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  • Articles  (11,891)
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  • 2010-2014  (11,891)
  • Nucleic Acids Research  (3,764)
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  • 1
    Publication Date: 2013-09-07
    Description: Bile acid diarrhoea (BAD) is a common disease that requires expensive imaging to diagnose. We have tested the efficacy of a new method to identify BAD, based on the detection of differences in volatile organic compounds (VOC) in urine headspace of BAD vs. ulcerative colitis and healthy controls. A total of 110 patients were recruited; 23 with BAD, 42 with ulcerative colitis (UC) and 45 controls. Patients with BAD also received standard imaging (Se75HCAT) for confirmation. Urine samples were collected and the headspace analysed using an AlphaMOS Fox 4000 electronic nose in combination with an Owlstone Lonestar Field Asymmetric Ion Mobility Spectrometer (FAIMS). A subset was also tested by gas chromatography, mass spectrometry (GCMS). Linear Discriminant Analysis (LDA) was used to explore both the electronic nose and FAIMS data. LDA showed statistical differences between the groups, with reclassification success rates (using an n-1 approach) at typically 83%. GCMS experiments confirmed these results and showed that patients with BAD had two chemical compounds, 2-propanol and acetamide, that were either not present or were in much reduced quantities in the ulcerative colitis and control samples. We believe that this work may lead to a new tool to diagnose BAD, which is cheaper, quicker and easier that current methods.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
    Published by MDPI Publishing
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  • 2
    Publication Date: 2013-09-07
    Description: This paper is a theoretical analysis of mirror tilt in a Michelson interferometer and its effect on the radiant flux over the active area of a rectangular photodetector or image sensor pixel. It is relevant to sensor applications using homodyne interferometry where these opto-electronic devices are employed for partial fringe counting. Formulas are derived for radiant flux across the detector for variable location within the fringe pattern and with varying wave front angle. The results indicate that the flux is a damped sine function of the wave front angle, with a decay constant of the ratio of wavelength to detector width. The modulation amplitude of the dynamic fringe pattern reduces to zero at wave front angles that are an integer multiple of this ratio and the results show that the polarity of the radiant flux changes exclusively at these multiples. Varying tilt angle causes radiant flux oscillations under an envelope curve, the frequency of which is dependent on the location of the detector with the fringe pattern. It is also shown that a fringe count of zero can be obtained for specific photodetector locations and wave front angles where the combined effect of fringe contraction and fringe tilt can have equal and opposite effects. Fringe tilt as a result of a wave front angle of 0.05° can introduce a phase measurement difference of 16° between a photodetector/pixel located 20 mm and one located 100 mm from the optical origin.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 3
    Publication Date: 2013-09-11
    Description: In this study, a miniaturized high fundamental frequency quartz crystal microbalance (QCM) is fabricated for sensor applications using a wet etching technique. The vibration area is reduced in the fabrication of the high frequency QCM with an inverted mesa structure. To reduce the complexity of the side wall profile that results from anisotropic quartz etching, a rectangular vibration area is used instead of the conventional circular structure. QCMs with high Q values exceeding 25,000 at 47 MHz, 27,000 at 60 MHz, 24,000 at 73 MHz and 25,000 at 84 MHz are fabricated on 4 × 4 mm2 chips with small vibration areas of 1.2 × 1.4 mm2. A PMMA-based flow cell is designed and manufactured to characterize the behavior of the fabricated QCM chip in a liquid. Q values as high as 1,006 at 47 MHz, 904 at 62 MHz, 867 at 71 MHz and 747 at 84 MHz are obtained when one side of the chip is exposed to pure water. These results show that fabricated QCM chips can be used for bio- and chemical sensor applications in liquids.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 4
    Publication Date: 2013-09-11
    Description: Finger vein recognition is a promising biometric recognition technology, which verifies identities via the vein patterns in the fingers. Binary pattern based methods were thoroughly studied in order to cope with the difficulties of extracting the blood vessel network. However, current binary pattern based finger vein matching methods treat every bit of feature codes derived from different image of various individuals as equally important and assign the same weight value to them. In this paper, we propose a finger vein recognition method based on personalized weight maps (PWMs). The different bits have different weight values according to their stabilities in a certain number of training samples from an individual. Firstly we present the concept of PWM, and then propose the finger vein recognition framework, which mainly consists of preprocessing, feature extraction, and matching. Finally, we design extensive experiments to evaluate the effectiveness of our proposal. Experimental results show that PWM achieves not only better performance, but also high robustness and reliability. In addition, PWM can be used as a general framework for binary pattern based recognition.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 5
    Publication Date: 2013-09-11
    Description: The aim of this work is to study the sensing behavior of Sr-doped hematite for soil water content measurement. The material was prepared by solid state reaction from commercial hematite and strontium carbonate heat treated at 900 °C. X-Ray diffraction, scanning electron microscopy and mercury intrusion porosimetry were used for microstructural characterization of the synthesized powder. Sensors were then prepared by uniaxially pressing and by screen-printing, on an alumina substrate, the prepared powder and subsequent firing in the 800–1,000 °C range. These sensors were first tested in a laboratory apparatus under humid air and then in an homogenized soil and finally in field. The results evidenced that the screen printed film was able to give a response for a soil matric potential from about 570 kPa, that is to say well below the wilting point in the used soil.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 6
    Publication Date: 2013-09-12
    Description: Since the mechanical properties of single cells together with the intercellular adhesive properties determine the macro-mechanical properties of plants, a method for evaluation of the cell elastic properties is needed to help explanation of the behavior of fruits and vegetables in handling and food processing. For this purpose, indentation of tomato mesocarp cells with an atomic force microscope was used. The Young’s modulus of a cell using the Hertz and Sneddon models, and stiffness were calculated from force-indentation curves. Use of two probes of distinct radius of curvature (20 nm and 10,000 nm) showed that the measured elastic properties were significantly affected by tip geometry. The Young’s modulus was about 100 kPa ± 35 kPa and 20 kPa ± 14 kPa for the sharper tip and a bead tip, respectively. Moreover, large variability regarding elastic properties (>100%) among cells sampled from the same region in the fruit was observed. We showed that AFM provides the possibility of combining nano-mechanical properties with topography imaging, which could be very useful for the study of structure-related properties of fruits and vegetables at the cellular and sub-cellular scale.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 7
    Publication Date: 2013-09-12
    Description: Active magnetic bearings (AMBs) have become a key technology in various industrial applications. Self-sensing AMBs provide an integrated sensorless solution for position estimation, consolidating the sensing and actuating functions into a single electromagnetic transducer. The approach aims to reduce possible hardware failure points, production costs, and system complexity. Despite these advantages, self-sensing methods must address various technical challenges to maximize the performance thereof. This paper presents the direct current measurement (DCM) approach for self-sensing AMBs, denoting the direct measurement of the current ripple component. In AMB systems, switching power amplifiers (PAs) modulate the rotor position information onto the current waveform. Demodulation self-sensing techniques then use bandpass and lowpass filters to estimate the rotor position from the voltage and current signals. However, the additional phase-shift introduced by these filters results in lower stability margins. The DCM approach utilizes a novel PA switching method that directly measures the current ripple to obtain duty-cycle invariant position estimates. Demodulation filters are largely excluded to minimize additional phase-shift in the position estimates. Basic functionality and performance of the proposed self-sensing approach are demonstrated via a transient simulation model as well as a high current (10 A) experimental system. A digital implementation of amplitude modulation self-sensing serves as a comparative estimator.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 8
    Publication Date: 2013-09-12
    Description: The stability of radiance measurements taken by the Sky Quality Meter (SQM)was tested under rapidly changing temperature conditions during exposure to a stable lightfield in the laboratory. The reported radiance was found to be negatively correlated withtemperature, but remained within 7% of the initial reported radiance over a temperaturerange of -15 °C to 35 °C, and during temperature changes of -33 °C/h and +70 °C/h.This is smaller than the manufacturer’s quoted unit-to-unit systematic uncertainty of 10%,indicating that the temperature compensation of the SQM is adequate under expected outdooroperating conditions.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 9
    Publication Date: 2013-09-13
    Description: This paper investigates the linear separation requirements for Angle-of-Arrival (AoA) and range sensors, in order to achieve the optimal performance in estimating the position of a target from multiple and typically noisy sensor measurements. We analyse the sensor-target geometry in terms of the Cramer–Rao inequality and the corresponding Fisher information matrix, in order to characterize localization performance with respect to the linear spatial distribution of sensors. Here in this paper, we consider both fixed and adjustable linear sensor arrays.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 10
    Publication Date: 2013-09-13
    Description: The problem of drifting charge-induced currents is considered in order to predict the pulsed operational characteristics in photo-and particle-detectors with a junction controlled active area. The direct analysis of the field changes induced by drifting charge in the abrupt junction devices with a plane-parallel geometry of finite area electrodes is presented. The problem is solved using the one-dimensional approach. The models of the formation of the induced pulsed currents have been analyzed for the regimes of partial and full depletion. The obtained solutions for the current density contain expressions of a velocity field dependence on the applied voltage, location of the injected surface charge domain and carrier capture parameters. The drift component of this current coincides with Ramo’s expression. It has been illustrated, that the synchronous action of carrier drift, trapping, generation and diffusion can lead to a vast variety of possible current pulse waveforms. Experimental illustrations of the current pulse variations determined by either the rather small or large carrier density within the photo-injected charge domain are presented, based on a study of Si detectors.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 11
    Publication Date: 2013-09-13
    Description: A visible light communication (VLC) system using an organic bulk heterojunction photodetector (OPD) is presented. The system has been successfully proven indoors with an audio signal. The emitter consists of three commercial high-power white LEDs connected in parallel. The receiver is based on an organic photodetector having as active layer a blend of poly(3-hexylthiophene) (P3HT) and phenyl C61-butyric acid methyl ester (PCBM). The OPD is opto-electrically characterized, showing a responsivity of 0.18 A/W and a modulation response of 790 kHz at −6 V.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 12
    Publication Date: 2013-09-14
    Description: Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW) biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 13
    Publication Date: 2013-09-14
    Description: Hull cleaning before repainting is a key operation in the maintenance of ships. For years, a method to improve such operation has been sought by means of the robotization of techniques such as grit blasting and ultra high pressure water jetting. Despite this, it continues to be standard practice in shipyards that this process is carried out manually because the developed robotized systems are too expensive to be widely accepted by shipyards. We have chosen to apply a more conservative and realistic approach to this problem, which has resulted in the development of several solutions that have been designed with different automation and operation range degrees. These solutions are fitted with most of the elements already available in many shipyards, so the installation of additional machinery in the workplace would not be necessary. This paper describes the evolutionary development of sensor systems for the automation of the preparation process of ship hull surfaces before the painting process is performed. Such evolution has given rise to the development of new technologies for coating removal.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 14
    Publication Date: 2013-09-14
    Description: Stress corrosion cracks (SCC) in low-pressure steam turbine discs are serious hidden dangers to production safety in the power plants, and knowing the orientation and depth of the initial cracks is essential for the evaluation of the crack growth rate, propagation direction and working life of the turbine disc. In this paper, a method based on phased array ultrasonic transducer and artificial neural network (ANN), is proposed to estimate both the depth and orientation of initial cracks in the turbine discs. Echo signals from cracks with different depths and orientations were collected by a phased array ultrasonic transducer, and the feature vectors were extracted by wavelet packet, fractal technology and peak amplitude methods. The radial basis function (RBF) neural network was investigated and used in this application. The final results demonstrated that the method presented was efficient in crack estimation tasks.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 15
    Publication Date: 2013-09-24
    Description: The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular “identity.” This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 16
    Publication Date: 2013-09-26
    Description: We have developed a new screening methodology for identifying all genes that control the expression of a target gene through genetic or metabolic interactions. The screen combines mutant libraries with luciferase reporter constructs, whose expression can be monitored in vivo and over time in different environmental conditions. We apply the method to identify the genes that control the expression of the gene acs , encoding the acetyl coenzyme A synthetase, in Escherichia coli . We confirm most of the known genetic regulators, including CRP–cAMP, IHF and components of the phosphotransferase system. In addition, we identify new regulatory interactions, many of which involve metabolic intermediates or metabolic sensing, such as the genes pgi, pfkA , sucB and lpdA , encoding enzymes in glycolysis and the TCA cycle. Some of these novel interactions were validated by quantitative reverse transcriptase-polymerase chain reaction. More generally, we observe that a large number of mutants directly or indirectly influence acs expression, an effect confirmed for a second promoter, sdhC . The method is applicable to any promoter fused to a luminescent reporter gene in combination with a deletion mutant library.
