culture, and in vitro conversion assays offer higher sensitivity but lack the high-throughput the immunological assays offer. Mass spectrometry is an attractive alternative to the above assays as it offers high-throughput, direct measurement of a protein's signature peptide, often with subfemtomole sensitivities. Although a liquid chromatography-multiple reaction monitoring (LC-MRM) method has been reported for PrPTSE, the chemical composition and lack of amino acid sequence conservation of the signature peptide may compromise its accuracy and make it difficult to apply to multiple species. Here, we demonstrate that an alternative protease (chymotrypsin) can produce signature peptides suitable for a LC-MRM absolute quantification (AQUA) experiment. The new method offers several advantages, including: (1) a chymotryptic signature peptide lacking chemically active residues (Cys, Met) that can confound assay accuracy; (2) low attomole limits of detection and quantitation (LOD and LOQ); and (3) a signature peptide retaining the same amino acid sequence across most mammals naturally susceptible to prion infection as well as important laboratory models. To the authors' knowledge, this is the first report on the use of a non-tryptic peptide in a LC-MRM AQUA workflow.

Serum microRNAs as biomarkers for recurrence in melanoma

PubMed Central

2012-01-01

Background Identification of melanoma patients at high risk for recurrence and monitoring for recurrence are critical for informed management decisions. We hypothesized that serum microRNAs (miRNAs) could provide prognostic information at the time of diagnosis unaccounted for by the current staging system and could be useful in detecting recurrence after resection. Methods We screened 355 miRNAs in sera from 80 melanoma patients at primary diagnosis (discovery cohort) using a unique quantitative reverse transcription-PCR (qRT-PCR) panel. Cox proportional hazard models and Kaplan-Meier recurrence-free survival (RFS) curves were used to identify a miRNA signature with prognostic potential adjusting for stage. We then tested the miRNA signature in an independent cohort of 50 primary melanoma patients (validation cohort). Logistic regression analysis was performed to determine if the miRNA signature can determine risk of recurrence in both cohorts. Selected miRNAs were measured longitudinally in subsets of patients pre-/post-operatively and pre-/post-recurrence. Results A signature of 5 miRNAs successfully classified melanoma patients into high and low recurrence risk groups with significant separation of RFS in both discovery and validation cohorts (p = 0.0036, p = 0.0093, respectively). Significant separation of RFS was maintained when a logistic model containing the same signature set was used to predict recurrence risk in both discovery and validation cohorts (p < 0.0001, p = 0.033, respectively). Longitudinal expression of 4 miRNAs in a subset of patients was dynamic, suggesting miRNAs can be associated with tumor burden. Conclusion Our data demonstrate that serum miRNAs can improve accuracy in identifying primary melanoma patients with high recurrence risk and in monitoring melanoma tumor burden over time. PMID:22857597

RIDES: Robust Intrusion Detection System for IP-Based Ubiquitous Sensor Networks

PubMed Central

Amin, Syed Obaid; Siddiqui, Muhammad Shoaib; Hong, Choong Seon; Lee, Sungwon

2009-01-01

The IP-based Ubiquitous Sensor Network (IP-USN) is an effort to build the “Internet of things”. By utilizing IP for low power networks, we can benefit from existing well established tools and technologies of IP networks. Along with many other unresolved issues, securing IP-USN is of great concern for researchers so that future market satisfaction and demands can be met. Without proper security measures, both reactive and proactive, it is hard to envisage an IP-USN realm. In this paper we present a design of an IDS (Intrusion Detection System) called RIDES (Robust Intrusion DEtection System) for IP-USN. RIDES is a hybrid intrusion detection system, which incorporates both Signature and Anomaly based intrusion detection components. For signature based intrusion detection this paper only discusses the implementation of distributed pattern matching algorithm with the help of signature-code, a dynamically created attack-signature identifier. Other aspects, such as creation of rules are not discussed. On the other hand, for anomaly based detection we propose a scoring classifier based on the SPC (Statistical Process Control) technique called CUSUM charts. We also investigate the settings and their effects on the performance of related parameters for both of the components. PMID:22412321

RIDES: Robust Intrusion Detection System for IP-Based Ubiquitous Sensor Networks.

PubMed

Amin, Syed Obaid; Siddiqui, Muhammad Shoaib; Hong, Choong Seon; Lee, Sungwon

2009-01-01

The IP-based Ubiquitous Sensor Network (IP-USN) is an effort to build the "Internet of things". By utilizing IP for low power networks, we can benefit from existing well established tools and technologies of IP networks. Along with many other unresolved issues, securing IP-USN is of great concern for researchers so that future market satisfaction and demands can be met. Without proper security measures, both reactive and proactive, it is hard to envisage an IP-USN realm. In this paper we present a design of an IDS (Intrusion Detection System) called RIDES (Robust Intrusion DEtection System) for IP-USN. RIDES is a hybrid intrusion detection system, which incorporates both Signature and Anomaly based intrusion detection components. For signature based intrusion detection this paper only discusses the implementation of distributed pattern matching algorithm with the help of signature-code, a dynamically created attack-signature identifier. Other aspects, such as creation of rules are not discussed. On the other hand, for anomaly based detection we propose a scoring classifier based on the SPC (Statistical Process Control) technique called CUSUM charts. We also investigate the settings and their effects on the performance of related parameters for both of the components.

On the information content of hydrological signatures and their relationship to catchment attributes

NASA Astrophysics Data System (ADS)

Addor, Nans; Clark, Martyn P.; Prieto, Cristina; Newman, Andrew J.; Mizukami, Naoki; Nearing, Grey; Le Vine, Nataliya

2017-04-01

Hydrological signatures, which are indices characterizing hydrologic behavior, are increasingly used for the evaluation, calibration and selection of hydrological models. Their key advantage is to provide more direct insights into specific hydrological processes than aggregated metrics (e.g., the Nash-Sutcliffe efficiency). A plethora of signatures now exists, which enable characterizing a variety of hydrograph features, but also makes the selection of signatures for new studies challenging. Here we propose that the selection of signatures should be based on their information content, which we estimated using several approaches, all leading to similar conclusions. To explore the relationship between hydrological signatures and the landscape, we extended a previously published data set of hydrometeorological time series for 671 catchments in the contiguous United States, by characterizing the climatic conditions, topography, soil, vegetation and stream network of each catchment. This new catchment attributes data set will soon be in open access, and we are looking forward to introducing it to the community. We used this data set in a data-learning algorithm (random forests) to explore whether hydrological signatures could be inferred from catchment attributes alone. We find that some signatures can be predicted remarkably well by random forests and, interestingly, the same signatures are well captured when simulating discharge using a conceptual hydrological model. We discuss what this result reveals about our understanding of hydrological processes shaping hydrological signatures. We also identify which catchment attributes exert the strongest control on catchment behavior, in particular during extreme hydrological events. Overall, climatic attributes have the most significant influence, and strongly condition how well hydrological signatures can be predicted by random forests and simulated by the hydrological model. In contrast, soil characteristics at the catchment scale are not found to be significant predictors by random forests, which raises questions on how to best use soil data for hydrological modeling, for instance for parameter estimation. We finally demonstrate that signatures with high spatial variability are poorly captured by random forests and model simulations, which makes their regionalization delicate. We conclude with a ranking of signatures based on their information content, and propose that the signatures with high information content are best suited for model calibration, model selection and understanding hydrologic similarity.

A Click Chemistry-Based Proteomic Approach Reveals that 1,2,4-Trioxolane and Artemisinin Antimalarials Share a Common Protein Alkylation Profile.

PubMed

Ismail, Hanafy M; Barton, Victoria E; Panchana, Matthew; Charoensutthivarakul, Sitthivut; Biagini, Giancarlo A; Ward, Stephen A; O'Neill, Paul M

2016-05-23

In spite of the recent increase in endoperoxide antimalarials under development, it remains unclear if all these chemotypes share a common mechanism of action. This is important since it will influence cross-resistance risks between the different classes. Here we investigate this proposition using novel clickable 1,2,4-trioxolane activity based protein-profiling probes (ABPPs). ABPPs with potent antimalarial activity were able to alkylate protein target(s) within the asexual erythrocytic stage of Plasmodium falciparum (3D7). Importantly, comparison of the alkylation fingerprint with that generated from an artemisinin ABPP equivalent confirms a highly conserved alkylation profile, with both endoperoxide classes targeting proteins in the glycolytic, hemoglobin degradation, antioxidant defence, protein synthesis and protein stress pathways, essential biological processes for plasmodial survival. The alkylation signatures of the two chemotypes show significant overlap (ca. 90 %) both qualitatively and semi-quantitatively, suggesting a common mechanism of action that raises concerns about potential cross-resistance liabilities.

Seismic Measurement of the Locations of the Base of Convection Zone and Helium Ionization Zone for Stars in the Kepler Seismic LEGACY Sample

NASA Astrophysics Data System (ADS)

Verma, Kuldeep; Raodeo, Keyuri; Antia, H. M.; Mazumdar, Anwesh; Basu, Sarbani; Lund, Mikkel N.; Silva Aguirre, Víctor

2017-03-01

Acoustic glitches are regions inside a star where the sound speed or its derivatives change abruptly. These leave a small characteristic oscillatory signature in the stellar oscillation frequencies. With the precision achieved by Kepler seismic data, it is now possible to extract these small amplitude oscillatory signatures, and infer the locations of the glitches. We perform glitch analysis for all the 66 stars in the Kepler seismic LEGACY sample to derive the locations of the base of the envelope convection zone (CZ) and the helium ionization zone. The signature from helium ionization zone is found to be robust for all stars in the sample, whereas the CZ signature is found to be weak and problematic, particularly for relatively massive stars with large errorbars on the oscillation frequencies. We demonstrate that the helium glitch signature can be used to constrain the properties of the helium ionization layers and the helium abundance.

Epithelial–mesenchymal transition-associated secretory phenotype predicts survival in lung cancer patients

PubMed Central

Reka, Ajaya Kumar; Chen, Guoan; Keshamouni, Venkateshwar G.

2014-01-01

In cancer cells, the process of epithelial–mesenchymal transition (EMT) confers migratory and invasive capacity, resistance to apoptosis, drug resistance, evasion of host immune surveillance and tumor stem cell traits. Cells undergoing EMT may represent tumor cells with metastatic potential. Characterizing the EMT secretome may identify biomarkers to monitor EMT in tumor progression and provide a prognostic signature to predict patient survival. Utilizing a transforming growth factor-β-induced cell culture model of EMT, we quantitatively profiled differentially secreted proteins, by GeLC-tandem mass spectrometry. Integrating with the corresponding transcriptome, we derived an EMT-associated secretory phenotype (EASP) comprising of proteins that were differentially upregulated both at protein and mRNA levels. Four independent primary tumor-derived gene expression data sets of lung cancers were used for survival analysis by the random survival forests (RSF) method. Analysis of 97-gene EASP expression in human lung adenocarcinoma tumors revealed strong positive correlations with lymph node metastasis, advanced tumor stage and histological grade. RSF analysis built on a training set (n = 442), including age, sex and stage as variables, stratified three independent lung cancer data sets into low-, medium- and high-risk groups with significant differences in overall survival. We further refined EASP to a 20 gene signature (rEASP) based on variable importance scores from RSF analysis. Similar to EASP, rEASP predicted survival of both adenocarcinoma and squamous carcinoma patients. More importantly, it predicted survival in the early-stage cancers. These results demonstrate that integrative analysis of the critical biological process of EMT provides mechanism-based and clinically relevant biomarkers with significant prognostic value. PMID:24510113

Quantitative sediment source attribution with compound-specific isotope analysis in a C3 plant-dominated catchment (central Switzerland)

NASA Astrophysics Data System (ADS)

Alewell, Christine; Birkholz, Axel; Meusburger, Katrin; Schindler Wildhaber, Yael; Mabit, Lionel

2016-03-01

As sediment loads impact freshwater systems and infrastructure, their origin in complex landscape systems is of crucial importance for sustainable management of agricultural catchments. We differentiated the sediment source contribution to a lowland river in central Switzerland by using compound-specific isotope analysis (CSIA). We found a clear distinction of sediment sources originating from forest and agricultural land use. Our results demonstrate that it is possible to reduce the uncertainty of sediment source attribution in: (i) using compound content (in our case, long-chain fatty acids; FAs) rather than soil organic matter content to transfer δ13C signal of FAs to soil contribution and (ii) restricting the investigation to the long-chain FAs (> C22 : 0) not to introduce errors due to aquatic contributions from algae and microorganisms. Results showed unambiguously that during base flow, agricultural land contributed up to 65 % of the suspended sediments, while forest was the dominant sediment source during high flow. This indicates that connectivity of sediment source areas within the river changes between base and high flow conditions. Uncertainty, which might occur in complex, large-scale studies due to undetected source attribution and/or CSSI signature degradation, is low because of limited data complexity in our study (i.e., two-three sources and two tracers). Our findings are the first published results highlighting (i) significant differences in compound-specific stable isotope (CSSI) signature of sediment sources from land uses dominated by C3 plant cultivation and (ii) the use of these differences to quantify sediment contribution to a small river.

Cross-study projections of genomic biomarkers: an evaluation in cancer genomics.

PubMed

Lucas, Joseph E; Carvalho, Carlos M; Chen, Julia Ling-Yu; Chi, Jen-Tsan; West, Mike

2009-01-01

Human disease studies using DNA microarrays in both clinical/observational and experimental/controlled studies are having increasing impact on our understanding of the complexity of human diseases. A fundamental concept is the use of gene expression as a "common currency" that links the results of in vitro controlled experiments to in vivo observational human studies. Many studies--in cancer and other diseases--have shown promise in using in vitro cell manipulations to improve understanding of in vivo biology, but experiments often simply fail to reflect the enormous phenotypic variation seen in human diseases. We address this with a framework and methods to dissect, enhance and extend the in vivo utility of in vitro derived gene expression signatures. From an experimentally defined gene expression signature we use statistical factor analysis to generate multiple quantitative factors in human cancer gene expression data. These factors retain their relationship to the original, one-dimensional in vitro signature but better describe the diversity of in vivo biology. In a breast cancer analysis, we show that factors can reflect fundamentally different biological processes linked to molecular and clinical features of human cancers, and that in combination they can improve prediction of clinical outcomes.

Hyperspectral analysis for qualitative and quantitative features related to acid mine drainage at a remediated open-pit mine

NASA Astrophysics Data System (ADS)

Davies, G.; Calvin, W. M.

2015-12-01

The exposure of pyrite to oxygen and water in mine waste environments is known to generate acidity and the accumulation of secondary iron minerals. Sulfates and secondary iron minerals associated with acid mine drainage (AMD) exhibit diverse spectral properties in the ultraviolet, visible and near-infrared regions of the electromagnetic spectrum. The use of hyperspectral imagery for identification of AMD mineralogy and contamination has been well studied. Fewer studies have examined the impacts of hydrologic variations on mapping AMD or the unique spectral signatures of mine waters. Open-pit mine lakes are an additional environmental hazard which have not been widely studied using imaging spectroscopy. A better understanding of AMD variation related to climate fluctuations and the spectral signatures of contaminated surface waters will aid future assessments of environmental contamination. This study examined the ability of multi-season airborne hyperspectral data to identify the geochemical evolution of substances and contaminant patterns at the Leviathan Mine Superfund site. The mine is located 24 miles southeast of Lake Tahoe and contains remnant tailings piles and several AMD collection ponds. The objectives were to 1) distinguish temporal changes in mineralogy at a the remediated open-pit sulfur mine, 2) identify the absorption features of mine affected waters, and 3) quantitatively link water spectra to known dissolved iron concentrations. Images from NASA's AVIRIS instrument were collected in the spring, summer, and fall seasons for two consecutive years at Leviathan (HyspIRI campaign). Images had a spatial resolution of 15 meters at nadir. Ground-based surveys using the ASD FieldSpecPro spectrometer and laboratory spectral and chemical analysis complemented the remote sensing data. Temporal changes in surface mineralogy were difficult to distinguish. However, seasonal changes in pond water quality were identified. Dissolved ferric iron and chlorophyll-a concentrations were determined to be the major influences on pond water spectral variation.

Field Demonstration of a Centrifugal Ultra High Pressure (UHP) P-19

DTIC Science & Technology

2010-03-01

States Air Force  Tyndall Air Force Base, FL 32403-5323 DISTRIBUTION A: Approved for public release; distribution unlimited. NOTICE AND SIGNATURE...PUBLICATION IN ACCORDANCE WITH ASSIGNED DISTRIBUTION STATEMENT. ___//SIGNATURE//______________________ ___//SIGNATURE//______________________ R...PROGRAM ELEMENT NUMBER 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 6. AUTHOR(S) 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8

Mesoscale Numerical Investigations of Air Traffic Emissions over the North Atlantic during SONEX Flight 8: A Case Study

NASA Technical Reports Server (NTRS)

Bieberbach, George, Jr.; Fuelberg, Henry E.; Thompson, Anne M.; Schmitt, Alf; Hannan, John R.; Gregory, G. L.; Kondo, Yutaka; Knabb, Richard D.; Sachse, G. W.; Talbot, R. W.

1999-01-01

Chemical data from flight 8 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) exhibited signatures consistent with aircraft emissions, stratospheric air, and surface-based pollution. These signatures are examined in detail, focussing on the broad aircraft emission signatures that are several hundred kilometers in length. A mesoscale meteorological model provides high resolution wind data that are used to calculate backward trajectories arriving at locations along the flight track. These trajectories are compared to aircraft locations in the North Atlantic Flight Corridor over a 27-33 hour period. Time series of flight level NO and the number of trajectory/aircraft encounters within the NAFC show excellent agreement. Trajectories arriving within the stratospheric and surface-based pollution regions are found to experience very few aircraft encounters. Conversely, there are many trajectory/aircraft encounters within the two chemical signatures corresponding to aircraft emissions. Even many detailed fluctuations of NO within the two aircraft signature regions correspond to similar fluctuations in aircraft encountered during the previous 27-33 hours. Results indicate that high resolution meteorological modeling, when coupled with detailed aircraft location data, is useful for understanding chemical signatures from aircraft emissions at scales of several hundred kilometers.

ARMOR Dual-Polarimetric Radar Observations of Tornadic Debris Signatures

NASA Technical Reports Server (NTRS)

Petersen, W. A,; Carey, L. D.; Knupp, K. R.; Schultz, C.; Johnson, E.

2008-01-01

During the Super-Tuesday tornado outbreak of 5-6 February 2008, two EF-4 tornadoes occurred in Northern Alabama within 75 km range of the University of Alabama in Huntsville (UAH) Advanced Radar for Meteorological and Operational Research (ARMOR, C-band dual-polarimetric). This study will present an analysis of ARMOR radar-indicated dual-polarimetric tornadic debris signatures. The debris signatures were associated with spatially-confined large decreases in the copolar correlation coefficient (rho(hv)hv) that were embedded within broader mesocyclone "hook" signatures. These debris signatures were most obviously manifest during the F-3 to F-4 intensity stages of the tornado(s) and extended to altitudes of approximately 3 km. The rho(hv) signatures of the tornadic debris were the most easily distinguished relative to other polarimetric and radial velocity parameters (e.g., associated with large hail and/or the incipient mesocyclone). Based on our analysis, and consistent with the small number of studies found in the literature, we conclude that dual-polarimetric radar data offer at least the possibility for enhancing specificity and confidence in the process of issuing tornado warnings based only on radar detection of threatening circulation features.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine

PubMed Central

Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma’ayan, Avi

2016-01-01

The library of integrated network-based cellular signatures (LINCS) L1000 data set currently comprises of over a million gene expression profiles of chemically perturbed human cell lines. Through unique several intrinsic and extrinsic benchmarking schemes, we demonstrate that processing the L1000 data with the characteristic direction (CD) method significantly improves signal to noise compared with the MODZ method currently used to compute L1000 signatures. The CD processed L1000 signatures are served through a state-of-the-art web-based search engine application called L1000CDS2. The L1000CDS2 search engine provides prioritization of thousands of small-molecule signatures, and their pairwise combinations, predicted to either mimic or reverse an input gene expression signature using two methods. The L1000CDS2 search engine also predicts drug targets for all the small molecules profiled by the L1000 assay that we processed. Targets are predicted by computing the cosine similarity between the L1000 small-molecule signatures and a large collection of signatures extracted from the gene expression omnibus (GEO) for single-gene perturbations in mammalian cells. We applied L1000CDS2 to prioritize small molecules that are predicted to reverse expression in 670 disease signatures also extracted from GEO, and prioritized small molecules that can mimic expression of 22 endogenous ligand signatures profiled by the L1000 assay. As a case study, to further demonstrate the utility of L1000CDS2, we collected expression signatures from human cells infected with Ebola virus at 30, 60 and 120 min. Querying these signatures with L1000CDS2 we identified kenpaullone, a GSK3B/CDK2 inhibitor that we show, in subsequent experiments, has a dose-dependent efficacy in inhibiting Ebola infection in vitro without causing cellular toxicity in human cell lines. In summary, the L1000CDS2 tool can be applied in many biological and biomedical settings, while improving the extraction of knowledge from the LINCS L1000 resource. PMID:28413689

Supervised Multi-Authority Scheme with Blind Signature for IoT with Attribute Based Encryption

NASA Astrophysics Data System (ADS)

Nissenbaum, O. V.; Ponomarov, K. Y.; Zaharov, A. A.

2018-04-01

This article proposes a three-side cryptographic scheme for verifying device attributes with a Supervisor and a Certification Authority (CA) for attribute-based encryption. Two options are suggested: using a message authentication code and using a digital signature. The first version is suitable for networks with one CA, and the second one for networks with several CAs, including dynamic systems. Also, the addition of this scheme with a blind signature is proposed to preserve the confidentiality of the device attributes from the CA. The introduction gives a definition and a brief historical overview of attribute-based encryption (ABE), addresses the use of ABE in the Internet of Things.

Benchmarking desktop and mobile handwriting across COTS devices: The e-BioSign biometric database

PubMed Central

Tolosana, Ruben; Vera-Rodriguez, Ruben; Fierrez, Julian; Morales, Aythami; Ortega-Garcia, Javier

2017-01-01

This paper describes the design, acquisition process and baseline evaluation of the new e-BioSign database, which includes dynamic signature and handwriting information. Data is acquired from 5 different COTS devices: three Wacom devices (STU-500, STU-530 and DTU-1031) specifically designed to capture dynamic signatures and handwriting, and two general purpose tablets (Samsung Galaxy Note 10.1 and Samsung ATIV 7). For the two Samsung tablets, data is collected using both pen stylus and also the finger in order to study the performance of signature verification in a mobile scenario. Data was collected in two sessions for 65 subjects, and includes dynamic information of the signature, the full name and alpha numeric sequences. Skilled forgeries were also performed for signatures and full names. We also report a benchmark evaluation based on e-BioSign for person verification under three different real scenarios: 1) intra-device, 2) inter-device, and 3) mixed writing-tool. We have experimented the proposed benchmark using the main existing approaches for signature verification: feature- and time functions-based. As a result, new insights into the problem of signature biometrics in sensor-interoperable scenarios have been obtained, namely: the importance of specific methods for dealing with device interoperability, and the necessity of a deeper analysis on signatures acquired using the finger as the writing tool. This e-BioSign public database allows the research community to: 1) further analyse and develop signature verification systems in realistic scenarios, and 2) investigate towards a better understanding of the nature of the human handwriting when captured using electronic COTS devices in realistic conditions. PMID:28475590

Benchmarking desktop and mobile handwriting across COTS devices: The e-BioSign biometric database.

PubMed

Tolosana, Ruben; Vera-Rodriguez, Ruben; Fierrez, Julian; Morales, Aythami; Ortega-Garcia, Javier

2017-01-01

This paper describes the design, acquisition process and baseline evaluation of the new e-BioSign database, which includes dynamic signature and handwriting information. Data is acquired from 5 different COTS devices: three Wacom devices (STU-500, STU-530 and DTU-1031) specifically designed to capture dynamic signatures and handwriting, and two general purpose tablets (Samsung Galaxy Note 10.1 and Samsung ATIV 7). For the two Samsung tablets, data is collected using both pen stylus and also the finger in order to study the performance of signature verification in a mobile scenario. Data was collected in two sessions for 65 subjects, and includes dynamic information of the signature, the full name and alpha numeric sequences. Skilled forgeries were also performed for signatures and full names. We also report a benchmark evaluation based on e-BioSign for person verification under three different real scenarios: 1) intra-device, 2) inter-device, and 3) mixed writing-tool. We have experimented the proposed benchmark using the main existing approaches for signature verification: feature- and time functions-based. As a result, new insights into the problem of signature biometrics in sensor-interoperable scenarios have been obtained, namely: the importance of specific methods for dealing with device interoperability, and the necessity of a deeper analysis on signatures acquired using the finger as the writing tool. This e-BioSign public database allows the research community to: 1) further analyse and develop signature verification systems in realistic scenarios, and 2) investigate towards a better understanding of the nature of the human handwriting when captured using electronic COTS devices in realistic conditions.

Genome-Wide Mutagenesis in Borrelia burgdorferi.

PubMed

Lin, Tao; Gao, Lihui

2018-01-01

Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector. STM procedure combined with Luminex Flex ® Map™ technology and next-generation sequencing (e.g., Tn-seq) are the powerful high-throughput tools for the determination of Borrelia burgdorferi virulence determinants. The assessment of multiple tissue sites and two DNA resources at two different time points using Luminex Flex ® Map™ technology provides a robust data set. B. burgdorferi transposon mutant screening indicates that a high proportion of genes are the novel virulence determinants that are required for mouse and tick infection. In this protocol, an effective signature-tagged Himar1-based transposon suicide vector was developed and used to generate a sequence-defined library of nearly 4800 mutants in the infectious B. burgdorferi B31 clone. In STM, signature-tagged suicide vectors are constructed by inserting unique DNA sequences (tags) into the transposable elements. The signature-tagged transposon mutants are generated when transposon suicide vectors are transformed into an infectious B. burgdorferi clone, and the transposable element is transposed into the 5'-TA-3' sequence in the B. burgdorferi genome with the signature tag. The transposon library is created and consists of many sub-libraries, each sub-library has several hundreds of mutants with same tags. A group of mice or ticks are infected with a mixed population of mutants with different tags, after recovered from different tissues of infected mice and ticks, mutants from output pool and input pool are detected using high-throughput, semi-quantitative Luminex ® FLEXMAP™ or next-generation sequencing (Tn-seq) technologies. Thus far, we have created a high-density, sequence-defined transposon library of over 6600 STM mutants for the efficient genome-wide investigation of genes and gene products required for wild-type pathogenesis, host-pathogen interactions, in vitro growth, in vivo survival, physiology, morphology, chemotaxis, motility, structure, metabolism, gene regulation, plasmid maintenance and replication, etc. The insertion sites of 4480 transposon mutants have been determined. About 800 predicted protein-encoding genes in the genome were disrupted in the STM transposon library. The infectivity and some functions of 800 mutants in 500 genes have been determined. Analysis of these transposon mutants has yielded valuable information regarding the genes and gene products important in the pathogenesis and biology of B. burgdorferi and its tick vectors.

