STM-SQUID probe microscope

International Nuclear Information System (INIS)

Hayashi, Tadayuki; Tachiki, Minoru; Itozaki, Hideo

2007-01-01

We have developed a STM-SQUID probe microscope. A high T C SQUID probe microscope was combined with a scanning tunneling microscope for investigation of samples at room temperature in air. A high permeability probe needle was used as a magnetic flux guide to improve the spatial resolution. The probe with tip radius of less than 100 nm was prepared by microelectropolishing. The probe was also used as a scanning tunneling microscope tip. Topography of the sample surface could be measured by the scanning tunneling microscope with high spatial resolution prior to observation by SQUID microscopy. The SQUID probe microscope image could be observed while keeping the distance from the sample surface to the probe tip constant. We observed a topographic image and a magnetic image of Ni fine pattern and also a magnetically recorded hard disk. Furthermore we have investigated a sample vibration method of the static magnetic field emanating from a sample with the aim of achieving a higher signal-to-noise (S/N) ratio

Measurement of local flow pattern in boiling R12 simulating PWR conditions with multiple optical probes

International Nuclear Information System (INIS)

Garnier, J.

1998-01-01

For a comprehensive approach of boiling crisis phenomenon in order to get more reliable predictions of critical heat flux in PWR core, a flow pattern study is under progress at CEA GRENOBLE (in a joint program with Electricite de France: EdF). The first aim is to get experimental results on flow structure in the range of thermal hydraulic parameters involved in the core of a PWR (pressure up to 16 MPa, heat flux about 1 MW/m 2 , mass velocity up to 5000 kg/s/m 2 . As critical heat flux is a local phenomenon and is the result of the flow development, the data has to be measured from the beginning of boiling until boiling crisis, and from the bulk flow until the boundary layer close to the heating walls. Therefore, these results will be useful in modeling not only boiling crisis phenomenon but also condensation in subcooled boiling, coalescence, splitting up, mass and energy transfers at interfaces, and so on. In a first step, the test section is a vertical tube 19.2 mm internal diameter with an axial uniform heat flux over a 3.5m length. The study is performed on the DEBORA loop with Freon 12 as coolant fluid. We assume that basic boiling phenomena (and the knowledge we get about them) only depend on the fluid properties by means of dimensionless parameters but not on the fluid itself. In a first part, we briefly recall that interfacial detection is the most important parameter of a flow pattern study. Therefore, the use of probes able to measure the Phase Indicator Function (P.I.F.) is necessary. A first study of flow conditions shows that the flow pattern is essentially a bubbly one with vapor particles of low diameter (about 300 clm) and high velocity (up to 7 m/s). These criteria induce that a multiple optical probe is the most appropriate tool provided we improve the technology. We detail the way to obtain probes able to detect small particles at high velocity. Each fiber is stretched to get a tip of 10 Clm with the cladding kept on 50 μm length which defines

Characterization of near-field optical probes

DEFF Research Database (Denmark)

Vohnsen, Brian; Bozhevolnyi, Sergey I.

1999-01-01

Radiation and collection characteristics of four different near-field optical-fiber probes, namely, three uncoated probes and an aluminium-coated small-aperture probe, are investigated and compared. Their radiation properties are characterized by observation of light-induced topography changes...... in a photo-sensitive film illuminated with the probes, and it is confirmed that the radiated optical field is unambigiously confined only for the coated probe. Near-field optical imaging of a standing evanescent-wave pattern is used to compare the detection characteristics of the probes, and it is concluded...... that, for the imaging of optical-field intensity distributions containing predominantly evanescent-wave components, a sharp uncoated tip is the probe of choice. Complementary results obtained with optical phase-conjugation experiments with he uncoated probes are discussed in relation to the probe...

Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

Directory of Open Access Journals (Sweden)

Nina P. L. Junager

2016-07-01

Full Text Available Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.

Scanning probe lithography for nanoimprinting mould fabrication

International Nuclear Information System (INIS)

Luo Gang; Xie Guoyong; Zhang Yongyi; Zhang Guoming; Zhang Yingying; Carlberg, Patrick; Zhu Tao; Liu Zhongfan

2006-01-01

We propose a rational fabrication method for nanoimprinting moulds by scanning probe lithography. By wet chemical etching, different kinds of moulds are realized on Si(110) and Si(100) surfaces according to the Si crystalline orientation. The structures have line widths of about 200 nm with a high aspect ratio. By reactive ion etching, moulds with patterns free from the limitation of Si crystalline orientation are also obtained. With closed-loop scan control of a scanning probe microscope, the length of patterned lines is more than 100 μm by integrating several steps of patterning. The fabrication process is optimized in order to produce a mould pattern with a line width about 10 nm. The structures on the mould are further duplicated into PMMA resists through the nanoimprinting process. The method of combining scanning probe lithography with wet chemical etching or reactive ion etching (RIE) provides a resistless route for the fabrication of nanoimprinting moulds

Multivariate pattern classification reveals autonomic and experiential representations of discrete emotions.

Science.gov (United States)

Kragel, Philip A; Labar, Kevin S

2013-08-01

Defining the structural organization of emotions is a central unresolved question in affective science. In particular, the extent to which autonomic nervous system activity signifies distinct affective states remains controversial. Most prior research on this topic has used univariate statistical approaches in attempts to classify emotions from psychophysiological data. In the present study, electrodermal, cardiac, respiratory, and gastric activity, as well as self-report measures were taken from healthy subjects during the experience of fear, anger, sadness, surprise, contentment, and amusement in response to film and music clips. Information pertaining to affective states present in these response patterns was analyzed using multivariate pattern classification techniques. Overall accuracy for classifying distinct affective states was 58.0% for autonomic measures and 88.2% for self-report measures, both of which were significantly above chance. Further, examining the error distribution of classifiers revealed that the dimensions of valence and arousal selectively contributed to decoding emotional states from self-report, whereas a categorical configuration of affective space was evident in both self-report and autonomic measures. Taken together, these findings extend recent multivariate approaches to study emotion and indicate that pattern classification tools may improve upon univariate approaches to reveal the underlying structure of emotional experience and physiological expression. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Light distribution analysis of optical fibre probe-based near-field optical tweezers using FDTD

Energy Technology Data Exchange (ETDEWEB)

Liu, B H; Yang, L J; Wang, Y [School of Mechanical and Electrical Engineering, Harbin Institute of Technology, Heilongjiang, Harbin, 150001 (China)], E-mail: richelaw@163.com

2009-09-01

Optical fibre probe-based near-field optical tweezers overcomes the diffraction limit of conventional optical tweezers, utilizing strong mechanical forces and torque associated with highly enhanced electric fields to trap and manipulate nano-scale particles. Near-field evanescent wave generated at optical fibre probe decays rapidly with the distance that results a significant reduced trapping volume, thus it is necessary to analyze the near-field distribution of optical fibre probe. The finite difference time domain (FDTD) method is applied to characterize the near-field distribution of optical fibre probe. In terms of the distribution patterns, depolarization and polarization, the near-field distributions in longitudinal sections and cross-sections of tapered metal-coated optical fibre probe are calculated. The calculation results reveal that the incident polarized wave becomes depolarized after exiting from the nano-scale aperture of probe. The near-field distribution of the probe is unsymmetrical, and the near-field distribution in the cross-section vertical to the incident polarized wave is different from that in the cross-section parallel to the incident polarized wave. Moreover, the polarization of incident wave has a great impact on the light intensity distribution.

Social patterns revealed through random matrix theory

Science.gov (United States)

Sarkar, Camellia; Jalan, Sarika

2014-11-01

Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

Scanning microscopic four-point conductivity probes

DEFF Research Database (Denmark)

Petersen, Christian Leth; Hansen, Torben Mikael; Bøggild, Peter

2002-01-01

A method for fabricating microscopic four-point probes is presented. The method uses silicon-based microfabrication technology involving only two patterning steps. The last step in the fabrication process is an unmasked deposition of the conducting probe material, and it is thus possible to select...... the conducting material either for a silicon wafer or a single probe unit. Using shadow masking photolithography an electrode spacing (pitch) down to 1.1 mum was obtained, with cantilever separation down to 200 run. Characterisation measurements have shown the microscopic probes to be mechanically very flexible...

Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

International Nuclear Information System (INIS)

Pillay, K.K.S.; Driscoll, D.C.; Jester, W.A.

1975-01-01

A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

Magnetization measurements reveal the local shear stiffness of hydrogels probed by ferromagnetic nanorods

Energy Technology Data Exchange (ETDEWEB)

Bender, P., E-mail: nano@p-bender.de; Tschöpe, A., E-mail: antsch@mx.uni-saarland.de; Birringer, R., E-mail: r.birringer@nano.uni-saarland.de

2014-12-15

The local mechanical coupling of ferromagnetic nanorods in hydrogels was characterized by magnetization measurements. Nickel nanorods were synthesized by the AAO-template method and embedded in gelatine hydrogels with mechanically soft or hard matrix properties determined by the gelatine weight fraction. By applying a homogeneous magnetic field during gelation the nanorods were aligned along the field resulting in uniaxially textured ferrogels. The magnetization curves of the soft ferrogel exhibited not only important similarities but also characteristic differences as compared to the hard ferrogel. The hystereses measured in a field parallel to the texture axis were almost identical for both samples indicating effective coupling of the nanorods with the polymer network. By contrast, measurements in a magnetic field perpendicular to the texture axis revealed a much higher initial susceptibility of the soft as compared to the hard ferrogel. This difference was attributed to the additional rotation of the nanorods allowed by the reduced shear modulus in the soft ferrogel matrix. Two methods for data analysis were presented which enabled us to determine the shear modulus of the gelatine matrix which was interpreted as a local rather than macroscopic quantity in consideration of the nanoscale of the probe particles. - Highlights: • Nanorods are embedded as magnetic probes in gelatine gels. • Elastic rotation of the rods can be induced by applying a homogeneous magnetic field. • Rod rotation has significant influence on the magnetization curves. • Two methods are presented to estimate the shear modulus of the matrix from the magnetization curves.

A new theoretical probe for the magnetic force microscope

Energy Technology Data Exchange (ETDEWEB)

Windmill, J.F.C. E-mail: jwindmill@plymouth.ac.uk; Clegg, W.W.; Jenkins, D.F.L.; Davey, P.J

2001-05-01

The magnetic force microscope (MFM) is established as a valuable tool for the analysis of magnetic structures. The standard design of MFM incorporates a silicon tip coated with a magnetic material. However, these tips are subject to several inherent problems, e.g. changing characteristics over time due to damage or magnetic hysteresis. A new theoretical electromagnetic MFM probe is introduced here. Although electromagnetic MFM has been discussed before by Zhou et al. (J. Vac. Sci. Technol. A 17 (1999) 2233), the design presented here is a different approach. Two different probe iterations and their magnetic field intensity distribution are modelled. The probe imaging capability is compared using the reciprocity principle (Wright and Hill, Appl. Phys. Lett. 68 (1996) 1726) to image the simulated force interaction between a sample and the probe fields. Thus, images of a sample's magnetic distribution are produced by the convolution of the different probe gradient field distributions and the sample magnetisation. Both perpendicular and longitudinal magnetisation patterns were simulated with the different probe iterations. This clearly showed the improvement of the second probe iteration, particularly for longitudinal patterns. The practical use of the new probe is also discussed, and future work outlined.

TreeNetViz: revealing patterns of networks over tree structures.

Science.gov (United States)

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Scanning vector Hall probe microscopy

International Nuclear Information System (INIS)

Cambel, V.; Gregusova, D.; Fedor, J.; Kudela, R.; Bending, S.J.

2004-01-01

We have developed a scanning vector Hall probe microscope for mapping magnetic field vector over magnetic samples. The microscope is based on a micromachined Hall sensor and the cryostat with scanning system. The vector Hall sensor active area is ∼5x5 μm 2 . It is realized by patterning three Hall probes on the tilted faces of GaAs pyramids. Data from these 'tilted' Hall probes are used to reconstruct the full magnetic field vector. The scanning area of the microscope is 5x5 mm 2 , space resolution 2.5 μm, field resolution ∼1 μT Hz -1/2 at temperatures 10-300 K

Genotypic characterization of Rickettsiae by DNA probes generated from Rickettsia Prowazekii DNA

International Nuclear Information System (INIS)

Demkin, V.V.; Rydkina, E.B.; Likhoded, L.Ya.; Ignatovich, V.F.; Genig, V.A.; Balayeva, N.M.

1994-01-01

Southern blot analysis of HindIII-cleaved rickettsial DNA was used for genotypic characterization of the typhus group (TG) species (R. prowazekii, R. typhi, R. canada) and a few species were of the spotted fever group (SFG)rickettsiae (R. sibirica, R. conorii, R. akari). Four different DNA probes were employed. PBH11 and PBH13 probes were morphospecific HindIII fragment of R prowazekii DNA. MW218 probe contained the gene for 51 K antigen and MW264 probe contained the citrate synthase gene of R. prowazekii. All the probes hybridized with the tested TG and SFG rickettsial DNAs, forming from 1 to 5 bands, but they did not with R. tsutsudamushi or C. burnetii DNAs. All the probes demonstrated specific hybridization pattern with TG species and R. akari. PBH11. PBH13 and MW264 probes clearly distinguished R. sibirica and R. conorii from the other tested rickettsiae, but not from each other. However, these two species differed slightly with MW218 probe. Several strains of each species were analyzed in this way and except for strains of R. conorii identical intra-species pattern were obtained. These data lead us to consider the obtained hybridization patterns as criteria for genotypic identification. (author)

Computational procedures for probing interactions in OLS and logistic regression: SPSS and SAS implementations.

Science.gov (United States)

Hayes, Andrew F; Matthes, Jörg

2009-08-01

Researchers often hypothesize moderated effects, in which the effect of an independent variable on an outcome variable depends on the value of a moderator variable. Such an effect reveals itself statistically as an interaction between the independent and moderator variables in a model of the outcome variable. When an interaction is found, it is important to probe the interaction, for theories and hypotheses often predict not just interaction but a specific pattern of effects of the focal independent variable as a function of the moderator. This article describes the familiar pick-a-point approach and the much less familiar Johnson-Neyman technique for probing interactions in linear models and introduces macros for SPSS and SAS to simplify the computations and facilitate the probing of interactions in ordinary least squares and logistic regression. A script version of the SPSS macro is also available for users who prefer a point-and-click user interface rather than command syntax.