    Keywords: Genomics, Transcriptome Mapping - Monitoring Gene Expression
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    Electronic ISSN: 1362-4962
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  • 17
    Publication Date: 2013-09-26
    Description: Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.
    Keywords: Computational Methods, Genomics
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  • 18
    Publication Date: 2013-09-26
    Description: A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
    Keywords: RNA characterisation and manipulation
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  • 19
    Publication Date: 2013-09-26
    Description: The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary significantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete understanding of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as translation, being more robust than those linked to regulation. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression.
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  • 20
    Publication Date: 2013-09-26
    Description: Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein–binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap .
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  • 21
    Publication Date: 2013-09-26
    Description: Escherichia coli Exonuclease IX (ExoIX), encoded by the xni gene, was the first identified member of a novel subfamily of ubiquitous flap endonucleases (FENs), which possess only one of the two catalytic metal-binding sites characteristic of other FENs. We have solved the first structure of one of these enzymes, that of ExoIX itself, at high resolution in DNA-bound and DNA-free forms. In the enzyme–DNA cocrystal, the single catalytic site binds two magnesium ions. The structures also reveal a binding site in the C-terminal domain where a potassium ion is directly coordinated by five main chain carbonyl groups, and we show this site is essential for DNA binding. This site resembles structurally and functionally the potassium sites in the human FEN1 and exonuclease 1 enzymes. Fluorescence anisotropy measurements and the crystal structures of the ExoIX:DNA complexes show that this potassium ion interacts directly with a phosphate diester in the substrate DNA.
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  • 22
    Publication Date: 2013-09-26
    Description: One of the obstacles hindering a better understanding of cancer is its heterogeneity. However, computational approaches to model cancer heterogeneity have lagged behind. To bridge this gap, we have developed a new probabilistic approach that models individual cancer cases as mixtures of subtypes. Our approach can be seen as a meta-model that summarizes the results of a large number of alternative models. It does not assume predefined subtypes nor does it assume that such subtypes have to be sharply defined. Instead given a measure of phenotypic similarity between patients and a list of potential explanatory features, such as mutations, copy number variation, microRNA levels, etc., it explains phenotypic similarities with the help of these features. We applied our approach to Glioblastoma Multiforme (GBM). The resulting model Prob_GBM, not only correctly inferred known relationships but also identified new properties underlining phenotypic similarities. The proposed probabilistic framework can be applied to model relations between similarity of gene expression and a broad spectrum of potential genetic causes.
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  • 23
    Publication Date: 2013-09-26
    Description: Estrogen regulates over a thousand genes, with an equal number of them being induced or repressed. The distinct mechanisms underlying these dual transcriptional effects remain largely unknown. We derived comprehensive views of the transcription machineries assembled at estrogen-responsive genes through integrating multiple types of genomic data. In the absence of estrogen, the majority of genes formed higher-order chromatin structures, including DNA loops tethered to protein complexes involving RNA polymerase II (Pol II), estrogen receptor alpha (ERα) and ERα-pioneer factors. Genes to be ‘repressed’ by estrogen showed active transcription at promoters and throughout the gene bodies; genes to be ‘induced’ exhibited active transcription initiation at promoters, but with transcription paused in gene bodies. In the presence of estrogen, the majority of estrogen-induced genes retained the original higher-order chromatin structures, whereas most estrogen-repressed genes underwent a chromatin reconfiguration. For estrogen-induced genes, estrogen enhances transcription elongation, potentially through recruitment of co-activators or release of co-repressors with unique roles in elongation. For estrogen-repressed genes, estrogen treatment leads to chromatin structure reconfiguration, thereby disrupting the originally transcription-efficient chromatin structures. Our in silico studies have shown that estrogen regulates gene expression, at least in part, through modifying previously assembled higher-order complexes, rather than by facilitating de novo assembly of machineries.
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  • 24
    Publication Date: 2013-09-26
    Description: The mineralocorticoid receptor (MR) is a ligand-induced transcription factor belonging to the steroid receptor family and involved in water-electrolyte homeostasis, blood pressure regulation, inflammation and fibrosis in the renocardiovascular system. The MR shares a common hormone-response-element with the glucocorticoid receptor but nevertheless elicits MR-specific effects including enhanced epidermal growth factor receptor (EGFR) expression via unknown mechanisms. The EGFR is a receptor tyrosine kinase that leads to activation of MAP kinases, but that can also function as a signal transducer for other signaling pathways. In the present study, we mechanistically investigate the interaction between a newly discovered MR- but not glucocorticoid receptor- responsive-element (=MRE1) of the EGFR promoter, specificity protein 1 (SP1) and MR to gain general insights into MR-specificity. Biological relevance of the interaction for EGFR expression and consequently for different signaling pathways in general is demonstrated in human, rat and murine vascular smooth muscle cells and cells of EGFR knockout mice. A genome-wide promoter search for identical binding regions followed by quantitative PCR validation suggests that the identified MR-SP1–MRE1 interaction might be applicable to other genes. Overall, a novel principle of MR-specific gene expression is explored that applies to the pathophysiologically relevant expression of the EGFR and potentially also to other genes.
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  • 25
    Publication Date: 2013-09-26
    Description: Selective inhibitory crosstalk has been known to occur within the signaling pathways of the dioxin (AhR) and estrogen (ERα) receptors. More specifically, ERα represses a cytochrome P450-encoding gene ( CYP1A1 ) that converts cellular estradiol into a metabolite that inhibits the cell cycle, while it has no effect on a P450-encoding gene ( CYP1B1 ) that converts estrodiol into a genotoxic product. Here we show that ERα represses CYP1A1 by targeting the Dnmt3B DNA methyltransferase and concomitant DNA methylation of the promoter. We also find that histone H2A.Z can positively contribute to CYP1A1 gene expression, and its presence at that gene is inversely correlated with DNA methylation. Taken together, our results provide a framework for how ERα can repress transcription, and how that impinges on the production of an enzyme that generates genotoxic estradiol metabolites, and potential breast cancer progression. Finally, our results reveal a new mechanism for how H2A.Z can positively influence gene expression, which is by potentially competing with DNA methylation events in breast cancer cells.
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  • 26
    Publication Date: 2013-09-26
    Description: TFIIIB and TFIIIC are multi-subunit factors required for transcription by RNA polymerase III. We present a genome-wide high-resolution footprint map of TFIIIB–TFIIIC complexes in Saccharomyces cerevisiae , obtained by paired-end sequencing of micrococcal nuclease-resistant DNA. On tRNA genes, TFIIIB and TFIIIC form stable complexes with the same distinctive occupancy pattern but in mirror image, termed ‘bootprints’. Global analysis reveals that the TFIIIB–TFIIIC transcription complex exhibits remarkable structural elasticity: tRNA genes vary significantly in length but remain protected by TFIIIC. Introns, when present, are markedly less protected. The RNA polymerase III transcription terminator is flexibly accommodated within the transcription complex and, unexpectedly, plays a major structural role by delimiting its 3'-boundary. The ETC sites, where TFIIIC binds without TFIIIB, exhibit different bootprints, suggesting that TFIIIC forms complexes involving other factors. We confirm six ETC sites and report a new site ( ETC10 ). Surprisingly, TFIIIC, but not TFIIIB, interacts with some centromeric nucleosomes, suggesting that interactions between TFIIIC and the centromere may be important in the 3D organization of the nucleus.