Development of integrated platform based on chalcogenides for sensing applications in the mid-infrared

NASA Astrophysics Data System (ADS)

Gutierrez-Arroyo, Aldo; Bodiou, Loïc.; Lemaitre, Jonathan; Baudet, Emeline; Baillieul, Marion; Hardy, Isabelle; Caillaud, Celine; Colas, Florent; Boukerma, Kada; Rinnert, Emmanuel; Michel, Karine; Bureau, Bruno; Nazabal, Virginie; Charrier, Joël.

2018-03-01

Mid-Infrared (mid-IR) spectral range, spanning from 2 μm to 20 μm, is ideal for chemical sensing using spectroscopy thanks to the presence of vibrational absorption bands of many liquid and gas substances in this wavelength range. Indeed, mid-IR spectroscopy allows simultaneous qualitative and quantitative analysis by, respectively, identifying molecules from their spectral signature and relating the concentrations of different chemical agents to their absorption coefficient according to Beer-Lambert law. In the last years, photonic integrated sensors based on mid-IR spectroscopy have emerged as a cheap, accurate, and compact solution that would enable continuous real-time on-site diagnostics and monitoring of molecular species without the need to collect samples for off-site measurements. Here, we report the design, processing and characterization of a photonic integrated transducer based on selenide ridge waveguides. Evanescent wave detection of chemical substances in liquid phase (isopropyl alcohol, C3H8O, and acetic acid, C2H4O2, both dissolved in cyclohexane) is presented using their absorption at a wavelength of 7.7 μm.

Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature

PubMed Central

De Pittà, Cristiano; Bertolucci, Cristiano; Mazzotta, Gabriella M; Bernante, Filippo; Rizzo, Giorgia; De Nardi, Barbara; Pallavicini, Alberto; Lanfranchi, Gerolamo; Costa, Rodolfo

2008-01-01

Background Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from different tissues of Euphausia superba (the Antarctic krill). Results We have constructed and sequenced five cDNA libraries from different Antarctic krill tissues: head, abdomen, thoracopods and photophores. We have identified 1.770 high-quality ESTs which were assembled into 216 overlapping clusters and 801 singletons resulting in a total of 1.017 non-redundant sequences. Quantitative RT-PCR analysis was performed to quantify and validate the expression levels of ten genes presenting different EST countings in krill tissues. In addition, bioinformatic screening of the non-redundant E. superba sequences identified 69 microsatellite containing ESTs. Clusters, consensuses and related similarity and gene ontology searches were organized in a dedicated E. superba database . Conclusion We defined the first tissue transcriptional signatures of E. superba based on functional categorization among the examined tissues. The analyses of annotated transcripts showed a higher similarity with genes from insects with respect to Malacostraca possibly as an effect of the limited number of Malacostraca sequences in the public databases. Our catalogue provides for the first time a genomic tool to investigate the biology of the Antarctic krill. PMID:18226200

High spin states in 162Lu

NASA Astrophysics Data System (ADS)

Gupta, S. L.; Pancholi, S. C.; Juneja, P.; Mehta, D.; Kumar, Ashok; Bhowmik, R. K.; Muralithar, S.; Rodrigues, G.; Singh, R. P.

1997-09-01

An experimental investigation of the odd-odd 162Lu nucleus, following the 148Sm(19F,5n) reaction at beam energy Elab=112 MeV, has been performed through in-beam gamma-ray spectroscopy. It revealed three signature-split bands. The yrast band based on πh11/2⊗νi13/2 configuration exhibits anomalous signature splitting (the unfavored signature Routhian lying lower than the favored one) whose magnitude Δe'~25 keV, is considerably reduced in contrast to sizable normal signature splitting Δe'~125 and 60 keV observed in the yrast πh11/2 bands of the neighboring odd-A 161,163Lu nuclei, respectively. The signature inversion in this band occurs at spin ~20ħ (frequency=0.37 MeV). The second signature-split band, observed above the band crossing associated with the alignment of a pair of i13/2 quasineutrons, is a band based on the four-quasiparticle [πh11/2[523]7/2-⊗νh9/2[521]3/2-⊗(νi13/2)2], i.e., EABAp(Bp), configuration. The third signature-split band is also likely to be a four-quasiparticle band with configuration similar to the second band but involving F quasineutron, i.e., FABAp(Bp). The experimental results are discussed in comparison with the existing data in the neighboring nuclei and in the framework of the cranking shell model.

FIR signature verification system characterizing dynamics of handwriting features

NASA Astrophysics Data System (ADS)

Thumwarin, Pitak; Pernwong, Jitawat; Matsuura, Takenobu

2013-12-01

This paper proposes an online signature verification method based on the finite impulse response (FIR) system characterizing time-frequency characteristics of dynamic handwriting features. First, the barycenter determined from both the center point of signature and two adjacent pen-point positions in the signing process, instead of one pen-point position, is used to reduce the fluctuation of handwriting motion. In this paper, among the available dynamic handwriting features, motion pressure and area pressure are employed to investigate handwriting behavior. Thus, the stable dynamic handwriting features can be described by the relation of the time-frequency characteristics of the dynamic handwriting features. In this study, the aforesaid relation can be represented by the FIR system with the wavelet coefficients of the dynamic handwriting features as both input and output of the system. The impulse response of the FIR system is used as the individual feature for a particular signature. In short, the signature can be verified by evaluating the difference between the impulse responses of the FIR systems for a reference signature and the signature to be verified. The signature verification experiments in this paper were conducted using the SUBCORPUS MCYT-100 signature database consisting of 5,000 signatures from 100 signers. The proposed method yielded equal error rate (EER) of 3.21% on skilled forgeries.

On the usability and security of pseudo-signatures

NASA Astrophysics Data System (ADS)

Chen, Jin; Lopresti, Daniel

2010-01-01

Handwriting has been proposed as a possible biometric for a number of years. However, recent work has shown that handwritten passphrases are vulnerable to both human-based and machine-based forgeries. Pseudosignatures as an alternative are designed to thwart such attacks while still being easy for users to create, remember, and reproduce. In this paper, we briefly review the concept of pseudo-signatures, then describe an evaluation framework that considers aspects of both usability and security. We present results from preliminary experiments that examine user choice in creating pseudo-signatures and discuss the implications when sketching is used for generating cryptographic keys.

A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts.

PubMed

Duffy, Fergal J; Thompson, Ethan; Downing, Katrina; Suliman, Sara; Mayanja-Kizza, Harriet; Boom, W Henry; Thiel, Bonnie; Weiner Iii, January; Kaufmann, Stefan H E; Dover, Drew; Tabb, David L; Dockrell, Hazel M; Ottenhoff, Tom H M; Tromp, Gerard; Scriba, Thomas J; Zak, Daniel E; Walzl, Gerhard

2018-01-01

Biomarkers that predict who among recently Mycobacterium tuberculosis (MTB)-exposed individuals will progress to active tuberculosis are urgently needed. Intracellular microRNAs (miRNAs) regulate the host response to MTB and circulating miRNAs (c-miRNAs) have been developed as biomarkers for other diseases. We performed machine-learning analysis of c-miRNA measurements in the serum of adult household contacts (HHCs) of TB index cases from South Africa and Uganda and developed a c-miRNA-based signature of risk for progression to active TB. This c-miRNA-based signature significantly discriminated HHCs within 6 months of progression to active disease from HHCs that remained healthy in an independent test set [ROC area under the ROC curve (AUC) 0.74, progressors < 6 Mo to active TB and ROC AUC 0.66, up to 24 Mo to active TB], and complements the predictions of a previous cellular mRNA-based signature of TB risk.

Color-Tunable Mirrors Based on Electrically Regulated Bandwidth Broadening in Polymer-Stabilized Cholesteric Liquid Crystals (Postprint)

DTIC Science & Technology

2014-10-01

DISTRIBUTION STATEMENT. //Signature// //Signature// TIMOTHY J. WHITE CHRISTOPHER D. BREWER, Chief Photonic Materials Branch... Photonic Materials Branch Functional Materials Division Functional Materials Division //Signature// TIMOTHY J. BUNNING, Chief Functional...LIQUID CRYSTALS (POSTPRINT) 5a. CONTRACT NUMBER FA8650-09-D-5434-0009 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62102F 6. AUTHOR(S

Learning semantic and visual similarity for endomicroscopy video retrieval.

PubMed

Andre, Barbara; Vercauteren, Tom; Buchner, Anna M; Wallace, Michael B; Ayache, Nicholas

2012-06-01

Content-based image retrieval (CBIR) is a valuable computer vision technique which is increasingly being applied in the medical community for diagnosis support. However, traditional CBIR systems only deliver visual outputs, i.e., images having a similar appearance to the query, which is not directly interpretable by the physicians. Our objective is to provide a system for endomicroscopy video retrieval which delivers both visual and semantic outputs that are consistent with each other. In a previous study, we developed an adapted bag-of-visual-words method for endomicroscopy retrieval, called "Dense-Sift," that computes a visual signature for each video. In this paper, we present a novel approach to complement visual similarity learning with semantic knowledge extraction, in the field of in vivo endomicroscopy. We first leverage a semantic ground truth based on eight binary concepts, in order to transform these visual signatures into semantic signatures that reflect how much the presence of each semantic concept is expressed by the visual words describing the videos. Using cross-validation, we demonstrate that, in terms of semantic detection, our intuitive Fisher-based method transforming visual-word histograms into semantic estimations outperforms support vector machine (SVM) methods with statistical significance. In a second step, we propose to improve retrieval relevance by learning an adjusted similarity distance from a perceived similarity ground truth. As a result, our distance learning method allows to statistically improve the correlation with the perceived similarity. We also demonstrate that, in terms of perceived similarity, the recall performance of the semantic signatures is close to that of visual signatures and significantly better than those of several state-of-the-art CBIR methods. The semantic signatures are thus able to communicate high-level medical knowledge while being consistent with the low-level visual signatures and much shorter than them. In our resulting retrieval system, we decide to use visual signatures for perceived similarity learning and retrieval, and semantic signatures for the output of an additional information, expressed in the endoscopist own language, which provides a relevant semantic translation of the visual retrieval outputs.

A Prognostic Gene Signature for Metastasis-Free Survival of Triple Negative Breast Cancer Patients

PubMed Central

Yun, Jieun; Bevilacqua, Elena; Caldas, Carlos; Chin, Suet-Feung; Rueda, Oscar M.; Reinitz, John; Rosner, Marsha Rich

2013-01-01

Although triple negative breast cancers (TNBC) are the most aggressive subtype of breast cancer, they currently lack targeted therapies. Because this classification still includes a heterogeneous collection of tumors, new tools to classify TNBCs are urgently required in order to improve our prognostic capability for high risk patients and predict response to therapy. We previously defined a gene expression signature, RKIP Pathway Metastasis Signature (RPMS), based upon a metastasis-suppressive signaling pathway initiated by Raf Kinase Inhibitory Protein (RKIP). We have now generated a new BACH1 Pathway Metastasis gene signature (BPMS) that utilizes targets of the metastasis regulator BACH1. Specifically, we substituted experimentally validated target genes to generate a new BACH1 metagene, developed an approach to optimize patient tumor stratification, and reduced the number of signature genes to 30. The BPMS significantly and selectively stratified metastasis-free survival in basal-like and, in particular, TNBC patients. In addition, the BPMS further stratified patients identified as having a good or poor prognosis by other signatures including the Mammaprint® and Oncotype® clinical tests. The BPMS is thus complementary to existing signatures and is a prognostic tool for high risk ER-HER2- patients. We also demonstrate the potential clinical applicability of the BPMS as a single sample predictor. Together, these results reveal the potential of this pathway-based BPMS gene signature to identify high risk TNBC patients that can respond effectively to targeted therapy, and highlight BPMS genes as novel drug targets for therapeutic development. PMID:24349199

Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis

PubMed Central

Akilesh, Shreeram; Shaffer, Daniel J.; Roopenian, Derry

2003-01-01

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an easy to use statistical algorithm—Global Pattern Recognition—to readily identify genes whose expression has changed significantly from healthy baseline profiles. This approach provides unique molecular signatures for rheumatoid arthritis, systemic lupus erythematosus, and graft versus host disease, and can also be applied to defining the molecular phenotype of a variety of other normal and pathological processes. PMID:12840047

Biomass measurement of methane forming bacteria in environmental samples

NASA Technical Reports Server (NTRS)

Martz, R. F.; Sebacher, D. I.; White, D. C.

1983-01-01

Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 x 10(-14) moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid 'signature'. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.

Preliminary sonic boom correlation of predicted and measured levels for STS-1 entry

NASA Technical Reports Server (NTRS)

Garcia, F., Jr.; Morrison, K. M.; Jones, J. H.; Henderson, H. R.

1982-01-01

A preliminary analysis correlating peaks from sonic boom pressure signatures recorded during the descent trajectory of the Orbiter Columbia, which landed in the dry lake bed at Edwards Air Force Base (EAFB), California, with measured wind tunnel signatures extrapolated from flight altitudes to the ground has been made for Mach numbers ranging from 1.3 to 6. The flight pressure signatures were recorded by microphones positioned at ground level near the groundtrack, whereas the wind tunnel signatures were measured during a test of a 0.0041-scale model Orbiter. The agreement between overpressure estimates based on wind tunnel data using preliminary flight trajectory data and oscillograph traces from ground measurements appears reasonable at this time for the range of Mach numbers considered. More detailed studies using final flight trajectory data and digitized ground measured data will be performed.

Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples

PubMed Central

Cheng, Jun; He, Jun; Liu, Huaping; Cai, Hao; Hong, Guini; Zhang, Jiahui; Li, Na; Ao, Lu; Guo, Zheng

2017-01-01

Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA. PMID:28036264

A study to explore the use of orbital remote sensing to determine native arid plant distribution. [Arizona

NASA Technical Reports Server (NTRS)

Mcginnies, W. G. (Principal Investigator); Conn, J. S.; Haase, E. F.; Lepley, L. K.; Musick, H. B.; Foster, K. E.

1975-01-01

The author has identified the following significant results. Research results include a method for determining the reflectivities of natural areas from ERTS data taking into account sun angle and atmospheric effects on the radiance seen by the satellite sensor. Ground truth spectral signature data for various types of scenes, including ground with and without annuals, and various shrubs were collected. Large areas of varnished desert pavement are visible and mappable on ERTS and high altitude aircraft imagery. A large scale and a small scale vegetation pattern were found to be correlated with presence of desert pavement. A comparison of radiometric data with video recordings shows quantitatively that for most areas of desert vegetation, soils are the most influential factor in determining the signature of a scene. Additive and subtractive image processing techniques were applied in the dark room to enhance vegetational aspects of ERTS.

Security-enhanced chaos communication with time-delay signature suppression and phase encryption.

PubMed

Xue, Chenpeng; Jiang, Ning; Lv, Yunxin; Wang, Chao; Li, Guilan; Lin, Shuqing; Qiu, Kun

2016-08-15

A security-enhanced chaos communication scheme with time delay signature (TDS) suppression and phase-encrypted feedback light is proposed, in virtue of dual-loop feedback with independent high-speed phase modulation. We numerically investigate the property of TDS suppression in the intensity and phase space and quantitatively discuss security of the proposed system by calculating the bit error rate of eavesdroppers who try to crack the system by directly filtering the detected signal or by using a similar semiconductor laser to synchronize the link signal and extract the data. The results show that TDS embedded in the chaotic carrier can be well suppressed by properly setting the modulation frequency, which can keep the time delay a secret from the eavesdropper. Moreover, because the feedback light is encrypted, without the accurate time delay and key, the eavesdropper cannot reconstruct the symmetric operation conditions and decode the correct data.

Global spectral graph wavelet signature for surface analysis of carpal bones

NASA Astrophysics Data System (ADS)

Masoumi, Majid; Rezaei, Mahsa; Ben Hamza, A.

2018-02-01

Quantitative shape comparison is a fundamental problem in computer vision, geometry processing and medical imaging. In this paper, we present a spectral graph wavelet approach for shape analysis of carpal bones of the human wrist. We employ spectral graph wavelets to represent the cortical surface of a carpal bone via the spectral geometric analysis of the Laplace-Beltrami operator in the discrete domain. We propose global spectral graph wavelet (GSGW) descriptor that is isometric invariant, efficient to compute, and combines the advantages of both low-pass and band-pass filters. We perform experiments on shapes of the carpal bones of ten women and ten men from a publicly-available database of wrist bones. Using one-way multivariate analysis of variance (MANOVA) and permutation testing, we show through extensive experiments that the proposed GSGW framework gives a much better performance compared to the global point signature embedding approach for comparing shapes of the carpal bones across populations.

THE VIOLATION OF THE TAYLOR HYPOTHESIS IN MEASUREMENTS OF SOLAR WIND TURBULENCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, K. G.; Howes, G. G.; TenBarge, J. M.

2014-08-01

Motivated by the upcoming Solar Orbiter and Solar Probe Plus missions, qualitative and quantitative predictions are made for the effects of the violation of the Taylor hypothesis on the magnetic energy frequency spectrum measured in the near-Sun environment. The synthetic spacecraft data method is used to predict observational signatures of the violation for critically balanced Alfvénic turbulence or parallel fast/whistler turbulence. The violation of the Taylor hypothesis can occur in the slow flow regime, leading to a shift of the entire spectrum to higher frequencies, or in the dispersive regime, in which the dissipation range spectrum flattens at high frequencies.more » It is found that Alfvénic turbulence will not significantly violate the Taylor hypothesis, but whistler turbulence will. The flattening of the frequency spectrum is therefore a key observational signature for fast/whistler turbulence.« less

Optical analyzer

DOEpatents

Hansen, A.D.

1987-09-28

An optical analyzer wherein a sample of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter is placed in a combustion tube, and light from a light source is passed through the sample. The temperature of the sample is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample is detected as the temperature is raised. A data processor, differentiator and a two pen recorder provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample. These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample. Additional information is obtained by repeating the run in different atmospheres and/or different rates or heating with other samples of the same particulate material collected on other filters. 7 figs.

Global spectral graph wavelet signature for surface analysis of carpal bones.

PubMed

Masoumi, Majid; Rezaei, Mahsa; Ben Hamza, A

2018-02-05

Quantitative shape comparison is a fundamental problem in computer vision, geometry processing and medical imaging. In this paper, we present a spectral graph wavelet approach for shape analysis of carpal bones of the human wrist. We employ spectral graph wavelets to represent the cortical surface of a carpal bone via the spectral geometric analysis of the Laplace-Beltrami operator in the discrete domain. We propose global spectral graph wavelet (GSGW) descriptor that is isometric invariant, efficient to compute, and combines the advantages of both low-pass and band-pass filters. We perform experiments on shapes of the carpal bones of ten women and ten men from a publicly-available database of wrist bones. Using one-way multivariate analysis of variance (MANOVA) and permutation testing, we show through extensive experiments that the proposed GSGW framework gives a much better performance compared to the global point signature embedding approach for comparing shapes of the carpal bones across populations.

Prediction of sonic boom at a focus

NASA Technical Reports Server (NTRS)

Plotkin, K. J.; Cantril, J. M.

1976-01-01

The behavior of sonic boom at a focus has been reviewed for the purpose of extending present sonic boom computational methods to include focal zones. The geometry of a focal zone - whether a smooth caustic, a cusped caustic, or a perfect focus to a point - determines the character of focused signatures. The seeming contradiction of various experimental data can be resolved by noting these differences. A ray acoustic analysis has been developed for quantitative determination of caustic geometry. The only reliable theory presently available for signatures at a focus is for a smooth caustic. There has been some controversy between theoretical and experimental values of a constant in the scaling law for this case. It has been found that this discrepancy can be resolved by accounting for the finite thickness of real sonic boom shock waves. These findings have been incorporated into an existing sonic boom computer program.

Radiation and polarization signatures of the 3D multizone time-dependent hadronic blazar model

DOE PAGES

Zhang, Haocheng; Diltz, Chris; Bottcher, Markus

2016-09-23

We present a newly developed time-dependent three-dimensional multizone hadronic blazar emission model. By coupling a Fokker–Planck-based lepto-hadronic particle evolution code, 3DHad, with a polarization-dependent radiation transfer code, 3DPol, we are able to study the time-dependent radiation and polarization signatures of a hadronic blazar model for the first time. Our current code is limited to parameter regimes in which the hadronic γ-ray output is dominated by proton synchrotron emission, neglecting pion production. Our results demonstrate that the time-dependent flux and polarization signatures are generally dominated by the relation between the synchrotron cooling and the light-crossing timescale, which is largely independent ofmore » the exact model parameters. We find that unlike the low-energy polarization signatures, which can vary rapidly in time, the high-energy polarization signatures appear stable. Lastly, future high-energy polarimeters may be able to distinguish such signatures from the lower and more rapidly variable polarization signatures expected in leptonic models.« less

Quantitative Morphologic Analysis of Boulder Shape and Surface Texture to Infer Environmental History: A Case Study of Rock Breakdown at the Ephrata Fan, Channeled Scabland, Washington

NASA Technical Reports Server (NTRS)

Ehlmann, Bethany L.; Viles, Heather A.; Bourke, Mary C.

2008-01-01

Boulder morphology reflects both lithology and climate and is dictated by the combined effects of erosion, transport, and weathering. At present, morphologic information at the boulder scale is underutilized as a recorder of environmental processes, partly because of the lack of a systematic quantitative parameter set for reporting and comparing data sets. We develop such a parameter set, incorporating a range of measures of boulder form and surface texture. We use standard shape metrics measured in the field and fractal and morphometric classification methods borrowed from landscape analysis and applied to laser-scanned molds. The parameter set was pilot tested on three populations of basalt boulders with distinct breakdown histories in the Channeled Scabland, Washington: (1) basalt outcrop talus; (2) flood-transported boulders recently excavated from a quarry; and (3) flood-transported boulders, extensively weathered in situ on the Ephrata Fan surface. Size and shape data were found to distinguish between flood-transported and untransported boulders. Size and edge angles (approximately 120 degrees) of flood-transported boulders suggest removal by preferential fracturing along preexisting columnar joints, and curvature data indicate rounding relative to outcrop boulders. Surface textural data show that boulders which have been exposed at the surface are significantly rougher than those buried by fan sediments. Past signatures diagnostic of flood transport still persist on surface boulders, despite ongoing overprinting by processes in the present breakdown environment through roughening and fracturing in situ. Further use of this quantitative boulder parameter set at other terrestrial and planetary sites will aid in cataloging and understanding morphologic signatures of environmental processes.

Correlation of Rock Spectra with Quantitative Morphologic Indices: Evidence for a Single Rock Type at the Mars Pathfinder Landing Site

NASA Technical Reports Server (NTRS)

Yingst, R. A.; Biedermann, K. L.; Pierre, N. M.; Haldemann, A. F. C.; Johnson, J. R.

2005-01-01

The Mars Pathfinder (MPF) landing site was predicted to contain a broad sampling of rock types varying in mineralogical, physical, mechanical and geochemical characteristics. Although rocks have been divided into several spectral categories based on Imager for Mars Pathfinder (IMP) visible/near-infrared data, efforts in isolating and classifying spectral units among MPF rocks and soils have met with varying degrees of success, as many factors influencing spectral signatures cannot be quantified to a sufficient level to be removed. It has not been fully determined which spectral categories stem from intrinsic mineralogical differences between rocks or rock surfaces, and which result from factors such as physical or chemical weathering. This has made isolation of unique rock mineralogies difficult. Morphology, like composition, is a characteristic tied to the intrinsic properties and geologic and weathering history of rocks. Rock morphologies can be assessed quantitatively and compared with spectral data, to identify and classify rock types at the MPF landing site. They can also isolate actual rock spectra from spectral types that are surficial in origin, as compositions associated with mantling dust or chemical coatings would presumably not influence rock morphology during weathering events. We previously reported on an initial classification of rocks using the quantitative morphologic indices of size, roundness, sphericity and elongation. Here, we compare this database of rock characteristics with associated rock surface spectra to improve our ability to discriminate between spectra associated with rock types and those from other sources.

In-vitro analysis of early calcification in aortic valvular interstitial cells using Laser-Induced Breakdown Spectroscopy (LIBS).

PubMed

Davari, Seyyed Ali; Masjedi, Shirin; Ferdous, Zannatul; Mukherjee, Dibyendu

2018-01-01

Calcific aortic valve disease (CAVD) is a major cardiovascular disorder caused by osteogenic differentiation of valvular interstitial cells (VICs) within aortic valves. Conventional methods like colorimetric assays and histology fail to detect small calcium depositions during in-vitro VIC cultures. Laser-induced breakdown spectroscopy (LIBS) is a robust analytical tool used for inorganic materials characterizations, but relatively new to biomedical applications. We employ LIBS, for the first time, for quantitative in-vitro detection of calcium depositions in VICs at various osteogenic differentiation stages. VICs isolated from porcine aortic valves were cultured in osteogenic media over various days. Colorimetric calcium assays based on arsenazo dye and Von Kossa staining measured the calcium depositions within VICs. Simultaneously, LIBS signatures for Ca I (422.67 nm) atomic emission lines were collected for estimating calcium depositions in lyophilized VIC samples. Our results indicate excellent linear correlation between the calcium assay and our LIBS measurements. Furthermore, unlike the assay results, the LIBS results could resolve calcium signals from cell samples with as early as 2 days of osteogenic culture. Quantitatively, the LIBS measurements establish the limit of detection for calcium content in VICs to be ∼0.17±0.04 μg which indicates a 5-fold improvement over calcium assay. Picture: Quantitative LIBS enables in-vitro analysis for early stage detection of calcium deposition within aortic valvular interstitial cells (VICs). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease.

PubMed

Winfree, Seth; Dagher, Pierre C; Dunn, Kenneth W; Eadon, Michael T; Ferkowicz, Michael; Barwinska, Daria; Kelly, Katherine J; Sutton, Timothy A; El-Achkar, Tarek M

2018-06-05

Kidney biopsy remains the gold standard for uncovering the pathogenesis of acute and chronic kidney diseases. However, the ability to perform high resolution, quantitative, molecular and cellular interrogation of this precious tissue is still at a developing stage compared to other fields such as oncology. Here, we discuss recent advances in performing large-scale, three-dimensional (3D), multi-fluorescence imaging of kidney biopsies and quantitative analysis referred to as 3D tissue cytometry. This approach allows the accurate measurement of specific cell types and their spatial distribution in a thick section spanning the entire length of the biopsy. By uncovering specific disease signatures, including rare occurrences, and linking them to the biology in situ, this approach will enhance our understanding of disease pathogenesis. Furthermore, by providing accurate quantitation of cellular events, 3D cytometry may improve the accuracy of prognosticating the clinical course and response to therapy. Therefore, large-scale 3D imaging and cytometry of kidney biopsy is poised to become a bridge towards personalized medicine for patients with kidney disease. © 2018 S. Karger AG, Basel.

Passive Fourier-transform infrared spectroscopy of chemical plumes: an algorithm for quantitative interpretation and real-time background removal

NASA Astrophysics Data System (ADS)

Polak, Mark L.; Hall, Jeffrey L.; Herr, Kenneth C.