Development of gamma probe technique for monitoring rooting pattern of pearl millet under field conditions

International Nuclear Information System (INIS)

Vittal, K.P.R.; Subbiah, B.V.

1982-01-01

For the root distribution studies, methods are not available to measure the growth in situ and in toto under field conditions without destroying the plants. A non-destructive method was developed for measuring the gamma activity in root using a probe that was administered through the stem. Five isotopes viz. 86 Rb, 134 Cs, 59 Fe, 65 Zn and 54 Mn tested, were found to represent almost similar rooting pattern for pearl millet from flowering to harvesting stages. Among these isotopes 59 Fe was found to be suitable for field use. This method also enabled to successfully monitor the root activity over time and avoided the sampling errors. Since laboratory processing of samples was eliminated, the process of measurement was hastened. (author)

Inheritance Patterns in Citation Networks Reveal Scientific Memes

Directory of Open Access Journals (Sweden)

Tobias Kuhn

2014-11-01

Full Text Available Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

Inheritance Patterns in Citation Networks Reveal Scientific Memes

Science.gov (United States)

Kuhn, Tobias; Perc, Matjaž; Helbing, Dirk

2014-10-01

Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

Directory of Open Access Journals (Sweden)

Paules Richard S

2007-11-01

Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

Increased detectability of somatic changes in the DNA from human tumours after probing with "synthetic" and "genome-derived" hypervariable multilocus probes

DEFF Research Database (Denmark)

Lagoda, P J; Seitz, G; Epplen, J T

1989-01-01

intensities were observed. Together the probes 33.15 and (CAC)5/(GTG)5 detected deviating fingerprint patterns in 63% of the colorectal carcinomas investigated. In mammary and stomach carcinomas, only 1/11 and 2/11 tumours, respectively, showed differences with either of the three probes, 33.15, (GACA)4...

In situ X-ray probing reveals fingerprints of surface platinum oxide.

Science.gov (United States)

Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

2011-01-07

In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

Instantaneous, Simple, and Reversible Revealing of Invisible Patterns Encrypted in Robust Hollow Sphere Colloidal Photonic Crystals.

Science.gov (United States)

Zhong, Kuo; Li, Jiaqi; Liu, Liwang; Van Cleuvenbergen, Stijn; Song, Kai; Clays, Koen

2018-05-04

The colors of photonic crystals are based on their periodic crystalline structure. They show clear advantages over conventional chromophores for many applications, mainly due to their anti-photobleaching and responsiveness to stimuli. More specifically, combining colloidal photonic crystals and invisible patterns is important in steganography and watermarking for anticounterfeiting applications. Here a convenient way to imprint robust invisible patterns in colloidal crystals of hollow silica spheres is presented. While these patterns remain invisible under static environmental humidity, even up to near 100% relative humidity, they are unveiled immediately (≈100 ms) and fully reversibly by dynamic humid flow, e.g., human breath. They reveal themselves due to the extreme wettability of the patterned (etched) regions, as confirmed by contact angle measurements. The liquid surface tension threshold to induce wetting (revealing the imprinted invisible images) is evaluated by thermodynamic predictions and subsequently verified by exposure to various vapors with different surface tension. The color of the patterned regions is furthermore independently tuned by vapors with different refractive indices. Such a system can play a key role in applications such as anticounterfeiting, identification, and vapor sensing. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Working in Separate Silos? What Citation Patterns Reveal about Higher Education Research Internationally

Science.gov (United States)

Tight, Malcolm

2014-01-01

Higher education research is a growing, inter-disciplinary and increasingly international field of study. This article examines the citation patterns of articles published in six leading higher education journals--three published in the United States and three published elsewhere in the world--for what they reveal about the development of this…

Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

Science.gov (United States)

Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

2014-01-01

The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

Blinded Comparison between an In-Air Reverberation Method and an Electronic Probe Tester in the Detection of Ultrasound Probe Faults.

Science.gov (United States)

Dudley, Nicholas J; Woolley, Darren J

2017-12-01

The aim of this study was to perform a blinded trial, comparing the results of a visual inspection of the in-air reverberation pattern with the results of an electronic probe tester in detecting ultrasound probe faults. Sixty-two probes were tested. A total of 28 faults were found, 3 only by in-air reverberation assessment and 2 only by the electronic probe tester. The electronic probe tester provided additional information regarding the location of the fault in 74% of the cases in which both methods detected a fault. It is possible to detect the majority of probe faults by visual inspection and in-air reverberation assessment. The latter provides an excellent first-line test, easily performed on a daily basis by equipment users. An electronic probe tester is required if detailed evaluation of faults is necessary. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. All rights reserved.

Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing.

Science.gov (United States)

Cébron, Aurélie; Bodrossy, Levente; Chen, Yin; Singer, Andrew C; Thompson, Ian P; Prosser, James I; Murrell, J Colin

2007-10-01

A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with (13)C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of (13)C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in (13)C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs.

Multivoxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

DEFF Research Database (Denmark)

Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.

2013-01-01

The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection, and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations...... within a multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while...... human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during...

NeuroMEMS: Neural Probe Microtechnologies

Directory of Open Access Journals (Sweden)

Sam Musallam

2008-10-01

Full Text Available Neural probe technologies have already had a significant positive effect on our understanding of the brain by revealing the functioning of networks of biological neurons. Probes are implanted in different areas of the brain to record and/or stimulate specific sites in the brain. Neural probes are currently used in many clinical settings for diagnosis of brain diseases such as seizers, epilepsy, migraine, Alzheimer’s, and dementia. We find these devices assisting paralyzed patients by allowing them to operate computers or robots using their neural activity. In recent years, probe technologies were assisted by rapid advancements in microfabrication and microelectronic technologies and thus are enabling highly functional and robust neural probes which are opening new and exciting avenues in neural sciences and brain machine interfaces. With a wide variety of probes that have been designed, fabricated, and tested to date, this review aims to provide an overview of the advances and recent progress in the microfabrication techniques of neural probes. In addition, we aim to highlight the challenges faced in developing and implementing ultralong multi-site recording probes that are needed to monitor neural activity from deeper regions in the brain. Finally, we review techniques that can improve the biocompatibility of the neural probes to minimize the immune response and encourage neural growth around the electrodes for long term implantation studies.

Employment of a self-made probe in galactography

International Nuclear Information System (INIS)

Zhong Meihua; Lv Dunzhao; Yang Zhihong

2009-01-01

Objective: To discuss the usefulness of a self-made probe in galactography. Methods: 45 cases performed galactography with self-made probe and other 56 cases performed routine galactography were compared. The occurrence of pain and ductal injuries during galactography and the rate of satisfactory between the two groups were noted. Results: In the group using self-made probe, pain was revealed in 2 cases without ductal injuries and satisfactory galactography was performed in 43 cases. In the routine group, pain was revealed in 15 cases, with ductal injuries in 3 cases during galactography and satisfactory galactography was performed in 41 cases. Significant difference was found in the occurrence of pain and the rate of satisfactory galactorgraphy. Conclusion: Galactography with self-made probe can greatly lessen the appearance of pain and ductal injuries during galactography and increase the rate of satisfactory examination and diagnostic accuracy of galactography. (authors)

Time-Varying Networks of Inter-Ictal Discharging Reveal Epileptogenic Zone.

Science.gov (United States)

Zhang, Luyan; Liang, Yi; Li, Fali; Sun, Hongbin; Peng, Wenjing; Du, Peishan; Si, Yajing; Song, Limeng; Yu, Liang; Xu, Peng

2017-01-01

The neuronal synchronous discharging may cause an epileptic seizure. Currently, most of the studies conducted to investigate the mechanism of epilepsy are based on EEGs or functional magnetic resonance imaging (fMRI) recorded during the ictal discharging or the resting-state, and few studies have probed into the dynamic patterns during the inter-ictal discharging that are much easier to record in clinical applications. Here, we propose a time-varying network analysis based on adaptive directed transfer function to uncover the dynamic brain network patterns during the inter-ictal discharging. In addition, an algorithm based on the time-varying outflow of information derived from the network analysis is developed to detect the epileptogenic zone. The analysis performed revealed the time-varying network patterns during different stages of inter-ictal discharging; the epileptogenic zone was activated prior to the discharge onset then worked as the source to propagate the activity to other brain regions. Consistence between the epileptogenic zones detected by our proposed approach and the actual epileptogenic zones proved that time-varying network analysis could not only reveal the underlying neural mechanism of epilepsy, but also function as a useful tool in detecting the epileptogenic zone based on the EEGs in the inter-ictal discharging.

Void fraction and flow regime determination by optical probe for boiling two-phase flow in a tube subchannel

International Nuclear Information System (INIS)

Cheng Huiping; Wu Hongtao; Ba Changxi; Yan Xiaoming; Huang Suyi

1995-12-01

In view of the need to determine void fraction and flow regime of vapor-liquid two-phase flow in the steam generator test model, domestic made optical probe was applied on a small-scale freon two-phase flow test rig. Optical probe signals were collected at a sampling rate up to 500 Hz and converted into digital form. Both the time signal, and the amplitude probability density function and FFT spectrum function calculated thereof were analysed in the time and frequency domains respectively. The threshold characterizing vapor or liquid contact with the probe tip was determined from the air-water two-phase flow pressure drop test results. Then, the boiling freon two-phase flow void fraction was determined by single threshold method, and compared with numerical heat transfer computation. Typical patterns which were revealed by the above-mentioned time signal and the functions were found corresponding to distinct flow regimes, as corroborated by visual observation. The experiment shows that the optical probe was a promising technique for two-phase flow void fraction measurement and flow regime identification (3 refs., 15 figs., 1 tab.)

Sandwich hybridization probes for the detection of Pseudo-nitzschia (Bacillariophyceae) species: An update to existing probes and a description of new probes.

Science.gov (United States)

Bowers, Holly A; Marin, Roman; Birch, James M; Scholin, Christopher A

2017-12-01

New sandwich hybridization assay (SHA) probes for detecting Pseudo-nitzschia species (P. arenysensis, P. fraudulenta, P. hasleana, P. pungens) are presented, along with updated cross-reactivity information on historical probes (SHA and FISH; fluorescence in situ hybridization) targeting P. australis and P. multiseries. Pseudo-nitzschia species are a cosmopolitan group of diatoms that produce varying levels of domoic acid (DA), a neurotoxin that can accumulate in finfish and shellfish and transfer throughout the food web. Consumption of infected food sources can lead to illness in humans (amnesic shellfish poisoning; ASP) and marine wildlife (domoic acid poisoning; DAP). The threat of human illness, along with economic loss from fishery closures has resulted in the implementation of monitoring protocols and intensive ecological studies. SHA probes have been instrumental in some of these efforts, as the technique performs well in complex heterogeneous sample matrices and has been adapted to benchtop and deployable (Environmental Sample Processor) platforms. The expanded probe set will enhance future efforts towards understanding spatial, temporal and successional patterns in species during bloom and non-bloom periods. Copyright © 2017 Elsevier B.V. All rights reserved.

Practical aspects of spherical near-field antenna measurements using a high-order probe

DEFF Research Database (Denmark)

Laitinen, Tommi; Pivnenko, Sergey; Nielsen, Jeppe Majlund

2006-01-01

Two practical aspects related to accurate antenna pattern characterization by probe-corrected spherical near-field antenna measurements with a high-order probe are examined. First, the requirements set by an arbitrary high-order probe on the scanning technique are pointed out. Secondly, a channel...... balance calibration procedure for a high-order dual-port probe with non-identical ports is presented, and the requirements set by this procedure for the probe are discussed....

Life in Ice: Microbial Growth Dynamics and Greenhouse Gas Production During Winter in a Thermokarst Bog Revealed by Stable Isotope Probing Targeted Metagenomics

Science.gov (United States)

Blazewicz, S.; White, R. A., III; Tas, N.; Euskirchen, E. S.; Mcfarland, J. W.; Jansson, J.; Waldrop, M. P.

2016-12-01

Permafrost contains a reservoir of frozen C estimated to be twice the size of the current atmospheric C pool. In response to changing climate, permafrost is rapidly warming which could result in widespread seasonal thawing. When permafrost thaws, soils that are rich in ice and C often transform into thermokarst wetlands with anaerobic conditions and significant production of atmospheric CH4. While most C flux research in recently thawed permafrost concentrates on the few summer months when seasonal thaw has occurred, there is mounting evidence that sizeable portions of annual CO2 and CH4 efflux occurs over winter or during a rapid burst of emissions associated with seasonal thaw. A potential mechanism for such efflux patterns is microbial activity in frozen soils over winter where gasses produced are partially trapped within ice until spring thaw. In order to better understand microbial transformation of soil C to greenhouse gas over winter, we applied stable isotope probing (SIP) targeted metagenomics combined with process measurements and field flux data to reveal activities of microbial communities in `frozen' soil from an Alaskan thermokarst bog. Field studies revealed build-up of CO2 and CH4 in frozen soils suggesting that microbial activity persisted throughout the winter in soils poised just below the freezing point. Laboratory incubations designed to simulate in-situ winter conditions (-1.5 °C and anaerobic) revealed continuous CH4 and CO2 production. Strikingly, the quantity of CH4 produced in 6 months in frozen soil was equivalent to approximately 80% of CH4 emitted during the 3 month summer `active' season. Heavy water SIP targeted iTag sequencing revealed growing bacteria and archaea in the frozen anaerobic soil. Growth was primarily observed in two bacterial phyla, Firmicutes and Bacteroidetes, suggesting that fermentation was likely the major C mineralization pathway. SIP targeted metagenomics facilitated characterization of the primary metabolic

Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

Science.gov (United States)

Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

1991-01-01

Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

Small molecule probes for cellular death machines.