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  • 27
    Publication Date: 2013-09-26
    Description: The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.
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  • 28
    Publication Date: 2013-09-26
    Description: Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the regulation of H4S47ph levels was unknown. Here, we show that three phosphatases (PP1α, PP1β and Wip1) regulate H4S47ph levels and H3.3 deposition. Depletion of each of the three phosphatases results in increased H4S47ph levels. Moreover, PP1α, PP1β and Wip1 bind H3-H4 in vitro and in vivo , whereas only PP1α and PP1β, but not Wip1, interact with Pak2 in vivo . These results suggest that PP1α, PP1β and Wip1 regulate the levels of H4S47ph through directly acting on H4S47ph, with PP1α and PP1β also likely regulating the activity of Pak2. Finally, depletion of PP1α, PP1β and Wip1 leads to increased H3.3 occupancy at candidate genes tested, elevated H3.3 deposition and enhanced association of H3.3 with its chaperones HIRA and Daxx. These results reveal a novel role of three phosphatases in chromatin dynamics in mammalian cells.
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  • 29
    Publication Date: 2013-09-26
    Description: Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe . Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 form co-localizing methyl methanesulphonate–induced foci in nuclei, further suggesting they function as a complex. To place the Rrp1/2 proteins more accurately within HR sub-pathways, we carried out extensive epistasis analysis between mutants defining Rrp1/2, Rad51 (recombinase), Swi5 and Rad57 (HR-mediators) plus the anti-recombinogenic helicases Srs2 and Rqh1. We confirm that Rrp1 and Rrp2 act together with Srs2 and Swi5 and independently of Rad57 and show that Rqh1 also acts independently of Rrp1/2. Mutants devoid of Srs2 are characterized by elevated recombination frequency with a concomitant increase in the percentage of conversion-type recombinants. Strains devoid of Rrp1 or Rrp2 did not show a change in HR frequency, but the number of conversion-type recombinants was increased, suggesting a possible function for Rrp1/2 with Srs2 in counteracting Rad51 activity. Our data allow us to propose a model placing Rrp1 and Rrp2 functioning together with Swi5 and Srs2 in a synthesis-dependent strand annealing HR repair pathway.
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  • 30
    Publication Date: 2013-09-26
    Description: In eukaryotic cells, gene expression is mediated by enhancer activation of RNA polymerase at distant promoters. Recently, distinctions between enhancers and promoters have been blurred by the discovery that enhancers are associated with RNA polymerase and are sites of RNA synthesis. Here, we present an analysis of the insulin-like growth factor 2/H19 muscle enhancer. This enhancer includes a short conserved core element that is organized into chromatin typical of mammalian enhancers, binds tissue-specific transcription factors and functions on its own in vitro to activate promoter transcription. However, in a chromosomal context, this element is not sufficient to activate distant promoters. Instead, enhancer function also requires transcription in cis of a long non-coding RNA, Nctc1 . Thus, the insulin-like growth factor 2/H19 enhancer is an active transcriptional complex whose own transcription is essential to its function.
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  • 31
    Publication Date: 2013-09-26
    Description: Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies 〉4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1 . This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.
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  • 32
    Publication Date: 2013-09-26
    Description: The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.
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  • 33
    Publication Date: 2013-09-26
    Description: RNA-based therapeutic approaches using splice-switching oligonucleotides have been successfully applied to rescue dystrophin in Duchenne muscular dystrophy (DMD) preclinical models and are currently being evaluated in DMD patients. Although the modular structure of dystrophin protein tolerates internal deletions, many mutations that affect nondispensable domains of the protein require further strategies. Among these, trans -splicing technology is particularly attractive, as it allows the replacement of any mutated exon by its normal version as well as introducing missing exons or correcting duplication mutations. We have applied such a strategy in vitro by using cotransfection of pre– trans -splicing molecule (PTM) constructs along with a reporter minigene containing part of the dystrophin gene harboring the stop-codon mutation found in the mdx mouse model of DMD. Optimization of the different functional domains of the PTMs allowed achieving accurate and efficient trans -splicing of up to 30% of the transcript encoded by the cotransfected minigene. Optimized parameters included mRNA stabilization, choice of splice site sequence, inclusion of exon splice enhancers and artificial intronic sequence. Intramuscular delivery of adeno-associated virus vectors expressing PTMs allowed detectable levels of dystrophin in mdx and mdx4Cv , illustrating that a given PTM can be suitable for a variety of mutations.
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  • 34
    Publication Date: 2013-09-26
    Description: Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast.
    Electronic ISSN: 1424-8220
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  • 35
    Publication Date: 2013-09-26
    Description: This paper presents a bio-inspired networking strategy to support the cooperation between static sensors on the ground and mobile sensors in the air to perform surveillance missions in large areas. The goal of the proposal is to provide low overhead in the communication among sensor nodes, while allocating the mobile sensors to perform sensing activities requested by the static ones. Simulations have shown that the strategy is efficient in maintaining low overhead and achieving the desired coordination.
    Electronic ISSN: 1424-8220
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  • 36
    Publication Date: 2013-09-26
    Description: In the face recognition field, principal component analysis is essential to the reduction of the image dimension. In spite of frequent use of this analysis, it is commonly believed that the basis faces with large eigenvalues are chosen as the best subset in the nearest neighbor classifiers. We propose an alternative that can predict the classification error during the training steps and find the useful basis faces for the similarity metrics of the classical pattern algorithms. In addition, we also show the need for the eye-aligned dataset to have the pure face. The experiments using face images verify that our method reduces the negative effect on the misaligned face images and decreases the weights of the useful basis faces in order to improve the classification accuracy.
    Electronic ISSN: 1424-8220
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  • 37
    Publication Date: 2013-09-26
    Description: Automatic detection of pig wasting diseases is an important issue in the management of group-housed pigs. Further, respiratory diseases are one of the main causes of mortality among pigs and loss of productivity in intensive pig farming. In this study, we propose an efficient data mining solution for the detection and recognition of pig wasting diseases using sound data in audio surveillance systems. In this method, we extract the Mel Frequency Cepstrum Coefficients (MFCC) from sound data with an automatic pig sound acquisition process, and use a hierarchical two-level structure: the Support Vector Data Description (SVDD) and the Sparse Representation Classifier (SRC) as an early anomaly detector and a respiratory disease classifier, respectively. Our experimental results show that this new method can be used to detect pig wasting diseases both economically (even a cheap microphone can be used) and accurately (94% detection and 91% classification accuracy), either as a standalone solution or to complement known methods to obtain a more accurate solution.
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  • 38
    Publication Date: 2013-09-26
    Description: Automated methods of real-time, unobtrusive, human ambulation, activity, and wellness monitoring and data analysis using various algorithmic techniques have been subjects of intense research. The general aim is to devise effective means of addressing the demands of assisted living, rehabilitation, and clinical observation and assessment through sensor-based monitoring. The research studies have resulted in a large amount of literature. This paper presents a holistic articulation of the research studies and offers comprehensive insights along four main axes: distribution of existing studies; monitoring device framework and sensor types; data collection, processing and analysis; and applications, limitations and challenges. The aim is to present a systematic and most complete study of literature in the area in order to identify research gaps and prioritize future research directions.
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  • 39
    Publication Date: 2013-10-01
    Description: The corrosion of reinforcements induced by chloride has resulted to be one of the most frequent causes of their premature damage. Most corrosion sensors were designed to monitor corrosion state in concrete, such as Anode-Ladder-System and Corrowatch System, which are widely used to monitor chloride ingress in marine concrete. However, the monitoring principle of these corrosion sensors is based on the macro-cell test method, so erroneous information may be obtained, especially from concrete under drying or saturated conditions due to concrete resistance taking control in macro-cell corrosion. In this paper, a fast weak polarization method to test corrosion state of reinforcements based on electrochemical polarization dynamics was proposed. Furthermore, a new corrosion sensor for monitoring the corrosion state of concrete cover was developed based on the proposed test method. The sensor was tested in cement mortar, with dry-wet cycle tests to accelerate the chloride ingress rate. The results show that the corrosion sensor can effectively monitor chloride penetration into concrete with little influence of the relative humidity in the concrete. With a reasonable corrosion sensor electrode arrangement, it seems the Ohm-drop effect measured by EIS can be ignored, which makes the tested electrochemical parameters more accurate.
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  • 40
    Publication Date: 2013-10-01
    Description: This study describes a wireless laser displacement sensor node that measures displacement as a representative damage index for structural health monitoring (SHM). The proposed measurement system consists of a laser displacement sensor (LDS) and a customized wireless sensor node. Wireless communication is enabled by a sensor node that consists of a sensor module, a code division multiple access (CDMA) communication module, a processor, and a power module. An LDS with a long measurement distance is chosen to increase field applicability. For a wireless sensor node driven by a battery, we use a power control module with a low-power processor, which facilitates switching between the sleep and active modes, thus maximizing the power consumption efficiency during non-measurement and non-transfer periods. The CDMA mode is also used to overcome the limitation of communication distance, which is a challenge for wireless sensor networks and wireless communication. To evaluate the reliability and field applicability of the proposed wireless displacement measurement system, the system is tested onsite to obtain the required vertical displacement measurements during the construction of mega-trusses and an edge truss, which are the primary structural members in a large-scale irregular building currently under construction. The measurement values confirm the validity of the proposed wireless displacement measurement system and its potential for use in safety evaluations of structural elements.