1995-08-01

We present a ratioing algorithm for quantitative analysis of the passive Fourier-transform infrared spectrum of a chemical plume. We show that the transmission of a near-field plume is given by tau plume = (Lobsd - Lbb-plume)/(Lbkgd - Lbb-plume), where tau _{plume is the frequency-dependent transmission of the plume, L obsd is the spectral radiance of the scene that contains the plume, Lbkgd is the spectral radiance of the same scene without the plume, and Lbb-plume is the spectral radiance of a blackbody at the plume temperature. The algorithm simultaneously achieves background removal, elimination of the spectrometer internal signature, and quantification of the plume spectral transmission. It has applications to both real-time processing for plume visualization and quantitative measurements of plume column densities. The plume temperature (Lbb-plume ), which is not always precisely known, can have a profound effect on the quantitative interpretation of the algorithm and is discussed in detail. Finally, we provide an illustrative example of the use of the algorithm on a trichloroethylene and acetone plume.}

A Fast lattice-based polynomial digital signature system for m-commerce

NASA Astrophysics Data System (ADS)

Wei, Xinzhou; Leung, Lin; Anshel, Michael

2003-01-01

The privacy and data integrity are not guaranteed in current wireless communications due to the security hole inside the Wireless Application Protocol (WAP) version 1.2 gateway. One of the remedies is to provide an end-to-end security in m-commerce by applying application level security on top of current WAP1.2. The traditional security technologies like RSA and ECC applied on enterprise's server are not practical for wireless devices because wireless devices have relatively weak computation power and limited memory compared with server. In this paper, we developed a lattice based polynomial digital signature system based on NTRU's Polynomial Authentication and Signature Scheme (PASS), which enabled the feasibility of applying high-level security on both server and wireless device sides.

The Search for Hydrologic Signatures: The Effect of Data Transformations on Bayesian Model Calibration

NASA Astrophysics Data System (ADS)

Sadegh, M.; Vrugt, J. A.

2011-12-01

In the past few years, several contributions have begun to appear in the hydrologic literature that introduced and analyzed the benefits of using a signature based approach to watershed analysis. This signature-based approach abandons the standard single criteria model-data fitting paradigm in favor of a diagnostic approach that better extracts the available information from the available data. Despite the prospects of this new viewpoint, rather ad-hoc criteria have hitherto been proposed to improve watershed modeling. Here, we aim to provide a proper mathematical foundation to signature based analysis. We analyze the information content of different data transformation by analyzing their convergence speed with Markov Chain Monte Carlo (MCMC) simulation using the Generalized Likelihood function of Schousp and Vrugt (2010). We compare the information content of the original discharge data against a simple square root and Box-Cox transformation of the streamflow data. We benchmark these results against wavelet and flow duration curve transformations that temporally disaggregate the discharge data. Our results conclusive demonstrate that wavelet transformations and flow duration curves significantly reduce the information content of the streamflow data and consequently unnecessarily increase the uncertainty of the HYMOD model parameters. Hydrologic signatures thus need to be found in the original data, without temporal disaggregation.

On the security of a novel probabilistic signature based on bilinear square Diffie-Hellman problem and its extension.

PubMed

Zhao, Zhenguo; Shi, Wenbo

2014-01-01

Probabilistic signature scheme has been widely used in modern electronic commerce since it could provide integrity, authenticity, and nonrepudiation. Recently, Wu and Lin proposed a novel probabilistic signature (PS) scheme using the bilinear square Diffie-Hellman (BSDH) problem. They also extended it to a universal designated verifier signature (UDVS) scheme. In this paper, we analyze the security of Wu et al.'s PS scheme and UDVS scheme. Through concrete attacks, we demonstrate both of their schemes are not unforgeable. The security analysis shows that their schemes are not suitable for practical applications.

Generating quantitative palaeoflood data from homogeneous lake sediments: a case-study from Brotherswater, northwest England

NASA Astrophysics Data System (ADS)

Schillereff, Daniel; Chiverrell, Richard; Macdonald, Neil; Hooke, Janet

2016-04-01

The scarcity of long-term hydrological data is a barrier to reliably determining the likelihood of floods becoming more frequent and/or intense in a warmer world. Lakes and their sediments are increasingly being used to reconstruct long-term, highly-resolved datasets of past floods but the ultimate goal, generating quantitative palaeohydrological data to augment flood frequency analyses, is a persistent challenge. To this end, ascertaining the autogenic and allogenic processes influencing the character and preservation potential of palaeoflood laminations and determining the minimum discharge at which a sedimentary imprint will be deposited in a particular system are two key precursors. Some success has been achieved at lakes containing annually-laminated sequences or where event layers exhibit well-defined lithological contacts. Many non-alpine and non-polar lakes, especially those in temperate regions, are instead characterised by visually-homogeneous, organic-rich sediments from which discrete flood laminations are difficult to discriminate. Working at Brotherswater, a small upland lake in northwest England, we have successfully demonstrated an approach to obtain flood frequency and magnitude data from this type of lake system by integrating a 16 month sediment trap deployment (CE 2013-2014) with the recent (CE 1962 - 2014) depositional record. The geochemical composition and end-member modelling of the trap data shed light on the seasonal variation in background sedimentation dynamics, specifically enhanced sediment supply during winter, spring diatom blooms and heightened summer productivity, which alter the signature of coarse-grained deposition in response to higher flows. Having pinpointed the characteristic flood end-member, comparison of the short-core palaeoflood reconstruction to local river discharge data was able to reveal the hydrological thresholds of this system: flood magnitudes calculated to have a four year recurrence interval are preserved in delta-proximal sediments but the central basin was less sensitive, declining to nine years. These results have been further contextualised through comparison with the sedimentological signature of a recent extreme flood captured by sediment traps and in short cores extracted immediately post-event. On the 5-6 December Storm Desmond delivered unprecedented rainfall and multiple gauging stations in the region surpassed record river flow, offering a unique opportunity to test a sediment-based palaeoflood record. These data re-emphasise the need for systematic process monitoring and calibration of the depositional record to obtain a site-specific understanding of internal and external factors controlling event signature preservation. Wider implementation of this approach at equivalent lakes offers a vast, untapped archive of palaeohydrological data for hydrologists, climate modellers, engineers and policy makers addressing future flood risks.

Offline signature verification using convolution Siamese network

NASA Astrophysics Data System (ADS)

Xing, Zi-Jian; Yin, Fei; Wu, Yi-Chao; Liu, Cheng-Lin

2018-04-01

This paper presents an offline signature verification approach using convolutional Siamese neural network. Unlike the existing methods which consider feature extraction and metric learning as two independent stages, we adopt a deepleaning based framework which combines the two stages together and can be trained end-to-end. The experimental results on two offline public databases (GPDSsynthetic and CEDAR) demonstrate the superiority of our method on the offline signature verification problem.

Quantum Proxy Multi-Signature Scheme Using Genuinely Entangled Six Qubits State

NASA Astrophysics Data System (ADS)

Cao, Hai-Jing; Wang, Huai-Sheng; Li, Peng-Fei

2013-04-01

A quantum proxy multi-signature scheme is presented based on controlled teleportation. Genuinely entangled six qubits quantum state functions as quantum channel. The scheme uses the physical characteristics of quantum mechanics to implement delegation, signature and verification. Quantum key distribution and one-time pad are adopted in our scheme, which could guarantee not only the unconditional security of the scheme but also the anonymity of the messages owner.

Output-Adaptive Tetrahedral Cut-Cell Validation for Sonic Boom Prediction

NASA Technical Reports Server (NTRS)

Park, Michael A.; Darmofal, David L.

2008-01-01

A cut-cell approach to Computational Fluid Dynamics (CFD) that utilizes the median dual of a tetrahedral background grid is described. The discrete adjoint is also calculated, which permits adaptation based on improving the calculation of a specified output (off-body pressure signature) in supersonic inviscid flow. These predicted signatures are compared to wind tunnel measurements on and off the configuration centerline 10 body lengths below the model to validate the method for sonic boom prediction. Accurate mid-field sonic boom pressure signatures are calculated with the Euler equations without the use of hybrid grid or signature propagation methods. Highly-refined, shock-aligned anisotropic grids were produced by this method from coarse isotropic grids created without prior knowledge of shock locations. A heuristic reconstruction limiter provided stable flow and adjoint solution schemes while producing similar signatures to Barth-Jespersen and Venkatakrishnan limiters. The use of cut-cells with an output-based adaptive scheme completely automated this accurate prediction capability after a triangular mesh is generated for the cut surface. This automation drastically reduces the manual intervention required by existing methods.

Fault-tolerant quantum blind signature protocols against collective noise

NASA Astrophysics Data System (ADS)

Zhang, Ming-Hui; Li, Hui-Fang

2016-10-01

This work proposes two fault-tolerant quantum blind signature protocols based on the entanglement swapping of logical Bell states, which are robust against two kinds of collective noises: the collective-dephasing noise and the collective-rotation noise, respectively. Both of the quantum blind signature protocols are constructed from four-qubit decoherence-free (DF) states, i.e., logical Bell qubits. The initial message is encoded on the logical Bell qubits with logical unitary operations, which will not destroy the anti-noise trait of the logical Bell qubits. Based on the fundamental property of quantum entanglement swapping, the receiver simply performs two Bell-state measurements (rather than four-qubit joint measurements) on the logical Bell qubits to verify the signature, which makes the protocols more convenient in a practical application. Different from the existing quantum signature protocols, our protocols can offer the high fidelity of quantum communication with the employment of logical qubits. Moreover, we hereinafter prove the security of the protocols against some individual eavesdropping attacks, and we show that our protocols have the characteristics of unforgeability, undeniability and blindness.

Quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets.

PubMed

Wise, M G; Siragusa, G R

2007-04-01

To explore the effect of drug-free poultry production on the intestinal microflora of broiler chickens, the bacterial community of this environment was quantitatively profiled in both conventionally reared birds and birds reared without antibiotic growth promotants (AGPs) on a vegetable-based diet. Quantitative, real-time PCR with group-specific 16S rDNA primer sets was used to enumerate the abundance of the following chicken gastrointestinal (GI) tract phylogenetic groups: the Clostridium leptum-Faecalibacterium prausnitzii subgroup (Clostridium genus cluster IV), the Clostridium coccoides - Eubacterium rectale subgroup (Clostridium cluster XIVa and XIVb), the Bacteroides group (including Prevotella and Porphyromonas), Bifidobacterium spp., the Enterobacteriaceae, the Lactobacillus group (including the genera Leuconostoc, Pediococcus, Aerococcus and Weissella), the Clostridium perfringens subgroup (Clostridium cluster I), Enterococcus spp., Veillonella spp., Atopobium spp., Campylobacter spp. and the domain Bacteria. A species-specific 5'-nuclease (Taqman) assay was also employed to specifically assess Cl. perfringens abundance. Ten birds were sampled from each of two commercial chicken houses, one in which feed was supplemented with AGPs and exogenous animal protein, and the other vegetable-based and drug-free, at 7, 14 and 21 days of age. The ileal community was dominated by two large populations, the lactobacilli and the Enterobacteriaceae, with those taxa much more numerous in drug-free vegetable-based diet fed birds than those conventionally reared at the 7- and 14-day time periods. The progressive changes in microflora in both the conventional and drug-free caeca were similar to each other, with the Enterobacteriaceae sequences dominating at day 7, but being replaced by obligate anaerobe signature sequences by day 14. Of note was the finding that all the day 14 and day 21 replicate caecal samples from the drug-free house were positive for Campylobacter spp. averaging >10(8) 16S rDNA gene copies per gram wet weight. Quantitative, real-time PCR indicates that the effects of drug-free rearing on the chicken GI tract microbial community are most pronounced in the ileal region, but AGPs may be important in controlling Campylobacter colonization of the caecum. A quantitative taxonomic understanding of the shifting microbial ecology of the broiler chicken gut microbiota is important in the light of AGP withdrawal. AGP withdrawal has occurred in response to concerns over the transfer of antimicrobial-resistant bacteria to humans via the food production chain.

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. | Office of Cancer Genomics

Cancer.gov

We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined.

Quantum dual signature scheme based on coherent states with entanglement swapping

NASA Astrophysics Data System (ADS)

Liu, Jia-Li; Shi, Rong-Hua; Shi, Jin-Jing; Lv, Ge-Li; Guo, Ying

2016-08-01

A novel quantum dual signature scheme, which combines two signed messages expected to be sent to two diverse receivers Bob and Charlie, is designed by applying entanglement swapping with coherent states. The signatory Alice signs two different messages with unitary operations (corresponding to the secret keys) and applies entanglement swapping to generate a quantum dual signature. The dual signature is firstly sent to the verifier Bob who extracts and verifies the signature of one message and transmits the rest of the dual signature to the verifier Charlie who verifies the signature of the other message. The transmission of the dual signature is realized with quantum teleportation of coherent states. The analysis shows that the security of secret keys and the security criteria of the signature protocol can be greatly guaranteed. An extensional multi-party quantum dual signature scheme which considers the case with more than three participants is also proposed in this paper and this scheme can remain secure. The proposed schemes are completely suited for the quantum communication network including multiple participants and can be applied to the e-commerce system which requires a secure payment among the customer, business and bank. Project supported by the National Natural Science Foundation of China (Grant Nos. 61272495, 61379153, and 61401519) and the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20130162110012).

Adaptive Aft Signature Shaping of a Low-Boom Supersonic Aircraft Using Off-Body Pressures

NASA Technical Reports Server (NTRS)

Ordaz, Irian; Li, Wu

2012-01-01

The design and optimization of a low-boom supersonic aircraft using the state-of-the- art o -body aerodynamics and sonic boom analysis has long been a challenging problem. The focus of this paper is to demonstrate an e ective geometry parameterization scheme and a numerical optimization approach for the aft shaping of a low-boom supersonic aircraft using o -body pressure calculations. A gradient-based numerical optimization algorithm that models the objective and constraints as response surface equations is used to drive the aft ground signature toward a ramp shape. The design objective is the minimization of the variation between the ground signature and the target signature subject to several geometric and signature constraints. The target signature is computed by using a least-squares regression of the aft portion of the ground signature. The parameterization and the deformation of the geometry is performed with a NASA in- house shaping tool. The optimization algorithm uses the shaping tool to drive the geometric deformation of a horizontal tail with a parameterization scheme that consists of seven camber design variables and an additional design variable that describes the spanwise location of the midspan section. The demonstration cases show that numerical optimization using the state-of-the-art o -body aerodynamic calculations is not only feasible and repeatable but also allows the exploration of complex design spaces for which a knowledge-based design method becomes less effective.

Mesoscale numerical investigations of air traffic emissions over the North Atlantic during SONEX flight 8: A case study

NASA Astrophysics Data System (ADS)

Bieberbach, George; Fuelberg, Henry E.; Thompson, Anne M.; Schmitt, Alfons; Hannan, John R.; Gregory, G. L.; Kondo, Yutaka; Knabb, Richard D.; Sachse, G. W.; Talbot, R. W.

2000-02-01

Chemical data from flight 8 of NASA's Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX) exhibited signatures consistent with aircraft emissions, stratospheric air, and surface-based pollution. These signatures are examined in detail, focusing on the broad aircraft emission signatures that are several hundred kilometers in length. A mesoscale meteorological model provides high-resolution wind data that are used to calculate backward trajectories arriving at locations along the flight track. These trajectories are compared to aircraft locations in the North Atlantic Flight Corridor (NAFC) over a 27-33 hour period. Time series of flight level NO and the number of trajectory/aircraft encounters within the NAFC show excellent agreement. Trajectories arriving within the stratospheric and surface-based pollution regions are found to experience very few aircraft encounters. Conversely, there are many trajectory/aircraft encounters within the two chemical signatures corresponding to aircraft emissions. Even many detailed fluctuations of NO within the two aircraft signature regions correspond to similar fluctuations in aircraft encountered. These NO spikes are due to the superposition of 14 to 25 aircraft plumes transported to the DC-8 flight track during the previous 33 hours. Results confirm that aircraft emissions were responsible for two chemical signatures observed during SONEX flight 8. They also indicate that high-resolution meteorological modeling, when coupled with detailed aircraft location data, is useful for understanding chemical signatures from aircraft emissions at scales of several hundred kilometers.

Source signature estimation from multimode surface waves via mode-separated virtual real source method

NASA Astrophysics Data System (ADS)

Gao, Lingli; Pan, Yudi

2018-05-01

The correct estimation of the seismic source signature is crucial to exploration geophysics. Based on seismic interferometry, the virtual real source (VRS) method provides a model-independent way for source signature estimation. However, when encountering multimode surface waves, which are commonly seen in the shallow seismic survey, strong spurious events appear in seismic interferometric results. These spurious events introduce errors in the virtual-source recordings and reduce the accuracy of the source signature estimated by the VRS method. In order to estimate a correct source signature from multimode surface waves, we propose a mode-separated VRS method. In this method, multimode surface waves are mode separated before seismic interferometry. Virtual-source recordings are then obtained by applying seismic interferometry to each mode individually. Therefore, artefacts caused by cross-mode correlation are excluded in the virtual-source recordings and the estimated source signatures. A synthetic example showed that a correct source signature can be estimated with the proposed method, while strong spurious oscillation occurs in the estimated source signature if we do not apply mode separation first. We also applied the proposed method to a field example, which verified its validity and effectiveness in estimating seismic source signature from shallow seismic shot gathers containing multimode surface waves.

Numerical Predictions of Sonic Boom Signatures for a Straight Line Segmented Leading Edge Model

NASA Technical Reports Server (NTRS)

Elmiligui, Alaa A.; Wilcox, Floyd J.; Cliff, Susan; Thomas, Scott

2012-01-01

A sonic boom wind tunnel test was conducted on a straight-line segmented leading edge (SLSLE) model in the NASA Langley 4- by 4- Foot Unitary Plan Wind Tunnel (UPWT). The purpose of the test was to determine whether accurate sonic boom measurements could be obtained while continuously moving the SLSLE model past a conical pressure probe. Sonic boom signatures were also obtained using the conventional move-pause data acquisition method for comparison. The continuous data acquisition approach allows for accurate signatures approximately 15 times faster than a move-pause technique. These successful results provide an incentive for future testing with greatly increased efficiency using the continuous model translation technique with the single probe to measure sonic boom signatures. Two widely used NASA codes, USM3D (Navier-Stokes) and CART3D-AERO (Euler, adjoint-based adaptive mesh), were used to compute off-body sonic boom pressure signatures of the SLSLE model at several different altitudes below the model at Mach 2.0. The computed pressure signatures compared well with wind tunnel data. The effect of the different altitude for signature extraction was evaluated by extrapolating the near field signatures to the ground and comparing pressure signatures and sonic boom loudness levels.

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples.

PubMed

Díaz-Gay, Marcos; Vila-Casadesús, Maria; Franch-Expósito, Sebastià; Hernández-Illán, Eva; Lozano, Juan José; Castellví-Bel, Sergi

2018-06-14

Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts. In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions. MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica .

Jahn-Teller versus quantum effects in the spin-orbital material LuVO 3

DOE PAGES

Skoulatos, M.; Toth, S.; Roessli, B.; ...

2015-04-13

In this article, we report on combined neutron and resonant x-ray scattering results, identifying the nature of the spin-orbital ground state and magnetic excitations in LuVO 3 as driven by the orbital parameter. In particular, we distinguish between models based on orbital-Peierls dimerization, taken as a signature of quantum effects in orbitals, and Jahn-Teller distortions, in favor of the latter. In order to solve this long-standing puzzle, polarized neutron beams were employed as a prerequisite in order to solve details of the magnetic structure, which allowed quantitative intensity analysis of extended magnetic-excitation data sets. The results of this detailed studymore » enabled us to draw definite conclusions about the classical versus quantum behavior of orbitals in this system and to discard the previous claims about quantum effects dominating the orbital physics of LuVO 3 and similar systems.« less

A quantitative investigation of the fracture pump-in/flowback test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plahn, S.V.; Nolte, K.G.; Thompson, L.G.

1997-02-01

Fracture-closure pressure is an important parameter for fracture treatment design and evaluation. The pump-in/flowback (PIFB) test is frequently used to estimate its magnitude. The test is attractive because bottomhole pressures (BHP`s) during flowback develop a distinct and repeatable signature. This is in contrast to the pump-in/shut-in test, where strong indications of fracture closure are rarely seen. Various techniques are used to extract closure pressure from the flowback-pressure response. Unfortunately, these techniques give different estimates for closure pressure, and their theoretical bases are not well established. The authors present results that place the PIFB test on a firmer foundation. A numericalmore » model is used to simulate the PIFB test and glean physical mechanisms contributing to the response. On the basis of their simulation results, they propose interpretation techniques that give better estimates of closure pressure than existing techniques.« less

Regression away from the mean: Theory and examples.

PubMed

Schwarz, Wolf; Reike, Dennis

2018-02-01

Using a standard repeated measures model with arbitrary true score distribution and normal error variables, we present some fundamental closed-form results which explicitly indicate the conditions under which regression effects towards (RTM) and away from the mean are expected. Specifically, we show that for skewed and bimodal distributions many or even most cases will show a regression effect that is in expectation away from the mean, or that is not just towards but actually beyond the mean. We illustrate our results in quantitative detail with typical examples from experimental and biometric applications, which exhibit a clear regression away from the mean ('egression from the mean') signature. We aim not to repeal cautionary advice against potential RTM effects, but to present a balanced view of regression effects, based on a clear identification of the conditions governing the form that regression effects take in repeated measures designs. © 2017 The British Psychological Society.

Geologic remote sensing - New technology, new information

NASA Technical Reports Server (NTRS)

Kruse, F. A.

1992-01-01

Results of geologic studies using data collected by the NASA/JPL Thermal Infrared Imaging Spectrometer (TIMS), Airborne Visible/Infrared Imaging Spectrometer (AVIRIS), and the Airborne Synthetic Aperture Radar (AIRSAR) are discussed. These instruments represent prototypes for the Earth Observing System (EOS) satellite instruments ASTER, High Resolution Imaging Spectrometer (HIRIS), and EOS SAR. Integrated analysis of this data type is one of the keys to successful geologic research using EOS. TIMS links the physical properties of surface materials in the 8-12-*mm region to their composition. Calibrated aircraft data make direct lithological mapping possible. AVIRIS, an analog for HIRIS, provides quantitative information about the surface composition of materials based on their detailed visible and infrared spectral signatures (0.4-2.45 mm). Calibrated AVIRIS data make direct identification of minerals possible. The AIRSAR provides additional complementary information about the surface morphology of rocks and soils.

Clinical Electroencephalography for Anesthesiologists Part I: Background and Basic Signatures

PubMed Central

Purdon, Patrick L.; Sampson, Aaron; Pavone, Kara J.; Brown, Emery N.

2015-01-01

The widely used electroencephalogram-based indices for depth-of-anesthesia monitoring assume that the same index value defines the same level of unconsciousness for all anesthetics. In contrast, we show that different anesthetics act at different molecular targets and neural circuits to produce distinct brain states that are readily visible in the electroencephalogram. We present a two-part review to educate anesthesiologists on use of the unprocessed electroencephalogram and its spectrogram to track the brain states of patients receiving anesthesia care. Here in Part I, we review the biophysics of the electroencephalogram, and the neurophysiology of the electroencephalogram signatures of three intravenous anesthetics: propofol, dexmedetomidine and ketamine; and four inhaled anesthetics: sevoflurane, isoflurane, desflurane and nitrous oxide. Later in Part II, we discuss patient management using these electroencephalogram signatures. Use of these electroencephalogram signatures suggests a neurophysiologically-based paradigm for brain-state monitoring of patients receiving anesthesia care. PMID:26275092

Estimating physiological skin parameters from hyperspectral signatures

NASA Astrophysics Data System (ADS)

Vyas, Saurabh; Banerjee, Amit; Burlina, Philippe

2013-05-01

We describe an approach for estimating human skin parameters, such as melanosome concentration, collagen concentration, oxygen saturation, and blood volume, using hyperspectral radiometric measurements (signatures) obtained from in vivo skin. We use a computational model based on Kubelka-Munk theory and the Fresnel equations. This model forward maps the skin parameters to a corresponding multiband reflectance spectra. Machine-learning-based regression is used to generate the inverse map, and hence estimate skin parameters from hyperspectral signatures. We test our methods using synthetic and in vivo skin signatures obtained in the visible through the short wave infrared domains from 24 patients of both genders and Caucasian, Asian, and African American ethnicities. Performance validation shows promising results: good agreement with the ground truth and well-established physiological precepts. These methods have potential use in the characterization of skin abnormalities and in minimally-invasive prescreening of malignant skin cancers.

Explosives Detection: Exploitation of the Physical Signatures

NASA Astrophysics Data System (ADS)

Atkinson, David

2010-10-01

Explosives based terrorism is an ongoing threat that is evolving with respect to implementation, configuration and materials used. There are a variety of devices designed to detect explosive devices, however, each technology has limitations and operational constraints. A full understanding of the signatures available for detection coupled with the array of detection choices can be used to develop a conceptual model of an explosives screening operation. Physics based sensors provide a robust approach to explosives detection, typically through the identification of anomalies, and are currently used for screening in airports around the world. The next generation of detectors for explosives detection will need to be more sensitive and selective, as well as integrate seamlessly with devices focused on chemical signatures. An appreciation for the details of the physical signature exploitation in cluttered environments with time, space, and privacy constraints is necessary for effective explosives screening of people, luggage, cargo, and vehicles.

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Genomic scar signatures associated with homologous recombination deficiency predict adverse clinical outcomes in patients with ovarian clear cell carcinoma.

PubMed

Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Jung, Shih-Ming; Lee, Yun-Shien; Chang, Wei-Yang; Yang, Lan-Yang; Ku, Fei-Chun; Huang, Huei-Jean; Chao, An-Shine; Wang, Chin-Jung; Chang, Ting-Chang; Wu, Ren-Chin

2018-05-03

We investigated whether genomic scar signatures associated with homologous recombination deficiency (HRD), which include telomeric allelic imbalance (TAI), large-scale transition (LST), and loss of heterozygosity (LOH), can predict clinical outcomes in patients with ovarian clear cell carcinoma (OCCC). We enrolled patients with OCCC (n = 80) and high-grade serous carcinoma (HGSC; n = 92) subjected to primary cytoreductive surgery, most of whom received platinum-based adjuvant chemotherapy. Genomic scar signatures based on genome-wide copy number data were determined in all participants and investigated in relation to prognosis. OCCC had significantly lower genomic scar signature scores than HGSC (p < 0.001). Near-triploid OCCC specimens showed higher TAI and LST scores compared with diploid tumors (p < 0.001). While high scores of these genomic scar signatures were significantly associated with better clinical outcomes in patients with HGSC, the opposite was evident for OCCC. Multivariate survival analysis in patients with OCCC identified high LOH scores as the main independent adverse predictor for both cancer-specific (hazard ratio [HR] = 3.22, p = 0.005) and progression-free survival (HR = 2.54, p = 0.01). In conclusion, genomic scar signatures associated with HRD predict adverse clinical outcomes in patients with OCCC. The LOH score was identified as the strongest prognostic indicator in this patient group. Genomic scar signatures associated with HRD are less frequent in OCCC than in HGSC. Genomic scar signatures associated with HRD have an adverse prognostic impact in patients with OCCC. LOH score is the strongest adverse prognostic factor in patients with OCCC.