Science.gov (United States)

Li, Ying; Qian, Lihui; Yuan, Junying

2017-08-01

The past decade has witnessed a significant expansion of our understanding about the regulated cell death mechanisms beyond apoptosis. The application of chemical biological approaches had played a major role in driving these exciting discoveries. The discovery and use of small molecule probes in cell death research has not only revealed significant insights into the regulatory mechanism of cell death but also provided new drug targets and lead drug candidates for developing therapeutics of human diseases with huge unmet need. Here, we provide an overview of small molecule modulators for necroptosis and ferroptosis, two non-apoptotic cell death mechanisms, and discuss the molecular pathways and relevant pathophysiological mechanisms revealed by the judicial applications of such small molecule probes. We suggest that the development and applications of small molecule probes for non-apoptotic cell death mechanisms provide an outstanding example showcasing the power of chemical biology in exploring novel biological mechanisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Time displacement pictures with multi-mode probes from circumferential welds

International Nuclear Information System (INIS)

Wustenberg, H.; Jaffrey, D.; Ludwig, B.; Bertus, N.; Erhard, A.

1985-01-01

If a creeping wave probe is applied to butt welds typical echo patterns from weld defects can be received. It seems possible that echoes from the geometric shape of the root or the crown and defect echoes can be separated by simple means. This has been the reason for the development of a special presentation of the echo patterns received by this multi-mode creeping wave probe. The so called time displacement pictures show the AD-converted A-scans in a gray scale along a line corresponding to the time axis of the propagation. Perpendicular to this time axis results obtained from displacement of the probe parallel to the weld are presented. This kind of picture immediately provides the whole A-scan information. This paper presents some first results on simulated welds with artificial defects and on circumferential welds with typical geometric imperfections

Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

Science.gov (United States)

Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

Active cancellation of probing in linear dipole phased array

CERN Document Server

Singh, Hema; Jha, Rakesh Mohan

2015-01-01

In this book, a modified improved LMS algorithm is employed for weight adaptation of dipole array for the generation of beam pattern in multiple signal environments. In phased arrays, the generation of adapted pattern according to the signal scenario requires an efficient adaptive algorithm. The antenna array is expected to maintain sufficient gain towards each of the desired source while at the same time suppress the probing sources. This cancels the signal transmission towards each of the hostile probing sources leading to active cancellation. In the book, the performance of dipole phased array is demonstrated in terms of fast convergence, output noise power and output signal-to-interference-and noise ratio. The mutual coupling effect and role of edge elements are taken into account. It is established that dipole array along with an efficient algorithm is able to maintain multilobe beamforming with accurate and deep nulls towards each probing source. This work has application to the active radar cross secti...

Femtosecond Pump-Push-Probe and Pump-Dump-Probe Spectroscopy of Conjugated Polymers: New Insight and Opportunities.

Science.gov (United States)

Kee, Tak W

2014-09-18

Conjugated polymers are an important class of soft materials that exhibit a wide range of applications. The excited states of conjugated polymers, often referred to as excitons, can either deactivate to yield the ground state or dissociate in the presence of an electron acceptor to form charge carriers. These interesting properties give rise to their luminescence and the photovoltaic effect. Femtosecond spectroscopy is a crucial tool for studying conjugated polymers. Recently, more elaborate experimental configurations utilizing three optical pulses, namely, pump-push-probe and pump-dump-probe, have been employed to investigate the properties of excitons and charge-transfer states of conjugated polymers. These studies have revealed new insight into femtosecond torsional relaxation and detrapping of bound charge pairs of conjugated polymers. This Perspective highlights (1) the recent achievements by several research groups in using pump-push-probe and pump-dump-probe spectroscopy to study conjugated polymers and (2) future opportunities and potential challenges of these techniques.

Long-term acoustical observations of the mesopelagic fish Maurolicus muelleri reveal novel and varied vertical migration patterns

KAUST Repository

Staby, A; Rø stad, Anders; Kaartvedt, Stein

2011-01-01

. The data revealed known patterns as normal diel vertical migration (DVM), midnight sinking between dusk and dawn, and periods without migrations, as well as novel behaviours consisting of early morning ascents, reverse diel vertical migrations

Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

Directory of Open Access Journals (Sweden)

Hines Heather M

2012-06-01

Full Text Available Abstract Background Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. Results We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. Conclusions This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.

How They Move Reveals What Is Happening: Understanding the Dynamics of Big Events from Human Mobility Pattern

Directory of Open Access Journals (Sweden)

Jean Damascène Mazimpaka

2017-01-01

Full Text Available The context in which a moving object moves contributes to the movement pattern observed. Likewise, the movement pattern reflects the properties of the movement context. In particular, big events influence human mobility depending on the dynamics of the events. However, this influence has not been explored to understand big events. In this paper, we propose a methodology for learning about big events from human mobility pattern. The methodology involves extracting and analysing the stopping, approaching, and moving-away interactions between public transportation vehicles and the geographic context. The analysis is carried out at two different temporal granularity levels to discover global and local patterns. The results of evaluating this methodology on bus trajectories demonstrate that it can discover occurrences of big events from mobility patterns, roughly estimate the event start and end time, and reveal the temporal patterns of arrival and departure of event attendees. This knowledge can be usefully applied in transportation and event planning and management.

Movement patterns and dispersal potential of Pecos bluntnose shiner (Notropis simus pecosensis) revealed using otolith microchemistry

Science.gov (United States)

Chase, Nathan M.; Caldwell, Colleen A.; Carleton, Scott A.; Gould, William R.; Hobbs, James A.

2015-01-01

Natal origin and dispersal potential of the federally threatened Pecos bluntnose shiner (Notropis simus pecosensis) were successfully characterized using otolith microchemistry and swimming performance trials. Strontium isotope ratios (87Sr:86Sr) of otoliths within the resident plains killifish (Fundulus zebrinus) were successfully used as a surrogate for strontium isotope ratios in water and revealed three isotopically distinct reaches throughout 297 km of the Pecos River, New Mexico, USA. Two different life history movement patterns were revealed in Pecos bluntnose shiner. Eggs and fry were either retained in upper river reaches or passively dispersed downriver followed by upriver movement during the first year of life, with some fish achieving a minimum movement of 56 km. Swimming ability of Pecos bluntnose shiner confirmed upper critical swimming speeds (Ucrit) as high as 43.8 cm·s−1 and 20.6 body lengths·s−1 in 30 days posthatch fish. Strong swimming ability early in life supports our observations of upriver movement using otolith microchemistry and confirms movement patterns that were previously unknown for the species. Understanding patterns of dispersal of this and other small-bodied fishes using otolith microchemistry may help redirect conservation and management efforts for Great Plains fishes.

Probing the reaching-grasping network in humans through multivoxel pattern decoding.

Science.gov (United States)

Di Bono, Maria Grazia; Begliomini, Chiara; Castiello, Umberto; Zorzi, Marco

2015-11-01

The quest for a putative human homolog of the reaching-grasping network identified in monkeys has been the focus of many neuropsychological and neuroimaging studies in recent years. These studies have shown that the network underlying reaching-only and reach-to-grasp movements includes the superior parieto-occipital cortex (SPOC), the anterior part of the human intraparietal sulcus (hAIP), the ventral and the dorsal portion of the premotor cortex, and the primary motor cortex (M1). Recent evidence for a wider frontoparietal network coding for different aspects of reaching-only and reach-to-grasp actions calls for a more fine-grained assessment of the reaching-grasping network in humans by exploiting pattern decoding methods (multivoxel pattern analysis--MVPA). Here, we used MPVA on functional magnetic resonance imaging (fMRI) data to assess whether regions of the frontoparietal network discriminate between reaching-only and reach-to-grasp actions, natural and constrained grasping, different grasp types, and object sizes. Participants were required to perform either reaching-only movements or two reach-to-grasp types (precision or whole hand grasp) upon spherical objects of different sizes. Multivoxel pattern analysis highlighted that, independently from the object size, all the selected regions of both hemispheres contribute in coding for grasp type, with the exception of SPOC and the right hAIP. Consistent with recent neurophysiological findings on monkeys, there was no evidence for a clear-cut distinction between a dorsomedial and a dorsolateral pathway that would be specialized for reaching-only and reach-to-grasp actions, respectively. Nevertheless, the comparison of decoding accuracy across brain areas highlighted their different contributions to reaching-only and grasping actions. Altogether, our findings enrich the current knowledge regarding the functional role of key brain areas involved in the cortical control of reaching-only and reach-to-grasp actions

RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats.

Science.gov (United States)

Merrick, B Alex; Phadke, Dhiral P; Auerbach, Scott S; Mav, Deepak; Stiegelmeyer, Suzy M; Shah, Ruchir R; Tice, Raymond R

2013-01-01

Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1), a potent hepatocarcinogen, on the male rat liver transcriptome prior to onset of histopathological lesions or tumors. We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL). Paired-end reads were mapped to the rat genome (Rn4) with TopHat and further analyzed by DESeq and Cufflinks-Cuffdiff pipelines to identify differentially expressed transcripts, new exons and unannotated transcripts. PCA and cluster analysis of DEGs showed clear separation between AFB1 and CTRL treatments and concordance among group replicates. qPCR of eight high and medium DEGs and three low DEGs showed good comparability among RNA-Seq and microarray transcripts. DESeq analysis identified 1,026 differentially expressed transcripts at greater than two-fold change (p<0.005) compared to 626 transcripts by microarray due to base pair resolution of transcripts by RNA-Seq, probe placement within transcripts or an absence of probes to detect novel transcripts, splice variants and exons. Pathway analysis among DEGs revealed signaling of Ahr, Nrf2, GSH, xenobiotic, cell cycle, extracellular matrix, and cell differentiation networks consistent with pathways leading to AFB1 carcinogenesis, including almost 200 upregulated transcripts controlled by E2f1-related pathways related to kinetochore structure, mitotic spindle assembly and tissue remodeling. We report 49 novel, differentially-expressed transcripts including confirmation by PCR-cloning of two unique, unannotated, hepatic AFB1-responsive transcripts (HAfT's) on chromosomes 1.q55 and 15.q11, overexpressed by 10 to 25-fold. Several potentially novel exons were found and exon refinements were made including AFB1 exon-specific induction of homologous family members, Ugt1a6 and Ugt1a7c. We find the

Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes.

Directory of Open Access Journals (Sweden)

Wayne Chadwick

Full Text Available The central nervous system normally functions at O(2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O(2-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O(2 tensions compared to the cell culture standard of 20% O(2, to investigate their ability to sense and translate this O(2 information to transcriptional activity. Variance of ambient O(2 tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O(2 tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O(2 tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O(2 tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional 'programs' may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.

Analysis of main artifacts in scanning probe microscopy (1)

International Nuclear Information System (INIS)

Alekperov, S.D.; Alekperov, S.D.

2012-01-01

The analysis of experiment carrying methodology in the scanning probe microscopy (SPM) region is carried out, the main parameters influencing on image quality are revealed. In order to reveal the artifact reason the main components of SPM signal which are divided on 5 groups : the useful signal; noises connected with external influences and temperature drift; distortions connected with piezoceramics and piezo-scanner non-ideality; probe geometry influence; apparatus noises are considered. The main methods of removal and minimization of the given artifacts are considered. The second and third groups of main components of SPM signal are considered in the articles first part

Reproducibility of the cutoff probe for the measurement of electron density

Energy Technology Data Exchange (ETDEWEB)

Kim, D. W.; Oh, W. Y. [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of); You, S. J., E-mail: sjyou@cnu.ac.kr [Department of Physics, Chungnam National University, Daejeon 305-701 (Korea, Republic of); Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H., E-mail: jhkim86@kriss.re.kr [Center for Vacuum Technology, Korea Research Institute of Standards and Science, Daejeon 305-306 (Korea, Republic of); Yoon, J.-S. [Plasma Technology Research Center, National Fusion Research Institute, Gunsan 573-540 (Korea, Republic of)

2016-06-15

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

Reproducibility of the cutoff probe for the measurement of electron density

International Nuclear Information System (INIS)

Kim, D. W.; Oh, W. Y.; You, S. J.; Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H.; Yoon, J.-S.

2016-01-01

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

Plasmonic direct writing lithography with a macroscopical contact probe

Science.gov (United States)

Huang, Yuerong; Liu, Ling; Wang, Changtao; Chen, Weidong; Liu, Yunyue; Li, Ling

2018-05-01

In this work, we design a plasmonic direct writing lithography system with a macroscopical contact probe to achieve nanometer scale spots. The probe with bowtie-shaped aperture array adopts spring hinge and beam deflection method (BDM) to realize near-field lithography. Lithography results show that a macroscopical plasmonic contact probe can achieve a patterning resolution of around 75 nm at 365 nm wavelength, and demonstrate that the lithography system is promising for practical applications due to beyond the diffraction limit, low cost, and simplification of system configuration. CST calculations provide a guide for the design of recording structure and the arrangement of placing polarizer.

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

Directory of Open Access Journals (Sweden)

Jasper J. van Thor

2015-01-01

Full Text Available In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe” which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

Calibration of the DLP-SC-3300-02 probe

DEFF Research Database (Denmark)

Pivnenko, Sergey; Breinbjerg, Olav

This report douments the calibration measurement of the DLP-SC-3300-02 dual-linearly polarized near-field probe. The measurement comprises radiation pattern, diretivity, gain, spetra of spherial wave coefients, polarization charateristis, and complex channel balance at 41 frequencies, as well...

Serial assessment of doxorubicin cardiomyopathy with the computerized scintillation probe

International Nuclear Information System (INIS)

Strashun, A.; Goldsmith, S.J.; Horowitz, S.F.

1982-01-01

Cardiac function was serially monitored in 55 patients receiving adriamycin chemotherapy over 18 months with quantitative radionuclide assessment by both a nonimaging computerized scintillation probe and gamma camera-computer imaging. Interval ejection fraction change was comparable with both techniques and predicted incipient cardiotoxicity. Probe data revealed ejection fraction decline was antedated by decline left ventricular emptying and filling rates

Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

Science.gov (United States)

Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

2008-10-01

Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

Effects of Mach number on pitot-probe displacement in a turbulent boundary layer

Science.gov (United States)

Allen, J. M.

1974-01-01

Experimental pitot-probe-displacement data have been obtained in a turbulent boundary layer at a local free-stream Mach number of 4.63 and unit Reynolds number of 6.46 million meter. The results of this study were compared with lower Mach number results of previous studies. It was found that small probes showed displacement only, whereas the larger probes showed not only displacement but also distortion of the shape of the boundary-layer profile. The distortion pattern occurred lower in the boundary layer at the higher Mach number than at the the lower Mach number. The maximum distortion occurred when the center of the probe was about one probe diameter off the test surface. For probes in the wall contact position, the indicated Mach numbers were, for all probes tested, close to the true profile. Pitot-probe displacement was found to increase significantly with increasing Mach number.

RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats.

Directory of Open Access Journals (Sweden)

B Alex Merrick

Full Text Available Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1, a potent hepatocarcinogen, on the male rat liver transcriptome prior to onset of histopathological lesions or tumors. We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL. Paired-end reads were mapped to the rat genome (Rn4 with TopHat and further analyzed by DESeq and Cufflinks-Cuffdiff pipelines to identify differentially expressed transcripts, new exons and unannotated transcripts. PCA and cluster analysis of DEGs showed clear separation between AFB1 and CTRL treatments and concordance among group replicates. qPCR of eight high and medium DEGs and three low DEGs showed good comparability among RNA-Seq and microarray transcripts. DESeq analysis identified 1,026 differentially expressed transcripts at greater than two-fold change (p<0.005 compared to 626 transcripts by microarray due to base pair resolution of transcripts by RNA-Seq, probe placement within transcripts or an absence of probes to detect novel transcripts, splice variants and exons. Pathway analysis among DEGs revealed signaling of Ahr, Nrf2, GSH, xenobiotic, cell cycle, extracellular matrix, and cell differentiation networks consistent with pathways leading to AFB1 carcinogenesis, including almost 200 upregulated transcripts controlled by E2f1-related pathways related to kinetochore structure, mitotic spindle assembly and tissue remodeling. We report 49 novel, differentially-expressed transcripts including confirmation by PCR-cloning of two unique, unannotated, hepatic AFB1-responsive transcripts (HAfT's on chromosomes 1.q55 and 15.q11, overexpressed by 10 to 25-fold. Several potentially novel exons were found and exon refinements were made including AFB1 exon-specific induction of homologous family members, Ugt1a6 and Ugt1a7c

CMOS Compatibility of a Micromachining Process Developed for Semiconductor Neural Probe

National Research Council Canada - National Science Library

An, S

2001-01-01

.... Test transistor patterns generated using standard CMOS fabrication line were exposed to a post-CMOS probe making process including dielectric deposition, gold metalization and the dry etching step...

Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

Science.gov (United States)

Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

2013-09-03

Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes.

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Bowden, G; Johnson, J; Schachtele, C

1993-08-01

Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

Network based approaches reveal clustering in protein point patterns

Science.gov (United States)

Parker, Joshua; Barr, Valarie; Aldridge, Joshua; Samelson, Lawrence E.; Losert, Wolfgang

2014-03-01

Recent advances in super-resolution imaging have allowed for the sub-diffraction measurement of the spatial location of proteins on the surfaces of T-cells. The challenge is to connect these complex point patterns to the internal processes and interactions, both protein-protein and protein-membrane. We begin analyzing these patterns by forming a geometric network amongst the proteins and looking at network measures, such the degree distribution. This allows us to compare experimentally observed patterns to models. Specifically, we find that the experimental patterns differ from heterogeneous Poisson processes, highlighting an internal clustering structure. Further work will be to compare our results to simulated protein-protein interactions to determine clustering mechanisms.

Molecular cloning and construction of the coding region for human acetylcholinesterase reveals a G + C-rich attenuating structure

International Nuclear Information System (INIS)

Soreq, H.; Ben-Aziz, R.; Prody, C.A.; Seidman, S.; Gnatt, A.; Neville, L.; Lieman-Hurwitz, J.; Lev-Lehman, E.; Ginzberg, D.; Lapidot-Lifson, Y.; Zakut, H.

1990-01-01

To study the primary structure of human acetylcholinesterase and its gene expression and amplification, cDNA libraries from human tissues expressing oocyte-translatable AcChoEase mRNA were constructed and screened with labeled oligodeoxynucleotide probes. Several cDNA clones were isolated that encoded a polypeptide with ≥50% identically aligned amino acids to Torpedo AcChoEase and human butyrylcholinesterase. However, these cDNA clones were all truncated within a 300-nucleotide-long G + C-rich region with a predicted pattern of secondary structure having a high Gibbs free energy downstream from the expected 5' end of the coding region. Screening of a genomic DNA library revealed the missing 5' domain. When ligated to the cDNA and constructed into a transcription vector, this sequence encoded a synthetic mRNA translated in microinjected oocytes into catalytically active AcChoEase with marked preference for acetylthiocholine over butyrylthiocholine as a substrate, susceptibility to inhibition by the AcChoEase inhibitor BW284C51, and resistance to the AcChoEase inhibitor tetraisopropylpyrophosphoramide. Blot hybridization of genomic DNA from different individuals carrying amplified AcChoEase genes revealed variable intensities and restriction patterns with probes from the regions upstream and downstream from the predicted G + C-rich structure. Thus, the human AcChoEase gene includes a putative G + C-rich attenuator domain and is subject to structural alterations in cases of AcChoEase gene amplification

Probing Dynamics in Colloidal Crystals with Pump-Probe Experiments at LCLS: Methodology and Analysis

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Nastasia Mukharamova

2017-05-01

Full Text Available We present results of the studies of dynamics in colloidal crystals performed by pump-probe experiments using an X-ray free-electron laser (XFEL. Colloidal crystals were pumped with an infrared laser at a wavelength of 800 nm with varying power and probed by XFEL pulses at an energy of 8 keV with a time delay up to 1000 ps. The positions of the Bragg peaks, and their radial and azimuthal widths were analyzed as a function of the time delay. The spectral analysis of the data did not reveal significant enhancement of frequencies expected in this experiment. This allowed us to conclude that the amplitude of vibrational modes excited in colloidal crystals was less than the systematic error caused by the noise level.

Mobile Probing and Probes

DEFF Research Database (Denmark)

Duvaa, Uffe; Ørngreen, Rikke; Weinkouff Mathiasen, Anne-Gitte

2013-01-01

Mobile probing is a method, developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time and space......). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings point...... to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face). The development...

Mobile Probing and Probes

DEFF Research Database (Denmark)

Duvaa, Uffe; Ørngreen, Rikke; Weinkouff, Anne-Gitte

2012-01-01

Mobile probing is a method, which has been developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time...... and space). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings...... point to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face...

Three-dimensional macroporous nanoelectronic networks as minimally invasive brain probes

Science.gov (United States)

Xie, Chong; Liu, Jia; Fu, Tian-Ming; Dai, Xiaochuan; Zhou, Wei; Lieber, Charles M.

2015-12-01

Direct electrical recording and stimulation of neural activity using micro-fabricated silicon and metal micro-wire probes have contributed extensively to basic neuroscience and therapeutic applications; however, the dimensional and mechanical mismatch of these probes with the brain tissue limits their stability in chronic implants and decreases the neuron-device contact. Here, we demonstrate the realization of a three-dimensional macroporous nanoelectronic brain probe that combines ultra-flexibility and subcellular feature sizes to overcome these limitations. Built-in strains controlling the local geometry of the macroporous devices are designed to optimize the neuron/probe interface and to promote integration with the brain tissue while introducing minimal mechanical perturbation. The ultra-flexible probes were implanted frozen into rodent brains and used to record multiplexed local field potentials and single-unit action potentials from the somatosensory cortex. Significantly, histology analysis revealed filling-in of neural tissue through the macroporous network and attractive neuron-probe interactions, consistent with long-term biocompatibility of the device.

A Network Based Methodology to Reveal Patterns in Knowledge Transfer

Directory of Open Access Journals (Sweden)

Orlando López-Cruz

2015-12-01

Full Text Available This paper motivates, presents and demonstrates in use a methodology based in complex network analysis to support research aimed at identification of sources in the process of knowledge transfer at the interorganizational level. The importance of this methodology is that it states a unified model to reveal knowledge sharing patterns and to compare results from multiple researches on data from different periods of time and different sectors of the economy. This methodology does not address the underlying statistical processes. To do this, national statistics departments (NSD provide documents and tools at their websites. But this proposal provides a guide to model information inferences gathered from data processing revealing links between sources and recipients of knowledge being transferred and that the recipient detects as main source to new knowledge creation. Some national statistics departments set as objective for these surveys the characterization of innovation dynamics in firms and to analyze the use of public support instruments. From this characterization scholars conduct different researches. Measures of dimensions of the network composed by manufacturing firms and other organizations conform the base to inquiry the structure that emerges from taking ideas from other organizations to incept innovations. These two sets of data are actors of a two- mode-network. The link between two actors (network nodes, one acting as the source of the idea. The second one acting as the destination comes from organizations or events organized by organizations that “provide” ideas to other group of firms. The resulting demonstrated design satisfies the objective of being a methodological model to identify sources in knowledge transfer of knowledge effectively used in innovation.

A Space-Based Observational Strategy for Hydrogen Cosmology Using Dynamic Polarimetry and Pattern Recognition

Science.gov (United States)

Burns, Jack O.; Nhan, Bang; Bradley, Richard F.; Tauscher, Keith A.; Rapetti, David; Switzer, Eric

2018-06-01

The redshifted 21-cm monopole is expected to be a powerful probe of the epoch of the first stars and galaxies (10 polarimetry that separates the polarized foreground from the unpolarized 21-cm signal. Initial results from a ground-based prototype called the Cosmic Twilight Polarimeter will be described which tentatively reveal the presence of the expected polarization signature from the foreground. Dynamic polarimetry, when combined with sophisticated pattern recognition techniques based on training sets, machine learning, and statistical information criteria offer promise for precise extraction of the 21-cm spectrum. We describe a new SmallSat mission concept, the Dark Ages Polarimetry Pathfinder (DAPPer), that will utilize these novel approaches for extending the recent detection of a 78 MHz signal down to lower frequencies where we can uniquely probe evidence for the first stars and dark matter.

Microdiffraction: X-rays as a probe to reveal flux divergences ininterconnects

Energy Technology Data Exchange (ETDEWEB)

Spolenak, R.; Tamura, N.; Patel, J.R.

2006-01-01

Most reliability issues in interconnect systems occur at a local scale and many of them include the local build-up of stresses. Typical failure mechanisms are electromigration and stress voiding in interconnect lines and fatigue in surface acoustic wave devices. Thus a local probe is required for the investigation of these phenomena. In this paper the application of the Laue microdiffraction technique to investigate flux divergences in interconnect systems will be described. The deviatoric strain tensor of single grains can be correlated with the local microstructure, orientation and defect density. Especially the latter led to recent results about the correlation of stress build-up and orientation in Cu lines and electromigration-induced grain rotation in Cu and Al lines.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

Science.gov (United States)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

A novel polymer probe for Zn(II) detection with ratiometric fluorescence signal

Science.gov (United States)

Diao, Haipeng; Guo, Lixia; Liu, Wen; Feng, Liheng

2018-05-01

A conjugated polymer probe comprised of fluorene, quinolone and benzothiazole units was designed and synthesized by the Suzuki coupling reaction. Through the studies of photophysical and thermal properties, the polymer displays blue-emitting feature and good thermal stability. A ratiometric fluorescence signal of the probe for Zn(II) was observed in ethanol with a new emission peak at 555 nm. The probe possesses a high selectivity and sensitivity for Zn(II) during familiar metal ions in ethanol. The detection limit of the probe for Zn (II) is up to 10-8 mol/L. The electron distributions of the polymer before and after bonding with Zn (II) were investigated by the Gaussian 09 software, which agreed with the experimental results. Noticeably, based on the color property of the probe with Zn(II), a series of color test paper were developed for visual detecting Zn(II) ions. This work helps to provide a platform or pattern for the development of polymer fluorescence probe in the chemosensor field.

Constructive nanolithography and nanochemistry : local probe oxidation and chemical modification

NARCIS (Netherlands)

Wouters, D.; Schubert, U.S.

2003-01-01

The possibility to prepare and use submicrometer-sized patterns in successive functionalization reactions with quaternary ammonium salts and (functional) chlorosilanes, as well as cationic gold nanoparticles, is presented. Submicrometer-sized structures were prepared by local probe oxidation of

A novel analysis strategy for HLA typing using a sequence-specific oligonucleotide probe method.

Science.gov (United States)

Won, D I

2017-11-01

The technique of reverse sequence-specific oligonucleotide probes (SSOPs) is commonly used in human leukocyte antigen (HLA) typing. In the conventional method for data analysis (exact pattern matching, EPM), the larger is the number of mismatched probes, the longer the time for final typing assignment. A novel strategy, filtering and scoring (FnS), has been developed to easily assign the best-fit allele pair. In the FnS method, candidate alleles and allele pairs were filtered based on (1) subject's ethnicity, and (2) the measured partial reaction pattern with only definitely negative or positive probes. Then, the complete reaction pattern for all probes (CRPoAPs) were compared between the raw sample and expected residual allele pairs to obtain mismatch scores. To compare the FnS and EPM methods, each analysis time (minutes:seconds) for reverse SSOP HLA typing with intermediate resolution (n = 507) was measured. The analysis time with FnS method was shorter than that of the EPM method [00:21 (00:08-01:47) and 01:04 (00:15-23:45), respectively, P typing in a comprehensive and quantitative comparison between measured and expected CRPoAPs of candidate allele pairs. Therefore, this analysis strategy might be useful in a clinical setting. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Accumulation of polyunsaturated aldehydes in the gonads of the copepod Acartia tonsa revealed by tailored fluorescent probes.

Science.gov (United States)

Wolfram, Stefanie; Nejstgaard, Jens C; Pohnert, Georg

2014-01-01

Polyunsaturated aldehydes (PUAs) are released by several diatom species during predation. Besides other attributed activities, these oxylipins can interfere with the reproduction of copepods, important predators of diatoms. While intensive research has been carried out to document the effects of PUAs on copepod reproduction, little is known about the underlying mechanistic aspects of PUA action. Especially PUA uptake and accumulation in copepods has not been addressed to date. To investigate how PUAs are taken up and interfere with the reproduction in copepods we developed a fluorescent probe containing the α,β,γ,δ-unsaturated aldehyde structure element that is essential for the activity of PUAs as well as a set of control probes. We developed incubation and monitoring procedures for adult females of the calanoid copepod Acartia tonsa and show that the PUA derived fluorescent molecular probe selectively accumulates in the gonads of this copepod. In contrast, a saturated aldehyde derived probe of an inactive parent molecule was enriched in the lipid sac. This leads to a model for PUAs' teratogenic mode of action involving accumulation and covalent interaction with nucleophilic moieties in the copepod reproductive tissue. The teratogenic effect of PUAs can therefore be explained by a selective targeting of the molecules into the reproductive tissue of the herbivores, while more lipophilic but otherwise strongly related structures end up in lipid bodies.