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  • 41
    Publication Date: 2013-10-01
    Description: Bacterial cell-to-cell communication (quorum sensing) refers to the regulation of bacterial gene expression in response to changes in microbial population density. Quorum sensing bacteria produce, release and respond to chemical signal molecules called autoinducers. Bacteria use two types of autoinducers, namely autoinducer-1 (AI-1) and autoinducer-2 (AI-2) where the former are N-acylhomoserine lactones and the latter is a product of the luxS gene. Most of the reported literatures show that the majority of oral bacteria use AI-2 for quorum sensing but rarely the AI-1 system. Here we report the isolation of Pseudomonas putida strain T2-2 from the oral cavity. Using high resolution mass spectrometry, it is shown that this isolate produced N-octanoylhomoserine lactone (C8-HSL) and N-dodecanoylhomoserine lactone (C12-HSL) molecules. This is the first report of the finding of quorum sensing of P. putida strain T2-2 isolated from the human tongue surface and their quorum sensing molecules were identified.
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  • 42
    Publication Date: 2013-10-01
    Description: Presented here is a slotted-quad-beam structure sensor for the measurement of friction in micro bearings. Stress concentration slots are incorporated into a conventional quad-beam structure to improve the sensitivity of force measurements. The performance comparison between the quad-beam structure sensor and the slotted-quad-beam structure sensor are performed by theoretical modeling and finite element (FE) analysis. A hollow stainless steel probe is attached to the mesa of the sensor chip by a tailor-made organic glass fixture. Concerning the overload protection of the fragile beams, a glass wafer is bonded onto the bottom of sensor chip to limit the displacement of the mesa. The calibration of the packaged device is experimentally performed by a tri-dimensional positioning stage, a precision piezoelectric ceramic and an electronic analytical balance, which indicates its favorable sensitivity and overload protection. To verify the potential of the proposed sensor being applied in micro friction measurement, a measurement platform is established. The output of the sensor reflects the friction of bearing resulting from dry friction and solid lubrication. The results accord with the theoretical modeling and demonstrate that the sensor has the potential application in measuring the micro friction force under stable stage in MEMS machines.
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  • 43
    Publication Date: 2013-10-01
    Description: A novel approach for identifying explosive species is reported, using Raman spectroscopy in suspended core optical fibers. Numerical simulations are presented that predict the strength of the observed signal as a function of fiber geometry, with the calculated trends verified experimentally and used to optimize the sensors. This technique is used to identify hydrogen peroxide in water solutions at volumes less than 60 nL and to quantify microgram amounts of material using the solvent’s Raman signature as an internal calibration standard. The same system, without further modifications, is also used to detect 1,4-dinitrobenzene, a model molecule for nitrobenzene-based explosives such as 2,4,6-trinitrotoluene (TNT).
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  • 44
    Publication Date: 2013-10-01
    Description: In the bacteria kingdom, quorum sensing (QS) is a cell-to-cell communication that relies on the production of and response to specific signaling molecules. In proteobacteria, N-acylhomoserine lactones (AHLs) are the well-studied signaling molecules. The present study aimed to characterize the production of AHL of a bacterial strain A9 isolated from a Malaysian tropical soil. Strain A9 was identified as Burkholderia sp. using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rDNA nucleotide sequence analysis. AHL production by A9 was detected with two biosensors, namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Thin layer chromatography results showed N–hexanoylhomoserine lactone (C6-HSL) and N–octanoylhomoserine lactone (C8-HSL) production. Unequivocal identification of C6-HSL and C8-HSL was achieved by high resolution triple quadrupole liquid chromatography-mass spectrometry analysis. We have demonstrated that Burkholderia sp. strain A9 produces AHLs that are known to be produced by other Burkholderia spp. with CepI/CepR homologs.
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  • 45
    Publication Date: 2013-10-02
    Description: In this paper, we present an approach to sense human body capacitance and apply it to recognize lower limb locomotion modes. The proposed wearable sensing system includes sensing bands, a signal processing circuit and a gait event detection module. Experiments on long-term working stability, adaptability to disturbance and locomotion mode recognition are carried out to validate the effectiveness of the proposed approach. Twelve able-bodied subjects are recruited, and eleven normal gait modes are investigated. With an event-dependent linear discriminant analysis classifier and feature selection procedure, four time-domain features are used for pattern recognition and satisfactory recognition accuracies (97:3% ± 0:5%, 97:0% ± 0:4%, 95:6% ± 0:9% and 97:0% ± 0:4% for four phases of one gait cycle respectively) are obtained. The accuracies are comparable with that from electromyography-based systems and inertial-based systems. The results validate the effectiveness of the proposed lower limb capacitive sensing approach in recognizing human normal gaits.
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  • 46
    Publication Date: 2013-10-02
    Description: Projector-camera systems are currently used in a wide field of applications, such as 3D reconstruction and augmented reality, and can provide accurate measurements, depending on the configuration and calibration. Frequently, the calibration task is divided into two steps: camera calibration followed by projector calibration. The latter still poses certain problems that are not easy to solve, such as the difficulty in obtaining a set of 2D–3D points to compute the projection matrix between the projector and the world. Existing methods are either not sufficiently accurate or not flexible. We propose an easy and automatic method to calibrate such systems that consists in projecting a calibration pattern and superimposing it automatically on a known printed pattern. The projected pattern is provided by a virtual camera observing a virtual pattern in an OpenGL model. The projector displays what the virtual camera visualizes. Thus, the projected pattern can be controlled and superimposed on the printed one with the aid of visual servoing. Our experimental results compare favorably with those of other methods considering both usability and accuracy.
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  • 47
    Publication Date: 2013-10-03
    Description: The world-wide sensor web has become a very useful technique for monitoring the physical world at spatial and temporal scales that were previously impossible. Yet we believe that the full potential of sensor web has thus far not been revealed. In order to harvest the world-wide sensor web’s full potential, a geospatial cyberinfrastructure is needed to store, process, and deliver large amount of sensor data collected worldwide. In this paper, we first define the issue of the sensor web long tail followed by our view of the world-wide sensor web architecture. Then, we introduce the Geospatial Cyberinfrastructure for Environmental Sensing (GeoCENS) architecture and explain each of its components. Finally, with demonstration of three real-world powered-by-GeoCENS sensor web applications, we believe that the GeoCENS architecture can successfully address the sensor web long tail issue and consequently realize the world-wide sensor web vision.
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  • 48
    Publication Date: 2013-09-10
    Description: Impact detection in aeronautical structures allows predicting their future reliability and performance. An impact can produce microscopic fissures that could evolve into fractures or even the total collapse of the structure, so it is important to know the location and severity of each impact. For this purpose, optical fibers with Bragg gratings are used to analyze each impact and the vibrations generated by them. In this paper it is proven that optical fibers with Bragg gratings can be used to detect impacts, and also that a high-frequency interrogator is necessary to collect valuable information about the impacts. The use of two interrogators constitutes the main novelty of this paper.
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  • 49
    Publication Date: 2013-09-10
    Description: The Rational Function Model (RFM) has been widely used as an alternative to rigorous sensor models of high-resolution optical imagery in photogrammetry and remote sensing geometric processing. However, not much work has been done to evaluate the applicability of the RF model for Synthetic Aperture Radar (SAR) image processing. This paper investigates how to generate a Rational Polynomial Coefficient (RPC) for high-resolution TerraSAR-X imagery using an independent approach. The experimental results demonstrate that the RFM obtained using the independent approach fits the Range-Doppler physical sensor model with an accuracy of greater than 10−3 pixel. Because independent RPCs indicate absolute errors in geolocation, two methods can be used to improve the geometric accuracy of the RFM. In the first method, Ground Control Points (GCPs) are used to update SAR sensor orientation parameters, and the RPCs are calculated using the updated parameters. Our experiment demonstrates that by using three control points in the corners of the image, an accuracy of 0.69 pixels in range and 0.88 pixels in the azimuth direction is achieved. For the second method, we tested the use of an affine model for refining RPCs. In this case, by applying four GCPs in the corners of the image, the accuracy reached 0.75 pixels in range and 0.82 pixels in the azimuth direction.
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  • 50
    Publication Date: 2013-09-10
    Description: Currently there are a few fields of application using quartz crystal microbalances (QCM). Because of environmental conditions and insufficient resolution of the microbalance, chemical sensing of volatile organic compounds in an open system was as yet not possible. In this study we present strategies on how to use 195 MHz fundamental quartz resonators for a mobile sensor platform to detect airborne analytes. Commonly the use of devices with a resonant frequency of about 10 MHz is standard. By increasing the frequency to 195 MHz the frequency shift increases by a factor of almost 400. Unfortunately, such kinds of quartz crystals tend to exhibit some challenges to obtain a reasonable signal-to-noise ratio. It was possible to reduce the noise in frequency in a continuous air flow of 7.5 m/s to 0.4 Hz [i.e., σ(τ) = 2 × 10−9] by elucidating the major source of noise. The air flow in the vicinity of the quartz was analyzed to reduce turbulences. Furthermore, we found a dependency between the acceleration sensitivity and mechanical stress induced by an internal thermal gradient. By reducing this gradient, we achieved reduction of the sensitivity to acceleration by more than one decade. Hence, the resulting sensor is more robust to environmental conditions such as temperature, acceleration and air flow.
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  • 51
    Publication Date: 2013-09-10
    Description: In this study, readily available antibodies that are used in standard agglutination tests were evaluated for their use in ABO blood typing by a surface plasmon resonance imaging (SPR imaging) technique. Five groups of antibodies, including mixed clones of anti-A, anti-B, and anti-AB, and single clones of anti-A and anti-B, were used to construct the five-line detection arrays using a multichannel flow cell in the SPR imager. The red blood cell (RBC) samples were applied to a multichannel flow cell that was orthogonal to the detection line arrays for blood group typing. We found that the blood samples were correctly grouped in less than 12 min by the SPR imaging technique, and the results were consistent with those of the standard agglutination technique for all 60 samples. We found that mixed clones of antibodies provided 33%–68% greater change in the SPR signal than the single-clone antibodies. Applying the SPR imaging technique using readily available antibodies may reduce the costs of the antibodies, shorten the measurement time, and increase the throughput.