A Real-Time Infrared Ultra-Spectral Signature Classification Method via Spatial Pyramid Matching

PubMed Central

Mei, Xiaoguang; Ma, Yong; Li, Chang; Fan, Fan; Huang, Jun; Ma, Jiayi

2015-01-01

The state-of-the-art ultra-spectral sensor technology brings new hope for high precision applications due to its high spectral resolution. However, it also comes with new challenges, such as the high data dimension and noise problems. In this paper, we propose a real-time method for infrared ultra-spectral signature classification via spatial pyramid matching (SPM), which includes two aspects. First, we introduce an infrared ultra-spectral signature similarity measure method via SPM, which is the foundation of the matching-based classification method. Second, we propose the classification method with reference spectral libraries, which utilizes the SPM-based similarity for the real-time infrared ultra-spectral signature classification with robustness performance. Specifically, instead of matching with each spectrum in the spectral library, our method is based on feature matching, which includes a feature library-generating phase. We calculate the SPM-based similarity between the feature of the spectrum and that of each spectrum of the reference feature library, then take the class index of the corresponding spectrum having the maximum similarity as the final result. Experimental comparisons on two publicly-available datasets demonstrate that the proposed method effectively improves the real-time classification performance and robustness to noise. PMID:26205263

Microwave signatures of ice hydrometeors from ground-based observations above Summit, Greenland

DOE PAGES

Pettersen, Claire; Bennartz, Ralf; Kulie, Mark S.; ...

2016-04-15

Multi-instrument, ground-based measurements provide unique and comprehensive data sets of the atmosphere for a specific location over long periods of time and resulting data compliment past and existing global satellite observations. Our paper explores the effect of ice hydrometeors on ground-based, high-frequency passive microwave measurements and attempts to isolate an ice signature for summer seasons at Summit, Greenland, from 2010 to 2013. Furthermore, data from a combination of passive microwave, cloud radar, radiosonde, and ceilometer were examined to isolate the ice signature at microwave wavelengths. By limiting the study to a cloud liquid water path of 40 g m -2more » or less, the cloud radar can identify cases where the precipitation was dominated by ice. These cases were examined using liquid water and gas microwave absorption models, and brightness temperatures were calculated for the high-frequency microwave channels: 90, 150, and 225GHz. By comparing the measured brightness temperatures from the microwave radiometers and the calculated brightness temperature using only gas and liquid contributions, any residual brightness temperature difference is due to emission and scattering of microwave radiation from the ice hydrometeors in the column. The ice signature in the 90, 150, and 225 GHz channels for the Summit Station summer months was isolated. Then, this measured ice signature was compared to an equivalent brightness temperature difference calculated with a radiative transfer model including microwave single-scattering properties for several ice habits. Furthermore, initial model results compare well against the 4 years of summer season isolated ice signature in the high-frequency microwave channels.« less

SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

PubMed Central

Vervoort, Mariëtte T. W.; Vonk, J. Arie; Mooijman, Paul J. W.; Van den Elsen, Sven J. J.; Van Megen, Hanny H. B.; Veenhuizen, Peter; Landeweert, Renske; Bakker, Jaap; Mulder, Christian; Helder, Johannes

2012-01-01

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked. PMID:23112818

CRISPR Spacer Arrays for Detection of Viral Signatures from Acidic Hot Springs

NASA Astrophysics Data System (ADS)

Snyder, J. C.; Bateson, M. M.; Suciu, D.; Young, M. J.

2010-04-01

Viruses are the most abundant life-like entities on the planet Earth. Using CRISPR spacer sequences, we have developed a microarray-based approach to detecting viral signatures in the acidic hot springs of Yellowstone.

Propulsion

NASA Astrophysics Data System (ADS)

Smith, P. K.

1993-06-01

Current requirements for missile systems increasingly stress the need for stealth capability. For the majority of missile systems and missions, the exhaust plume is likely to be the major contributor to overall missile signature, especially considering the recent developments in low emission and low Radar Cross Section coatings for motor bodies. This implies the need for the lowest possible rocket exhaust signature over a wide range of frequencies from the UV through visible and IR to microwave and radio frequencies. The choice of propellant type, Double Base; Composite etc, plays a significant part in determining the exhaust signature of the rocket motor as does the selection of inert materials for liners, inhibitors, and nozzles. It is also possible with certain propellants to incorporate additives which reduce exhaust signature either by modifying the chemistry or the afterburning plume or more significantly by suppressing secondary combustion and hence dramatically reducing plume temperature. The feasibility of plume signature control on the various missions envisaged by the missile designer is considered. The choice of propellant type and hardware components to give low signature is discussed together with performance implications. Signature reduction results obtained over a wide range of frequencies are also presented.

DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition.

PubMed

Peter, Cyril J; Fischer, Laura K; Kundakovic, Marija; Garg, Paras; Jakovcevski, Mira; Dincer, Aslihan; Amaral, Ana C; Ginns, Edward I; Galdzicka, Marzena; Bryce, Cyralene P; Ratner, Chana; Waber, Deborah P; Mokler, David; Medford, Gayle; Champagne, Frances A; Rosene, Douglas L; McGaughy, Jill A; Sharp, Andrew J; Galler, Janina R; Akbarian, Schahram

2016-11-15

Early childhood malnutrition affects 113 million children worldwide, impacting health and increasing vulnerability for cognitive and behavioral disorders later in life. Molecular signatures after childhood malnutrition, including the potential for intergenerational transmission, remain unexplored. We surveyed blood DNA methylomes (~483,000 individual CpG sites) in 168 subjects across two generations, including 50 generation 1 individuals hospitalized during the first year of life for moderate to severe protein-energy malnutrition, then followed up to 48 years in the Barbados Nutrition Study. Attention deficits and cognitive performance were evaluated with the Connors Adult Attention Rating Scale and Wechsler Abbreviated Scale of Intelligence. Expression of nutrition-sensitive genes was explored by quantitative reverse transcriptase polymerase chain reaction in rat prefrontal cortex. We identified 134 nutrition-sensitive, differentially methylated genomic regions, with most (87%) specific for generation 1. Multiple neuropsychiatric risk genes, including COMT, IFNG, MIR200B, SYNGAP1, and VIPR2 showed associations of specific methyl-CpGs with attention and IQ. IFNG expression was decreased in prefrontal cortex of rats showing attention deficits after developmental malnutrition. Early childhood malnutrition entails long-lasting epigenetic signatures associated with liability for attention and cognition, and limited potential for intergenerational transmission. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Blood plasma lipidomic signature of epicardial fat in healthy obese women.

PubMed

Scherer, Max; Montoliu, Ivan; Qanadli, Salah D; Collino, Sebastiano; Rezzi, Serge; Kussmann, Martin; Giusti, Vittorio; Martin, François-Pierre J

2015-01-01

A lipidomic approach was employed in a clinically well-defined cohort of healthy obese women to explore blood lipidome phenotype ascribed to body fat deposition, with emphasis on epicardial adipose tissue (EAT). The present investigation delivered a lipidomics signature of epicardial adiposity under healthy clinical conditions using a cohort of 40 obese females (age: 25-45 years, BMI: 28-40 kg/m(2) ) not showing any metabolic disease traits. Lipidomics analysis of blood plasma was employed in combination with in vivo quantitation of mediastinal fat depots by computerized tomography. All cardiac fat depots correlated to indicators of hepatic dysfunctions (ALAT and ASAT), which describe physiological connections between hepatic and cardiac steatosis. Plasma lipidomics encompassed overall levels of lipid classes, fatty acid profiles, and individual lipid species. EAT and visceral fat associated with diacylglycerols (DAG), triglycerides, and distinct phospholipid and sphingolipid species. A pattern of DAG and phosphoglycerols was specific to EAT. Human blood plasma lipidomics appears to be a promising clinical and potentially diagnostic readout for patient stratification and monitoring. Association of blood lipidomics signature to regio-specific mediastinal and visceral adiposity under healthy clinical conditions may help provide more biological insights into obese patient stratification for cardiovascular disease risks. © 2014 The Obesity Society.

Bioinspired magnetoreception and navigation using magnetic signatures as waypoints.

PubMed

Taylor, Brian K

2018-05-15

Diverse taxa use Earth's magnetic field in conjunction with other sensory modalities to accomplish navigation tasks ranging from local homing to long-distance migration across continents and ocean basins. However, despite extensive research, the mechanisms that underlie animal magnetoreception are not clearly understood, and how animals use Earth's magnetic field to navigate is an active area of investigation. Concurrently, Earth's magnetic field offers a signal that engineered systems can leverage for navigation in environments where man-made systems such as GPS are unavailable or unreliable. Using a proxy for Earth's magnetic field, and inspired by migratory animal behavior, this work implements a behavioral strategy that uses combinations of magnetic field properties as rare or unique signatures that mark specific locations. Using a discrete number of these signatures as goal waypoints, the strategy navigates through a closed set of points several times in a variety of environmental conditions, and with various levels of sensor noise. The results from this engineering/quantitative biology approach support existing notions that some animals may use combinations of magnetic properties as navigational markers, and provides insights into features and constraints that would enable navigational success or failure. The findings also offer insights into how autonomous engineered platforms might be designed to leverage the magnetic field as a navigational resource.

On the Security of a Novel Probabilistic Signature Based on Bilinear Square Diffie-Hellman Problem and Its Extension

PubMed Central

Zhao, Zhenguo; Shi, Wenbo

2014-01-01

Probabilistic signature scheme has been widely used in modern electronic commerce since it could provide integrity, authenticity, and nonrepudiation. Recently, Wu and Lin proposed a novel probabilistic signature (PS) scheme using the bilinear square Diffie-Hellman (BSDH) problem. They also extended it to a universal designated verifier signature (UDVS) scheme. In this paper, we analyze the security of Wu et al.'s PS scheme and UDVS scheme. Through concrete attacks, we demonstrate both of their schemes are not unforgeable. The security analysis shows that their schemes are not suitable for practical applications. PMID:25025083

Validation of a national hydrological model

NASA Astrophysics Data System (ADS)

McMillan, H. K.; Booker, D. J.; Cattoën, C.

2016-10-01

Nationwide predictions of flow time-series are valuable for development of policies relating to environmental flows, calculating reliability of supply to water users, or assessing risk of floods or droughts. This breadth of model utility is possible because various hydrological signatures can be derived from simulated flow time-series. However, producing national hydrological simulations can be challenging due to strong environmental diversity across catchments and a lack of data available to aid model parameterisation. A comprehensive and consistent suite of test procedures to quantify spatial and temporal patterns in performance across various parts of the hydrograph is described and applied to quantify the performance of an uncalibrated national rainfall-runoff model of New Zealand. Flow time-series observed at 485 gauging stations were used to calculate Nash-Sutcliffe efficiency and percent bias when simulating between-site differences in daily series, between-year differences in annual series, and between-site differences in hydrological signatures. The procedures were used to assess the benefit of applying a correction to the modelled flow duration curve based on an independent statistical analysis. They were used to aid understanding of climatological, hydrological and model-based causes of differences in predictive performance by assessing multiple hypotheses that describe where and when the model was expected to perform best. As the procedures produce quantitative measures of performance, they provide an objective basis for model assessment that could be applied when comparing observed daily flow series with competing simulated flow series from any region-wide or nationwide hydrological model. Model performance varied in space and time with better scores in larger and medium-wet catchments, and in catchments with smaller seasonal variations. Surprisingly, model performance was not sensitive to aquifer fraction or rain gauge density.

Inductive Approaches to Improving Diagnosis and Design for Diagnosability

NASA Technical Reports Server (NTRS)

Fisher, Douglas H. (Principal Investigator)

1995-01-01

The first research area under this grant addresses the problem of classifying time series according to their morphological features in the time domain. A supervised learning system called CALCHAS, which induces a classification procedure for signatures from preclassified examples, was developed. For each of several signature classes, the system infers a model that captures the class's morphological features using Bayesian model induction and the minimum message length approach to assign priors. After induction, a time series (signature) is classified in one of the classes when there is enough evidence to support that decision. Time series with sufficiently novel features, belonging to classes not present in the training set, are recognized as such. A second area of research assumes two sources of information about a system: a model or domain theory that encodes aspects of the system under study and data from actual system operations over time. A model, when it exists, represents strong prior expectations about how a system will perform. Our work with a diagnostic model of the RCS (Reaction Control System) of the Space Shuttle motivated the development of SIG, a system which combines information from a model (or domain theory) and data. As it tracks RCS behavior, the model computes quantitative and qualitative values. Induction is then performed over the data represented by both the 'raw' features and the model-computed high-level features. Finally, work on clustering for operating mode discovery motivated some important extensions to the clustering strategy we had used. One modification appends an iterative optimization technique onto the clustering system; this optimization strategy appears to be novel in the clustering literature. A second modification improves the noise tolerance of the clustering system. In particular, we adapt resampling-based pruning strategies used by supervised learning systems to the task of simplifying hierarchical clusterings, thus making post-clustering analysis easier.

Fault Diagnosis Strategies for SOFC-Based Power Generation Plants

PubMed Central

Costamagna, Paola; De Giorgi, Andrea; Gotelli, Alberto; Magistri, Loredana; Moser, Gabriele; Sciaccaluga, Emanuele; Trucco, Andrea

2016-01-01

The success of distributed power generation by plants based on solid oxide fuel cells (SOFCs) is hindered by reliability problems that can be mitigated through an effective fault detection and isolation (FDI) system. However, the numerous operating conditions under which such plants can operate and the random size of the possible faults make identifying damaged plant components starting from the physical variables measured in the plant very difficult. In this context, we assess two classical FDI strategies (model-based with fault signature matrix and data-driven with statistical classification) and the combination of them. For this assessment, a quantitative model of the SOFC-based plant, which is able to simulate regular and faulty conditions, is used. Moreover, a hybrid approach based on the random forest (RF) classification method is introduced to address the discrimination of regular and faulty situations due to its practical advantages. Working with a common dataset, the FDI performances obtained using the aforementioned strategies, with different sets of monitored variables, are observed and compared. We conclude that the hybrid FDI strategy, realized by combining a model-based scheme with a statistical classifier, outperforms the other strategies. In addition, the inclusion of two physical variables that should be measured inside the SOFCs can significantly improve the FDI performance, despite the actual difficulty in performing such measurements. PMID:27556472

Thermal Signature Measurements for Ammonium Nitrate/Fuel Mixtures by Laser Heating.

PubMed

Nazarian, Ashot; Presser, Cary

2016-01-10

Measurements were carried out to obtain thermal signatures of several ammonium nitrate/fuel (ANF) mixtures, using a laser-heating technique referred to as the laser-driven thermal reactor (LDTR). The mixtures were ammonium nitrate (AN)/kerosene, AN/ethylene glycol, AN/paraffin wax, AN/petroleum jelly, AN/confectioner's sugar, AN/cellulose (tissue paper), nitromethane/cellulose, nitrobenzene/cellulose, AN/cellulose/nitromethane, AN/cellulose/nitrobenzene. These mixtures were also compared with AN/nitromethane and AN/diesel fuel oil, obtained from an earlier investigation. Thermograms for the mixtures, as well as individual constituents, were compared to better understand how the sample thermal signature changes with mixture composition. This is the first step in development of a thermal-signature database, to be used along with other signature databases, to improve identification of energetic substances of unknown composition. The results indicated that each individual thermal signature was associated unambiguously with a particular mixture composition. The signature features of a particular mixture were shaped by the individual constituent signatures. It was also uncovered that the baseline signature was modified after an experiment due to coating of unreacted residue on the substrate surface and a change in the reactor sphere oxide layer. Thus, care was required to pre-oxidize the sphere prior to an experiment. A minimum sample mass (which was dependent on composition) was required to detect the signature characteristics. Increased laser power served to magnify signal strength while preserving the signature features. For the mixtures examined, the thermal response of each ANF mixture was found to be different, which was based on the mixture composition and the thermal behavior of each mixture constituent.

Multivariate Protein Signatures of Pre-Clinical Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Plasma Proteome Dataset

PubMed Central

Johnstone, Daniel; Milward, Elizabeth A.; Berretta, Regina; Moscato, Pablo

2012-01-01

Background Recent Alzheimer's disease (AD) research has focused on finding biomarkers to identify disease at the pre-clinical stage of mild cognitive impairment (MCI), allowing treatment to be initiated before irreversible damage occurs. Many studies have examined brain imaging or cerebrospinal fluid but there is also growing interest in blood biomarkers. The Alzheimer's Disease Neuroimaging Initiative (ADNI) has generated data on 190 plasma analytes in 566 individuals with MCI, AD or normal cognition. We conducted independent analyses of this dataset to identify plasma protein signatures predicting pre-clinical AD. Methods and Findings We focused on identifying signatures that discriminate cognitively normal controls (n = 54) from individuals with MCI who subsequently progress to AD (n = 163). Based on p value, apolipoprotein E (APOE) showed the strongest difference between these groups (p = 2.3×10−13). We applied a multivariate approach based on combinatorial optimization ((α,β)-k Feature Set Selection), which retains information about individual participants and maintains the context of interrelationships between different analytes, to identify the optimal set of analytes (signature) to discriminate these two groups. We identified 11-analyte signatures achieving values of sensitivity and specificity between 65% and 86% for both MCI and AD groups, depending on whether APOE was included and other factors. Classification accuracy was improved by considering “meta-features,” representing the difference in relative abundance of two analytes, with an 8-meta-feature signature consistently achieving sensitivity and specificity both over 85%. Generating signatures based on longitudinal rather than cross-sectional data further improved classification accuracy, returning sensitivities and specificities of approximately 90%. Conclusions Applying these novel analysis approaches to the powerful and well-characterized ADNI dataset has identified sets of plasma biomarkers for pre-clinical AD. While studies of independent test sets are required to validate the signatures, these analyses provide a starting point for developing a cost-effective and minimally invasive test capable of diagnosing AD in its pre-clinical stages. PMID:22485168

Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells.

PubMed

Mariappan, Devi; Winkler, Johannes; Chen, Shuhua; Schulz, Herbert; Hescheler, Jürgen; Sachinidis, Agapios

2009-02-01

Identification of genes involved in endothelial differentiation is of great interest for the understanding of the cellular and molecular mechanisms involved in the development of new blood vessels. Mouse embryonic stem (mES) cells serve as a potential source of endothelial cells for transcriptomic analysis. We isolated endothelial cells from 8-days old embryoid bodies by immuno-magnetic separation using platelet endothelial cell adhesion molecule-1 (also known as CD31) expressed on both early and mature endothelial cells. CD31(+) cells exhibit endothelial-like behavior by being able to incorporate DiI-labeled acetylated low-density lipoprotein as well as form tubular structures on matrigel. Quantitative and semi-quantitative PCR analysis further demonstrated the increased expression of endothelial transcripts. To ascertain the specific transcriptomic identity of the CD31(+) cells, large-scale microarray analysis was carried out. Comparative bioinformatic analysis reveals an enrichment of the gene ontology categories angiogenesis, blood vessel morphogenesis, vasculogenesis and blood coagulation in the CD31(+) cell population. Based on the transcriptomic signatures of the CD31(+) cells, we conclude that this ES cell-derived population contains endothelial-like cells expressing a mesodermal marker BMP2 and possess an angiogenic potential. The transcriptomic characterization of CD31(+) cells enables an in vitro functional genomic model to identify genes required for angiogenesis.

Secure Obfuscation for Encrypted Group Signatures

PubMed Central

Fan, Hongfei; Liu, Qin

2015-01-01

In recent years, group signature techniques are widely used in constructing privacy-preserving security schemes for various information systems. However, conventional techniques keep the schemes secure only in normal black-box attack contexts. In other words, these schemes suppose that (the implementation of) the group signature generation algorithm is running in a platform that is perfectly protected from various intrusions and attacks. As a complementary to existing studies, how to generate group signatures securely in a more austere security context, such as a white-box attack context, is studied in this paper. We use obfuscation as an approach to acquire a higher level of security. Concretely, we introduce a special group signature functionality-an encrypted group signature, and then provide an obfuscator for the proposed functionality. A series of new security notions for both the functionality and its obfuscator has been introduced. The most important one is the average-case secure virtual black-box property w.r.t. dependent oracles and restricted dependent oracles which captures the requirement of protecting the output of the proposed obfuscator against collision attacks from group members. The security notions fit for many other specialized obfuscators, such as obfuscators for identity-based signatures, threshold signatures and key-insulated signatures. Finally, the correctness and security of the proposed obfuscator have been proven. Thereby, the obfuscated encrypted group signature functionality can be applied to variants of privacy-preserving security schemes and enhance the security level of these schemes. PMID:26167686

RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.

PubMed

Auerbach, Scott S; Phadke, Dhiral P; Mav, Deepak; Holmgren, Stephanie; Gao, Yuan; Xie, Bin; Shin, Joo Heon; Shah, Ruchir R; Merrick, B Alex; Tice, Raymond R

2015-07-01

Formalin-fixed, paraffin-embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic-based biomarker discovery. We present here a comparison of results from a whole transcriptome RNA-Seq analysis of RNA extracted from fresh frozen and FFPE livers. The samples were derived from rats exposed to aflatoxin B1 (AFB1 ) and a corresponding set of control animals. Principal components analysis indicated that samples were separated in the two groups representing presence or absence of chemical exposure, both in fresh frozen and FFPE sample types. Sixty-five percent of the differentially expressed transcripts (AFB1 vs. controls) in fresh frozen samples were also differentially expressed in FFPE samples (overlap significance: P < 0.0001). Genomic signature and gene set analysis of AFB1 differentially expressed transcript lists indicated highly similar results between fresh frozen and FFPE at the level of chemogenomic signatures (i.e., single chemical/dose/duration elicited transcriptomic signatures), mechanistic and pathology signatures, biological processes, canonical pathways and transcription factor networks. Overall, our results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples. These results indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature-based biomarker discovery and mechanistic characterization of toxicity. Copyright © 2014 John Wiley & Sons, Ltd.

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

PubMed Central

Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel J; Turner, John P; Vidović, Dušica; Forlin, Michele; Kelley, Tanya T; D’Urso, Alessandro; Allen, Bryce K; Torre, Denis; Jagodnik, Kathleen M; Wang, Lily; Jenkins, Sherry L; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma’ayan, Avi; Pillai, Ajay

2018-01-01

Abstract The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content. PMID:29140462

In situ spectroradiometric quantification of ERTS data

NASA Technical Reports Server (NTRS)

Yost, E. (Principal Investigator)

1972-01-01

The author has identified the following significant results. Additive color photographic analysis of ERTS-1 multispectral imagery indicates that the presence of soil moisture in playas (desert dry lakes) can be readily detected from space. Time sequence additive color presentations in which 600-700 nm bands taken at three successive 18-day cycles show that changes in soil moisture of playas with time can be detected as unique color signatures and can probably be quantitatively measured using photographic images of multispectral scanner data.

Critical Point in Self-Organized Tissue Growth

NASA Astrophysics Data System (ADS)

Aguilar-Hidalgo, Daniel; Werner, Steffen; Wartlick, Ortrud; González-Gaitán, Marcos; Friedrich, Benjamin M.; Jülicher, Frank

2018-05-01

We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and advection. We identify a critical point of this feedback dynamics, which is characterized by spatially homogeneous growth and proportional scaling of patterns with tissue length. We apply this theory to the biological model system of the developing wing of the fruit fly Drosophila melanogaster and quantitatively identify signatures of the critical point.

Development of a flash, bang, and smoke simulation of a shell burst

NASA Technical Reports Server (NTRS)

Williamson, F. R.; Kinney, J. F.; Wallace, T. V.

1982-01-01

A large number of experiments (cue test firings) were performed in the definition of the cue concepts and packaging configurations. A total of 344 of these experiments were recorded with instrumentation photography to allow a quantitative analysis of the smoke cloud to be made as a function of time. These analyses were predominantly made using a short test site. Supplementary long range visibility tests were conducted to insure the required 3 kilometer visibility of the smoke signature.

Prediction of sonic boom from experimental near-field overpressure data. Volume 1: Method and results

NASA Technical Reports Server (NTRS)

Glatt, C. R.; Hague, D. S.; Reiners, S. J.

1975-01-01

A computerized procedure for predicting sonic boom from experimental near-field overpressure data has been developed. The procedure extrapolates near-field pressure signatures for a specified flight condition to the ground by the Thomas method. Near-field pressure signatures are interpolated from a data base of experimental pressure signatures. The program is an independently operated ODIN (Optimal Design Integration) program which obtains flight path information from other ODIN programs or from input.

On Entropy Trail

NASA Astrophysics Data System (ADS)

Farokhi, Saeed; Taghavi, Ray; Keshmiri, Shawn

2015-11-01

Stealth technology is developed for military aircraft to minimize their signatures. The primary attention was focused on radar signature, followed by the thermal and noise signatures of the vehicle. For radar evasion, advanced configuration designs, extensive use of carbon composites and radar-absorbing material, are developed. On thermal signature, mainly in the infra-red (IR) bandwidth, the solution was found in blended rectangular nozzles of high aspect ratio that are shielded from ground detectors. For noise, quiet and calm jets are integrated into vehicles with low-turbulence configuration design. However, these technologies are totally incapable of detecting new generation of revolutionary aircraft. These shall use all electric, distributed, propulsion system that are thermally transparent. In addition, composite skin and non-emitting sensors onboard the aircraft will lead to low signature. However, based on the second-law of thermodynamics, there is no air vehicle that can escape from leaving an entropy trail. Entropy is thus the only inevitable signature of any system, that once measured, can detect the source. By characterizing the entropy field based on its statistical properties, the source may be recognized, akin to face recognition technology. Direct measurement of entropy is cumbersome, however as a derived property, it can be easily measured. The measurement accuracy depends on the probe design and the sensors onboard. One novel air data sensor suite is introduced with promising potential to capture the entropy trail.

Generation of signature databases with fast codes

NASA Astrophysics Data System (ADS)

Bradford, Robert A.; Woodling, Arthur E.; Brazzell, James S.

1990-09-01

Using the FASTSIG signature code to generate optical signature databases for the Ground-based Surveillance and Traking System (GSTS) Program has improved the efficiency of the database generation process. The goal of the current GSTS database is to provide standardized, threat representative target signatures that can easily be used for acquisition and trk studies, discrimination algorithm development, and system simulations. Large databases, with as many as eight interpolalion parameters, are required to maintain the fidelity demands of discrimination and to generalize their application to other strateg systems. As the need increases for quick availability of long wave infrared (LWIR) target signatures for an evolving design4o-threat, FASTSIG has become a database generation alternative to using the industry standard OptiCal Signatures Code (OSC). FASTSIG, developed in 1985 to meet the unique strategic systems demands imposed by the discrimination function, has the significant advantage of being a faster running signature code than the OSC, typically requiring two percent of the cpu time. It uses analytical approximations to model axisymmetric targets, with the fidelity required for discrimination analysis. Access of the signature database is accomplished through use of the waveband integration and interpolation software, INTEG and SIGNAT. This paper gives details of this procedure as well as sample interpolated signatures and also covers sample verification by comparison to the OSC, in order to establish the fidelity of the FASTSIG generated database.

Post interaural neural net-based vowel recognition

NASA Astrophysics Data System (ADS)

Jouny, Ismail I.