Accumulation of polyunsaturated aldehydes in the gonads of the copepod Acartia tonsa revealed by tailored fluorescent probes.

Directory of Open Access Journals (Sweden)

Stefanie Wolfram

Full Text Available Polyunsaturated aldehydes (PUAs are released by several diatom species during predation. Besides other attributed activities, these oxylipins can interfere with the reproduction of copepods, important predators of diatoms. While intensive research has been carried out to document the effects of PUAs on copepod reproduction, little is known about the underlying mechanistic aspects of PUA action. Especially PUA uptake and accumulation in copepods has not been addressed to date. To investigate how PUAs are taken up and interfere with the reproduction in copepods we developed a fluorescent probe containing the α,β,γ,δ-unsaturated aldehyde structure element that is essential for the activity of PUAs as well as a set of control probes. We developed incubation and monitoring procedures for adult females of the calanoid copepod Acartia tonsa and show that the PUA derived fluorescent molecular probe selectively accumulates in the gonads of this copepod. In contrast, a saturated aldehyde derived probe of an inactive parent molecule was enriched in the lipid sac. This leads to a model for PUAs' teratogenic mode of action involving accumulation and covalent interaction with nucleophilic moieties in the copepod reproductive tissue. The teratogenic effect of PUAs can therefore be explained by a selective targeting of the molecules into the reproductive tissue of the herbivores, while more lipophilic but otherwise strongly related structures end up in lipid bodies.

Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

Directory of Open Access Journals (Sweden)

Sagar Singh

2016-03-01

should be over-designed to ensure successful insertion. Probability color maps were generated to visually compare the influence of design parameters. Statistical metrics derived from the color maps and multi-variable regression analysis confirmed that coating thickness and probe length were the most important features in influencing insertion potential. The model also revealed the effects of manufacturing flaws on insertion potential.

Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef

Science.gov (United States)

Edwards, Clinton B.; Eynaud, Yoan; Williams, Gareth J.; Pedersen, Nicole E.; Zgliczynski, Brian J.; Gleason, Arthur C. R.; Smith, Jennifer E.; Sandin, Stuart A.

2017-12-01

For sessile organisms such as reef-building corals, differences in the degree of dispersion of individuals across a landscape may result from important differences in life-history strategies or may reflect patterns of habitat availability. Descriptions of spatial patterns can thus be useful not only for the identification of key biological and physical mechanisms structuring an ecosystem, but also by providing the data necessary to generate and test ecological theory. Here, we used an in situ imaging technique to create large-area photomosaics of 16 plots at Palmyra Atoll, central Pacific, each covering 100 m2 of benthic habitat. We mapped the location of 44,008 coral colonies and identified each to the lowest taxonomic level possible. Using metrics of spatial dispersion, we tested for departures from spatial randomness. We also used targeted model fitting to explore candidate processes leading to differences in spatial patterns among taxa. Most taxa were clustered and the degree of clustering varied by taxon. A small number of taxa did not significantly depart from randomness and none revealed evidence of spatial uniformity. Importantly, taxa that readily fragment or tolerate stress through partial mortality were more clustered. With little exception, clustering patterns were consistent with models of fragmentation and dispersal limitation. In some taxa, dispersion was linearly related to abundance, suggesting density dependence of spatial patterning. The spatial patterns of stony corals are non-random and reflect fundamental life-history characteristics of the taxa, suggesting that the reef landscape may, in many cases, have important elements of spatial predictability.

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

Science.gov (United States)

Watters, Kyle E; Choudhary, Krishna; Aviran, Sharon; Perry, Keith L

2018-01-01

Abstract In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3′ untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites. PMID:29294088

Darkfield microspectroscopy of nanostructures on silver tip-enhanced Raman scattering probes

Energy Technology Data Exchange (ETDEWEB)

Itoh, Tamitake, E-mail: tamitake-itou@aist.go.jp [Nano-Bioanalysis Team, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395 (Japan); Yamamoto, Yuko S., E-mail: yamayulab@gmail.com [Research Fellow of the Japan Society for the Promotion of Science, Chiyoda, Tokyo 102-8472 (Japan); Department of Chemistry, School of Science and Technology, Kagawa University, Takamatsu, Kagawa 761-0396 (Japan); Suzuki, Toshiaki [UNISOKU Co. Ltd., 2-4-3 Kasugano, Hirakata, Osaka 573-0131 (Japan); Kitahama, Yasutaka; Ozaki, Yukihiro [Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337 (Japan)

2016-01-11

We report an evaluation method employing darkfield microspectroscopy for silver probes used in tip-enhanced Raman scattering (TERS). By adjusting the darkfield illumination, the diffracted light from the probe outlines disappears and the diffracted light from the surface nanostructures and tips of the probes appears as colorful spots. Scanning electron microscopy reveals that the spectral variations in these spots reflect the shapes of the surface nanostructures. The tip curvatures correlate to the spectral maxima of their spots. Temporal color changes in the spots indicate the deterioration due to the oxidation of the silver surfaces. These results show that the proposed method is useful for in situ evaluation of plasmonic properties of TERS probes.

Development and Characterization of Complex DNA Fingerprinting Probes for the Infectious Yeast Candida dubliniensis

Science.gov (United States)

Joly, Sophie; Pujol, Claude; Rysz, Michal; Vargas, Kaaren; Soll, David R.

1999-01-01

Using a strategy to clone large genomic sequences containing repetitive elements from the infectious yeast Candida dubliniensis, the three unrelated sequences Cd1, Cd24, and Cd25, with respective molecular sizes of 15,500, 10,000, and 16,000 bp, were cloned and analyzed for their efficacy as DNA fingerprinting probes. Each generated a complex Southern blot hybridization pattern with endonuclease-digested genomic DNA. Cd1 generated an extremely variable pattern that contained all of the bands of the pattern generated by the repeat element RPS of Candida albicans. We demonstrated that Cd1 does not contain RPS but does contain a repeat element associated with RPS throughout the C. dubliniensis genome. The Cd1 pattern was the least stable over time both in vitro and in vivo and for that reason proved most effective in assessing microevolution. Cd24, which did not exhibit microevolution in vitro, was highly variable in vivo, suggesting in vivo-dependent microevolution. Cd25 was deemed the best probe for broad epidemiological studies, since it was the most stable over time, was the only truly C. dubliniensis-specific probe of the three, generated the most complex pattern, was distributed throughout all C. dubliniensis chromosomes, and separated a worldwide collection of 57 C. dubliniensis isolates into two distinct groups. The presence of a species-specific repetitive element in Cd25 adds weight to the already substantial evidence that C. dubliniensis represents a bona fide species. PMID:10074523

Comparative Analysis of WUSCHEL-Related Homeobox Genes Revealed Their Parent-of-Origin and Cell Type-Specific Expression Pattern During Early Embryogenesis in Tobacco

Directory of Open Access Journals (Sweden)

Xuemei Zhou

2018-03-01

Full Text Available WUSCHEL-related homeobox (WOX gene is a plant-specific clade of homeobox transcription factors. Increasing evidences reveal that WOXs play critical roles in early embryogenesis, which involves zygote development, initiation of zygote division, and apical or basal cell lineage establishment. However, how WOXs regulate these developmental events remains largely unknown, and even detailed expression pattern in gametes and early proembryos is not yet available. Here, 13 WOX family genes were identified in Nicotiana tabacum genome. Comparative analysis of 13 WOX family genes with their homologs in Arabidopsis thaliana reveals relatively conserved expression pattern of WUS and WOX5 in shoot/root apical meristem. Whereas variations were also found, e.g., lacking homolog of WOX8 (a marker for suspensor cell in tobacco genome and the expression of WOX2/WOX9 in both apical cell and basal cell. Transient transcriptional activity analysis revealed that WOXs in WUS clade have repressive activities for their target's transcription, whereas WOXs in ancient and intermediate clade have activation activities, giving a molecular basis for the phylogenetic classification of tobacco WOXs into three major clades. Expression pattern analysis revealed that some WOXs (e.g., WOX 13a expressed in both male and female gametes and some WOXs (e.g., WOX 11 and WOX 13b displayed the characteristics of parent-of-origin genes. Interestingly, some WOXs (e.g., WOX2 and WOX9, which are essential for early embryo patterning, were de novo transcribed in zygote, indicating relevant mechanism for embryo pattern formation is only established in zygote right after fertilization and not carried in by gametes. We also found that most WOXs displayed a stage-specific and cell type-specific expression pattern. Taken together, this work provides a detailed landscape of WOXs in tobacco during fertilization and early embryogenesis, which will facilitate the understanding of their specific roles

A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar

2017-05-17

Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.

Electromechanical response of amorphous LaAlO3 thin film probed by scanning probe microscopies

Science.gov (United States)

Borowiak, Alexis S.; Baboux, Nicolas; Albertini, David; Vilquin, Bertrand; Saint Girons, Guillaume; Pelloquin, Sylvain; Gautier, Brice

2014-07-01

The electromechanical response of a 3 nm thick amorphous LaAlO3 layer obtained by molecular beam epitaxy has been studied using scanning probe microscopies. Although this kind of sample is not ferroelectric due to its amorphous nature, the resulting images are identical to what is generally obtained on truly ferroelectric samples probed by piezoresponse force microscopy: domains of apparently opposite polarisation are detected, and perfect, square shaped hysteresis loops are recorded. Moreover, written patterns are stable within 72 h. We discuss in the general case the possible origins of this behaviour in terms of charge injection, ionic conduction and motion of oxygen vacancies. In the case presented in this paper, since the writing process has been conducted with applied voltages lower than the injection threshold measured by conductive atomic force Microscopy, allowing to withdraw the hypothesis of charge injection in the sample, we propose that a bistable distribution of oxygen vacancies is responsible for this contrast.

Electromechanical response of amorphous LaAlO3 thin film probed by scanning probe microscopies

International Nuclear Information System (INIS)

Borowiak, Alexis S.; Baboux, Nicolas; Albertini, David; Gautier, Brice; Vilquin, Bertrand; Saint Girons, Guillaume; Pelloquin, Sylvain

2014-01-01

The electromechanical response of a 3 nm thick amorphous LaAlO 3 layer obtained by molecular beam epitaxy has been studied using scanning probe microscopies. Although this kind of sample is not ferroelectric due to its amorphous nature, the resulting images are identical to what is generally obtained on truly ferroelectric samples probed by piezoresponse force microscopy: domains of apparently opposite polarisation are detected, and perfect, square shaped hysteresis loops are recorded. Moreover, written patterns are stable within 72 h. We discuss in the general case the possible origins of this behaviour in terms of charge injection, ionic conduction and motion of oxygen vacancies. In the case presented in this paper, since the writing process has been conducted with applied voltages lower than the injection threshold measured by conductive atomic force Microscopy, allowing to withdraw the hypothesis of charge injection in the sample, we propose that a bistable distribution of oxygen vacancies is responsible for this contrast.

Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity.

Science.gov (United States)

Dakin, Roslyn; Fellows, Tyee K; Altshuler, Douglas L

2016-08-02

Information about self-motion and obstacles in the environment is encoded by optic flow, the movement of images on the eye. Decades of research have revealed that flying insects control speed, altitude, and trajectory by a simple strategy of maintaining or balancing the translational velocity of images on the eyes, known as pattern velocity. It has been proposed that birds may use a similar algorithm but this hypothesis has not been tested directly. We examined the influence of pattern velocity on avian flight by manipulating the motion of patterns on the walls of a tunnel traversed by Anna's hummingbirds. Contrary to prediction, we found that lateral course control is not based on regulating nasal-to-temporal pattern velocity. Instead, birds closely monitored feature height in the vertical axis, and steered away from taller features even in the absence of nasal-to-temporal pattern velocity cues. For vertical course control, we observed that birds adjusted their flight altitude in response to upward motion of the horizontal plane, which simulates vertical descent. Collectively, our results suggest that birds avoid collisions using visual cues in the vertical axis. Specifically, we propose that birds monitor the vertical extent of features in the lateral visual field to assess distances to the side, and vertical pattern velocity to avoid collisions with the ground. These distinct strategies may derive from greater need to avoid collisions in birds, compared with small insects.

Dynamics of Exciton Relaxation in LH2 Antenna Probed by Multipulse Nonlinear Spectroscopy

NARCIS (Netherlands)

Novoderezhkin, V.I.; Cohen Stuart, T.A.; van Grondelle, R.

2011-01-01

We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump - dump - probe spectroscopy (Th. A. Cohen StuartM. VengrisV. I. NovoderezhkinR. J. CogdellC. N. HunterR. van Grondelle, submitted). The theory of pump - dump - probe response is evaluated using the doorway -

Complex (Nonstandard) Six-Layer Polytypes of Lizardite Revealed from Oblique-Texture Electron Diffraction Patterns

International Nuclear Information System (INIS)

Zhukhlistov, A.P.; Zinchuk, N.N.; Kotel'nikov, D.D.

2004-01-01

Association of simple (1T and 3R) and two complex (nonstandard) orthogonal polytypes of the serpentine mineral lizardite from the Catoca kimberlite pipe (West Africa) association is revealed from oblique-texture electron diffraction patterns. A six-layer polytype with an ordered superposition of equally oriented layers (notation 3 2 3 2 3 4 3 4 3 6 3 6 or ++ - -00) belonging to the structural group A and a three-layer (336 or I,I,II) or a six-layer (336366 or I,I,II,I,II,II) polytype with alternating oppositely oriented layers and semi-disordered structure are identified using polytype analysis

[Transmission efficiency analysis of near-field fiber probe using FDTD simulation].

Science.gov (United States)

Huang, Wei; Dai, Song-Tao; Wang, Huai-Yu; Zhou, Yun-Song

2011-10-01

A fiber probe is the key component of near-field optical technology which is widely used in high resolution imaging, spectroscopy detection and nano processing. How to improve the transmission efficiency of the fiber probe is a very important problem in the application of near-field optical technology. Based on the results of 3D-FDTD computation, the dependence of the transmission efficiency on the cone angle, the aperture diameter, the wavelength and the thickness of metal cladding is revealed. The authors have also made a comparison between naked probe and the probe with metal cladding in terms of transmission efficiency and spatial resolution. In addition, the authors have discovered the fluctuation phenomena of transmission efficiency as the wavelength of incident laser increases.