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  • 52
    Publication Date: 2013-09-10
    Description: In the case of through-the-wall localization of moving targets by ultra wideband (UWB) radars, there are applications in which handheld sensors equipped only with one transmitting and two receiving antennas are applied. Sometimes, the radar using such a small antenna array is not able to localize the target with the required accuracy. With a view to improve through-the-wall target localization, cooperative positioning based on a fusion of data retrieved from two independent radar systems can be used. In this paper, the novel method of the cooperative localization referred to as joining intersections of the ellipses is introduced. This method is based on a geometrical interpretation of target localization where the target position is estimated using a properly created cluster of the ellipse intersections representing potential positions of the target. The performance of the proposed method is compared with the direct calculation method and two alternative methods of cooperative localization using data obtained by measurements with the M-sequence UWB radars. The direct calculation method is applied for the target localization by particular radar systems. As alternative methods of cooperative localization, the arithmetic average of the target coordinates estimated by two single independent UWB radars and the Taylor series method is considered.
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  • 53
    Publication Date: 2013-09-10
    Description: In this paper, different polymer optical fibres for applications in force sensing systems in textile fabrics are reported. The proposed method is based on the deflection of the light in fibre waveguides. Applying a force on the fibre changes the geometry and affects the wave guiding properties and hence induces light loss in the optical fibre. Fibres out of three different elastic and transparent copolymer materials were successfully produced and tested. Moreover, the influence of the diameter on the sensing properties was studied. The detectable force ranges from 0.05 N to 40 N (applied on 3 cm of fibre length), which can be regulated with the material and the diameter of the fibre. The detected signal loss varied from 0.6% to 78.3%. The fibres have attenuation parameters between 0.16–0.25 dB/cm at 652 nm. We show that the cross-sensitivies to temperature, strain and bends are low. Moreover, the high yield strength (0.0039–0.0054 GPa) and flexibility make these fibres very attractive candidates for integration into textiles to form wearable sensors, medical textiles or even computing systems.
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  • 54
    Publication Date: 2013-09-10
    Description: Proton Transfer Reaction Mass Spectrometry (PTR-MS) has evolved in the last decade as a fast and high sensitivity sensor for the real-time monitoring of volatile compounds. Its applications range from environmental sciences to medical sciences, from food technology to bioprocess monitoring. Italian scientists and institutions participated from the very beginning in fundamental and applied research aiming at exploiting the potentialities of this technique and providing relevant methodological advances and new fundamental indications. In this review we describe this activity on the basis of the available literature. The Italian scientific community has been active mostly in food science and technology, plant physiology and environmental studies and also pioneered the applications of the recently released PTR-ToF-MS (Proton Transfer Reaction—Time of Flight—Mass Spectrometry) in food science and in plant physiology. In the very last years new results related to bioprocess monitoring and health science have been published as well. PTR-MS data analysis, particularly in the case of the ToF based version, and the application of advanced chemometrics and data mining are also aspects characterising the activity of the Italian community.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 55
    Publication Date: 2013-09-11
    Description: Agriculture and Forestry are two broad and promising areas demanding technological solutions with the aim of increasing production or accurate inventories for sustainability while the environmental impact is minimized by reducing the application of agro-chemicals and increasing the use of environmental friendly agronomical practices. In addition, the immediate consequence of this “trend” is the reduction of production costs.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 56
    Publication Date: 2013-09-11
    Description: Large amounts of low-grade heat are emitted by various industries and exhausted into the environment. This heat energy can be used as a free source for pyroelectric power generation. A three-dimensional pattern helps to improve the temperature variation rates in pyroelectric elements by means of lateral temperature gradients induced on the sidewalls of the responsive elements. A novel method using sandblast etching is successfully applied in fabricating the complex pattern of a vortex-like electrode. Both experiment and simulation show that the proposed design of the vortex-like electrode improved the electrical output of the pyroelectric cells and enhanced the efficiency of pyroelectric harvesting converters. A three-dimensional finite element model is generated by commercial software for solving the transient temperature fields and exploring the temperature variation rate in the PZT pyroelectric cells with various designs. The vortex-like type has a larger temperature variation rate than the fully covered type, by about 53.9%.The measured electrical output of the vortex-like electrode exhibits an obvious increase in the generated charge and the measured current, as compared to the fully covered electrode, by of about 47.1% and 53.1%, respectively.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 57
    Publication Date: 2013-09-13
    Description: An analytic method for predicting the performance of track-to-track association (TTTA) with biased data in multi-sensor multi-target tracking scenarios is proposed in this paper. The proposed method extends the existing results of the bias-free situation by accounting for the impact of sensor biases. Since little insight of the intrinsic relationship between scenario parameters and the performance of TTTA can be obtained by numerical simulations, the proposed analytic approach is a potential substitute for the costly Monte Carlo simulation method. Analytic expressions are developed for the global nearest neighbor (GNN) association algorithm in terms of correct association probability. The translational biases of sensors are incorporated in the expressions, which provide good insight into how the TTTA performance is affected by sensor biases, as well as other scenario parameters, including the target spatial density, the extraneous track density and the average association uncertainty error. To show the validity of the analytic predictions, we compare them with the simulation results, and the analytic predictions agree reasonably well with the simulations in a large range of normally anticipated scenario parameters.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 58
    Publication Date: 2013-09-13
    Description: A crucial aspect in rowing is having a synchronized, highly-efficient stroke. This is very difficult to obtain, due to the many interacting factors that each rower of the crew must perceive. Having a system that monitors and represents the crew coordination would be of great help to the coach during training sessions. In the literature, some methods already employ wireless sensors for capturing motion patterns that affect rowing performance. A challenging problem is to support the coach’s decisions at his same level of knowledge, using a limited number of sensors and avoiding the complexity of the biomechanical analysis of human movements. In this paper, we present a multi-agent information-processing system for on-water measuring of both the overall crew asynchrony and the individual rower asynchrony towards the crew. More specifically, in the system, the first level of processing is managed by marking agents, which release marks in a sensing space, according to the rowers’ motion. The accumulation of marks enables a stigmergic cooperation mechanism, generating collective marks, i.e., short-term memory structures in the sensing space. At the second level of processing, information provided by marks is observed by similarity agents, which associate a similarity degree with respect to optimal marks. Finally, the third level is managed by granulation agents, which extract asynchrony indicators for different purposes. The effectiveness of the system has been experimented on real-world scenarios. The study includes the problem statement and its characterization in the literature, as well as the proposed solving approach and initial experimental setting.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 59
    Publication Date: 2013-09-14
    Description: Considering the characteristics of wind tunnel tests, a position measurement system that can minimize the effects on the flow of simulated wind must be established. In this study, a motion-capture camera was used to measure the displacement responses of structures in a wind tunnel test, and the applicability of the system was tested. A motion-capture system (MCS) could output 3D coordinates using two-dimensional image coordinates obtained from the camera. Furthermore, this remote sensing system had some flexibility regarding lab installation because of its ability to measure at relatively long distances from the target structures. In this study, we performed wind tunnel tests on a pylon specimen and compared the measured responses of the MCS with the displacements measured with a laser displacement sensor (LDS). The results of the comparison revealed that the time-history displacement measurements from the MCS slightly exceeded those of the LDS. In addition, we confirmed the measuring reliability of the MCS by identifying the dynamic properties (natural frequency, damping ratio, and mode shape) of the test specimen using system identification methods (frequency domain decomposition, FDD). By comparing the mode shape obtained using the aforementioned methods with that obtained using the LDS, we also confirmed that the MCS could construct a more accurate mode shape (bending-deflection mode shape) with the 3D measurements.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 60
    Publication Date: 2013-09-19
    Description: Oil sand pumps are widely used in the mining industry for the delivery of mixtures of abrasive solids and liquids. Because they operate under highly adverse conditions, these pumps usually experience significant wear. Consequently, equipment owners are quite often forced to invest substantially in system maintenance to avoid unscheduled downtime. In this study, an approach combining relevance vector machines (RVMs) with a sum of two exponential functions was developed to predict the remaining useful life (RUL) of field pump impellers. To handle field vibration data, a novel feature extracting process was proposed to arrive at a feature varying with the development of damage in the pump impellers. A case study involving two field datasets demonstrated the effectiveness of the developed method. Compared with standalone exponential fitting, the proposed RVM-based model was much better able to predict the remaining useful life of pump impellers.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 61
    Publication Date: 2013-09-19