2001-10-01

Interaural head related transfer functions are used to process speech signatures prior to neural net based recognition. Data representing the head related transfer function of a dummy has been collected at MIT and made available on the Internet. This data is used to pre-process vowel signatures to mimic the effects of human ear on speech perception. Signatures representing various vowels of the English language are then presented to a multi-layer perceptron trained using the back propagation algorithm for recognition purposes. The focus in this paper is to assess the effects of human interaural system on vowel recognition performance particularly when using a classification system that mimics the human brain such as a neural net.

Precision diagnostics: moving towards protein biomarker signatures of clinical utility in cancer.

PubMed

Borrebaeck, Carl A K

2017-03-01

Interest in precision diagnostics has been fuelled by the concept that early detection of cancer would benefit patients; that is, if detected early, more tumours should be resectable and treatment more efficacious. Serum contains massive amounts of potentially diagnostic information, and affinity proteomics has risen as an accurate approach to decipher this, to generate actionable information that should result in more precise and evidence-based options to manage cancer. To achieve this, we need to move from single to multiplex biomarkers, a so-called signature, that can provide significantly increased diagnostic accuracy. This Opinion article focuses on the progress being made in identifying protein biomarker signatures of clinical utility, using blood-based proteomics.

A Dynamic Time Warping based covariance function for Gaussian Processes signature identification

NASA Astrophysics Data System (ADS)

Silversides, Katherine L.; Melkumyan, Arman

2016-11-01

Modelling stratiform deposits requires a detailed knowledge of the stratigraphic boundaries. In Banded Iron Formation (BIF) hosted ores of the Hamersley Group in Western Australia these boundaries are often identified using marker shales. Both Gaussian Processes (GP) and Dynamic Time Warping (DTW) have been previously proposed as methods to automatically identify marker shales in natural gamma logs. However, each method has different advantages and disadvantages. We propose a DTW based covariance function for the GP that combines the flexibility of the DTW with the probabilistic framework of the GP. The three methods are tested and compared on their ability to identify two natural gamma signatures from a Marra Mamba type iron ore deposit. These tests show that while all three methods can identify boundaries, the GP with the DTW covariance function combines and balances the strengths and weaknesses of the individual methods. This method identifies more positive signatures than the GP with the standard covariance function, and has a higher accuracy for identified signatures than the DTW. The combined method can handle larger variations in the signature without requiring multiple libraries, has a probabilistic output and does not require manual cut-off selections.

Human relevance of an in vitro gene signature in HaCaT for skin sensitization.

PubMed

van der Veen, Jochem W; Hodemaekers, Henny; Reus, Astrid A; Maas, Wilfred J M; van Loveren, Henk; Ezendam, Janine

2015-02-01

The skin sensitizing potential of chemicals is mainly assessed using animal methods, such as the murine local lymph node assay. Recently, an in vitro assay based on a gene expression signature in the HaCaT keratinocyte cell line was proposed as an alternative to these animal methods. Here, the human relevance of this gene signature is assessed through exposure of freshly isolated human skin to the chemical allergens dinitrochlorobenzene (DNCB) and diphenylcyclopropenone (DCP). In human skin, the gene signature shows similar direction of regulation as was previously observed in vitro, suggesting that the molecular processes that drive expression of these genes are similar between the HaCaT cell line and freshly isolated skin, providing evidence for the human relevance of the gene signature. Copyright © 2014 Elsevier Ltd. All rights reserved.

Blind Quantum Signature with Blind Quantum Computation

NASA Astrophysics Data System (ADS)

Li, Wei; Shi, Ronghua; Guo, Ying

2017-04-01

Blind quantum computation allows a client without quantum abilities to interact with a quantum server to perform a unconditional secure computing protocol, while protecting client's privacy. Motivated by confidentiality of blind quantum computation, a blind quantum signature scheme is designed with laconic structure. Different from the traditional signature schemes, the signing and verifying operations are performed through measurement-based quantum computation. Inputs of blind quantum computation are securely controlled with multi-qubit entangled states. The unique signature of the transmitted message is generated by the signer without leaking information in imperfect channels. Whereas, the receiver can verify the validity of the signature using the quantum matching algorithm. The security is guaranteed by entanglement of quantum system for blind quantum computation. It provides a potential practical application for e-commerce in the cloud computing and first-generation quantum computation.

A small noncoding RNA signature found in exosomes of GBM patient serum as a diagnostic tool.

PubMed

Manterola, Lorea; Guruceaga, Elizabeth; Gállego Pérez-Larraya, Jaime; González-Huarriz, Marisol; Jauregui, Patricia; Tejada, Sonia; Diez-Valle, Ricardo; Segura, Victor; Samprón, Nicolás; Barrena, Cristina; Ruiz, Irune; Agirre, Amaia; Ayuso, Angel; Rodríguez, Javier; González, Alvaro; Xipell, Enric; Matheu, Ander; López de Munain, Adolfo; Tuñón, Teresa; Zazpe, Idoya; García-Foncillas, Jesús; Paris, Sophie; Delattre, Jean Yves; Alonso, Marta M

2014-04-01

Glioblastoma multiforme (GBM) is the most frequent malignant brain tumor in adults, and its prognosis remains dismal despite intensive research and therapeutic advances. Diagnostic biomarkers would be clinically meaningful to allow for early detection of the tumor and for those cases in which surgery is contraindicated or biopsy results are inconclusive. Recent findings show that GBM cells release microvesicles that contain a select subset of cellular proteins and RNA. The aim of this hypothesis-generating study was to assess the diagnostic potential of miRNAs found in microvesicles isolated from the serum of GBM patients. To control disease heterogeneity, we used patients with newly diagnosed GBM. In the discovery stage, PCR-based TaqMan Low Density Arrays followed by individual quantitative reverse transcriptase polymerase chain reaction were used to test the differences in the miRNA expression levels of serum microvesicles among 25 GBM patients and healthy controls paired by age and sex. The detected noncoding RNAs were then validated in another 50 GBM patients. We found that the expression levels of 1 small noncoding RNA (RNU6-1) and 2 microRNAs (miR-320 and miR-574-3p) were significantly associated with a GBM diagnosis. In addition, RNU6-1 was consistently an independent predictor of a GBM diagnosis. Altogether our results uncovered a small noncoding RNA signature in microvesicles isolated from GBM patient serum that could be used as a fast and reliable differential diagnostic biomarker.

Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle

PubMed Central

Kim, Eui-Soo; Cole, John B.; Huson, Heather; Wiggans, George R.; Van Tassell, Curtis P.; Crooker, Brian A.; Liu, George; Da, Yang; Sonstegard, Tad S.

2013-01-01

The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins. PMID:24348915

HOX and TALE signatures specify human stromal stem cell populations from different sources.

PubMed

Picchi, Jacopo; Trombi, Luisa; Spugnesi, Laura; Barachini, Serena; Maroni, Giorgia; Brodano, Giovanni Barbanti; Boriani, Stefano; Valtieri, Mauro; Petrini, Mario; Magli, Maria Cristina

2013-04-01

Human stromal stem cell populations reside in different tissues and anatomical sites, however a critical question related to their efficient use in regenerative medicine is whether they exhibit equivalent biological properties. Here, we compared cellular and molecular characteristics of stromal stem cells derived from the bone marrow, at different body sites (iliac crest, sternum, and vertebrae) and other tissues (dental pulp and colon). In particular, we investigated whether homeobox genes of the HOX and TALE subfamilies might provide suitable markers to identify distinct stromal cell populations, as HOX proteins control cell positional identity and, together with their co-factors TALE, are involved in orchestrating differentiation of adult tissues. Our results show that stromal populations from different sources, although immunophenotypically similar, display distinct HOX and TALE signatures, as well as different growth and differentiation abilities. Stromal stem cells from different tissues are characterized by specific HOX profiles, differing in the number and type of active genes, as well as in their level of expression. Conversely, bone marrow-derived cell populations can be essentially distinguished for the expression levels of specific HOX members, strongly suggesting that quantitative differences in HOX activity may be crucial. Taken together, our data indicate that the HOX and TALE profiles provide positional, embryological and hierarchical identity of human stromal stem cells. Furthermore, our data suggest that cell populations derived from different body sites may not represent equivalent cell sources for cell-based therapeutical strategies for regeneration and repair of specific tissues. Copyright © 2012 Wiley Periodicals, Inc.

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

PubMed

Tan, Jie; Huyck, Matthew; Hu, Dongbo; Zelaya, René A; Hogan, Deborah A; Greene, Casey S

2017-11-22

Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologically relevant gene sets, which are currently curated manually, limiting their availability and accuracy in many organisms without extensively curated resources. New feature learning approaches can now be paired with existing data collections to directly extract functional gene sets from big data. Here we introduce a method to identify perturbed processes. In contrast with methods that use curated gene sets, this approach uses signatures extracted from public expression data. We first extract expression signatures from public data using ADAGE, a neural network-based feature extraction approach. We next identify signatures that are differentially active under a given treatment. Our results demonstrate that these signatures represent biological processes that are perturbed by the experiment. Because these signatures are directly learned from data without supervision, they can identify uncurated or novel biological processes. We implemented ADAGE signature analysis for the bacterial pathogen Pseudomonas aeruginosa. For the convenience of different user groups, we implemented both an R package (ADAGEpath) and a web server ( http://adage.greenelab.com ) to run these analyses. Both are open-source to allow easy expansion to other organisms or signature generation methods. We applied ADAGE signature analysis to an example dataset in which wild-type and ∆anr mutant cells were grown as biofilms on the Cystic Fibrosis genotype bronchial epithelial cells. We mapped active signatures in the dataset to KEGG pathways and compared with pathways identified using GSEA. The two approaches generally return consistent results; however, ADAGE signature analysis also identified a signature that revealed the molecularly supported link between the MexT regulon and Anr. We designed ADAGE signature analysis to perform gene set analysis using data-defined functional gene signatures. This approach addresses an important gap for biologists studying non-traditional model organisms and those without extensive curated resources available. We built both an R package and web server to provide ADAGE signature analysis to the community.

The CoRoT target HD 49933: a possible seismic signature of heavy elements ionization in the deep convective zone

NASA Astrophysics Data System (ADS)

Brito, Ana; Lopes, Ilídio

2017-04-01

We use a seismic diagnostic, based on the derivative of the phase shift of the acoustic waves reflected by the surface, to probe the outer layers of the star HD 49933. This diagnostic is particularly sensitive to partial ionization processes occurring above the base of the convective zone. The regions of partial ionization of light elements, hydrogen and helium, have well-known seismological signatures. In this work, we detect a different seismic signature in the acoustic frequencies, which we showed to correspond to the location where the partial ionization of heavy elements occurs. The location of the corresponding acoustic glitch lies between the region of the second ionization of helium and the base of the convective zone, approximately 5 per cent below the surface of the stars.

Waveform design for detection of weapons based on signature exploitation

NASA Astrophysics Data System (ADS)

Ahmad, Fauzia; Amin, Moeness G.; Dogaru, Traian

2010-04-01

We present waveform design based on signature exploitation techniques for improved detection of weapons in urban sensing applications. A single-antenna monostatic radar system is considered. Under the assumption of exact knowledge of the target orientation and, hence, known impulse response, matched illumination approach is used for optimal target detection. For the case of unknown target orientation, we analyze the target signatures as random processes and perform signal-to-noise-ratio based waveform optimization. Numerical electromagnetic modeling is used to provide the impulse responses of an AK-47 assault rifle for various target aspect angles relative to the radar. Simulation results depict an improvement in the signal-to-noise-ratio at the output of the matched filter receiver for both matched illumination and stochastic waveforms as compared to a chirp waveform of the same duration and energy.

Prediction of Chemical Respiratory Sensitizers Using GARD, a Novel In Vitro Assay Based on a Genomic Biomarker Signature

PubMed Central

Albrekt, Ann-Sofie; Borrebaeck, Carl A. K.; Lindstedt, Malin

2015-01-01

Background Repeated exposure to certain low molecular weight (LMW) chemical compounds may result in development of allergic reactions in the skin or in the respiratory tract. In most cases, a certain LMW compound selectively sensitize the skin, giving rise to allergic contact dermatitis (ACD), or the respiratory tract, giving rise to occupational asthma (OA). To limit occurrence of allergic diseases, efforts are currently being made to develop predictive assays that accurately identify chemicals capable of inducing such reactions. However, while a few promising methods for prediction of skin sensitization have been described, to date no validated method, in vitro or in vivo, exists that is able to accurately classify chemicals as respiratory sensitizers. Results Recently, we presented the in vitro based Genomic Allergen Rapid Detection (GARD) assay as a novel testing strategy for classification of skin sensitizing chemicals based on measurement of a genomic biomarker signature. We have expanded the applicability domain of the GARD assay to classify also respiratory sensitizers by identifying a separate biomarker signature containing 389 differentially regulated genes for respiratory sensitizers in comparison to non-respiratory sensitizers. By using an independent data set in combination with supervised machine learning, we validated the assay, showing that the identified genomic biomarker is able to accurately classify respiratory sensitizers. Conclusions We have identified a genomic biomarker signature for classification of respiratory sensitizers. Combining this newly identified biomarker signature with our previously identified biomarker signature for classification of skin sensitizers, we have developed a novel in vitro testing strategy with a potent ability to predict both skin and respiratory sensitization in the same sample. PMID:25760038

Comparison of Neural Networks and Tabular Nearest Neighbor Encoding for Hyperspectral Signature Classification in Unresolved Object Detection

NASA Astrophysics Data System (ADS)

Schmalz, M.; Ritter, G.; Key, R.

Accurate and computationally efficient spectral signature classification is a crucial step in the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications using linear mixing models, signature classification accuracy depends on accurate spectral endmember discrimination [1]. If the endmembers cannot be classified correctly, then the signatures cannot be classified correctly, and object recognition from hyperspectral data will be inaccurate. In practice, the number of endmembers accurately classified often depends linearly on the number of inputs. This can lead to potentially severe classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an comparison of emerging technologies for nonimaging spectral signature classfication based on a highly accurate, efficient search engine called Tabular Nearest Neighbor Encoding (TNE) [3,4] and a neural network technology called Morphological Neural Networks (MNNs) [5]. Based on prior results, TNE can optimize its classifier performance to track input nonergodicities, as well as yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., the neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement algorithms. The open architecture and programmability of TNE's agreement map processing allows a TNE programmer or user to determine classification accuracy, as well as characterize in detail the signatures for which TNE did not obtain classification matches, and why such mis-matches occurred. In this study, we will compare TNE and MNN based endmember classification, using performance metrics such as probability of correct classification (Pd) and rate of false detections (Rfa). As proof of principle, we analyze classification of multiple closely spaced signatures from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to Bayesian techniques based on classical neural networks. [1] Winter, M.E. "Fast autonomous spectral end-member determination in hyperspectral data," in Proceedings of the 13th International Conference On Applied Geologic Remote Sensing, Vancouver, B.C., Canada, pp. 337-44 (1999). [2] N. Keshava, "A survey of spectral unmixing algorithms," Lincoln Laboratory Journal 14:55-78 (2003). [3] Key, G., M.S. SCHMALZ, F.M. Caimi, and G.X. Ritter. "Performance analysis of tabular nearest neighbor encoding algorithm for joint compression and ATR", in Proceedings SPIE 3814:115-126 (1999). [4] Schmalz, M.S. and G. Key. "Algorithms for hyperspectral signature classification in unresolved object detection using tabular nearest neighbor encoding" in Proceedings of the 2007 AMOS Conference, Maui HI (2007). [5] Ritter, G.X., G. Urcid, and M.S. Schmalz. "Autonomous single-pass endmember approximation using lattice auto-associative memories", Neurocomputing (Elsevier), accepted (June 2008).

Role of moisture and density of sand for microwave enhancement of thermal detection of buried mines

NASA Astrophysics Data System (ADS)

Swiderski, Waldemar; Hlosta, Pawel; Jarzemski, Jozef; Szugajew, Leszek; Usowicz, Jerzy

2012-06-01

The main disadvantage of applying the IRT method is presence of plenty false indications in thermograms. A simple use of IRT equipment with better temperature resolution would not help in distinguishing the mines, since noise comes not from a camera, but from soil surface. Recognizing the role of moisture and density of sand and possibilities to express it quantitatively plays an important role. In our model of thermal properties of the soil the volumetric unit of the soil consists of mineral and organic particles, as well as water and air. All needed parameters can be calculated. Calculations of thermal signatures of the underground objects were made basing on 3D-heat equation for the sinus type heating of 3D model and cooling by convection. Measurements were made for field and laboratory stand-ups, using methodologies typical for "single-shot" measurements as well as analyses of transient processes based on sequence of thermograms. Results of simulations and measurements confirm expectation tha that high level of "radiant noises" is caused mainly by differences in the moisture and sand density levels.

Temporal complexity in emission from Anderson localized lasers

NASA Astrophysics Data System (ADS)

Kumar, Randhir; Balasubrahmaniyam, M.; Alee, K. Shadak; Mujumdar, Sushil

2017-12-01

Anderson localization lasers exploit resonant cavities formed due to structural disorder. The inherent randomness in the structure of these cavities realizes a probability distribution in all cavity parameters such as quality factors, mode volumes, mode structures, and so on, implying resultant statistical fluctuations in the temporal behavior. Here we provide direct experimental measurements of temporal width distributions of Anderson localization lasing pulses in intrinsically and extrinsically disordered coupled-microresonator arrays. We first illustrate signature exponential decays in the spatial intensity distributions of the lasing modes that quantify their localized character, and then measure the temporal width distributions of the pulsed emission over several configurations. We observe a dependence of temporal widths on the disorder strength, wherein the widths show a single-peaked, left-skewed distribution in extrinsic disorder and a dual-peaked distribution in intrinsic disorder. We propose a model based on coupled rate equations for an emitter and an Anderson cavity with a random mode structure, which gives excellent quantitative and qualitative agreement with the experimental observations. The experimental and theoretical analyses bring to the fore the temporal complexity in Anderson-localization-based lasing systems.

Comparisons of Robustness and Sensitivity between Cancer and Normal Cells by Microarray Data

PubMed Central

Chu, Liang-Hui; Chen, Bor-Sen

2008-01-01

Robustness is defined as the ability to uphold performance in face of perturbations and uncertainties, and sensitivity is a measure of the system deviations generated by perturbations to the system. While cancer appears as a robust but fragile system, few computational and quantitative evidences demonstrate robustness tradeoffs in cancer. Microarrays have been widely applied to decipher gene expression signatures in human cancer research, and quantification of global gene expression profiles facilitates precise prediction and modeling of cancer in systems biology. We provide several efficient computational methods based on system and control theory to compare robustness and sensitivity between cancer and normal cells by microarray data. Measurement of robustness and sensitivity by linear stochastic model is introduced in this study, which shows oscillations in feedback loops of p53 and demonstrates robustness tradeoffs that cancer is a robust system with some extreme fragilities. In addition, we measure sensitivity of gene expression to perturbations in other gene expression and kinetic parameters, discuss nonlinear effects in feedback loops of p53 and extend our method to robustness-based cancer drug design. PMID:19259409

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

PubMed Central

Bray, Mark-Anthony; Singh, Shantanu; Han, Han; Davis, Chadwick T.; Borgeson, Blake; Hartland, Cathy; Kost-Alimova, Maria; Gustafsdottir, Sigrun M.; Gibson, Christopher C.; Carpenter, Anne E.

2016-01-01

In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, a morphological profiling assay multiplexing six fluorescent dyes imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Cells are plated in multi-well plates, perturbed with the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Then, automated image analysis software identifies individual cells and measures ~1,500 morphological features (various measures of size, shape, texture, intensity, etc.) to produce a rich profile suitable for detecting subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes two weeks; feature extraction and data analysis take an additional 1-2 weeks. PMID:27560178

Note onset deviations as musical piece signatures.

PubMed

Serrà, Joan; Özaslan, Tan Hakan; Arcos, Josep Lluis

2013-01-01

A competent interpretation of a musical composition presents several non-explicit departures from the written score. Timing variations are perhaps the most important ones: they are fundamental for expressive performance and a key ingredient for conferring a human-like quality to machine-based music renditions. However, the nature of such variations is still an open research question, with diverse theories that indicate a multi-dimensional phenomenon. In the present study, we consider event-shift timing variations and show that sequences of note onset deviations are robust and reliable predictors of the musical piece being played, irrespective of the performer. In fact, our results suggest that only a few consecutive onset deviations are already enough to identify a musical composition with statistically significant accuracy. We consider a mid-size collection of commercial recordings of classical guitar pieces and follow a quantitative approach based on the combination of standard statistical tools and machine learning techniques with the semi-automatic estimation of onset deviations. Besides the reported results, we believe that the considered materials and the methodology followed widen the testing ground for studying musical timing and could open new perspectives in related research fields.

Grouping of Petroleum Substances as Example UVCBs by Ion Mobility-Mass Spectrometry to Enable Chemical Composition-Based Read-Across.

PubMed

Grimm, Fabian A; Russell, William K; Luo, Yu-Syuan; Iwata, Yasuhiro; Chiu, Weihsueh A; Roy, Tim; Boogaard, Peter J; Ketelslegers, Hans B; Rusyn, Ivan

2017-06-20

Substances of Unknown or Variable composition, Complex reaction products, and Biological materials (UVCBs), including many refined petroleum products, present a major challenge in regulatory submissions under the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) and US High Production Volume regulatory regimes. The inherent complexity of these substances, as well as variability in composition obfuscates detailed chemical characterization of each individual substance and their grouping for human and environmental health evaluation through read-across. In this study, we applied ion mobility mass spectrometry in conjunction with cheminformatics-based data integration and visualization to derive substance-specific signatures based on the distribution and abundance of various heteroatom classes. We used petroleum substances from four petroleum substance manufacturing streams and evaluated their chemical composition similarity based on high-dimensional substance-specific quantitative parameters including m/z distribution, drift time, carbon number range, and associated double bond equivalents and hydrogen-to-carbon ratios. Data integration and visualization revealed group-specific similarities for petroleum substances. Observed differences within a product group were indicative of batch- or manufacturer-dependent variation. We demonstrate how high-resolution analytical chemistry approaches can be used effectively to support categorization of UVCBs based on their heteroatom composition and how such data can be used in regulatory decision-making.

Motion-compensated optical coherence tomography using envelope-based surface detection and Kalman-based prediction

NASA Astrophysics Data System (ADS)

Irsch, Kristina; Lee, Soohyun; Bose, Sanjukta N.; Kang, Jin U.

2018-02-01

We present an optical coherence tomography (OCT) imaging system that effectively compensates unwanted axial motion with micron-scale accuracy. The OCT system is based on a swept-source (SS) engine (1060-nm center wavelength, 100-nm full-width sweeping bandwidth, and 100-kHz repetition rate), with axial and lateral resolutions of about 4.5 and 8.5 microns respectively. The SS-OCT system incorporates a distance sensing method utilizing an envelope-based surface detection algorithm. The algorithm locates the target surface from the B-scans, taking into account not just the first or highest peak but the entire signature of sequential A-scans. Subsequently, a Kalman filter is applied as predictor to make up for system latencies, before sending the calculated position information to control a linear motor, adjusting and maintaining a fixed system-target distance. To test system performance, the motioncorrection algorithm was compared to earlier, more basic peak-based surface detection methods and to performing no motion compensation. Results demonstrate increased robustness and reproducibility, particularly noticeable in multilayered tissues, while utilizing the novel technique. Implementing such motion compensation into clinical OCT systems may thus improve the reliability of objective and quantitative information that can be extracted from OCT measurements.

On the Eigenstrain Application of Shot-Peened Residual Stresses Within a Crystal Plasticity Framework: Application to Ni-Base Superalloy Specimens (Postprint)

DTIC Science & Technology

2016-01-06

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Thermal Signature Measurements for Ammonium Nitrate/Fuel Mixtures by Laser Heating

PubMed Central

Nazarian, Ashot; Presser, Cary

2016-01-01

Measurements were carried out to obtain thermal signatures of several ammonium nitrate/fuel (ANF) mixtures, using a laser-heating technique referred to as the laser-driven thermal reactor (LDTR). The mixtures were ammonium nitrate (AN)/kerosene, AN/ethylene glycol, AN/paraffin wax, AN/petroleum jelly, AN/confectioner’s sugar, AN/cellulose (tissue paper), nitromethane/cellulose, nitrobenzene/cellulose, AN/cellulose/nitromethane, AN/cellulose/nitrobenzene. These mixtures were also compared with AN/nitromethane and AN/diesel fuel oil, obtained from an earlier investigation. Thermograms for the mixtures, as well as individual constituents, were compared to better understand how the sample thermal signature changes with mixture composition. This is the first step in development of a thermal-signature database, to be used along with other signature databases, to improve identification of energetic substances of unknown composition. The results indicated that each individual thermal signature was associated unambiguously with a particular mixture composition. The signature features of a particular mixture were shaped by the individual constituent signatures. It was also uncovered that the baseline signature was modified after an experiment due to coating of unreacted residue on the substrate surface and a change in the reactor sphere oxide layer. Thus, care was required to pre-oxidize the sphere prior to an experiment. A minimum sample mass (which was dependent on composition) was required to detect the signature characteristics. Increased laser power served to magnify signal strength while preserving the signature features. For the mixtures examined, the thermal response of each ANF mixture was found to be different, which was based on the mixture composition and the thermal behavior of each mixture constituent. PMID:26955190

A sessional blind signature based on quantum cryptography

NASA Astrophysics Data System (ADS)

Khodambashi, Siavash; Zakerolhosseini, Ali

2014-01-01

In this paper, we present a sessional blind signature protocol whose security is guaranteed by fundamental principles of quantum physics. It allows a message owner to get his message signed by an authorized signatory. However, the signatory is not capable of reading the message contents and everyone can verify authenticity of the message. For this purpose, we took advantage of a sessional signature as well as quantum entangled pairs which are generated with respect to it in our proposed protocol. We describe our proposed blind signature through an example and briefly discuss about its unconditional security. Due to the feasibility of the protocol, it can be widely employed for e-payment, e-government, e-business and etc.

Security of the arbitrated quantum signature protocols revisited

NASA Astrophysics Data System (ADS)

Kejia, Zhang; Dan, Li; Qi, Su

2014-01-01

Recently, much attention has been paid to the study of arbitrated quantum signature (AQS). Among these studies, the cryptanalysis of some AQS protocols and a series of improved ideas have been proposed. Compared with the previous analysis, we present a security criterion, which can judge whether an AQS protocol is able to prevent the receiver (i.e. one participant in the signature protocol) from forging a legal signature. According to our results, it can be seen that most AQS protocols which are based on the Zeng and Keitel (ZK) model are susceptible to a forgery attack. Furthermore, we present an improved idea of the ZK protocol. Finally, some supplement discussions and several interesting topics are provided.

Practical quantum digital signature

NASA Astrophysics Data System (ADS)

Yin, Hua-Lei; Fu, Yao; Chen, Zeng-Bing

2016-03-01

Guaranteeing nonrepudiation, unforgeability as well as transferability of a signature is one of the most vital safeguards in today's e-commerce era. Based on fundamental laws of quantum physics, quantum digital signature (QDS) aims to provide information-theoretic security for this cryptographic task. However, up to date, the previously proposed QDS protocols are impractical due to various challenging problems and most importantly, the requirement of authenticated (secure) quantum channels between participants. Here, we present the first quantum digital signature protocol that removes the assumption of authenticated quantum channels while remaining secure against the collective attacks. Besides, our QDS protocol can be practically implemented over more than 100 km under current mature technology as used in quantum key distribution.