Influence of probe motion on laser probe temperature in circulating blood.

Science.gov (United States)

Hehrlein, C; Splinter, R; Littmann, L; Tuntelder, J R; Tatsis, G P; Svenson, R H

1991-01-01

The purpose of this study was to evaluate the effect of probe motion on laser probe temperature in various blood flow conditions. Laser probe temperatures were measured in an in vitro blood circulation model consisting of 3.2 nm-diameter plastic tubes. A 2.0 mm-diameter metal probe attached to a 300 microns optical quartz fiber was coupled to an argon laser. Continuous wave 4 watts and 8 watts of laser power were delivered to the fiber tip corresponding to a 6.7 +/- 0.5 and 13.2 +/- 0.7 watts power setting at the laser generator. The laser probe was either moved with constant velocity or kept stationary. A thermocouple inserted in the lateral portion of the probe was used to record probe temperatures. Probe temperature changes were found with the variation of laser power, probe velocity, blood flow, and duration of laser exposure. Probe motion significantly reduced probe temperatures. After 10 seconds of 4 watts laser power the probe temperature in stagnant blood decreased from 303 +/- 18 degrees C to 113 +/- 17 degrees C (63%) by moving the probe with a velocity of 5 cm/sec. Blood flow rates of 170 ml/min further decreased the probe temperature from 113 +/- 17 degrees C to 50 +/- 8 degrees C (56%). At 8 watts of laser power a probe temperature reduction from 591 +/- 25 degrees C to 534 +/- 36 degrees C (10%) due to 5 cm/sec probe velocity was noted. Probe temperatures were reduced to 130 +/- 30 degrees C (78%) under the combined influence of 5 cm/sec probe velocity and 170 ml/min blood flow.(ABSTRACT TRUNCATED AT 250 WORDS)

Clustering Patterns of Engagement in Massive Open Online Courses (MOOCs): The Use of Learning Analytics to Reveal Student Categories

Science.gov (United States)

Khalil, Mohammad; Ebner, Martin

2017-01-01

Massive Open Online Courses (MOOCs) are remote courses that excel in their students' heterogeneity and quantity. Due to the peculiarity of being massiveness, the large datasets generated by MOOC platforms require advanced tools and techniques to reveal hidden patterns for purposes of enhancing learning and educational behaviors. This publication…

Inhomogeneous distribution of manganese atoms in ferromagnetic ZnSnAs{sub 2}:Mn thin films on InP revealed by three-dimensional atom probe investigation

Energy Technology Data Exchange (ETDEWEB)

Uchitomi, Naotaka, E-mail: uchitomi@nagaokaut.ac.jp; Inoue, Hiroaki; Kato, Takahiro; Toyota, Hideyuki [Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka 940-2188 (Japan); Uchida, Hiroshi [Toshiba Nanoanalysis Corporation, 8 Shinsugita-cho, Isogo-ku, Yokohama 235-8522 (Japan)

2015-05-07

Atomic-scale Mn distributions in ferromagnetic ZnSnAs{sub 2}:Mn thin films grown on InP substrates have been studied by applying three-dimensional atom probe (3DAP) microscopy. It is found that Mn atoms in cross-sectional 3DAP maps show the presence of inhomogeneities in Mn distribution, which is characteristic patterns of a spinoidal decomposition phase with slightly high and low concentration regions. The high Mn concentration regions are expected to be coherently clustered MnAs in the zinc-blende structure, resulting in the formation of Mn-As random connecting patterns. The origin of room-temperature ferromagnetism in ZnSnAs{sub 2}:Mn on InP can be well explained by the formation of atomic-scale magnetic clustering by spinoidal decomposition without breaking the continuity of the zinc-blende structure, which has been suggested by previous theoretical works. The lattice-matching between magnetic epi-layers and substrates should be one of the most important factors to avoid the formation of secondary hexagonal MnAs phase precipitates in preparing ferromagnetic semiconductor thin films.

A novel dog-bone oscillating AFM probe with thermal actuation and piezoresistive detection.

Science.gov (United States)

Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

2014-10-31

In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments.

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents

Energy Technology Data Exchange (ETDEWEB)

Bendell, L.I., E-mail: bendell@sfu.ca

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of 'pulse' toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a 'snap-shot' of soil, plant or avian tissue trace metal analysis post-mining activity. - Research Highlights: {yields} Archived gizzard samples reveals mining history. {yields} Grit ingestion exposes grouse to cadmium and lead. {yields} Grit selection includes particles enriched in cadmium. {yields} Cadmium enriched particles are of toxicological significance.

Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

Directory of Open Access Journals (Sweden)

Liang-Hui Chu

Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

A Chemical Probe that Labels Human Pluripotent Stem Cells

Directory of Open Access Journals (Sweden)

Nao Hirata

2014-03-01

Full Text Available A small-molecule fluorescent probe specific for human pluripotent stem cells would serve as a useful tool for basic cell biology research and stem cell therapy. Screening of fluorescent chemical libraries with human induced pluripotent stem cells (iPSCs and subsequent evaluation of hit molecules identified a fluorescent compound (Kyoto probe 1 [KP-1] that selectively labels human pluripotent stem cells. Our analyses indicated that the selectivity results primarily from a distinct expression pattern of ABC transporters in human pluripotent stem cells and from the transporter selectivity of KP-1. Expression of ABCB1 (MDR1 and ABCG2 (BCRP, both of which cause the efflux of KP-1, is repressed in human pluripotent stem cells. Although KP-1, like other pluripotent markers, is not absolutely specific for pluripotent stem cells, the identified chemical probe may be used in conjunction with other reagents.

Outsourced Probe Data Effectiveness on Signalized Arterials

Energy Technology Data Exchange (ETDEWEB)

Young, Stanley E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sharifi, Elham [University of Maryland; Eshragh, Sepideh [University of Maryland; Hamedi, Masoud [University of Maryland; Juster, Reuben M. [University of Maryland; Kaushik, Kartik [University of Maryland

2017-07-31

This paper presents results of an I-95 Corridor Coalition sponsored project to assess the ability of outsourced vehicle probe data to provide accurate travel time on signalized roadways for the purposes of real-time operations as well as performance measures. The quality of outsourced probe data on freeways has led many departments of transportation to consider such data for arterial performance monitoring. From April 2013 through June of 2014, the University of Maryland Center for Advanced Transportation Technology gathered travel times from several arterial corridors within the mid-Atlantic region using Bluetooth traffic monitoring (BTM) equipment, and compared these travel times with the data reported to the I95 Vehicle Probe Project (VPP) from an outsourced probe data vendor. The analysis consisted of several methodologies: (1) a traditional analysis that used precision and bias speed metrics; (2) a slowdown analysis that quantified the percentage of significant traffic disruptions accurately captured in the VPP data; (3) a sampled distribution method that uses overlay methods to enhance and analyze recurring congestion patterns. (4) Last, the BTM and VPP data from each 24-hour period of data collection were reviewed by the research team to assess the extent to which VPP captured the nature of the traffic flow. Based on the analysis, probe data is recommended only on arterial roadways with signal densities (measured in signals per mile) up to one, and it should be tested and used with caution for signal densities between one and two, and is not recommended when signal density exceeds two.

Statistical decision making with a dual-detector probe

International Nuclear Information System (INIS)

Hickernell, T.S.

1988-01-01

Conventional imaging techniques for cancer detection have difficulty finding small, deep tumors. Single-detector radiation probes have been developed to search for deep lesions in a patient who has been given a tumor-seeking radiopharmaceutical. These probes perform poorly, however, when the background activity in the patient varies greatly from site to site. We have developed a surgical dual-detector probe that solves the problem of background activity variation, by simultaneously monitoring counts from a region of interest and counts from adjacent normal tissue. A comparison of counts from the detectors can reveal the class of tissue, tumor or normal, in the region of interest. In this study, we apply methods from statistical decision theory and derive a suitable comparison of counts to help us decide whether a tumor is present in the region of interest. We use the Hotelling trace criterion with a few assumptions to find a linear discriminant function, which can be reduced to a normalized subtraction of the counts for large background count-rate variations. Using a spatial response map of the dual probe, a computer torso phantom, and estimates of activity distribution, we simulate a surgical staging procedure to test the dual probe and the discriminant functions

Resting state fMRI entropy probes complexity of brain activity in adults with ADHD.

Science.gov (United States)

Sokunbi, Moses O; Fung, Wilson; Sawlani, Vijay; Choppin, Sabine; Linden, David E J; Thome, Johannes

2013-12-30

In patients with attention deficit hyperactivity disorder (ADHD), quantitative neuroimaging techniques have revealed abnormalities in various brain regions, including the frontal cortex, striatum, cerebellum, and occipital cortex. Nonlinear signal processing techniques such as sample entropy have been used to probe the regularity of brain magnetoencephalography signals in patients with ADHD. In the present study, we extend this technique to analyse the complex output patterns of the 4 dimensional resting state functional magnetic resonance imaging signals in adult patients with ADHD. After adjusting for the effect of age, we found whole brain entropy differences (P=0.002) between groups and negative correlation (r=-0.45) between symptom scores and mean whole brain entropy values, indicating lower complexity in patients. In the regional analysis, patients showed reduced entropy in frontal and occipital regions bilaterally and a significant negative correlation between the symptom scores and the entropy maps at a family-wise error corrected cluster level of Pentropy is a useful tool in revealing abnormalities in the brain dynamics of patients with psychiatric disorders. © 2013 Elsevier Ireland Ltd. All rights reserved.

Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

Directory of Open Access Journals (Sweden)

Jérémy R. Rouxel

2017-07-01

Full Text Available Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O provide different local windows onto the parity breaking geometry change thus revealing the enantiomer asymmetry.

Electromechanical response of amorphous LaAlO{sub 3} thin film probed by scanning probe microscopies

Energy Technology Data Exchange (ETDEWEB)

Borowiak, Alexis S.; Baboux, Nicolas; Albertini, David; Gautier, Brice, E-mail: brice.gautier@insa-lyon.fr [Institut des nanotechnologies de Lyon (INL), Institut National des Sciences Appliquées de Lyon, Université de Lyon, UMR CNRS 5270, 7 Avenue Capelle, F-69621 Villeurbanne Cedex (France); Vilquin, Bertrand; Saint Girons, Guillaume; Pelloquin, Sylvain [Institut des nanotechnologies de Lyon (INL), Ecole Centrale de Lyon, Université de Lyon, UMR CNRS 5270, 36 Avenue Guy de Collongues, F-69134 Ecully Cedex (France)

2014-07-07

The electromechanical response of a 3 nm thick amorphous LaAlO{sub 3} layer obtained by molecular beam epitaxy has been studied using scanning probe microscopies. Although this kind of sample is not ferroelectric due to its amorphous nature, the resulting images are identical to what is generally obtained on truly ferroelectric samples probed by piezoresponse force microscopy: domains of apparently opposite polarisation are detected, and perfect, square shaped hysteresis loops are recorded. Moreover, written patterns are stable within 72 h. We discuss in the general case the possible origins of this behaviour in terms of charge injection, ionic conduction and motion of oxygen vacancies. In the case presented in this paper, since the writing process has been conducted with applied voltages lower than the injection threshold measured by conductive atomic force Microscopy, allowing to withdraw the hypothesis of charge injection in the sample, we propose that a bistable distribution of oxygen vacancies is responsible for this contrast.

X-Ray Microdiffraction as a Probe to Reveal Flux Divergences in Interconnects

Science.gov (United States)

Spolenak, R.; Tamura, N.; Patel, J. R.

2006-02-01

Most reliability issues in interconnect systems occur at a local scale and many of them include the local build-up of stresses. Typical failure mechanisms are electromigration and stress voiding in interconnect lines and fatigue in surface acoustic wave devices. Thus a local probe is required for the investigation of these phenomena. In this paper the application of the Laue microdiffraction technique to investigate flux divergences in interconnect systems will be described. The deviatoric strain tensor of single grains can be correlated with the local microstructure, orientation and defect density. Especially the latter led to recent results about the correlation of stress build-up and orientation in Cu lines and electromigration-induced grain rotation in Cu and Al lines.

Development and implementation of UT procedures for nuclear and other applications using TRL phased array probes

International Nuclear Information System (INIS)

Chardome, V.; Delaide, M.; Cermak, J.; Cruysweegs, E.; Plateau, M.

2006-01-01

In the past, Vincotte developed, qualified and applied various UT procedures for the automated in-service inspection of austenitic and dissimilar metal welds, using conventional ultrasonic probes. In a process of continuous improvement, Vincotte is upgrading these existing procedures by applying low frequency TRL phased array probes. This presentation situates this recent innovation within the phased array history of Vincotte. Particular attention will be paid to these newest phased array developments, in terms of probe development, angled beam generation and scanning patterns. (orig.)

Spectro-temporal modulation masking patterns reveal frequency selectivity.

Science.gov (United States)

Oetjen, Arne; Verhey, Jesko L

2015-02-01

The present study investigated the possibility that the human auditory system demonstrates frequency selectivity to spectro-temporal amplitude modulations. Threshold modulation depth for detecting sinusoidal spectro-temporal modulations was measured using a generalized masked threshold pattern paradigm with narrowband masker modulations. Four target spectro-temporal modulations were examined, differing in their temporal and spectral modulation frequencies: a temporal modulation of -8, 8, or 16 Hz combined with a spectral modulation of 1 cycle/octave and a temporal modulation of 4 Hz combined with a spectral modulation of 0.5 cycles/octave. The temporal center frequencies of the masker modulation ranged from 0.25 to 4 times the target temporal modulation. The spectral masker-modulation center-frequencies were 0, 0.5, 1, 1.5, and 2 times the target spectral modulation. For all target modulations, the pattern of average thresholds for the eight normal-hearing listeners was consistent with the hypothesis of a spectro-temporal modulation filter. Such a pattern of modulation-frequency sensitivity was predicted on the basis of psychoacoustical data for purely temporal amplitude modulations and purely spectral amplitude modulations. An analysis of separability indicates that, for the present data set, selectivity in the spectro-temporal modulation domain can be described by a combination of a purely spectral and a purely temporal modulation filter function.