    Description: The time-average method currently available is limited to analyzing the specific performance of the automatic gain control-proportional and integral (AGC-PI) based velocity-controlled closed-loop in a micro-electro-mechanical systems (MEMS) vibratory gyroscope, since it is hard to solve nonlinear functions in the time domain when the control loop reaches to 3rd order. In this paper, we propose a linearization design approach to overcome this limitation by establishing a 3rd order linear model of the control loop and transferring the analysis to the frequency domain. Order reduction is applied on the built linear model’s transfer function by constructing a zero-pole doublet, and therefore mathematical expression of each control loop’s performance specification is obtained. Then an optimization methodology is summarized, which reveals that a robust, stable and swift control loop can be achieved by carefully selecting the system parameters following a priority order. Closed-loop drive circuits are designed and implemented using 0.35 μm complementary metal oxide semiconductor (CMOS) process, and experiments carried out on a gyroscope prototype verify the optimization methodology that an optimized stability of the control loop can be achieved by constructing the zero-pole doublet, and disturbance rejection capability (D.R.C) of the control loop can be improved by increasing the integral term.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 62
    Publication Date: 2013-09-19
    Description: Centrifugal compressors are a key piece of equipment for modern production. Among the components of the centrifugal compressor, the impeller is a pivotal part as it is used to transform kinetic energy into pressure energy. Blade crack condition monitoring and classification has been broadly investigated in the industrial and academic area. In this research, a pressure pulsation (PP) sensor arranged in close vicinity to the crack area and the corresponding casing vibration signals are used to monitor blade crack information. As these signals cannot directly demonstrate the blade crack, the method employed in this research is based on the extraction of weak signal characteristics that are induced by blade cracking. A method for blade crack classification based on the signals monitored by using a squared envelope spectrum (SES) is presented. Experimental investigations on blade crack classification are carried out to verify the effectiveness of this method. The results show that it is an effective tool for blade crack classification in centrifugal compressors.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 63
    Publication Date: 2013-09-19
    Description: This paper presents a CMOS temperature sensor based on the thermal dependencies of the leakage currents targeting the 65 nm node. To compensate for the effect of process fluctuations, the proposed sensor realizes the ratio of two measures of the time it takes a capacitor to discharge through a transistor in the subthreshold regime. Furthermore, a novel charging mechanism for the capacitor is proposed to further increase the robustness against fabrication variability. The sensor, including digitization and interfacing, occupies 0.0016 mm2 and has an energy consumption of 47.7–633 pJ per sample. The resolution of the sensor is 0.28 °C, and the 3σ inaccuracy over the range 40–110 °C is 1.17 °C.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 64
    Publication Date: 2013-09-24
    Description: This paper presents a low-cost hyperspectral measurement setup in a new application based on fluorescence detection in the visible (Vis) wavelength range. The aim of the setup is to take hyperspectral fluorescence images of viscous materials. Based on these images, fluorescent and non-fluorescent impurities in the viscous materials can be detected. For the illumination of the measurement object, a narrow-band high-power light-emitting diode (LED) with a center wavelength of 370 nm was used. The low-cost acquisition unit for the imaging consists of a linear variable filter (LVF) and a complementary metal oxide semiconductor (CMOS) 2D sensor array. The translucent wavelength range of the LVF is from 400 nm to 700 nm. For the confirmation of the concept, static measurements of fluorescent viscous materials with a non-fluorescent impurity have been performed and analyzed. With the presented setup, measurement surfaces in the micrometer range can be provided. The measureable minimum particle size of the impurities is in the nanometer range. The recording rate for the measurements depends on the exposure time of the used CMOS 2D sensor array and has been found to be in the microsecond range.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 65
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    Unknown
    Oxford University Press
    Publication Date: 2013-09-26
    Print ISSN: 0305-1048
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  • 66
    Publication Date: 2013-09-26
    Description: In reverse genetics, a gene’s function is elucidated through targeted modifications in the coding region or associated DNA cis -regulatory elements. To this purpose, recently developed customizable transcription activator-like effector nucleases (TALENs) have proven an invaluable tool, allowing introduction of double-strand breaks at predetermined sites in the genome. Here we describe a practical and efficient method for the targeted genome engineering in Drosophila . We demonstrate TALEN-mediated targeted gene integration and efficient identification of mutant flies using a traceable marker phenotype. Furthermore, we developed an easy TALEN assembly (easyT) method relying on simultaneous reactions of DNA Bae I digestion and ligation, enabling construction of complete TALENs from a monomer unit library in a single day. Taken together, our strategy with easyT and TALEN-plasmid microinjection simplifies mutant generation and enables isolation of desired mutant fly lines in the F 1 generation.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 67
    Publication Date: 2013-09-26
    Description: High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect , a tool that combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions directly in the vicinity of existing Alus. To set the parameters of our method, we use simulation of a faux reference, which allows us to compute the precision and recall of various parameter settings using real sequencing data. Applying our method to 100 bp paired Illumina data from seven individuals, including two trios, we detected on average 1519 novel Alus per sample. Based on the faux-reference simulation, we estimate that our method has 97% precision and 85% recall. We identify 808 novel Alus not previously described in other studies. We also demonstrate the use of alu-detect to study the local sequence and global location preferences for novel Alu insertions.
    Keywords: Polymorphism/mutation detection, Genomics
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  • 68
    Publication Date: 2013-09-26
    Description: DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, protein purification protocols and a well annotated protein database limits the utility of these cells for proteomic studies. Here we describe a fast and inexpensive experimental pipeline for protein localization, quantification and mass spectrometry–based interaction studies using DT40 cells. Our newly designed set of pQuant vectors and a sequence- and ligation-independent cloning (SLIC) strategy allow for simple and efficient generation of gene targeting constructs, facilitating homologous-recombination–based protein tagging on a multi-gene scale. We also report proof of principle results using the key proteins involved in RNA decay, namely EXOSC8, EXOSC9, CNOT7 and UPF1.
    Keywords: Synthetic Biology and Assembly Cloning, Protein-protein interaction, Recombinant DNA expression, Recombination
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  • 69
    Publication Date: 2013-09-26
    Description: Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein–protein binding experiments revealed that 〉65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action.
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  • 70
    Publication Date: 2013-09-26
    Description: HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA–HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ~2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.
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  • 71
    Publication Date: 2013-09-26
    Description: Magnetic isotope and magnetic field effects on the rate of DNA synthesis catalysed by polymerases β with isotopic ions 24 Mg 2+ , 25 Mg 2+ and 26 Mg 2+ in the catalytic sites were detected. No difference in enzymatic activity was found between polymerases β carrying 24 Mg 2+ and 26 Mg 2+ ions with spinless, non-magnetic nuclei 24 Mg and 26 Mg. However, 25 Mg 2+ ions with magnetic nucleus 25 Mg were shown to suppress enzymatic activity by two to three times with respect to the enzymatic activity of polymerases β with 24 Mg 2+ and 26 Mg 2+ ions. Such an isotopic dependence directly indicates that in the DNA synthesis magnetic mass-independent isotope effect functions. Similar effect is exhibited by polymerases β with Zn 2+ ions carrying magnetic 67 Zn and non-magnetic 64 Zn nuclei, respectively. A new, ion–radical mechanism of the DNA synthesis is suggested to explain these effects. Magnetic field dependence of the magnesium-catalysed DNA synthesis is in a perfect agreement with the proposed ion–radical mechanism. It is pointed out that the magnetic isotope and magnetic field effects may be used for medicinal purposes (trans-cranial magnetic treatment of cognitive deceases, cell proliferation, control of the cancer cells, etc).
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  • 72
    Publication Date: 2013-09-26
    Description: Translation of the sigma factor RpoS is activated by DsrA, RprA and ArcA, three small non-coding sRNAs (sRNA) that expose the ribosome-binding site (RBS) by opening up an inhibitory loop. In the RpoS network, no sRNAs have been found to pair with the RBS, a most common sRNA target site in bacteria. Here, we generate Ribo-0, an artificial sRNA, which represses rpoS translation by pairing with the RBS. Ribo-0 bypasses the RNA chaperon Hfq but requires the RBS to be loosely blocked. Ribo-0 interacts with DsrA and reshapes the RpoS network. Specifically, in the intact RpoS network, DsrA activates rpoS translation by freeing up the RBS. In the modified RpoS network where Ribo-0 is introduced, the DsrA-caused RBS exposure facilitates Ribo-0 binding, thereby strengthening Ribo-0 inhibition. In other words, Ribo-0 changes DsrA from an activator to an accomplice for repressing rpoS translation. This work presents an artificial mechanism of rpoS regulation, reveals mutual effects of native and synthetic players and demonstrates genetic context-dependency of their functions.
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  • 73
    Publication Date: 2013-09-26
    Description: Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
    Keywords: Computational Methods
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  • 74
    Publication Date: 2013-09-26
    Description: The nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons but also regulates the abundance of cellular RNAs. We sought to identify transcripts that are regulated by two novel NMD factors, DHX34 and neuroblastoma amplified sequence (NBAS), which were identified in a genome-wide RNA interference screen in Caenorhabditis elegans and later shown to mediate NMD in vertebrates. We performed microarray expression profile analysis in human cells, zebrafish embryos and C. elegans that were individually depleted of these factors. Our analysis revealed that a significant proportion of genes are co-regulated by DHX34, NBAS and core NMD factors in these three organisms. Further analysis indicates that NMD modulates cellular stress response pathways and membrane trafficking across species . Interestingly, transcripts encoding different NMD factors were sensitive to DHX34 and NBAS depletion, suggesting that these factors participate in a conserved NMD negative feedback regulatory loop, as was recently described for core NMD factors. In summary, we find that DHX34 and NBAS act in concert with core NMD factors to co-regulate a large number of endogenous RNA targets. Furthermore, the conservation of a mechanism to tightly control NMD homeostasis across different species highlights the importance of the NMD response in the control of gene expression.
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  • 75
    Publication Date: 2013-09-26
    Description: Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein–DNA nanostructures.