Identification of Mature Atherosclerotic Plaque Proteome Signatures Using Data-Independent Acquisition Mass Spectrometry.

PubMed

Hansmeier, Nicole; Buttigieg, Josef; Kumar, Pankaj; Pelle, Shaneen; Choi, Kyoo Yoon; Kopriva, David; Chao, Tzu-Chiao

2018-01-05

Atherosclerosis is a chronic inflammatory disease with complex pathobiology and one of the most common causes of cardiovascular events. The process is characterized by complex vascular remodeling processes that require the actions of numerous proteins. The composition of atherosclerotic plaque is increasingly recognized as a major factor governing the occurrence of cardiovascular or neurological symptoms. To gain deeper insights into the composition of atherosclerotic plaques, we created quantitative proteome profiles of advanced plaque tissues of six male patients undergoing carotid endarterectomy for stroke prevention. Using a quantitative, data-independent proteome approach, we identified 4181 proteins with an average protein coverage of 45%. An analysis of the quantitative composition of the tissue revealed key players of vascular remodeling processes. Moreover, compared with proximal arterial tissue, 20 proteins in mature plaques were enriched, whereas 52 proteins were found in lower quantities. Among the proteins with increased abundance were prominent extracellular matrix proteins such as biglycan and lumican, whereas cytoskeletal markers for contractile smooth muscle cells (SMCs) were decreased. Taken together, this study provides the most comprehensive quantitative assessment of mature human plaque tissue to date, which indicates a central role of SMCs in the structure of advanced atherosclerotic plaques.

Quantitative radiomic profiling of glioblastoma represents transcriptomic expression.

PubMed

Kong, Doo-Sik; Kim, Junhyung; Ryu, Gyuha; You, Hye-Jin; Sung, Joon Kyung; Han, Yong Hee; Shin, Hye-Mi; Lee, In-Hee; Kim, Sung-Tae; Park, Chul-Kee; Choi, Seung Hong; Choi, Jeong Won; Seol, Ho Jun; Lee, Jung-Il; Nam, Do-Hyun

2018-01-19

Quantitative imaging biomarkers have increasingly emerged in the field of research utilizing available imaging modalities. We aimed to identify good surrogate radiomic features that can represent genetic changes of tumors, thereby establishing noninvasive means for predicting treatment outcome. From May 2012 to June 2014, we retrospectively identified 65 patients with treatment-naïve glioblastoma with available clinical information from the Samsung Medical Center data registry. Preoperative MR imaging data were obtained for all 65 patients with primary glioblastoma. A total of 82 imaging features including first-order statistics, volume, and size features, were semi-automatically extracted from structural and physiologic images such as apparent diffusion coefficient and perfusion images. Using commercially available software, NordicICE, we performed quantitative imaging analysis and collected the dataset composed of radiophenotypic parameters. Unsupervised clustering methods revealed that the radiophenotypic dataset was composed of three clusters. Each cluster represented a distinct molecular classification of glioblastoma; classical type, proneural and neural types, and mesenchymal type. These clusters also reflected differential clinical outcomes. We found that extracted imaging signatures does not represent copy number variation and somatic mutation. Quantitative radiomic features provide a potential evidence to predict molecular phenotype and treatment outcome. Radiomic profiles represents transcriptomic phenotypes more well.

Constrained energy minimization applied to apparent reflectance and single-scattering albedo spectra: a comparison

NASA Astrophysics Data System (ADS)

Resmini, Ronald G.; Graver, William R.; Kappus, Mary E.; Anderson, Mark E.

1996-11-01

Constrained energy minimization (CEM) has been applied to the mapping of the quantitative areal distribution of the mineral alunite in an approximately 1.8 km2 area of the Cuprite mining district, Nevada. CEM is a powerful technique for rapid quantitative mineral mapping which requires only the spectrum of the mineral to be mapped. A priori knowledge of background spectral signatures is not required. Our investigation applies CEM to calibrated radiance data converted to apparent reflectance (AR) and to single scattering albedo (SSA) spectra. The radiance data were acquired by the 210 channel, 0.4 micrometers to 2.5 micrometers airborne Hyperspectral Digital Imagery Collection Experiment sensor. CEM applied to AR spectra assumes linear mixing of the spectra of the materials exposed at the surface. This assumption is likely invalid as surface materials, which are often mixtures of particulates of different substances, are more properly modeled as intimate mixtures and thus spectral mixing analyses must take account of nonlinear effects. One technique for approximating nonlinear mixing requires the conversion of AR spectra to SSA spectra. The results of CEM applied to SSA spectra are compared to those of CEM applied to AR spectra. The occurrence of alunite is similar though not identical to mineral maps produced with both the SSA and AR spectra. Alunite is slightly more widespread based on processing with the SSA spectra. Further, fractional abundances derived from the SSA spectra are, in general, higher than those derived from AR spectra. Implications for the interpretation of quantitative mineral mapping with hyperspectral remote sensing data are discussed.

Identification of gene expression signature for cigarette smoke exposure response--from man to mouse.

PubMed

Martin, F; Talikka, M; Hoeng, J; Peitsch, M C

2015-12-01

Gene expression profiling data can be used in toxicology to assess both the level and impact of toxicant exposure, aligned with a vision of 21st century toxicology. Here, we present a whole blood-derived gene signature that can distinguish current smokers from either nonsmokers or former smokers with high specificity and sensitivity. Such a signature that can be measured in a surrogate tissue (whole blood) may help in monitoring smoking exposure as well as discontinuation of exposure when the primarily impacted tissue (e.g., lung) is not readily accessible. The signature consisted of LRRN3, SASH1, PALLD, RGL1, TNFRSF17, CDKN1C, IGJ, RRM2, ID3, SERPING1, and FUCA1. Several members of this signature have been previously described in the context of smoking. The signature translated well across species and could distinguish mice that were exposed to cigarette smoke from ones exposed to air only or had been withdrawn from cigarette smoke exposure. Finally, the small signature of only 11 genes could be converted into a polymerase chain reaction-based assay that could serve as a marker to monitor compliance with a smoking abstinence protocol. © The Author(s) 2015.

Ground-based microwave radar and optical lidar signatures of volcanic ash plumes: models, observations and retrievals

NASA Astrophysics Data System (ADS)

Mereu, Luigi; Marzano, Frank; Mori, Saverio; Montopoli, Mario; Cimini, Domenico; Martucci, Giovanni

2013-04-01

The detection and quantitative retrieval of volcanic ash clouds is of significant interest due to its environmental, climatic and socio-economic effects. Real-time monitoring of such phenomena is crucial, also for the initialization of dispersion models. Satellite visible-infrared radiometric observations from geostationary platforms are usually exploited for long-range trajectory tracking and for measuring low level eruptions. Their imagery is available every 15-30 minutes and suffers from a relatively poor spatial resolution. Moreover, the field-of-view of geostationary radiometric measurements may be blocked by water and ice clouds at higher levels and their overall utility is reduced at night. Ground-based microwave radars may represent an important tool to detect and, to a certain extent, mitigate the hazard from the ash clouds. Ground-based weather radar systems can provide data for determining the ash volume, total mass and height of eruption clouds. Methodological studies have recently investigated the possibility of using ground-based single-polarization and dual-polarization radar system for the remote sensing of volcanic ash cloud. A microphysical characterization of volcanic ash was carried out in terms of dielectric properties, size distribution and terminal fall speed, assuming spherically-shaped particles. A prototype of volcanic ash radar retrieval (VARR) algorithm for single-polarization systems was proposed and applied to S-band and C-band weather radar data. The sensitivity of the ground-based radar measurements decreases as the ash cloud is farther so that for distances greater than about 50 kilometers fine ash might be not detected anymore by microwave radars. In this respect, radar observations can be complementary to satellite, lidar and aircraft observations. Active remote sensing retrieval from ground, in terms of detection, estimation and sensitivity, of volcanic ash plumes is not only dependent on the sensor specifications, but also on the range and ash cloud distribution. The minimum detectable signal can be increased, for a given system and ash plume scenario, by decreasing the observation range and increasing the operational frequency using a multi-sensor approach, but also exploiting possible polarimetric capabilities. In particular, multi-wavelengths lidars can be complementary systems useful to integrate radar-based ash particle measurement. This work, starting from the results of a previous study and from above mentioned issues, is aimed at quantitatively assessing the optimal choices for microwave and millimeter-wave radar systems with a dual-polarization capability for real-time ash cloud remote sensing to be used in combination with an optical lidar. The physical-electromagnetic model of ash particle distributions is systematically reviewed and extended to include non-spherical particle shapes, vesicular composition, silicate content and orientation phenomena. The radar and lidar scattering and absorption response is simulated and analyzed in terms of self-consistent polarimetric signatures for ash classification purposes and correlation with ash concentration and mean diameter for quantitative retrieval aims. A sensitivity analysis to ash concentration, as a function of sensor specifications, range and ash category, is carried out trying to assess the expected multi-sensor multi-spectral system performances and limitations. The multi-sensor multi-wavelength polarimetric model-based approach can be used within a particle classification and estimation scheme, based on the VARR Bayesian metrics. As an application, the ground-based observation of the Eyjafjallajökull volcanic ash plume on 15-16 May 2010, carried out at the Atmospheric Research Station at Mace Head, Carna (Ireland) with MIRA36 35-GHz Ka-Band Doppler cloud radar and CHM15K lidar/ceilometer at 1064-nm wavelength, has been considered. Results are discussed in terms of retrievals and intercomparison with other ground-based and satellite-based sensors.

Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas: Mutational signature associated with MUTYH deficiency in cancers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilati, Camilla; Shinde, Jayendra; Alexandrov, Ludmil B.

Germline alterations in DNA repair genes are implicated in cancer predisposition and can result in characteristic mutational signatures. However, specific mutational signatures associated with base excision repair (BER) defects remain to be characterized. Here, by analysing a series of colorectal cancers (CRCs) using exome sequencing, we identified a particular spectrum of somatic mutations characterized by an enrichment of C > A transversions in NpCpA or NpCpT contexts in three tumours from a MUTYH-associated polyposis (MAP) patient and in two cases harbouring pathogenic germline MUTYH mutations. In two series of adrenocortical carcinomas (ACCs), we identified four tumours with a similar signaturemore » also presenting germline MUTYH mutations. Altogether, these findings demonstrate that MUTYH inactivation results in a particular mutational signature, which may serve as a useful marker of BER-related genomic instability in new cancer types.« less

Mutational signature analysis identifies MUTYH deficiency in colorectal cancers and adrenocortical carcinomas: Mutational signature associated with MUTYH deficiency in cancers

DOE PAGES

Pilati, Camilla; Shinde, Jayendra; Alexandrov, Ludmil B.; ...

2017-03-29

Germline alterations in DNA repair genes are implicated in cancer predisposition and can result in characteristic mutational signatures. However, specific mutational signatures associated with base excision repair (BER) defects remain to be characterized. Here, by analysing a series of colorectal cancers (CRCs) using exome sequencing, we identified a particular spectrum of somatic mutations characterized by an enrichment of C > A transversions in NpCpA or NpCpT contexts in three tumours from a MUTYH-associated polyposis (MAP) patient and in two cases harbouring pathogenic germline MUTYH mutations. In two series of adrenocortical carcinomas (ACCs), we identified four tumours with a similar signaturemore » also presenting germline MUTYH mutations. Altogether, these findings demonstrate that MUTYH inactivation results in a particular mutational signature, which may serve as a useful marker of BER-related genomic instability in new cancer types.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verma, Kuldeep; Lund, Mikkel N.; Aguirre, Víctor Silva

Acoustic glitches are regions inside a star where the sound speed or its derivatives change abruptly. These leave a small characteristic oscillatory signature in the stellar oscillation frequencies. With the precision achieved by Kepler seismic data, it is now possible to extract these small amplitude oscillatory signatures, and infer the locations of the glitches. We perform glitch analysis for all the 66 stars in the Kepler seismic LEGACY sample to derive the locations of the base of the envelope convection zone (CZ) and the helium ionization zone. The signature from helium ionization zone is found to be robust for allmore » stars in the sample, whereas the CZ signature is found to be weak and problematic, particularly for relatively massive stars with large errorbars on the oscillation frequencies. We demonstrate that the helium glitch signature can be used to constrain the properties of the helium ionization layers and the helium abundance.« less

A feature based comparison of pen and swipe based signature characteristics.

PubMed

Robertson, Joshua; Guest, Richard

2015-10-01

Dynamic Signature Verification (DSV) is a biometric modality that identifies anatomical and behavioral characteristics when an individual signs their name. Conventionally signature data has been captured using pen/tablet apparatus. However, the use of other devices such as the touch-screen tablets has expanded in recent years affording the possibility of assessing biometric interaction on this new technology. To explore the potential of employing DSV techniques when a user signs or swipes with their finger, we report a study to correlate pen and finger generated features. Investigating the stability and correlation between a set of characteristic features recorded in participant's signatures and touch-based swipe gestures, a statistical analysis was conducted to assess consistency between capture scenarios. The results indicate that there is a range of static and dynamic features such as the rate of jerk, size, duration and the distance the pen traveled that can lead to interoperability between these two systems for input methods for use within a potential biometric context. It can be concluded that this data indicates that a general principle is that the same underlying constructional mechanisms are evident. Copyright © 2015 Elsevier B.V. All rights reserved.

Screening for angiogenic inhibitors in zebrafish to evaluate a predictive model for developmental vascular toxicity.

PubMed

Tal, Tamara; Kilty, Claire; Smith, Andrew; LaLone, Carlie; Kennedy, Brendán; Tennant, Alan; McCollum, Catherine W; Bondesson, Maria; Knudsen, Thomas; Padilla, Stephanie; Kleinstreuer, Nicole

2017-06-01

Chemically-induced vascular toxicity during embryonic development may cause a wide range of adverse effects. To identify putative vascular disrupting chemicals (pVDCs), a predictive pVDC signature was constructed from 124 U.S. EPA ToxCast high-throughput screening (HTS) assays and used to rank 1060 chemicals for their potential to disrupt vascular development. Thirty-seven compounds were selected for targeted testing in transgenic Tg(kdrl:EGFP) and Tg(fli1:EGFP) zebrafish embryos to identify chemicals that impair developmental angiogenesis. We hypothesized that zebrafish angiogenesis toxicity data would correlate with human cell-based and cell-free in vitro HTS ToxCast data. Univariate statistical associations used to filter HTS data based on correlations with zebrafish angiogenic inhibition in vivo revealed 132 total significant associations, 33 of which were already captured in the pVDC signature, and 689 non-significant assay associations. Correlated assays were enriched in cytokine and extracellular matrix pathways. Taken together, the findings indicate the utility of zebrafish assays to evaluate an HTS-based predictive toxicity signature and also provide an experimental basis for expansion of the pVDC signature with novel HTS assays. Published by Elsevier Inc.

Raman spectral signatures of cervical exfoliated cells from liquid-based cytology samples

NASA Astrophysics Data System (ADS)

Kearney, Padraig; Traynor, Damien; Bonnier, Franck; Lyng, Fiona M.; O'Leary, John J.; Martin, Cara M.

2017-10-01

It is widely accepted that cervical screening has significantly reduced the incidence of cervical cancer worldwide. The primary screening test for cervical cancer is the Papanicolaou (Pap) test, which has extremely variable specificity and sensitivity. There is an unmet clinical need for methods to aid clinicians in the early detection of cervical precancer. Raman spectroscopy is a label-free objective method that can provide a biochemical fingerprint of a given sample. Compared with studies on infrared spectroscopy, relatively few Raman spectroscopy studies have been carried out to date on cervical cytology. The aim of this study was to define the Raman spectral signatures of cervical exfoliated cells present in liquid-based cytology Pap test specimens and to compare the signature of high-grade dysplastic cells to each of the normal cell types. Raman spectra were recorded from single exfoliated cells and subjected to multivariate statistical analysis. The study demonstrated that Raman spectroscopy can identify biochemical signatures associated with the most common cell types seen in liquid-based cytology samples; superficial, intermediate, and parabasal cells. In addition, biochemical changes associated with high-grade dysplasia could be identified suggesting that Raman spectroscopy could be used to aid current cervical screening tests.

Quantitative characterization of crude oils and fuels in mineral substrates using reflectance spectroscopy: Implications for remote sensing

NASA Astrophysics Data System (ADS)

Scafutto, Rebecca Del'Papa Moreira; Souza Filho, Carlos Roberto de

2016-08-01

The near and shortwave infrared spectral reflectance properties of several mineral substrates impregnated with crude oils (°APIs 19.2, 27.5 and 43.2), diesel, gasoline and ethanol were measured and assembled in a spectral library. These data were examined using Principal Component Analysis (PCA) and Partial Least Squares (PLS) Regression. Unique and characteristic absorption features were identified in the mixtures, besides variations of the spectral signatures related to the compositional difference of the crude oils and fuels. These features were used for qualitative and quantitative determination of the contaminant impregnated in the substrates. Specific wavelengths, where key absorption bands occur, were used for the individual characterization of oils and fuels. The intensity of these features can be correlated to the abundance of the contaminant in the mixtures. Grain size and composition of the impregnated substrate directly influence the variation of the spectral signatures. PCA models applied to the spectral library proved able to differentiate the type and density of the hydrocarbons. The calibration models generated by PLS are robust, of high quality and can also be used to predict the concentration of oils and fuels in mixtures with mineral substrates. Such data and models are employable as a reference for classifying unknown samples of contaminated substrates. The results of this study have important implications for onshore exploration and environmental monitoring of oil and fuels leaks using proximal and far range multispectral, hyperspectral and ultraespectral remote sensing.

Predictions of runoff signatures in ungauged basins: Austrian case study

NASA Astrophysics Data System (ADS)

Viglione, A.; Parajka, J.; Salinas, J.; Rogger, M.; Sivapalan, M.; Bloeschl, G.

2012-12-01

Runoff variability can be broken up into several components, each of them meaningful of a certain class of applications of societal relevance: annual runoff, seasonal runoff, flow duration curve, low flows, floods and hydrographs. We call them runoff signatures and we view them as a manifestation of catchment functioning at different time scales, as emergent properties of the complex systems that catchments are. Just as a medical doctor has many different options for studying the state and functioning of a patient, we can infer the state and functioning of a catchment observing its runoff signatures. But what can we do in the absence of runoff data? This study aims to understand how well one can predict runoff signatures in ungauged catchments. The comparison across signatures is based on one consistent data set (Austria) and one regionalisation method (Top-Kriging) in order to explore the relative performance of the predictions of each of the signatures. Results indicate that the performance, assessed by cross-validation, is best for annual and seasonal runoff, it degrades as one moves to low flows and floods and goes up again to high values for runoff hydrographs. Also, dedicated regionalisation methods, i.e. focusing on particular signatures and their characteristics, provide better predictions of the signatures than regionalisation of the entire hydrograph. These results suggest that the use of signatures in the calibration or assessment of process models can be valuable, in that this can lead to models predicting runoff correctly for the right reasons.

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

PubMed Central

Dephoure, Noah; Hwang, Sunyoung; O'Sullivan, Ciara; Dodgson, Stacie E; Gygi, Steven P; Amon, Angelika; Torres, Eduardo M

2014-01-01

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms. DOI: http://dx.doi.org/10.7554/eLife.03023.001 PMID:25073701

Symbiodinium Clade Affects Coral Skeletal Isotopic Ratio

NASA Astrophysics Data System (ADS)

Carilli, J.; Charles, C. D.; Garren, M.; McField, M.; Norris, R. D.

2011-12-01

The influence of different physiologies of Symbiodinium dinoflagellate symbiont clades on the skeletal chemistry of associated coral hosts has not previously been investigated. This is an important issue because coral skeletons are routinely used for tropical paleoclimatic reconstructions. We analyzed coral skeletal samples collected simultaneously from neighboring colonies off Belize and found that those harboring different clades of Symbiodinium displayed significantly different skeletal oxygen isotopic compositions. We also found evidence for mean shifts in skeletal oxygen isotopic composition after coral bleaching (the loss and potential exchange of symbionts) in two of four longer coral cores from the Mesoamerican Reef, though all experienced similar climatic conditions. Thus, we suggest that symbiont clade identity leaves a signature in the coral skeletal archive and that this influence must be considered for quantitative environmental reconstruction. In addition, we suggest that the skeletal isotopic signature may be used to identify changes in the dominant symbiont clade that have occurred in the past, to identify how common and widespread this phenomenon is--a potential adaptation to climate change.

Optical analyzer

DOEpatents

Hansen, Anthony D.

1989-02-07

An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

Chemical ecology of interactions between human skin microbiota and mosquitoes.

PubMed

Verhulst, Niels O; Takken, Willem; Dicke, Marcel; Schraa, Gosse; Smallegange, Renate C

2010-10-01

Microbiota on the human skin plays a major role in body odour production. The human microbial and chemical signature displays a qualitative and quantitative correlation. Genes may influence the chemical signature by shaping the composition of the microbiota. Recent studies on human skin microbiota, using 16S rRNA gene sequencing, found a high inter- and intrapersonal variation in bacterial species on the human skin, which is relatively stable over time. Human body odours mediate the attraction of mosquitoes to their blood hosts. Odours produced by skin microbiota are attractive to mosquitoes as shown by in vitro studies, and variation in bacterial species on the human skin may explain the variation in mosquito attraction between humans. Detailed knowledge of the ecology and genetics of human skin microbiota is needed in order to unravel the evolutionary mechanisms that underlie the interactions between mosquitoes and their hosts. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Measurement of rock mass deformation with grouted coaxial antenna cables

NASA Astrophysics Data System (ADS)

Dowding, C. H.; Su, M. B.; O'Connor, K.

1989-01-01

Techniques presented herein show how reflected voltage pulses from coaxial antenna cable grouted in rock masses can be employed to quantify the type and magnitude of rock mass deformation. This measurement is similar to that obtained from a combined full profile extensometer (to measure local extension) and inclinometer (to measure local shearing). Rock mass movements deform the grouted cable, which locally changes cable capacitance and thereby the reflected wave form of the voltage pulse. Thus, by monitoring changes in these reflection signatures, it is possible to monitor rock mass deformation. This paper presents laboratory measurements necessary to quantitatively interpret the reflected voltage signatures. Cables were sheared and extended to correlate measured cable deformation with reflected voltage signals. Laboratory testing included development of grout mixtures with optimum properties for field installation and performance of a TDR (Time Domain Reflectometry) monitoring system. Finally, the interpretive techniques developed through laboratory measurements were applied to previously collected field data to extract hitherto unrealized information.

Optical analyzer

DOEpatents

Hansen, Anthony D.

1989-01-01

An optical analyzer (10) wherein a sample (19) of particulate matter, and particularly of organic matter, which has been collected on a quartz fiber filter (20) is placed in a combustion tube (11), and light from a light source (14) is passed through the sample (19). The temperature of the sample (19) is raised at a controlled rate and in a controlled atmosphere. The magnitude of the transmission of light through the sample (19) is detected (18) as the temperature is raised. A data processor (23), differentiator (28) and a two pen recorder (24) provide a chart of the optical transmission versus temperature and the rate of change of optical transmission versus temperature signatures (T and D) of the sample (19). These signatures provide information as to physical and chemical processes and a variety of quantitative and qualitative information about the sample (19). Additional information is obtained by repeating the run in different atmospheres and/or different rates of heating with other samples of the same particulate material collected on other filters.

Autophagy-related prognostic signature for breast cancer.

PubMed

Gu, Yunyan; Li, Pengfei; Peng, Fuduan; Zhang, Mengmeng; Zhang, Yuanyuan; Liang, Haihai; Zhao, Wenyuan; Qi, Lishuang; Wang, Hongwei; Wang, Chenguang; Guo, Zheng

2016-03-01

Autophagy is a process that degrades intracellular constituents, such as long-lived or damaged proteins and organelles, to buffer metabolic stress under starvation conditions. Deregulation of autophagy is involved in the progression of cancer. However, the predictive value of autophagy for breast cancer prognosis remains unclear. First, based on gene expression profiling, we found that autophagy genes were implicated in breast cancer. Then, using the Cox proportional hazard regression model, we detected autophagy prognostic signature for breast cancer in a training dataset. We identified a set of eight autophagy genes (BCL2, BIRC5, EIF4EBP1, ERO1L, FOS, GAPDH, ITPR1 and VEGFA) that were significantly associated with overall survival in breast cancer. The eight autophagy genes were assigned as a autophagy-related prognostic signature for breast cancer. Based on the autophagy-related signature, the training dataset GSE21653 could be classified into high-risk and low-risk subgroups with significantly different survival times (HR = 2.72, 95% CI = (1.91, 3.87); P = 1.37 × 10(-5)). Inactivation of autophagy was associated with shortened survival of breast cancer patients. The prognostic value of the autophagy-related signature was confirmed in the testing dataset GSE3494 (HR = 2.12, 95% CI = (1.48, 3.03); P = 1.65 × 10(-3)) and GSE7390 (HR = 1.76, 95% CI = (1.22, 2.54); P = 9.95 × 10(-4)). Further analysis revealed that the prognostic value of the autophagy signature was independent of known clinical prognostic factors, including age, tumor size, grade, estrogen receptor status, progesterone receptor status, ERBB2 status, lymph node status and TP53 mutation status. Finally, we demonstrated that the autophagy signature could also predict distant metastasis-free survival for breast cancer. © 2015 Wiley Periodicals, Inc.

Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses.

PubMed

Eng, Christine L P; Tong, Joo Chuan; Tan, Tin Wee

2016-01-01

Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.

Twenty-four signature genes predict the prognosis of oral squamous cell carcinoma with high accuracy and repeatability

PubMed Central

Gao, Jianyong; Tian, Gang; Han, Xu; Zhu, Qiang

2018-01-01

Oral squamous cell carcinoma (OSCC) is the sixth most common type cancer worldwide, with poor prognosis. The present study aimed to identify gene signatures that could classify OSCC and predict prognosis in different stages. A training data set (GSE41613) and two validation data sets (GSE42743 and GSE26549) were acquired from the online Gene Expression Omnibus database. In the training data set, patients were classified based on the tumor-node-metastasis staging system, and subsequently grouped into low stage (L) or high stage (H). Signature genes between L and H stages were selected by disparity index analysis, and classification was performed by the expression of these signature genes. The established classification was compared with the L and H classification, and fivefold cross validation was used to evaluate the stability. Enrichment analysis for the signature genes was implemented by the Database for Annotation, Visualization and Integration Discovery. Two validation data sets were used to determine the precise of classification. Survival analysis was conducted followed each classification using the package ‘survival’ in R software. A set of 24 signature genes was identified based on the classification model with the Fi value of 0.47, which was used to distinguish OSCC samples in two different stages. Overall survival of patients in the H stage was higher than those in the L stage. Signature genes were primarily enriched in ‘ether lipid metabolism’ pathway and biological processes such as ‘positive regulation of adaptive immune response’ and ‘apoptotic cell clearance’. The results provided a novel 24-gene set that may be used as biomarkers to predict OSCC prognosis with high accuracy, which may be used to determine an appropriate treatment program for patients with OSCC in addition to the traditional evaluation index. PMID:29257303

Probing the ToxCast Chemical Library for Predictive Signatures of Developmental Toxicity

EPA Science Inventory

EPA’s ToxCast™ project is profiling the in vitro bioactivity of chemical compounds to assess pathway-level and cell-based signatures that correlate with observed in vivo toxicity. We hypothesize that cell signaling pathways are primary targets for diverse environmental chemicals ...