Influence of an electric probe on the anode layer of a glow discharge in nitrogen

Science.gov (United States)

Taran, M. D.; Dyatko, N. A.; Kochetov, I. V.; Napartovich, A. P.; Akishev, Yu S.

2018-05-01

A two-dimensional (2D) numerical model of a DC glow discharge in nitrogen is developed for the case when the electric probe is mounted in the discharge gap. Within this model, calculations are performed for the gas pressure of 50 Torr and discharge current densities of 22 and 90 mA cm‑2. A cylindrical probe 1 mm in diameter is located parallel to the anode at a distance of 5 or 10 mm. The probe potential is varied in a wide range relative to the floating potential. Numerical simulations predict the 2D plasma perturbation pattern induced by the electric probe and the influence of the probe on anode layer characteristics. In particular, conditions are determined under which a region with no glow forms in the anode layer.

Transient light-induced intracellular oxidation revealed by redox biosensor

Energy Technology Data Exchange (ETDEWEB)

Kolossov, Vladimir L., E-mail: viadimer@illinois.edu [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Beaudoin, Jessica N. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Hanafin, William P. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); DiLiberto, Stephen J. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Kenis, Paul J.A. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801 (United States); Rex Gaskins, H. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 S. Lincoln Avenue, Urbana, IL 61801 (United States); Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 S. Goodwin Avenue, Urbana, IL 61801 (United States)

2013-10-04

Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition.

Transient light-induced intracellular oxidation revealed by redox biosensor

International Nuclear Information System (INIS)

Kolossov, Vladimir L.; Beaudoin, Jessica N.; Hanafin, William P.; DiLiberto, Stephen J.; Kenis, Paul J.A.; Rex Gaskins, H.

2013-01-01

Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition

Four-probe measurements with a three-probe scanning tunneling microscope

International Nuclear Information System (INIS)

Salomons, Mark; Martins, Bruno V. C.; Zikovsky, Janik; Wolkow, Robert A.

2014-01-01

We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe

Four-probe measurements with a three-probe scanning tunneling microscope

Energy Technology Data Exchange (ETDEWEB)

Salomons, Mark [National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta T6G 2M9 (Canada); Martins, Bruno V. C.; Zikovsky, Janik; Wolkow, Robert A., E-mail: rwolkow@ualberta.ca [National Institute for Nanotechnology, National Research Council of Canada, Edmonton, Alberta T6G 2M9 (Canada); Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1 (Canada)

2014-04-15

We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.

Four-probe measurements with a three-probe scanning tunneling microscope.

Science.gov (United States)

Salomons, Mark; Martins, Bruno V C; Zikovsky, Janik; Wolkow, Robert A

2014-04-01

We present an ultrahigh vacuum (UHV) three-probe scanning tunneling microscope in which each probe is capable of atomic resolution. A UHV JEOL scanning electron microscope aids in the placement of the probes on the sample. The machine also has a field ion microscope to clean, atomically image, and shape the probe tips. The machine uses bare conductive samples and tips with a homebuilt set of pliers for heating and loading. Automated feedback controlled tip-surface contacts allow for electrical stability and reproducibility while also greatly reducing tip and surface damage due to contact formation. The ability to register inter-tip position by imaging of a single surface feature by multiple tips is demonstrated. Four-probe material characterization is achieved by deploying two tips as fixed current probes and the third tip as a movable voltage probe.

Graphical representation of ribosomal RNA probe accessibility data using ARB software package

Directory of Open Access Journals (Sweden)

Amann Rudolf

2005-03-01

Full Text Available Abstract Background Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH, besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. Results The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool. Conclusion Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de.

A Novel Dog-Bone Oscillating AFM Probe with Thermal Actuation and Piezoresistive Detection †

Science.gov (United States)

Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

2014-01-01

In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments. PMID:25365463

Characterization of power induced heating and damage in fiber optic probes for near-field scanning optical microscopy

Science.gov (United States)

Dickenson, Nicholas E.; Erickson, Elizabeth S.; Mooren, Olivia L.; Dunn, Robert C.

2007-05-01

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ˜55-60°C as output powers reach ˜50nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ˜450nW. The sample heating profiles measured for etched NSOM probes are consistent with those previously measured for NSOM probes fabricated using the pulling method. At high powers, both pulled and etched NSOM probes fail as the aluminum coating is damaged. For probes fabricated in our laboratory we find failure occurring at input powers of 3.4±1.7 and 20.7±6.9mW for pulled and etched probes, respectively. The larger half-cone angle for etched probes (˜15° for etched and ˜6° for pulled probes) enables more light delivery and also apparently leads to a different failure mechanism. For pulled NSOM probes, high resolution images of NSOM probes as power is increased reveal the development of stress fractures in the coating at a taper diameter of ˜6μm. These stress fractures, arising from the differential heating expansion of the dielectric and the metal coating, eventually lead to coating removal and probe failure. For etched tips, the absence of clear stress fractures and the pooled morphology of the damaged aluminum coating following failure suggest that thermal damage may cause coating failure, although other mechanisms cannot be ruled out.

Potential for tree rings to reveal spatial patterns of past drought variability across western Australia

Science.gov (United States)

O'Donnell, Alison J.; Cook, Edward R.; Palmer, Jonathan G.; Turney, Chris S. M.; Grierson, Pauline F.

2018-02-01

Proxy records have provided major insights into the variability of past climates over long timescales. However, for much of the Southern Hemisphere, the ability to identify spatial patterns of past climatic variability is constrained by the sparse distribution of proxy records. This is particularly true for mainland Australia, where relatively few proxy records are located. Here, we (1) assess the potential to use existing proxy records in the Australasian region—starting with the only two multi-century tree-ring proxies from mainland Australia—to reveal spatial patterns of past hydroclimatic variability across the western third of the continent, and (2) identify strategic locations to target for the development of new proxy records. We show that the two existing tree-ring records allow robust reconstructions of past hydroclimatic variability over spatially broad areas (i.e. > 3° × 3°) in inland north- and south-western Australia. Our results reveal synchronous periods of drought and wet conditions between the inland northern and southern regions of western Australia as well as a generally anti-phase relationship with hydroclimate in eastern Australia over the last two centuries. The inclusion of 174 tree-ring proxy records from Tasmania, New Zealand and Indonesia and a coral record from Queensland did not improve the reconstruction potential over western Australia. However, our findings suggest that the addition of relatively few new proxy records from key locations in western Australia that currently have low reconstruction skill will enable the development of a comprehensive drought atlas for the region, and provide a critical link to the drought atlases of monsoonal Asia and eastern Australia and New Zealand.

Probing the topological properties of complex networks modeling short written texts.

Directory of Open Access Journals (Sweden)

Diego R Amancio

Full Text Available In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well-many informative discoveries have been made this way-but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks.

Mobile Game Probes

DEFF Research Database (Denmark)

Borup Lynggaard, Aviaja

2006-01-01

This paper will examine how probes can be useful for game designers in the preliminary phases of a design process. The work is based upon a case study concerning pervasive mobile phone games where Mobile Game Probes have emerged from the project. The new probes are aimed towards a specific target...... group and the goal is to specify the probes so they will cover the most relevant areas for our project. The Mobile Game Probes generated many interesting results and new issues occurred, since the probes came to be dynamic and favorable for the process in new ways....

A telemetry study on the chronic effects of microdialyis probe implantation on the activity pattern and temperature rhythm of the rat

NARCIS (Netherlands)

Drijfhout, W.J.; Kemper, R.H.A.; Meerlo, P.; Koolhaas, J.M.; Grol, C.J.; Westerink, B.H.C.

1995-01-01

The present study describes the effects of implantation of microdialysis probes on temperature and activity rhythms of the rat, measured with a telemetry system. For comparison two widely used types of microdialysis probes were investigated, a transcerebral probe, inserted into the pineal gland and

Effect of laser power and specimen temperature on atom probe analyses of magnesium alloys

International Nuclear Information System (INIS)

Oh-ishi, K.; Mendis, C.L.; Ohkubo, T.; Hono, K.

2011-01-01

The influence of laser power, wave length, and specimen temperature on laser assisted atom probe analyses for Mg alloys was investigated. Higher laser power and lower specimen temperature led to improved mass and spatial resolutions. Background noise and mass resolutions were degraded with lower laser power and higher specimen temperature. By adjusting the conditions for laser assisted atom probe analyses, atom probe results with atomic layer resolutions were obtained from all the Mg alloys so far investigated. Laser assisted atom probe investigations revealed detailed chemical information on Guinier-Preston zones in Mg alloys. -- Research highlights: → We study performance of UV laser assisted atom probe analysis for Mg alloys. → There is an optimized range of laser power and specimen temperature. → Optimized UV laser enables atom probe data of Mg alloys with high special resolution.

Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

Science.gov (United States)

Bendell, L I

2011-02-15

Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

Traversing probe system

Science.gov (United States)

Mashburn, Douglas N.; Stevens, Richard H.; Woodall, Harold C.

1977-01-01

This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride.

Traversing probe system

International Nuclear Information System (INIS)

Mashburn, D.N.; Stevens, R.H.; Woodall, H.C.

1977-01-01

This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride. 10 claims, 6 figures

Influence of probe geometry on the response of an electrostatic probe

DEFF Research Database (Denmark)

Johansson, Torben; Crichton, George C; McAllister, Iain Wilson

1999-01-01

The response of an electrostatic probe is examined with reference to the probe geometry. The study involves the evaluation of the probe lambda function, from which response-related characteristic parameters can be derived. These parameters enable the probe detection sensitivity Se and spatial...

Nuclear magnetic resonance probe head design for precision strain control

International Nuclear Information System (INIS)

Kissikov, T.; Sarkar, R.; Bush, B. T.; Lawson, M.; Canfield, P. C.; Curro, N. J.

2017-01-01

Here, we present the design and construction of an NMR probe to investigate single crystals under strain at cryogenic temperatures. The probe head incorporates a piezoelectric-based apparatus from Razorbill Instruments that enables both compressive and tensile strain tuning up to strain values on the order of 0.3% with a precision of 0.001%. 75 As NMR in BaFe 2 As 2 reveals large changes to the electric field gradient and indicates that the strain is homogeneous to within 16% over the volume of the NMR coil.

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

Science.gov (United States)

Ritchie, Scott C; Watts, Stephen; Fearnley, Liam G; Holt, Kathryn E; Abraham, Gad; Inouye, Michael

2016-07-01

Network modules-topologically distinct groups of edges and nodes-that are preserved across datasets can reveal common features of organisms, tissues, cell types, and molecules. Many statistics to identify such modules have been developed, but testing their significance requires heuristics. Here, we demonstrate that current methods for assessing module preservation are systematically biased and produce skewed p values. We introduce NetRep, a rapid and computationally efficient method that uses a permutation approach to score module preservation without assuming data are normally distributed. NetRep produces unbiased p values and can distinguish between true and false positives during multiple hypothesis testing. We use NetRep to quantify preservation of gene coexpression modules across murine brain, liver, adipose, and muscle tissues. Complex patterns of multi-tissue preservation were revealed, including a liver-derived housekeeping module that displayed adipose- and muscle-specific association with body weight. Finally, we demonstrate the broader applicability of NetRep by quantifying preservation of bacterial networks in gut microbiota between men and women. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Objective assessment of chromatic and achromatic pattern adaptation reveals the temporal response properties of different visual pathways.

Science.gov (United States)

Robson, Anthony G; Kulikowski, Janus J

2012-11-01

The aim was to investigate the temporal response properties of magnocellular, parvocellular, and koniocellular visual pathways using increment/decrement changes in contrast to elicit visual evoked potentials (VEPs). Static achromatic and isoluminant chromatic gratings were generated on a monitor. Chromatic gratings were modulated along red/green (R/G) or subject-specific tritanopic confusion axes, established using a minimum distinct border criterion. Isoluminance was determined using minimum flicker photometry. Achromatic and chromatic VEPs were recorded to contrast increments and decrements of 0.1 or 0.2 superimposed on the static gratings (masking contrast 0-0.6). Achromatic increment/decrement changes in contrast evoked a percept of apparent motion when the spatial frequency was low; VEPs to such stimuli were positive in polarity and largely unaffected by high levels of static contrast, consistent with transient response mechanisms. VEPs to finer achromatic gratings showed marked attenuation as static contrast was increased. Chromatic VEPs to R/G or tritan chromatic contrast increments were of negative polarity and showed progressive attenuation as static contrast was increased, in keeping with increasing desensitization of the sustained responses of the color-opponent visual pathways. Chromatic contrast decrement VEPs were of positive polarity and less sensitive to pattern adaptation. The relative contribution of sustained/transient mechanisms to achromatic processing is spatial frequency dependent. Chromatic contrast increment VEPs reflect the sustained temporal response properties of parvocellular and koniocellular pathways. Cortical VEPs can provide an objective measure of pattern adaptation and can be used to probe the temporal response characteristics of different visual pathways.

Carbon nanotube/carbon nanotube composite AFM probes prepared using ion flux molding

Science.gov (United States)

Chesmore, Grace; Roque, Carrollyn; Barber, Richard

The performance of carbon nanotube-carbon nanotube composite (CNT/CNT composite) atomic force microscopy (AFM) probes is compared to that of conventional Si probes in AFM tapping mode. The ion flux molding (IFM) process, aiming an ion beam at the CNT probe, aligns the tip to a desired angle. The result is a relatively rigid tip that is oriented to offset the cantilever angle. Scans using these probes reveal an improvement in image accuracy over conventional tips, while allowing higher aspect ratio imaging of 3D surface features. Furthermore, the lifetimes of CNT-CNT composite tips are observed to be longer than both conventional tips and those claimed for other CNT technologies. Novel applications include the imaging of embiid silk. Supported by the Clare Boothe Luce Research Scholars Award and Carbon Design Innovations.

The Oxford Probe: an open access five-hole probe for aerodynamic measurements

Science.gov (United States)

Hall, B. F.; Povey, T.

2017-03-01

The Oxford Probe is an open access five-hole probe designed for experimental aerodynamic measurements. The open access probe can be manufactured by the end user via additive manufacturing (metal or plastic). The probe geometry, drawings, calibration maps, and software are available under a creative commons license. The purpose is to widen access to aerodynamic measurement techniques in education and research environments. There are many situations in which the open access probe will allow results of comparable accuracy to a well-calibrated commercial probe. We discuss the applications and limitations of the probe, and compare the calibration maps for 16 probes manufactured in different materials and at different scales, but with the same geometrical design.