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  • 76
    Publication Date: 2013-09-28
    Description: This article deals with the application of the principles of SCD (Selective Change Driven) vision to 3D laser scanning. Two experimental sets have been implemented: one with a classical CMOS (Complementary Metal-Oxide Semiconductor) sensor, and the other one with a recently developed CMOS SCD sensor for comparative purposes, both using the technique known as Active Triangulation. An SCD sensor only delivers the pixels that have changed most, ordered by the magnitude of their change since their last readout. The 3D scanning method is based on the systematic search through the entire image to detect pixels that exceed a certain threshold, showing the SCD approach to be ideal for this application. Several experiments for both capturing strategies have been performed to try to find the limitations in high speed acquisition/processing. The classical approach is limited by the sequential array acquisition, as predicted by the Nyquist
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 77
    Publication Date: 2013-09-28
    Description: DC-offset and DC-suppression are key parameters in bioelectric amplifiers. However, specific DC analyses are not often explained. Several factors influence the DC-budget: the programmable gain, the programmable cut-off frequencies for high pass filtering and, the low cut-off values and the capacitor blocking issues involved. A new intermediate stage is proposed to address the DC problem entirely. Two implementations were tested. The stage is composed of a programmable gain amplifier (PGA) with DC-rejection and low output offset. Cut-off frequencies are selectable and values from 0.016 to 31.83 Hz were tested, and the capacitor deblocking is embedded in the design. Hence, this PGA delivers most of the required gain with constant low output offset, notwithstanding the gain or cut-off frequency selected.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 78
    Publication Date: 2013-09-28
    Description: This paper presents a method implemented in a system for automatic contactless calibration of gauge blocks designed at ISI ASCR. The system combines low-coherence interferometry and laser interferometry, where the first identifies the gauge block sides position and the second one measures the gauge block length itself. A crucial part of the system is the algorithm for gauge block alignment to the measuring beam which is able to compensate the gauge block lateral and longitudinal tilt up to 0.141 mrad. The algorithm is also important for the gauge block position monitoring during its length measurement.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 79
    Publication Date: 2013-09-28
    Description: Smartphone-based activity recognition (SP-AR) recognizes users’ activities using the embedded accelerometer sensor. Only a small number of previous works can be classified as online systems, i.e., the whole process (pre-processing, feature extraction, and classification) is performed on the device. Most of these online systems use either a high sampling rate (SR) or long data-window (DW) to achieve high accuracy, resulting in short battery life or delayed system response, respectively. This paper introduces a real-time/online SP-AR system that solves this problem. Exploratory data analysis was performed on acceleration signals of 6 activities, collected from 30 subjects, to show that these signals are generated by an autoregressive (AR) process, and an accurate AR-model in this case can be built using a low SR (20 Hz) and a small DW (3 s). The high within class variance resulting from placing the phone at different positions was reduced using kernel discriminant analysis to achieve position-independent recognition. Neural networks were used as classifiers. Unlike previous works, true subject-independent evaluation was performed, where 10 new subjects evaluated the system at their homes for 1 week. The results show that our features outperformed three commonly used features by 40% in terms of accuracy for the given SR and DW.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 80
    Publication Date: 2013-10-01
    Description: Spectroscopy has proven to be an efficient tool for measuring the properties of meat. In this article, hyperspectral imaging (HSI) techniques are used to determine the moisture content in cooked chicken breast over the VIS/NIR (400–1,000 nm) spectral range. Moisture measurements were performed using an oven drying method. A partial least squares regression (PLSR) model was developed to extract a relationship between the HSI spectra and the moisture content. In the full wavelength range, the PLSR model possessed a maximum  of 0.90 and an SEP of 0.74%. For the NIR range, the PLSR model yielded an  of 0.94 and an SEP of 0.71%. The majority of the absorption peaks occurred around 760 and 970 nm, representing the water content in the samples. Finally, PLSR images were constructed to visualize the dehydration and water distribution within different sample regions. The high correlation coefficient and low prediction error from the PLSR analysis validates that HSI is an effective tool for visualizing the chemical properties of meat.
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    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 81
    Publication Date: 2013-10-01
    Description: The paper presents a coaxial-like sensor operating in the 20 Hz–2 MHz frequency range used to determine the electrical properties of selected liquids of low electrical conductivity. Examined materials included low-concentrated aqueous solutions of potassium chloride, sodium chloride and trisodium citrate, which are common food additives. Impedance spectra of the measurement cell filled with particular liquids were obtained and analyzed using the electrical equivalent circuit approach. The values of physical quantities and parameters describing the equivalent circuit components, including a constant phase element, were calculated for each sample. The applied sensor was also calibrated for electrical conductivity measurements up to 8 mS/m. The constant phase element parameters differed among the studied solutions and concentrations. This may provide a basis for a detection method of small amounts of compounds, such as food additives in low-concentrated aqueous solutions. To demonstrate the potential of the presented method, samples of purchased mineral water and a flavored drink containing various additives were tested.
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  • 82
    Publication Date: 2013-10-01
    Description: An efficient and low cost optical method for directly measuring the concentration of homogenous biological solutes is proposed and demonstrated. The proposed system operates by Fresnel reflection, with a flat-cleaved single-mode fiber serving as the sensor probe. A laser provides a 12.9 dBm sensor signal at 1,550 nm, while a computer-controlled optical power meter measures the power of the signal returned by the probe. Three different mesenchymal stem cell (MSC) lines were obtained, sub-cultured and trypsinized daily over 9 days. Counts were measured using a haemocytometer and the conditioned media (CM) was collected daily and stored at −80 °C. MSCs release excretory biomolecules proportional to their growth rate into the CM, which changes the refractive index of the latter. The sensor is capable of detecting changes in the number of stem cells via correlation to the change in the refractive index of the CM, with the measured power loss decreasing approximately 0.4 dB in the CM sample per average 1,000 cells in the MSC subculture. The proposed system is highly cost-effective, simple to deploy, operate, and maintain, is non-destructive, and allows reliable real-time measurement of various stem cell proliferation parameters.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 83
    Publication Date: 2013-10-01
    Description: This paper proposes and implements a new TDMA-based MAC protocol for providing timely and reliable delivery of data and command for monitoring and control networks. In this kind of network, sensor nodes are required to sense data from the monitoring environment periodically and then send the data to a sink. The sink determines whether the environment is safe or not by analyzing the acquired data. Sometimes, a command or control message is sent from the sink to a particular node or a group of nodes to execute the services or request further interested data. The proposed MAC protocol enables bidirectional communication, controls active and sleep modes of a sensor node to conserve energy, and addresses the problem of load unbalancing between the nodes near a sink and the other nodes. It can improve reliability of communication significantly while extending network lifetime. These claims are supported by the experimental results.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 84
    Publication Date: 2013-10-02
    Description: To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 85
    Publication Date: 2013-10-03
    Description: Mobile wireless multimedia sensor networks (WMSNs), which consist of mobile sink or sensor nodes and use rich sensing information, require much faster and more reliable wireless links than static wireless sensor networks (WSNs). This paper proposes an adaptive multi-node (MN) multiple input and multiple output (MIMO) transmission to improve the transmission reliability and capacity of mobile sink nodes when they experience spatial correlation. Unlike conventional single-node (SN) MIMO transmission, the proposed scheme considers the use of transmission antennas from more than two sensor nodes. To find an optimal antenna set and a MIMO transmission scheme, a MN MIMO channel model is introduced first, followed by derivation of closed-form ergodic capacity expressions with different MIMO transmission schemes, such as space-time transmit diversity coding and spatial multiplexing. The capacity varies according to the antenna correlation and the path gain from multiple sensor nodes. Based on these statistical results, we propose an adaptive MIMO mode and antenna set switching algorithm that maximizes the ergodic capacity of mobile sink nodes. The ergodic capacity of the proposed scheme is compared with conventional SN MIMO schemes, where the gain increases as the antenna correlation and path gain ratio increase.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 86
    Publication Date: 2013-10-04
    Description: In this work we have developed a multiplex microarray system capable of detecting VEGF165 and thrombin. We recently described a Sandwich Aptamer Microarray (SAM) for thrombin detection feasible for use in multiplex microarrays; here we describe a new aptasensor for VEGF165 detection employing Vap7 and VEa5, two DNA aptamers recognizing different sites of the protein. The aptamers were modified to be adapted to the solid phase platform of SAM and their capability to simultaneously recognize VEGF165 by forming a ternary complex was analyzed in solution. Having so defined the best tandem arrangement of modified aptamers, we set up the aptasensor for VEGF165, and finally analyzed the multiplex system with the two aptasensors for the simultaneous detection of VEGF165 and thrombin. The results indicate that each sandwich is specific, even when the two proteins are mixed. The system performance is consistent with the behavior evidenced by the biochemical analysis, which proves to be valuable to drive the evaluation and refinement of aptamers prior to or along the development of a detection platform. Since thrombin upregulates VEGF expression, the simultaneous recognition of these two proteins could be useful in the analysis of biomarkers in pathologies characterized by neo-angiogenesis.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 87
    Publication Date: 2013-06-08
    Description: Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from many phyla. Pnkp is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase and a C-terminal ligase. The phosphatase module is a Mn 2+ -dependent phosphodiesterase–monoesterase that dephosphorylates 2',3'-cyclic phosphate RNA ends. Here we report the crystal structure of the phosphatase domain of Clostridium thermocellum Pnkp with Mn 2+ and citrate in the active site. The protein consists of a core binuclear metallo-phosphoesterase fold (exemplified by bacteriophage phosphatase) embellished by distinctive secondary structure elements. The active site contains a single Mn 2+ in an octahedral coordination complex with Asp187, His189, Asp233, two citrate oxygens and a water. The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237, Asn263 and His264. The citrate invades the site normally occupied by a second metal (engaged by Asp233, Asn263, His323 and His376), and thereby dislocates His376. A continuous tract of positive surface potential flanking the active site suggests an RNA binding site. The structure illuminates a large body of mutational data regarding the metal and substrate specificity of Clostridium thermocellum Pnkp phosphatase.
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  • 88
    Publication Date: 2013-06-08
    Description: The formation of the open promoter complex (RPo) in which the melted DNA containing the transcription start site is located at the RNA polymerase (RNAP) catalytic centre is an obligatory step in the transcription of DNA into RNA catalyzed by RNAP. In the RPo, an extensive network of interactions is established between DNA, RNAP and the -factor and the formation of functional RPo occurs via a series of transcriptional intermediates (collectively ‘RPi’). A single tryptophan is ideally positioned to directly engage with the flipped out base of the non-template strand at the +1 site. Evidence suggests that this tryptophan (i) is involved in either forward translocation or DNA scrunching and (ii) in 54 -regulated promoters limits the transcription activity of at least one intermediate complex (RPi) before the formation of a fully functional RPo. Limiting RPi activity may be important in preventing the premature synthesis of abortive transcripts, suggesting its involvement in a general mechanism driving the RPi to RPo transition for transcription initiation.
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  • 89
    Publication Date: 2013-06-08
    Description: Guanine-rich RNA sequences can fold into non-canonical, four stranded helical structures called G-quadruplexes that have been shown to be widely distributed within the mammalian transcriptome, as well as being key regulatory elements in various biological mechanisms. That said, their role within the 3'-untranslated region (UTR) of mRNA remains to be elucidated and appreciated. A bioinformatic analysis of the 3'-UTRs of mRNAs revealed enrichment in G-quadruplexes. To shed light on the role(s) of these structures, those found in the LRP5 and FXR1 genes were characterized both in vitro and in cellulo . The 3'-UTR G-quadruplexes were found to increase the efficiencies of alternative polyadenylation sites, leading to the expression of shorter transcripts and to possess the ability to interfere with the miRNA regulatory network of a specific mRNA. Clearly, G-quadruplexes located in the 3'-UTRs of mRNAs are cis -regulatory elements that have a significant impact on gene expression.