An Identity-Based Anti-Quantum Privacy-Preserving Blind Authentication in Wireless Sensor Networks.

PubMed

Zhu, Hongfei; Tan, Yu-An; Zhu, Liehuang; Wang, Xianmin; Zhang, Quanxin; Li, Yuanzhang

2018-05-22

With the development of wireless sensor networks, IoT devices are crucial for the Smart City; these devices change people's lives such as e-payment and e-voting systems. However, in these two systems, the state-of-art authentication protocols based on traditional number theory cannot defeat a quantum computer attack. In order to protect user privacy and guarantee trustworthy of big data, we propose a new identity-based blind signature scheme based on number theorem research unit lattice, this scheme mainly uses a rejection sampling theorem instead of constructing a trapdoor. Meanwhile, this scheme does not depend on complex public key infrastructure and can resist quantum computer attack. Then we design an e-payment protocol using the proposed scheme. Furthermore, we prove our scheme is secure in the random oracle, and satisfies confidentiality, integrity, and non-repudiation. Finally, we demonstrate that the proposed scheme outperforms the other traditional existing identity-based blind signature schemes in signing speed and verification speed, outperforms the other lattice-based blind signature in signing speed, verification speed, and signing secret key size.

An Identity-Based Anti-Quantum Privacy-Preserving Blind Authentication in Wireless Sensor Networks

PubMed Central

Zhu, Hongfei; Tan, Yu-an; Zhu, Liehuang; Wang, Xianmin; Zhang, Quanxin; Li, Yuanzhang

2018-01-01

With the development of wireless sensor networks, IoT devices are crucial for the Smart City; these devices change people’s lives such as e-payment and e-voting systems. However, in these two systems, the state-of-art authentication protocols based on traditional number theory cannot defeat a quantum computer attack. In order to protect user privacy and guarantee trustworthy of big data, we propose a new identity-based blind signature scheme based on number theorem research unit lattice, this scheme mainly uses a rejection sampling theorem instead of constructing a trapdoor. Meanwhile, this scheme does not depend on complex public key infrastructure and can resist quantum computer attack. Then we design an e-payment protocol using the proposed scheme. Furthermore, we prove our scheme is secure in the random oracle, and satisfies confidentiality, integrity, and non-repudiation. Finally, we demonstrate that the proposed scheme outperforms the other traditional existing identity-based blind signature schemes in signing speed and verification speed, outperforms the other lattice-based blind signature in signing speed, verification speed, and signing secret key size. PMID:29789475

Experiments on Adaptive Techniques for Host-Based Intrusion Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

DRAELOS, TIMOTHY J.; COLLINS, MICHAEL J.; DUGGAN, DAVID P.

2001-09-01

This research explores four experiments of adaptive host-based intrusion detection (ID) techniques in an attempt to develop systems that can detect novel exploits. The technique considered to have the most potential is adaptive critic designs (ACDs) because of their utilization of reinforcement learning, which allows learning exploits that are difficult to pinpoint in sensor data. Preliminary results of ID using an ACD, an Elman recurrent neural network, and a statistical anomaly detection technique demonstrate an ability to learn to distinguish between clean and exploit data. We used the Solaris Basic Security Module (BSM) as a data source and performed considerablemore » preprocessing on the raw data. A detection approach called generalized signature-based ID is recommended as a middle ground between signature-based ID, which has an inability to detect novel exploits, and anomaly detection, which detects too many events including events that are not exploits. The primary results of the ID experiments demonstrate the use of custom data for generalized signature-based intrusion detection and the ability of neural network-based systems to learn in this application environment.« less

Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

PubMed

Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

2011-01-01

The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Search by photo methodology for signature properties assessment by human observers

NASA Astrophysics Data System (ADS)

Selj, Gorm K.; Heinrich, Daniela H.

2015-05-01

Reliable, low-cost and simple methods for assessment of signature properties for military purposes are very important. In this paper we present such an approach that uses human observers in a search by photo assessment of signature properties of generic test targets. The method was carried out by logging a large number of detection times of targets recorded in relevant terrain backgrounds. The detection times were harvested by using human observers searching for targets in scene images shown by a high definition pc screen. All targets were identically located in each "search image", allowing relative comparisons (and not just rank by order) of targets. To avoid biased detections, each observer only searched for one target per scene. Statistical analyses were carried out for the detection times data. Analysis of variance was chosen if detection times distribution associated with all targets satisfied normality, and non-parametric tests, such as Wilcoxon's rank test, if otherwise. The new methodology allows assessment of signature properties in a reproducible, rapid and reliable setting. Such assessments are very complex as they must sort out what is of relevance in a signature test, but not loose information of value. We believe that choosing detection times as the primary variable for a comparison of signature properties, allows a careful and necessary inspection of observer data as the variable is continuous rather than discrete. Our method thus stands in opposition to approaches based on detections by subsequent, stepwise reductions in distance to target, or based on probability of detection.

Circulating neutrophil transcriptome may reveal intracranial aneurysm signature

PubMed Central

Tutino, Vincent M.; Poppenberg, Kerry E.; Jiang, Kaiyu; Jarvis, James N.; Sun, Yijun; Sonig, Ashish; Siddiqui, Adnan H.; Snyder, Kenneth V.; Levy, Elad I.; Kolega, John

2018-01-01

Background Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. Methods Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls. Samples from the two groups were paired based on demographics and comorbidities. RNA was extracted from isolated neutrophils and subjected to next-generation RNA sequencing to obtain differential expressions for identification of an IA-associated signature. Bioinformatics analyses, including gene set enrichment analysis and Ingenuity Pathway Analysis, were used to investigate the biological function of all differentially expressed transcripts. Results Transcriptome profiling identified 258 differentially expressed transcripts in patients with and without IAs. Expression differences were consistent with peripheral neutrophil activation. An IA-associated RNA expression signature was identified in 82 transcripts (p<0.05, fold-change ≥2). This signature was able to separate patients with and without IAs on hierarchical clustering. Furthermore, in an independent, unpaired, replication cohort of patients with IAs (n = 5) and controls (n = 5), the 82 transcripts separated 9 of 10 patients into their respective groups. Conclusion Preliminary findings show that RNA expression from circulating neutrophils carries an IA-associated signature. These findings highlight a potential to use predictive biomarkers from peripheral blood samples to identify patients with IAs. PMID:29342213

Automated road network extraction from high spatial resolution multi-spectral imagery

NASA Astrophysics Data System (ADS)

Zhang, Qiaoping

For the last three decades, the Geomatics Engineering and Computer Science communities have considered automated road network extraction from remotely-sensed imagery to be a challenging and important research topic. The main objective of this research is to investigate the theory and methodology of automated feature extraction for image-based road database creation, refinement or updating, and to develop a series of algorithms for road network extraction from high resolution multi-spectral imagery. The proposed framework for road network extraction from multi-spectral imagery begins with an image segmentation using the k-means algorithm. This step mainly concerns the exploitation of the spectral information for feature extraction. The road cluster is automatically identified using a fuzzy classifier based on a set of predefined road surface membership functions. These membership functions are established based on the general spectral signature of road pavement materials and the corresponding normalized digital numbers on each multi-spectral band. Shape descriptors of the Angular Texture Signature are defined and used to reduce the misclassifications between roads and other spectrally similar objects (e.g., crop fields, parking lots, and buildings). An iterative and localized Radon transform is developed for the extraction of road centerlines from the classified images. The purpose of the transform is to accurately and completely detect the road centerlines. It is able to find short, long, and even curvilinear lines. The input image is partitioned into a set of subset images called road component images. An iterative Radon transform is locally applied to each road component image. At each iteration, road centerline segments are detected based on an accurate estimation of the line parameters and line widths. Three localization approaches are implemented and compared using qualitative and quantitative methods. Finally, the road centerline segments are grouped into a road network. The extracted road network is evaluated against a reference dataset using a line segment matching algorithm. The entire process is unsupervised and fully automated. Based on extensive experimentation on a variety of remotely-sensed multi-spectral images, the proposed methodology achieves a moderate success in automating road network extraction from high spatial resolution multi-spectral imagery.

Cryptanalysis of an inter-bank E-payment protocol based on quantum proxy blind signature

NASA Astrophysics Data System (ADS)

Cai, Xiao-Qiu; Wei, Chun-Yan

2013-04-01

We analyze the security of an inter-bank E-payment protocol based on quantum proxy blind signature, and find that there is a security leak in the quantum channels of this protocol, which gives a chance for an outside opponent to launch a special denial-of-service attack. Furthermore, we show that the dishonest merchant can succeed to change the purchase information of the customer in this protocol.

SASS measurements of the Ku-band radar signature of the ocean

NASA Technical Reports Server (NTRS)

Schroeder, L. C.; Grantham, W. L.; Mitchell, J. L.; Sweet, J. L.

1982-01-01

SeaSat-A Satellite Scatterometer (SASS) measurements of normalized radar cross section (NRCS) have been merged with high quality surface-wind fields based on in situ, to create a large data base of NRCS-wind signature data. These data are compared to the existing NRCS-wind model used by the SASS to infer winds. Falso-color maps of SASS NRCS and ocean winds from multiple orbits show important synoptic trends.

A PRIM approach to predictive-signature development for patient stratification

PubMed Central

Chen, Gong; Zhong, Hua; Belousov, Anton; Devanarayan, Viswanath

2015-01-01

Patients often respond differently to a treatment because of individual heterogeneity. Failures of clinical trials can be substantially reduced if, prior to an investigational treatment, patients are stratified into responders and nonresponders based on biological or demographic characteristics. These characteristics are captured by a predictive signature. In this paper, we propose a procedure to search for predictive signatures based on the approach of patient rule induction method. Specifically, we discuss selection of a proper objective function for the search, present its algorithm, and describe a resampling scheme that can enhance search performance. Through simulations, we characterize conditions under which the procedure works well. To demonstrate practical uses of the procedure, we apply it to two real-world data sets. We also compare the results with those obtained from a recent regression-based approach, Adaptive Index Models, and discuss their respective advantages. In this study, we focus on oncology applications with survival responses. PMID:25345685

A New Method to Quantify the Isotopic Signature of Leaf Transpiration: Implications for Landscape-Scale Evapotranspiration Partitioning Studies

NASA Astrophysics Data System (ADS)

Wang, L.; Good, S. P.; Caylor, K. K.

2010-12-01

Characterizing the constituent components of evapotranspiration is crucial to better understand ecosystem-level water budgets and water use dynamics. Isotope based evapotranspiration partitioning methods are promising but their utility lies in the accurate estimation of the isotopic composition of underlying transpiration and evaporation. Here we report a new method to quantify the isotopic signature of leaf transpiration under field conditions. This method utilizes a commercially available laser-based isotope analyzer and a transparent leaf chamber, modified from Licor conifer leaf chamber. The method is based on the water mass balance in ambient air and leaf transpired air. We verified the method using “artificial leaves” and glassline extracted samples. The method provides a new and direct way to estimate leaf transpiration isotopic signatures and it has wide applications in ecology, hydrology and plant physiology.

Integrating Iris and Signature Traits for Personal Authentication Using User-Specific Weighting

PubMed Central

Viriri, Serestina; Tapamo, Jules R.

2012-01-01

Biometric systems based on uni-modal traits are characterized by noisy sensor data, restricted degrees of freedom, non-universality and are susceptible to spoof attacks. Multi-modal biometric systems seek to alleviate some of these drawbacks by providing multiple evidences of the same identity. In this paper, a user-score-based weighting technique for integrating the iris and signature traits is presented. This user-specific weighting technique has proved to be an efficient and effective fusion scheme which increases the authentication accuracy rate of multi-modal biometric systems. The weights are used to indicate the importance of matching scores output by each biometrics trait. The experimental results show that our biometric system based on the integration of iris and signature traits achieve a false rejection rate (FRR) of 0.08% and a false acceptance rate (FAR) of 0.01%. PMID:22666032

A Charge Coupled Device Imaging System For Ophthalmology

NASA Astrophysics Data System (ADS)

Rowe, R. Wanda; Packer, Samuel; Rosen, James; Bizais, Yves

1984-06-01

A digital camera system has been constructed for obtaining reflectance images of the fundus of the eye with monochromatic light. Images at wavelengths in the visible and near infrared regions of the spectrum are recorded by a charge-coupled device array and transferred to a computer. A variety of image processing operations are performed to restore the pictures, correct for distortions in the image formation process, and extract new and diagnostically useful information. The steps involved in calibrating the system to permit quantitative measurement of fundus reflectance are discussed. Three clinically important applications of such a quantitative system are addressed: the characterization of changes in the optic nerve arising from glaucoma, the diagnosis of choroidal melanoma through spectral signatures, and the early detection and improved management of diabetic retinopathy by measurement of retinal tissue oxygen saturation.

Glucose Sensing with Phenylboronic Acid Functionalized Hydrogel-Based Optical Diffusers

PubMed Central

2018-01-01

Phenylboronic acids have emerged as synthetic receptors that can reversibly bind to cis-diols of glucose molecules. The incorporation of phenylboronic acids in hydrogels offers exclusive attributes; for example, the binding process with glucose induces Donnan osmotic pressure resulting in volumetric changes in the matrix. However, their practical applications are hindered because of complex readout approaches and their time-consuming fabrication processes. Here, we demonstrate a microimprinting method to fabricate densely packed concavities in phenylboronic acid functionalized hydrogel films. A microengineered optical diffuser structure was imprinted on a phenylboronic acid based cis-diol recognizing motif prepositioned in a hydrogel film. The diffuser structure engineered on the hydrogel was based on laser-inscribed arrays of imperfect microlenses that focused the incoming light at different focal lengths and direction resulting in a diffused profile of light in transmission and reflection readout modes. The signature of the dimensional modulation was detected in terms of changing focal lengths of the microlenses due to the volumetric expansion of the hydrogel that altered the diffusion spectra and transmitted beam profile. The transmitted optical light spread and intensity through the sensor was measured to determine variation in glucose concentrations at physiological conditions. The sensor was integrated in a contact lens and placed over an artificial eye. Artificial stimulation of variation in glucose concentration allowed quantitative measurements using a smartphone’s photodiode. A smartphone app was utilized to convert the received light intensity to quantitative glucose concentration values. The developed sensing platform offers low cost, rapid fabrication, and easy detection scheme as compared to other optical sensing counterparts. The presented detection scheme may have applications in wearable real-time biomarker monitoring devices at point-of-care settings. PMID:29529366

A new method and application for determining the nitrogen isotopic composition of NOx

NASA Astrophysics Data System (ADS)

Hastings, M. G.; Miller, D. J.; Wojtal, P.; O'Connor, M.

2015-12-01

Atmospheric nitrogen oxides (NOx = NO + NO2) play key roles in atmospheric chemistry, air quality, and radiative forcing, and contribute to nitric acid deposition. Sources of NOx include both natural and anthropogenic emissions, which vary significantly in space and time. NOx isotopic signatures offer a potentially valuable tool to trace source impacts on atmospheric chemistry and regional acid deposition. Previous work on NOx isotopic signatures suggests large ranges in values, even from the same emission source, as well as overlapping ranges amongst different sources, making it difficult to use the isotopic composition as a quantitative tracer of source influences. These prior measurements have utilized a variety of methods for collecting the NOx as nitrate or nitrite for isotopic analysis, and testing of some of these methods (including active and passive collections) reveal inconsistencies in efficiency of collection, as well as issues related to changes in conditions such as humidity, temperature, and NOx fluxes. A recently developed method allows for accurately measuring the nitrogen isotopic composition of NOx (NOx = NO + NO2) after capturing the NOx in a potassium permanganate/sodium hydroxide solution as nitrate (Fibiger et al., Anal. Chem., 2014). The method has been thoroughly tested in the laboratory and field, and efficiently collects NO and NO2 under a variety of conditions. There are several advantages to collecting NOx actively, including the ability to collect over minutes to hourly time scales, and the ability to collect in environments with highly variable NOx sources and concentrations. Challenges include a nitrate background present in potassium permanganate (solid and liquid forms), accurately deriving ambient NOx concentrations based upon flow rate and solution concentrations above this variable background, and potential interferences from other nitrogen species. This method was designed to collect NOx in environments with very different emission source loadings in an effort to isotopically characterize NOx sources. Results to date suggest very different values, and less variability than previous work, particularly for vehicle emissions. Ultimately, we aim to determine whether the influence of NOx sources can be quantitatively tracked in the environment.

Flow and Transport in Complex Microporous Carbonates as a Consequence of Separation of Scales

NASA Astrophysics Data System (ADS)

Bijeljic, B.; Raeini, A. Q.; Lin, Q.; Blunt, M. J.

2017-12-01

Some of the most important examples of flow and transport in complex pore structures are found in subsurface applications such as contaminant hydrology, carbon storage and enhanced oil recovery. Carbonate rock structures contain most of the world's oil reserves, considerable amount of water reserves, and potentially hold a storage capacity for carbon dioxide. However, this type of pore space is difficult to represent due to complexities associated with a wide range of pore sizes and variation in connectivity which poses a considerable challenge for quantitative predictions of transport across multiple scales.A new concept unifying X-ray tomography experiment and direct numerical simulation has been developed that relies on full description flow and solute transport at the pore scale. Differential imaging method (Lin et al. 2016) provides rich information in microporous space, while advective and diffusive mass transport are simulated on micro-CT images of pore-space: Navier-Stokes equations are solved for flow in the image voxels comprising the pore space, streamline-based simulation is used to account for advection, and diffusion is superimposed by random walk.Quantitative validation has been done on analytical solutions for diffusion and by comparing the model predictions versus the experimental NMR measurements in the dual porosity beadpack. Furthermore, we discriminate signatures of multi-scale transport behaviour for a range of carbonate rock (Figure 1), dependent on the heterogeneity of the inter- and intra-grain pore space, heterogeneity in the flow field, and the mass transfer characteristics of the porous media. Finally, we demonstrate the predictive capabilities of the model through an analysis that includes a number of probability density functions flow and transport (PDFs) measures of non-Fickian transport on the micro-CT i935mages. In complex porous media separation of scales exists, leading to flow and transport signatures that need to be described by multiple functions with distinct flow field and transport characteristics. Reference: Lin, Q., Al-Khulaifi Y., Blunt, M.J. and Bijeljic B. (2016). Advances in Water Resources, 96, 306-322, doi:10.1016/j.advwatres.2016.08.002.

Melt production constrained by the topographic signature of the Altiplano-Puna Magma Body

NASA Astrophysics Data System (ADS)

Perkins, J. P.; Ward, K. M.; de Silva, S. L.; Zandt, G.; Beck, S. L.; Finnegan, N. J.

2015-12-01

The Altiplano-Puna Magma Body (APMB) is a ~200 km diameter, ~10 km thick elliptical zone of low seismic shear velocity interpreted as partial melt within the mid crust of the Central Andes (Ward et al., 2014). It is thought to be the crustal magmatic source for a flare-up of large-volume ignimbrites since 10 Ma (e.g. de Silva et al., 1989), and recent rapid uplift events such as those at Uturuncu volcano appear to be associated with magmatism from the APMB at depth (e.g., Fialko and Pearse, 2011). Hence, the APMB is a first-order geologic feature on par with the Sierra Nevada batholith in CA. Here we use the topographic signature of the low-density APMB in order to quantitatively constrain the melt production necessary to generate a magmatic zone of this size. A long-wavelength, ~1 km high topographic dome spatially coincides with the seismically measured extent of the APMB. The peak of the long wavelength dome acts as a regional drainage divide, and exposed basement rock elevations show that doming is a structural feature and does not reflect solely the accumulation of volcanic deposits on the plateau. Additionally, the minimal free-air gravity anomaly above the APMB and the dome's length scale suggest that the uplift is isostatically compensated. Based on a buried load isostatic model (e.g., Forsyth, 1985), the dome above the APMB implies that 5.6-5.8 km of crustal thickening occurred during the emplacement of the magma body. Our estimate compares well with calculations of crustal addition using magma chamber volume and a standard melt mixing model (Ward et al., 2014), and suggests that the magma production rate for the APMB may be within the range of 70-117 km3/km/yr, similar to rates of the Late Cretaceous magmatic episode in the Sierra Nevada Batholith (e.g., Ducea, 2001). Surface topography may therefore be able to provide quantitative constraints on the magnitude of pluton-scale melt fluxes.

The Long Noncoding RNA Landscape of the Mouse Eye.

PubMed

Chen, Weiwei; Yang, Shuai; Zhou, Zhonglou; Zhao, Xiaoting; Zhong, Jiayun; Reinach, Peter S; Yan, Dongsheng

2017-12-01

Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice. Quantitative RT-PCR analysis validated array findings. Cis analyses and Gene Ontology (GO) annotation of protein-coding genes adjacent to signature lncRNA loci clarified potential lncRNA roles in maintaining tissue identity and regulating eye maturation during the aforementioned phase. In newborn and 8-week-old mice, we identified 47,332 protein-coding and noncoding gene transcripts. LncRNAs comprise 19,313 of these transcripts annotated in public data banks. During this maturation phase of these six different tissue subsets, more than 1000 lncRNAs expression levels underwent ≥2-fold changes. qRT-PCR analysis confirmed part of the gene microarray analysis results. K-means clustering identified 910 lncRNAs in the P0 groups and 686 lncRNAs in the postnatal 8-week-old groups, suggesting distinct tissue-specific lncRNA clusters. GO analysis of protein-coding genes proximal to lncRNA signatures resolved close correlations with their tissue-specific functional maturation between P0 and 8 weeks of age in the 6 tissue subsets. Characterizating maturational changes in lncRNA expression patterns as well as tissue-specific lncRNA signatures in six ocular tissues suggest important contributions made by lncRNA to the control of developmental processes in the mouse eye.

HA117 endows HL60 cells with a stem-like signature by inhibiting the degradation of DNMT1 via its ability to down-regulate expression of the GGL domain of RGS6

PubMed Central

Li, Shuangshuang; Wu, Huan; Wang, Yi; Li, Xiaoqing; Guo, Yuxia; Liang, Shaoyan

2017-01-01

All-trans retinoic acid (ATRA) induces complete remission in almost all patients with acute promyelocytic leukemia (APL) via its ability to induce the in vivo differentiation of APL blasts. However, prolonged ATRA treatment can result in drug resistance. In previous studies, we generated a multi-drug-resistant HL60/ATRA cell line and found it to contain a new drug resistance-related gene segment, HA117. In this study, we demonstrate that ATRA induces multi-drug-resistant subpopulations of HL60 cells with a putative stem-like signature by up-regulating the expression of the new gene segment HA117. Western blot analysis and quantitative real-time PCR demonstrated that HA117 causes alternative splicing of regulator of G-protein signaling 6 (RGS6) and down-regulation of the expression of the GGL domain of RGS6, which plays an important role in DNA methyltransferase 1 (DNMT1) degradation. Moreover, DNMT1 expression was increased in multi-drug resistance HL60/ATRA cells. Knockdown of HA117 restored expression of the GGL domain and blocked DNMT1 expression. Moreover, resistant cells displayed a putative stem-like signature with increased expression of cancer steam cell markers CD133 and CD123. The stem cell marker, Nanog, was significantly up-regulated. In conclusion, our study shows that HA117 potentially promotes the stem-like signature of the HL60/ATRA cell line by inhibiting by the ubiquitination and degradation of DNMT1 and by down-regulating the expression of the GGL domain of RGS6. These results throw light on the cellular events associated with the ATRA-induced multi-drug resistance phenotype in acute leukemia. PMID:28665981

Type I IFN-related NETosis in ataxia telangiectasia and Artemis deficiency.

PubMed

Gul, Ersin; Sayar, Esra Hazar; Gungor, Bilgi; Eroglu, Fehime Kara; Surucu, Naz; Keles, Sevgi; Guner, Sukru Nail; Findik, Siddika; Alpdundar, Esin; Ayanoglu, Ihsan Cihan; Kayaoglu, Basak; Geckin, Busra Nur; Sanli, Hatice Asena; Kahraman, Tamer; Yakicier, Cengiz; Muftuoglu, Meltem; Oguz, Berna; Cagdas Ayvaz, Deniz Nazire; Gursel, Ihsan; Ozen, Seza; Reisli, Ismail; Gursel, Mayda

2017-11-16

Pathological inflammatory syndromes of unknown etiology are commonly observed in ataxia telangiectasia (AT) and Artemis deficiency. Similar inflammatory manifestations also exist in patients with STING-associated vasculopathy in infancy (SAVI). We sought to test the hypothesis that the inflammation-associated manifestations observed in patients with AT and Artemis deficiency stem from increased type I IFN signature leading to neutrophil-mediated pathological damage. Cytokine/protein signatures were determined by ELISA, cytometric bead array, or quantitative PCR. Stat1 phosphorylation levels were determined by flow cytometry. DNA species accumulating in the cytosol of patients' cells were quantified microscopically and flow cytometrically. Propensity of isolated polymorhonuclear granulocytes to form neutrophil extracellular traps (NETs) was determined using fluorescence microscopy and picogreen assay. Neutrophil reactive oxygen species levels and mitochondrial stress were assayed using fluorogenic probes, microscopy, and flow cytometry. Type I and III IFN signatures were elevated in plasma and peripheral blood cells of patients with AT, Artemis deficiency, and SAVI. Chronic IFN production stemmed from the accumulation of DNA in the cytoplasm of AT and Artemis-deficient cells. Neutrophils isolated from patients spontaneously produced NETs and displayed indicators of oxidative and mitochondrial stress, supportive of their NETotic tendencies. A similar phenomenon was also observed in neutrophils from healthy controls exposed to patient plasma samples or exogeneous IFN-α. Type I IFN-mediated neutrophil activation and NET formation may contribute to inflammatory manifestations observed in patients with AT, Artemis deficiency, and SAVI. Thus, neutrophils represent a promising target to manage inflammatory syndromes in diseases with active type I IFN signature. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Analysis of the microRNA signature driving adaptive right ventricular hypertrophy in an ovine model of congenital heart disease.

PubMed

Kameny, Rebecca Johnson; He, Youping; Zhu, Terry; Gong, Wenhui; Raff, Gary W; Chapin, Cheryl J; Datar, Sanjeev A; Boehme, Jason; Hata, Akiko; Fineman, Jeffrey R

2018-06-15

The right ventricular (RV) response to pulmonary arterial hypertension (PAH) is heterogeneous. Most patients have maladaptive changes with RV dilation and failure while some-especially patients with PAH secondary to congenital heart disease (CHD)-have an adaptive response with hypertrophy and preserved systolic function. Mechanisms for RV adaptation to PAH are unknown despite RV function being a primary determinant of mortality. In our CHD ovine model with fetally-implanted aortopulmonary shunt (shunt lambs), we previously demonstrated an adaptive physiologic RV response to increased afterload with hypertrophy. In this study, we examined small noncoding microRNA (miRNA) expression in shunt RV and characterized downstream effects of a key miRNA. RV tissue was harvested from 4-week-old shunt and control lambs (n=5) and miRNA, mRNA, and proteins were quantitated. We found differential expression of 40 cardiovascular-specific miRNA in shunt RV. Interestingly, this miRNA signature is distinct from models of RV failure, suggesting that miRNAs might contribute to adaptive RV hypertrophy. Among RV miRNAs, miR-199b is decreased in RV with eventual downregulation of nuclear factor of activated T-cells (NFAT)/calcineurin signaling. Furthermore, anti-fibrotic miR-29a is increased in shunt RV with reduction of miR-29 targets Collagen A1 and 3A1 and decreased fibrosis. Thus, we conclude that the miRNA signature specific to shunt lambs is distinct from RV failure and drives gene expression required for adaptive RV hypertrophy. We propose that the adaptive RV miRNA signature may serve as a prognostic and therapeutic tool in patients with PAH to attenuate or prevent progression of RV failure and premature death.

Ion channel gene expression predicts survival in glioma patients

PubMed Central

Wang, Rong; Gurguis, Christopher I.; Gu, Wanjun; Ko, Eun A; Lim, Inja; Bang, Hyoweon; Zhou, Tong; Ko, Jae-Hong

2015-01-01

Ion channels are important regulators in cell proliferation, migration, and apoptosis. The malfunction and/or aberrant expression of ion channels may disrupt these important biological processes and influence cancer progression. In this study, we investigate the expression pattern of ion channel genes in glioma. We designate 18 ion channel genes that are differentially expressed in high-grade glioma as a prognostic molecular signature. This ion channel gene expression based signature predicts glioma outcome in three independent validation cohorts. Interestingly, 16 of these 18 genes were down-regulated in high-grade glioma. This signature is independent of traditional clinical, molecular, and histological factors. Resampling tests indicate that the prognostic power of the signature outperforms random gene sets selected from human genome in all the validation cohorts. More importantly, this signature performs better than the random gene signatures selected from glioma-associated genes in two out of three validation datasets. This study implicates ion channels in brain cancer, thus expanding on knowledge of their roles in other cancers. Individualized profiling of ion channel gene expression serves as a superior and independent prognostic tool for glioma patients. PMID:26235283

Application of micro-attenuated total reflectance Fourier transform infrared spectroscopy to ink examination in signatures written with ballpoint pen on questioned documents.

PubMed

Nam, Yun Sik; Park, Jin Sook; Lee, Yeonhee; Lee, Kang-Bong

2014-05-01

Questioned documents examined in a forensic laboratory sometimes contain signatures written with ballpoint pen inks; these signatures were examined to assess the feasibility of micro-attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy as a forensic tool. Micro-ATR FTIR spectra for signatures written with 63 ballpoint pens available commercially in Korea were obtained and used to construct an FTIR spectral database. A library-searching program was utilized to identify the manufacturer, blend, and model of each black ballpoint pen ink based upon their FTIR peak intensities, positions, and patterns in the spectral database. This FTIR technique was also successfully used in determining the sequence of homogeneous line intersections from the crossing lines of two ballpoint pen signatures. We have demonstrated with a set of sample documents that micro-ATR FTIR is a viable nondestructive analytical method that can be used to identify the origin of the ballpoint pen ink used to mark signatures. © 2014 American Academy of Forensic Sciences.

Spatially Resolved Isotopic Source Signatures of Wetland Methane Emissions

NASA Astrophysics Data System (ADS)

Ganesan, A. L.; Stell, A. C.; Gedney, N.; Comyn-Platt, E.; Hayman, G.; Rigby, M.; Poulter, B.; Hornibrook, E. R. C.

2018-04-01

We present the first spatially resolved wetland δ13C(CH4) source signature map based on data characterizing wetland ecosystems and demonstrate good agreement with wetland signatures derived from atmospheric observations. The source signature map resolves a latitudinal difference of 10‰ between northern high-latitude (mean -67.8‰) and tropical (mean -56.7‰) wetlands and shows significant regional variations on top of the latitudinal gradient. We assess the errors in inverse modeling studies aiming to separate CH4 sources and sinks by comparing atmospheric δ13C(CH4) derived using our spatially resolved map against the common assumption of globally uniform wetland δ13C(CH4) signature. We find a larger interhemispheric gradient, a larger high-latitude seasonal cycle, and smaller trend over the period 2000-2012. The implication is that erroneous CH4 fluxes would be derived to compensate for the biases imposed by not utilizing spatially resolved signatures for the largest source of CH4 emissions. These biases are significant when compared to the size of observed signals.

Probing the ToxCastTM Chemical Library for Predictive Signatures of Developmental Toxicity -NLTO Poster

EPA Science Inventory

EPA’s ToxCast™ project is profiling the in vitro bioactivity of chemical compounds to assess pathway-level and cell-based signatures that correlate with observed in vivo toxicity. We hypothesize that cell signaling pathways are primary targets for diverse environmental chemicals ...

MIXING MODELS IN ANALYSES OF DIET USING MULTIPLE STABLE ISOTOPES: A CRITIQUE

EPA Science Inventory

Stable isotopes have become widely used in ecology to quantify the importance of different sources based on their isotopic signature. One example of this has been the determination of food webs, where the isotopic signatures of a predator and various prey items can be used to de...

77 FR 52313 - Notice of Scope Rulings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-29

..., 2012. A-570-506: Porcelain-On-Steel Cooking Ware from the People's Republic of China Requestor: The Coleman Company, Inc.; the stockpot locking lid of its Signature Series All-In-One Cooking System And Max Series is within the scope of the antidumping duty order; the stockpot cooking base of its Signature...

Sonic Booms And Building Vibration Revisited

NASA Astrophysics Data System (ADS)

Sutherland, Louis C.; Kryter, Karl D.; Czech, Joseph

2006-05-01

Lessons learned from the 1960's sonic boom tests at St. Louis, Oklahoma City and at Edwards Air Force Base (EAFB) and more recently in communities near EAFB and Nellis AFB are briefly reviewed from the standpoint of building vibration and rattle response induced by the sonic boom signature. Available data on the vibro-acoustic threshold of rattle are considered along with the principal sonic boom signature parameters, peak overpressure and duration, which drive the low frequency vibration response of buildings to sonic booms. Implications for the current effort to develop an acceptable sonic boom signature are considered with this overview of current understanding of building vibration response to sonic booms. Possible gaps in this current knowledge for current technology boom signatures are considered.

Classification and Verification of Handwritten Signatures with Time Causal Information Theory Quantifiers.

PubMed

Rosso, Osvaldo A; Ospina, Raydonal; Frery, Alejandro C

2016-01-01

We present a new approach for handwritten signature classification and verification based on descriptors stemming from time causal information theory. The proposal uses the Shannon entropy, the statistical complexity, and the Fisher information evaluated over the Bandt and Pompe symbolization of the horizontal and vertical coordinates of signatures. These six features are easy and fast to compute, and they are the input to an One-Class Support Vector Machine classifier. The results are better than state-of-the-art online techniques that employ higher-dimensional feature spaces which often require specialized software and hardware. We assess the consistency of our proposal with respect to the size of the training sample, and we also use it to classify the signatures into meaningful groups.

A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping.

PubMed

Wen, Qing; Kim, Chang-Sik; Hamilton, Peter W; Zhang, Shu-Dong

2016-05-11

Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research in connectivity mapping mainly focused on two of the key components in the framework, namely, the reference gene expression profiles and the connectivity mapping algorithms. The other key component in this framework, the query gene signature, has been left to users to construct without much consensus on how this should be done, albeit it has been an issue most relevant to end users. As a key input to the connectivity mapping process, gene signature is crucially important in returning biologically meaningful and relevant results. This paper intends to formulate a standardized procedure for constructing high quality gene signatures from a user's perspective. We describe a two-stage process for making quality gene signatures using gene expression data as initial inputs. First, a differential gene expression analysis comparing two distinct biological states; only the genes that have passed stringent statistical criteria are considered in the second stage of the process, which involves ranking genes based on statistical as well as biological significance. We introduce a "gene signature progression" method as a standard procedure in connectivity mapping. Starting from the highest ranked gene, we progressively determine the minimum length of the gene signature that allows connections to the reference profiles (drugs) being established with a preset target false discovery rate. We use a lung cancer dataset and a breast cancer dataset as two case studies to demonstrate how this standardized procedure works, and we show that highly relevant and interesting biological connections are returned. Of particular note is gefitinib, identified as among the candidate therapeutics in our lung cancer case study. Our gene signature was based on gene expression data from Taiwan female non-smoker lung cancer patients, while there is evidence from independent studies that gefitinib is highly effective in treating women, non-smoker or former light smoker, advanced non-small cell lung cancer patients of Asian origin. In summary, we introduced a gene signature progression method into connectivity mapping, which enables a standardized procedure for constructing high quality gene signatures. This progression method is particularly useful when the number of differentially expressed genes identified is large, and when there is a need to prioritize them to be included in the query signature. The results from two case studies demonstrate that the approach we have developed is capable of obtaining pertinent candidate drugs with high precision.

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

PubMed Central

Yu, Shunying; Yuan, Chengmei; Hong, Wu; Wang, Zuowei; Cui, Jian; Shi, Tieliu; Fang, Yiru

2012-01-01

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls. PMID:22348066

Exploring the Use of Radar for Physically-Based Nowcasting of Lightning Cessation

NASA Technical Reports Server (NTRS)

Schultz, Elise V.; Petersen, Walter A.; Carey, Lawrence D.

2011-01-01

NASA's Marshall Space Flight Center and the University of Alabama in Huntsville (UAHuntsville) are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. This project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically-based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms driven primarily by trending in the actual total lightning flash rate, we believe that dual polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and ice-microphysics. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can propagation phase-based ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UAHuntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the NASA-MSFC North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. Thus far our case study results suggest that the negative differential phase shift signature weakens and disappears after the analyzed storms ceased lightning production (i.e., after the last lightning flash occurred). This is a key observation because it suggests that while strong electric fields may still have been present, the lightning cessation signature was encompassed in the period of the polarimetric negative phase shift signature. To the extent this behavior is repeatable in other cases, even if only in a substantial fraction of those cases, the analysis suggests that differential propagation phase may prove to be a useful parameter for future lightning cessation algorithms. Indeed, a preliminary analysis of 15+ cases has shown additional indications of the weakening and disappearance of this ice alignment signature with lightning cessation. A summary of these case-study results is presented.

Vehicle Classification Using the Discrete Fourier Transform with Traffic Inductive Sensors.

PubMed

Lamas-Seco, José J; Castro, Paula M; Dapena, Adriana; Vazquez-Araujo, Francisco J

2015-10-26

Inductive Loop Detectors (ILDs) are the most commonly used sensors in traffic management systems. This paper shows that some spectral features extracted from the Fourier Transform (FT) of inductive signatures do not depend on the vehicle speed. Such a property is used to propose a novel method for vehicle classification based on only one signature acquired from a sensor single-loop, in contrast to standard methods using two sensor loops. Our proposal will be evaluated by means of real inductive signatures captured with our hardware prototype.

Spectral signature variations, atmospheric scintillations and sensor parameters

NASA Astrophysics Data System (ADS)

Berger, Henry; Neander, John

2002-11-01

The spectral signature of a material is the curve of power density vs. wavelength (λ) obtained from measurements of reflected light. It is used, among other things, for the identification of targets in remotely acquired images. Sometimes, however, unpredictable distortions may prevent this. In only a few cases have such distortions been explained. We propose some reasonable arguments that in a significant number of circumstances, atmospheric turbulence may contribute to such spectral signature distortion. We propose, based on this model, what appears to be one method that could combat such distortion.

Terrain type recognition using ERTS-1 MSS images

NASA Technical Reports Server (NTRS)

Gramenopoulos, N.

1973-01-01

For the automatic recognition of earth resources from ERTS-1 digital tapes, both multispectral and spatial pattern recognition techniques are important. Recognition of terrain types is based on spatial signatures that become evident by processing small portions of an image through selected algorithms. An investigation of spatial signatures that are applicable to ERTS-1 MSS images is described. Artifacts in the spatial signatures seem to be related to the multispectral scanner. A method for suppressing such artifacts is presented. Finally, results of terrain type recognition for one ERTS-1 image are presented.

Blind Quantum Signature with Controlled Four-Particle Cluster States

NASA Astrophysics Data System (ADS)

Li, Wei; Shi, Jinjing; Shi, Ronghua; Guo, Ying

2017-08-01

A novel blind quantum signature scheme based on cluster states is introduced. Cluster states are a type of multi-qubit entangled states and it is more immune to decoherence than other entangled states. The controlled four-particle cluster states are created by acting controlled-Z gate on particles of four-particle cluster states. The presented scheme utilizes the above entangled states and simplifies the measurement basis to generate and verify the signature. Security analysis demonstrates that the scheme is unconditional secure. It can be employed to E-commerce systems in quantum scenario.

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs

PubMed Central

Lafyatis, Robert; Burkly, Linda C.

2017-01-01

Systemic sclerosis (SSc) is a devastating disease affecting the skin and internal organs. Dermal fibrosis manifests early and Modified Rodnan Skin Scores (MRSS) correlate with disease progression. Transcriptomics of SSc skin biopsies suggest the role of the in vivo microenvironment in maintaining the pathological myofibroblasts. Therefore, defining the structural changes in dermal collagen in SSc patients could inform our understanding of fibrosis pathogenesis. Here, we report a method for quantitative whole-slide image analysis of dermal collagen from SSc patients, and our findings of more aligned dermal collagen bundles in diffuse cutaneous SSc (dcSSc) patients. Using the bleomycin-induced mouse model of SSc, we identified a distinct high dermal collagen bundle alignment gene signature, characterized by a concerted upregulation in cell migration, adhesion, and guidance pathways, and downregulation of spindle, replication, and cytokinesis pathways. Furthermore, increased bundle alignment induced a cell migration gene signature in fibroblasts in vitro, and these cells demonstrated increased directed migration on aligned ECM fibers that is dependent on expression of Arhgdib (Rho GDP-dissociation inhibitor 2). Our results indicate that increased cell migration is a cellular response to the increased collagen bundle alignment featured in fibrotic skin. Moreover, many of the cell migration genes identified in our study are shared with human SSc skin and may be new targets for therapeutic intervention. PMID:28662216

Secreted primary human malignant mesothelioma exosome signature reflects oncogenic cargo

PubMed Central

Greening, David W.; Ji, Hong; Chen, Maoshan; Robinson, Bruce W. S.; Dick, Ian M.; Creaney, Jenette; Simpson, Richard J.

2016-01-01

Malignant mesothelioma (MM) is a highly-aggressive heterogeneous malignancy, typically diagnosed at advanced stage. An important area of mesothelioma biology and progression is understanding intercellular communication and the contribution of the secretome. Exosomes are secreted extracellular vesicles shown to shuttle cellular cargo and direct intercellular communication in the tumour microenvironment, facilitate immunoregulation and metastasis. In this study, quantitative proteomics was used to investigate MM-derived exosomes from distinct human models and identify select cargo protein networks associated with angiogenesis, metastasis, and immunoregulation. Utilising bioinformatics pathway/network analyses, and correlation with previous studies on tumour exosomes, we defined a select mesothelioma exosomal signature (mEXOS, 570 proteins) enriched in tumour antigens and various cancer-specific signalling (HPGD/ENO1/OSMR) and secreted modulators (FN1/ITLN1/MAMDC2/PDGFD/GBP1). Notably, such circulating cargo offers unique insights into mesothelioma progression and tumour microenvironment reprogramming. Functionally, we demonstrate that oncogenic exosomes facilitate the migratory capacity of fibroblast/endothelial cells, supporting the systematic model of MM progression associated with vascular remodelling and angiogenesis. We provide biophysical and proteomic characterisation of exosomes, define a unique oncogenic signature (mEXOS), and demonstrate the regulatory capacity of exosomes in cell migration/tube formation assays. These findings contribute to understanding tumour-stromal crosstalk in the context of MM, and potential new diagnostic and therapeutic extracellular targets. PMID:27605433

Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

PubMed Central

Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R.; Messer, Philipp W.

2015-01-01

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks. PMID:26589239

Evaluating the performance of selection scans to detect selective sweeps in domestic dogs.

PubMed

Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R; Messer, Philipp W

2016-01-01

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks. © 2015 John Wiley & Sons Ltd.

Characterizing the anthropogenic signature in the LCLU dynamics in the Central Asia region

NASA Astrophysics Data System (ADS)

Tatarskii, V.; Sokolik, I. N.; de Beurs, K.; Shiklomanov, A. I.

2017-12-01

Humans have been changing the LCLU dynamics over time through the world. In the Central Asia region, these changes have been especially pronounced due to the political and economic transformation. We present a detailed analysis, focusing on identifying and quantifying the anthropogenic signature in the water and land use across the region. We have characterized the anthropogenic dust emission by combining the modeling and observations. The model is a fully coupled model called WRF-Chem-DuMo that takes explicitly into account the vegetation treatment in modeling the dust emission. We have reconstructed the anthropogenic dust sources in the region, such as the retreat of the Aral Sea, changes in agricultural fields, etc. In addition, we characterize the anthropogenic water use dynamics, including the changes in the water use for the agricultural production. Furthermore, we perform an analysis to identify the anthropogenic signature in the NDVI pattern. The NDVI were analyzed in conjunction with the meteorological fields that were simulated at the high special resolution using the WRF model. Meteorological fields of precipitation and temperature were used for the correlation analysis to separate the natural vs. anthropogenic changes. In this manner, we were able to identify the regions that have been affected by human activities. We will present the quantitative assessment of the anthropogenic changes. The diverse consequences for the economy of the region, as well as, the environment will be addressed.

From the surface to the deep critical zone: Linking soil carbon, fluid saturation and weathering rate

NASA Astrophysics Data System (ADS)

Druhan, Jennifer; Lawrence, Corey; Oster, Jessica; Rempe, Daniella; Dietrich, William

2017-04-01

Shallow soils from a wide range of ecosystems demonstrate a clear and consistent relationship between effective fluid saturation and the rate at which organic carbon is converted to CO2. While the underlying mechanisms contributing to this dependence are diverse, a consistent pattern of maximum CO2 production at intermediate soil moisture supports a generalized functional relationship, which may be incorporated into a quantitative reactive transport framework. A key result of this model development is a prediction of the extent to which the inorganic carbon content of water in biologically active soils varies as a function of hydrologic parameters (i.e. moisture content and residence time), and in turn influences weathering reactions. Deeper in the CZ, the consistency of this relationship and the influence of hydrologically - regulated CO2 production on the rates of water - rock interaction are largely unknown. Here, we use a novel reactive transport model incorporating this functional relationship to consider how variations in the reactive potential of water entering the vadose zone influences subsurface weathering rates. We leverage two examples of variably saturated natural systems to consider (1) CO2 production and associated weathering potential regulated by seasonal hydrologic shifts and (2) the preservation of soil carbon signatures in the deep CZ over millennial timescales. First, at the Eel River CZ Observatory in Northern California, USA, a novel Vadose Zone Monitoring System (VMS) installed in a 14 - 20 m thick unsaturated section offers an unprecedented view into the physical, chemical and biological behavior of the depth profile separating soils from groundwater. Based on soil moisture, gas and fluid phase samples, we demonstrate a predictive relationship between seasonal hydrologic variations and the location and magnitude of geochemical weathering rates. Second, an environmental monitoring project in the Blue Springs Cave, Sparta, TN, USA, provides chemical and isotopic signatures of both soil and cave drip water, allowing constraint of a model for the evolution of fluid with depth through a karst system. The carbon isotope signatures of these speleothems have been suggested as a record of long term variations in CZ vegetation, soil respiration and carbon stability. Using our modeling approach, we offer a prediction of the extent to which hydrologically - driven variations in carbon respiration are converted to weathering rates in karst systems and ultimately preserved within the speleothem record. By combining this novel modeling approach with these two examples, we illustrate a quantitative framework for (1) the influence of hydro-biological coupling in shallow soils on deep weathering regimes in the Critical Zone, and (2) the preservation of these signals in the geologic record.

Exploring the Use of Radar for a Physically Based Lightning Cessation Nowcasting Tool

NASA Technical Reports Server (NTRS)

Schultz, Elise V.; Petersen, Walter A.; Carey, Lawrence D.

2011-01-01

NASA s Marshall Space Flight Center (MSFC) and the University of Alabama in Huntsville (UAHuntsville) are collaborating with the 45th Weather Squadron (45WS) at Cape Canaveral Air Force Station (CCAFS) to enable improved nowcasting of lightning cessation. This project centers on use of dual-polarimetric radar capabilities, and in particular, the new C-band dual-polarimetric weather radar acquired by the 45WS. Special emphasis is placed on the development of a physically based operational algorithm to predict lightning cessation. While previous studies have developed statistically based lightning cessation algorithms, we believe that dual-polarimetric radar variables offer the possibility to improve existing algorithms through the inclusion of physically meaningful trends reflecting interactions between in-cloud electric fields and hydrometeors. Specifically, decades of polarimetric radar research using propagation differential phase has demonstrated the presence of distinct phase and ice crystal alignment signatures in the presence of strong electric fields associated with lightning. One question yet to be addressed is: To what extent can these ice-crystal alignment signatures be used to nowcast the cessation of lightning activity in a given storm? Accordingly, data from the UAHuntsville Advanced Radar for Meteorological and Operational Research (ARMOR) along with the NASA-MSFC North Alabama Lightning Mapping Array are used in this study to investigate the radar signatures present before and after lightning cessation. Thus far, our case study results suggest that the negative differential phase shift signature weakens and disappears after the analyzed storms ceased lightning production (i.e., after the last lightning flash occurred). This is a key observation because it suggests that while strong electric fields may still have been present, the lightning cessation signature encompassed the period of the polarimetric negative phase shift signature. To the extent this behavior is repeatable in other cases, even if only in a substantial fraction of those cases, the case analyses suggests that differential propagation phase may prove to be a useful parameter for future lightning cessation algorithms. Indeed, analysis of 15+ cases has shown additional indications of the weakening and disappearance of this ice alignment signature with lightning cessation. A summary of results will be presented.

Laboratory study of effects of sonic boom shaping on subjective loudness and acceptability

NASA Technical Reports Server (NTRS)

Leatherwood, Jack D.; Sullivan, Brenda M.

1992-01-01

A laboratory study was conducted to determine the effects of sonic boom signature shaping on subjective loudness and acceptability. The study utilized the sonic boom simulator at the Langley Research Center. A wide range of symmetrical, front-shock-minimized signature shapes were investigated together with a limited number of asymmetrical signatures. Subjective loudness judgments were obtained from 60 test subjects by using an 11-point numerical category scale. Acceptability judgments were obtained using the method of constant stimuli. Results were used to assess the relative predictive ability of several noise metrics, determine the loudness benefits of detailed boom shaping, and derive laboratory sonic boom acceptability criteria. These results indicated that the A-weighted sound exposure level, the Stevens Mark 7 Perceived Level, and the Zwicker Loudness Level metrics all performed well. Significant reductions in loudness were obtained by increasing front-shock rise time and/or decreasing front-shock overpressure of the front-shock minimized signatures. In addition, the asymmetrical signatures were rated to be slightly quieter than the symmetrical front-shock-minimized signatures of equal A-weighted sound exposure level. However, this result was based on a limited number of asymmetric signatures. The comparison of laboratory acceptability results with acceptability data obtained in more realistic situations also indicated good agreement.

Beyond the scope of Free-Wilson analysis: building interpretable QSAR models with machine learning algorithms.

PubMed

Chen, Hongming; Carlsson, Lars; Eriksson, Mats; Varkonyi, Peter; Norinder, Ulf; Nilsson, Ingemar

2013-06-24

A novel methodology was developed to build Free-Wilson like local QSAR models by combining R-group signatures and the SVM algorithm. Unlike Free-Wilson analysis this method is able to make predictions for compounds with R-groups not present in a training set. Eleven public data sets were chosen as test cases for comparing the performance of our new method with several other traditional modeling strategies, including Free-Wilson analysis. Our results show that the R-group signature SVM models achieve better prediction accuracy compared with Free-Wilson analysis in general. Moreover, the predictions of R-group signature models are also comparable to the models using ECFP6 fingerprints and signatures for the whole compound. Most importantly, R-group contributions to the SVM model can be obtained by calculating the gradient for R-group signatures. For most of the studied data sets, a significant correlation with that of a corresponding Free-Wilson analysis is shown. These results suggest that the R-group contribution can be used to interpret bioactivity data and highlight that the R-group signature based SVM modeling method is as interpretable as Free-Wilson analysis. Hence the signature SVM model can be a useful modeling tool for any drug discovery project.

A Trusted Third-Party E-Payment Protocol Based on Quantum Blind Signature Without Entanglement

NASA Astrophysics Data System (ADS)

Guo, Xi; Zhang, Jian-Zhong; Xie, Shu-Cui

2018-06-01

In this paper, we present a trusted third-party e-payment protocol which is designed based on quantum blind signature without entanglement. The security and verifiability of our scheme are guaranteed by using single-particle unitary operation, quantum key distribution (QKD) protocol and one-time pad. Furthermore, once there is a dispute among the participants, it can be solved with the assistance of the third-party platform which is reliant.

An Identity Based Key Exchange Protocol in Cloud Computing

NASA Astrophysics Data System (ADS)

Molli, Venkateswara Rao; Tiwary, Omkar Nath

2012-10-01

Workflow systems often use delegation to enhance the flexibility of authorization; delegation transfers privileges among users across different administrative domains and facilitates information sharing. We present an independently verifiable delegation mechanism, where a delegation credential can be verified without the participation of domain administrators. This protocol, called role-based cascaded delegation (RBCD), supports simple and efficient cross-domain delegation of authority. RBCD enables a role member to create delegations based on the dynamic needs of collaboration; in the meantime, a delegation chain canbe verified by anyone without the participation of role administrators. We also propose the Measurable Risk Adaptive decentralized Role-based Delegation framework to address this problem. Describe an efficient realization of RBCD by using aggregate signatures, where the authentication information for an arbitrarily long role-based delegation chain is captured by one short signature of constant size. RBCD enables a role member to create delegations based on the need of collaboration; in the meantime anyone can verify a delegation chain without the participation of role administrators. The protocol is general and can be realized by any signature scheme. We have described a specific realization with a hierarchical certificate-based encryption scheme that gives delegation compact credentials.

Detection of Rooftop Cooling Unit Faults Based on Electrical Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armstrong, Peter R.; Laughman, C R.; Leeb, S B.

Non-intrusive load monitoring (NILM) is accomplished by sampling voltage and current at high rates and reducing the resulting start transients or harmonic contents to concise ''signatures''. Changes in these signatures can be used to detect, and in many cases directly diagnose, equipment and component faults associated with roof-top cooling units. Use of the NILM for fault detection and diagnosis (FDD) is important because (1) it complements other FDD schemes that are based on thermo-fluid sensors and analyses and (2) it is minimally intrusive (one measuring point in the relatively protected confines of the control panel) and therefore inherently reliable. Thismore » paper describes changes in the power signatures of fans and compressors that were found, experimentally and theoretically, to be useful for fault detection.« less