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  • 90
    Publication Date: 2013-06-08
    Description: One of the primary aims of synthetic biology is to (re)design metabolic pathways towards the production of desired chemicals. The fast pace of developments in molecular biology increasingly makes it possible to experimentally redesign existing pathways and implement de novo ones in microbes or using in vitro platforms. For such experimental studies, the bottleneck is shifting from implementation of pathways towards their initial design. Here, we present an online tool called ‘Metabolic Tinker’, which aims to guide the design of synthetic metabolic pathways between any two desired compounds. Given two user-defined ‘target’ and ‘source’ compounds, Metabolic Tinker searches for thermodynamically feasible paths in the entire known metabolic universe using a tailored heuristic search strategy. Compared with similar graph-based search tools, Metabolic Tinker returns a larger number of possible paths owing to its broad search base and fast heuristic, and provides for the first time thermodynamic feasibility information for the discovered paths. Metabolic Tinker is available as a web service at http://osslab.ex.ac.uk/tinker.aspx . The same website also provides the source code for Metabolic Tinker, allowing it to be developed further or run on personal machines for specific applications.
    Keywords: Synthetic Biology and Assembly Cloning, Computational Methods
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  • 91
    Publication Date: 2013-06-08
    Description: COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing. The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites. COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with ~50% concordance with gene expression from both cell line data and heterogeneous patient data. For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression. COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression. This software is freely available at https://sourceforge.net/projects/cohcap/ .
    Keywords: Nucleic acid modification, Computational Methods, Genomics
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  • 92
    Publication Date: 2013-06-08
    Description: Tristetraprolin (TTP) and let-7 microRNA exhibit suppressive effects on cell growth through down-regulation of oncogenes. Both TTP and let-7 are often repressed in human cancers, thereby promoting oncogenesis by derepressing their target genes. However, the precise mechanism of this repression is unknown. We here demonstrate that p53 stimulated by the DNA-damaging agent doxorubicin (DOX) induced the expression of TTP in cancer cells. TTP in turn increased let-7 levels through down-regulation of Lin28a . Correspondingly, cancer cells with mutations or inhibition of p53 failed to induce the expression of both TTP and let-7 on treatment with DOX. Down-regulation of TTP by small interfering RNAs attenuated the inhibitory effect of DOX on let-7 expression and cell growth. Therefore, TTP provides an important link between p53 activation induced by DNA damage and let-7 biogenesis. These novel findings provide a mechanism for the widespread decrease in TTP and let-7 and chemoresistance observed in human cancers.
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  • 93
    Publication Date: 2013-06-08
    Description: The observation that long tracts of RNA are associated with replicating molecules of mitochondrial DNA (mtDNA) suggests that the mitochondrial genome of mammals is copied by an unorthodox mechanism. Here we show that these RNA-containing species are present in living cells and tissue, based on interstrand cross-linking. Using DNA synthesis in organello , we demonstrate that isolated mitochondria incorporate radiolabeled RNA precursors, as well as DNA precursors, into replicating DNA molecules. RNA-containing replication intermediates are chased into mature mtDNA, to which they are thus in precursor–product relationship. While a DNA chain terminator rapidly blocks the labeling of mitochondrial replication intermediates, an RNA chain terminator does not. Furthermore, processed L-strand transcripts can be recovered from gel-extracted mtDNA replication intermediates. Therefore, instead of concurrent DNA and RNA synthesis, respectively, on the leading and lagging strands, preformed processed RNA is incorporated as a provisional lagging strand during mtDNA replication. These findings indicate that RITOLS is a physiological mechanism of mtDNA replication, and that it involves a ‘bootlace' mechanism, in which processed transcripts are successively hybridized to the lagging-strand template, as the replication fork advances.
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  • 94
    Publication Date: 2013-06-08
    Description: Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3'-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an ‘anchor’ site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 Å, reveals an Mg 2+ ion bound to the scissile phosphate in a position corresponding to Mg B in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed.
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  • 95
    Publication Date: 2013-06-08
    Description: The rpoS mRNA, which encodes the master regulator S of general stress response, requires Hfq-facilitated base pairing with DsrA small RNA for efficient translation at low temperatures. It has recently been proposed that one mechanism underlying Hfq action is to bridge a transient ternary complex by simultaneously binding to rpoS and DsrA. However, no structural evidence of Hfq simultaneously bound to different RNAs has been reported. We detected simultaneous binding of Hfq to rpoS and DsrA fragments. Crystal structures of AU6A•Hfq•A7 and Hfq•A7 complexes were resolved using 1.8- and 1.9-Å resolution, respectively. Ternary complex has been further verified in solution by NMR. In vivo , activation of rpoS translation requires intact Hfq, which is capable of bridging rpoS and DsrA simultaneously into ternary complex. This ternary complex possibly corresponds to a meta-stable transition state in Hfq-facilitated small RNA–mRNA annealing process.
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  • 96
    Publication Date: 2013-06-08
    Description: Surface plasmon resonance (SPR) sensor is widely used for its high precision and real-time analysis. Fiber-optic SPR sensor is easy for miniaturization, so it is commonly used in the development of portable detection equipment. It can also be used for remote, real-time, and online detection. In this study, a wavelength modulation fiber-optic SPR sensor is designed, and theoretical analysis of optical propagation in the optical fiber is also done. Compared with existing methods, both the transmission of a skew ray and the influence of the chromatic dispersion are discussed. The resonance wavelength is calculated at two different cases, in which the chromatic dispersion in the fiber core is considered. According to the simulation results, a novel multi-channel fiber-optic SPR sensor is likewise designed to avoid defaults aroused by the complicated computation of the skew ray as well as the chromatic dispersion. Avoiding the impact of skew ray can do much to improve the precision of this kind of sensor.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 97
    Publication Date: 2013-06-08
    Description: A simple two-step method was employed for preparing nano-sized gold nanoparticles-graphene composite to construct a GNPs-GR-SDS modified electrode. Hemoglobin (Hb) was successfully immobilized on the surface of a basal plane graphite (BPG) electrode through a simple dropping technique. Direct electrochemistry and electrocatalysis of the hemoglobin-modified electrode was investigated. The as-prepared composites showed an obvious promotion of the direct electro-transfer between hemoglobin and the electrode. A couple of well-defined and quasi-reversible Hb CV peaks can be observed in a phosphate buffer solution (pH 7.0). The separation of anodic and cathodic peak potentials is 81 mV, indicating a fast electron transfer reaction. The experimental results also clarified that the immobilized Hb retained its biological activity for the catalysis toward NO. The biosensor showed high sensitivity and fast response upon the addition of NO, under the conditions of pH 7.0, potential ‒0.82 V. The time to reach the stable-state current was less than 3 s, and the linear response range of NO was 0.72–7.92 μM, with a correlation coefficient of 0.9991.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 98
    Publication Date: 2013-06-08
    Description: This paper presents an intelligent surveillance platform based on the usage of large numbers of inexpensive sensors designed and developed inside the European Eureka Celtic project HuSIMS. With the aim of maximizing the number of deployable units while keeping monetary and resource/bandwidth costs at a minimum, the surveillance platform is based on the usage of inexpensive visual sensors which apply efficient motion detection and tracking algorithms to transform the video signal in a set of motion parameters. In order to automate the analysis of the myriad of data streams generated by the visual sensors, the platform’s control center includes an alarm detection engine which comprises three components applying three different Artificial Intelligence strategies in parallel. These strategies are generic, domain-independent approaches which are able to operate in several domains (traffic surveillance, vandalism prevention, perimeter security, etc.). The architecture is completed with a versatile communication network which facilitates data collection from the visual sensors and alarm and video stream distribution towards the emergency teams. The resulting surveillance system is extremely suitable for its deployment in metropolitan areas, smart cities, and large facilities, mainly because cheap visual sensors and autonomous alarm detection facilitate dense sensor network deployments for wide and detailed coverage.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 99
    Publication Date: 2013-06-08
    Description: Network simulators are useful for researching protocol performance, appraising new hardware capabilities and evaluating real application scenarios. However, these tasks can only be achieved when using accurate models and real parameters that enable the extraction of trustworthy results and conclusions. This paper presents an underwater wireless sensor network ecosystem for the ns-3 simulator. This ecosystem is composed of a new energy-harvesting model and a low-cost, low-power underwater wake-up modem model that, alongside existing models, enables the performance of accurate simulations by providing real weather and marine conditions from the location where the real application is to be deployed.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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  • 100
    Publication Date: 2013-06-08
    Description: An essential application of wireless sensor networks is to successfully respond to user queries. Query packet losses occur in the query dissemination due to wireless communication problems such as interference, multipath fading, packet collisions, etc. The losses of query messages at sensor nodes result in the failure of sensor nodes reporting the requested data. Hence, the reliable and successful dissemination of query messages to sensor nodes is a non-trivial problem. The target of this paper is to enable highly successful query delivery to sensor nodes by localized and energy-efficient discovery, and recovery of query losses. We adopt local and collective cooperation among sensor nodes to increase the success rate of distributed discoveries and recoveries. To enable the scalability in the operations of discoveries and recoveries, we employ a distributed name resolution mechanism at each sensor node to allow sensor nodes to self-detect the correlated queries and query losses, and then efficiently locally respond to the query losses. We prove that the collective discovery of query losses has a high impact on the success of query dissemination and reveal that scalability can be achieved by using the proposed approach. We further study the novel features of the cooperation and competition in the collective recovery at PHY and MAC layers, and show that the appropriate number of detectors can achieve optimal successful recovery rate. We evaluate the proposed approach with both mathematical analyses and computer simulations. The proposed approach enables a high rate of successful delivery of query messages and it results in short route lengths to recover from query losses. The proposed approach is scalable and operates in a fully distributed manner.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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