The Oxford Probe: an open access five-hole probe for aerodynamic measurements

International Nuclear Information System (INIS)

Hall, B F; Povey, T

2017-01-01

The Oxford Probe is an open access five-hole probe designed for experimental aerodynamic measurements. The open access probe can be manufactured by the end user via additive manufacturing (metal or plastic). The probe geometry, drawings, calibration maps, and software are available under a creative commons license. The purpose is to widen access to aerodynamic measurement techniques in education and research environments. There are many situations in which the open access probe will allow results of comparable accuracy to a well-calibrated commercial probe. We discuss the applications and limitations of the probe, and compare the calibration maps for 16 probes manufactured in different materials and at different scales, but with the same geometrical design. (paper)

Probe Techniques. Introductory Remarks

Energy Technology Data Exchange (ETDEWEB)

Emeleus, K. G. [School of Physics and Applied Mathematics, Queen' s University, Belfast (United Kingdom)

1968-04-15

In this brief introduction to the session on probes, the history of theii development is first touched on briefly. Reference is then made to the significance of the work to be described by Medicus, for conductivity and recombination calculations, and by Lam and Su, for a wide range of medium and higher pressure plasmas. Finally, a number of other probe topics are mentioned, including multiple probes; probes in electronegative plasmas; resonance probes; probes in noisy discharges; probes as oscillation detectors; use of probes where space-charge is not negligible. (author)

Patterns of hybrid loss of imprinting reveal tissue- and cluster-specific regulation.

Directory of Open Access Journals (Sweden)

Christopher D Wiley

Full Text Available Crosses between natural populations of two species of deer mice, Peromyscus maniculatus (BW, and P. polionotus (PO, produce parent-of-origin effects on growth and development. BW females mated to PO males (bwxpo produce growth-retarded but otherwise healthy offspring. In contrast, PO females mated to BW males (POxBW produce overgrown and severely defective offspring. The hybrid phenotypes are pronounced in the placenta and include POxBW conceptuses which lack embryonic structures. Evidence to date links variation in control of genomic imprinting with the hybrid defects, particularly in the POxBW offspring. Establishment of genomic imprinting is typically mediated by gametic DNA methylation at sites known as gDMRs. However, imprinted gene clusters vary in their regulation by gDMR sequences.Here we further assess imprinted gene expression and DNA methylation at different cluster types in order to discern patterns. These data reveal POxBW misexpression at the Kcnq1ot1 and Peg3 clusters, both of which lose ICR methylation in placental tissues. In contrast, some embryonic transcripts (Peg10, Kcnq1ot1 reactivated the silenced allele with little or no loss of DNA methylation. Hybrid brains also display different patterns of imprinting perturbations. Several cluster pairs thought to use analogous regulatory mechanisms are differentially affected in the hybrids.These data reinforce the hypothesis that placental and somatic gene regulation differs significantly, as does that between imprinted gene clusters and between species. That such epigenetic regulatory variation exists in recently diverged species suggests a role in reproductive isolation, and that this variation is likely to be adaptive.

Label-free proteome profiling reveals developmental-dependent patterns in young barley grains.

Science.gov (United States)

Kaspar-Schoenefeld, Stephanie; Merx, Kathleen; Jozefowicz, Anna Maria; Hartmann, Anja; Seiffert, Udo; Weschke, Winfriede; Matros, Andrea; Mock, Hans-Peter

2016-06-30

Due to its importance as a cereal crop worldwide, high interest in the determination of factors influencing barley grain quality exists. This study focusses on the elucidation of protein networks affecting early grain developmental processes. NanoLC-based separation coupled to label-free MS detection was applied to gain insights into biochemical processes during five different grain developmental phases (pre-storage until storage phase, 3days to 16days after flowering). Multivariate statistics revealed two distinct developmental patterns during the analysed grain developmental phases: proteins showed either highest abundance in the middle phase of development - in the transition phase - or at later developmental stages - within the storage phase. Verification of developmental patterns observed by proteomic analysis was done by applying hypothesis-driven approaches, namely Western Blot analysis and enzyme assays. High general metabolic activity of the grain with regard to protein synthesis, cell cycle regulation, defence against oxidative stress, and energy production via photosynthesis was observed in the transition phase. Proteins upregulated in the storage phase are related towards storage protein accumulation, and interestingly to the defence of storage reserves against pathogens. A mixed regulatory pattern for most enzymes detected in our study points to regulatory mechanisms at the level of protein isoforms. In-depth understanding of early grain developmental processes of cereal caryopses is of high importance as they influence final grain weight and quality. Our knowledge about these processes is still limited, especially on proteome level. To identify key mechanisms in early barley grain development, a label-free data-independent proteomics acquisition approach has been applied. Our data clearly show, that proteins either exhibit highest expression during cellularization and the switch to the storage phase (transition phase, 5-7 DAF), or during storage

Probe-diverse ptychography

Energy Technology Data Exchange (ETDEWEB)

Peterson, I., E-mail: isaac.russellpeterson@rmit.edu.au [ARC Centre of Excellence for Coherent X-ray Science, the University of Melbourne, School of Physics, Victoria 3010 (Australia); Harder, R. [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Robinson, I.K. [Research Complex at Harwell, Didcot, Oxfordshire OX11 0DE (United Kingdom); London Centre for Nanotechnology, University College London, London WC1H 0AH (United Kingdom)

2016-12-15

We propose an extension of ptychography where the target sample is scanned separately through several probes with distinct amplitude and phase profiles and a diffraction image is recorded for each probe and each sample translation. The resulting probe-diverse dataset is used to iteratively retrieve high-resolution images of the sample and all probes simultaneously. The method is shown to yield significant improvement in the reconstructed sample image compared to the image obtained using the standard single-probe ptychographic phase-retrieval scheme.

Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

Science.gov (United States)

Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

2015-01-01

The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

Inspection of Pipe Inner Surface using Advanced Pipe Crawler Robot with PVDF Sensor based Rotating Probe

Directory of Open Access Journals (Sweden)

Vimal AGARWAL

2011-04-01

Full Text Available Due to corrosive environment, pipes used for transportation of water and gas at the plants often get damaged. Defects caused by corrosion and cracking may cause serious accidents like leakage, fire and blasts. It also reduces the life of the transportation system substantially. In order to inspect such defects, a Polyvinyledene Fluoride (PVDF based cantilever smart probe is developed to scan the surface quality of the pipes. The smart probe, during rotation, touches the inner surface of the pipe and experience a broad-band excitation in the absence of surface features. On the other hand, whenever the probe comes across any surface projection, there is a change in vibration pattern of the probe, which causes a high voltage peak/pulse. Such peaks/pulses could give useful information about the location and nature of a defect. Experiments are carried out on different patterns, sizes and shapes of surface projections artificially constructed inside the pipe. The sensor system has reliably predicted the presence and distribution of projections in every case. It is envisaged that the new sensing system could be used effectively for pipe health monitoring.

The Influence of Prosodic Stress Patterns and Semantic Depth on Novel Word Learning in Typically Developing Children.

Science.gov (United States)

Gladfelter, Allison; Goffman, Lisa

2013-01-01

The goal of this study was to investigate the effects of prosodic stress patterns and semantic depth on word learning. Twelve preschool-aged children with typically developing speech and language skills participated in a word learning task. Novel words with either a trochaic or iambic prosodic pattern were embedded in one of two learning conditions, either in children's stories (semantically rich) or picture matching games (semantically sparse). Three main analyses were used to measure word learning: comprehension and production probes, phonetic accuracy, and speech motor stability. Results revealed that prosodic frequency and density influence the learnability of novel words, or that there are prosodic neighborhood density effects. The impact of semantic depth on word learning was minimal and likely depends on the amount of experience with the novel words.

The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing

Energy Technology Data Exchange (ETDEWEB)

Tong, Hui [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China); Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Liu, Chengshuai [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009 (China); Li, Fangbai, E-mail: cefbli@soil.gd.cn [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China); Luo, Chunling [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Chen, Manjia; Hu, Min [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China)

2015-11-15

Highlights: • SIP suggested that Dechloromonas can mineralize PCP in soil. • Methanosaeta and Methanocella acquired PCP-derived carbon. • Lactate enhanced microbial degradation of PCP in soil. - Abstract: Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of {sup 13}CH{sub 4} and {sup 13}CO{sub 2} indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing

International Nuclear Information System (INIS)

Tong, Hui; Liu, Chengshuai; Li, Fangbai; Luo, Chunling; Chen, Manjia; Hu, Min

2015-01-01

Highlights: • SIP suggested that Dechloromonas can mineralize PCP in soil. • Methanosaeta and Methanocella acquired PCP-derived carbon. • Lactate enhanced microbial degradation of PCP in soil. - Abstract: Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of 13 CH 4 and 13 CO 2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil

Simultaneous surface and depth neural activity recording with graphene transistor-based dual-modality probes.

Science.gov (United States)

Du, Mingde; Xu, Xianchen; Yang, Long; Guo, Yichuan; Guan, Shouliang; Shi, Jidong; Wang, Jinfen; Fang, Ying

2018-05-15

Subdural surface and penetrating depth probes are widely applied to record neural activities from the cortical surface and intracortical locations of the brain, respectively. Simultaneous surface and depth neural activity recording is essential to understand the linkage between the two modalities. Here, we develop flexible dual-modality neural probes based on graphene transistors. The neural probes exhibit stable electrical performance even under 90° bending because of the excellent mechanical properties of graphene, and thus allow multi-site recording from the subdural surface of rat cortex. In addition, finite element analysis was carried out to investigate the mechanical interactions between probe and cortex tissue during intracortical implantation. Based on the simulation results, a sharp tip angle of π/6 was chosen to facilitate tissue penetration of the neural probes. Accordingly, the graphene transistor-based dual-modality neural probes have been successfully applied for simultaneous surface and depth recording of epileptiform activity of rat brain in vivo. Our results show that graphene transistor-based dual-modality neural probes can serve as a facile and versatile tool to study tempo-spatial patterns of neural activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Probing the Penetration of Antimicrobial Polymyxin Lipopeptides into Gram-Negative Bacteria

Science.gov (United States)

2015-01-01

The dry antibiotic development pipeline coupled with the emergence of multidrug resistant Gram-negative ‘superbugs’ has driven the revival of the polymyxin lipopeptide antibiotics. Polymyxin resistance implies a total lack of antibiotics for the treatment of life-threatening infections. The lack of molecular imaging probes that possess native polymyxin-like antibacterial activity is a barrier to understanding the resistance mechanisms and the development of a new generation of polymyxin lipopeptides. Here we report the regioselective modification of the polymyxin B core scaffold at the N-terminus with the dansyl fluorophore to generate an active probe that mimics polymyxin B pharmacologically. Time-lapse laser scanning confocal microscopy imaging of the penetration of probe (1) into Gram-negative bacterial cells revealed that the probe initially accumulates in the outer membrane and subsequently penetrates into the inner membrane and finally the cytoplasm. The implementation of this polymyxin-mimetic probe will advance the development of platforms for the discovery of novel polymyxin lipopeptides with efficacy against polymyxin-resistant strains. PMID:24635310

Electrical resistivity probes

Science.gov (United States)

Lee, Ki Ha; Becker, Alex; Faybishenko, Boris A.; Solbau, Ray D.

2003-10-21

A miniaturized electrical resistivity (ER) probe based on a known current-voltage (I-V) electrode structure, the Wenner array, is designed for local (point) measurement. A pair of voltage measuring electrodes are positioned between a pair of current carrying electrodes. The electrodes are typically about 1 cm long, separated by 1 cm, so the probe is only about 1 inch long. The electrodes are mounted to a rigid tube with electrical wires in the tube and a sand bag may be placed around the electrodes to protect the electrodes. The probes can be positioned in a borehole or on the surface. The electrodes make contact with the surrounding medium. In a dual mode system, individual probes of a plurality of spaced probes can be used to measure local resistance, i.e. point measurements, but the system can select different probes to make interval measurements between probes and between boreholes.

Transmission X-ray scattering as a probe for complex liquid-surface structures

Energy Technology Data Exchange (ETDEWEB)

Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; Kuzmenko, Ivan

2016-01-28

The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibility of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.

Synchronized and configurable source of electrical pulses for x-ray pump-probe experiments

International Nuclear Information System (INIS)

Strachan, J. P.; Chembrolu, V.; Yu, X. W.; Tyliszczak, T.; Acremann, Y.

2007-01-01

A method is described for the generation of software tunable patterns of nanosecond electrical pulses. The bipolar, high repetition rate (up to 250 MHz), fast rise time (<30 ps), square pulses are suitable for applications such as the excitation sequence in dynamic pump-probe experiments. Synchronization with the time structure of a synchrotron facility is possible as well as fine control of the relative delay in steps of 10 ps. The pulse generator described here is used to excite magnetic nanostructures with current pulses. Having an excitation system which can match the high repetition rate of a synchrotron allows for utilization of the full x-ray flux and is needed in experiments which require a large photon flux. The fast rise times allow for picosecond time resolution in pump-probe experiments. All pulse pattern parameters are configurable by software

Probe based manipulation and assembly of nanowires into organized mesostructures

Science.gov (United States)

Reynolds, K.; Komulainen, J.; Kivijakola, J.; Lovera, P.; Iacopino, D.; Pudas, M.; Vähäkangas, J.; Röning, J.; Redmond, G.

2008-12-01

A convenient approach to patterning inorganic and organic nanowires using a novel probe manipulator is presented. The system utilizes an electrochemically etched tungsten wire probe mounted onto a 3D actuator that is directed by a 3D controller. When it is engaged by the user, the movement of the probe and the forces experienced by the tip are simultaneously reported in real time. Platinum nanowires are manipulated into organized mesostructures on silicon chip substrates. In particular, individual nanowires are systematically removed from aggregates, transferred to a chosen location, and manipulated into complex structures in which selected wires occupy specific positions with defined orientations. Rapid prototyping of complex mesostructures, by pushing, rotating and bending conjugated polymer, i.e., polyfluorene, nanowires into various configurations, is also achieved. By exploiting the strong internal axial alignment of polymer chains within the polyfluorene nanowires, mesostructures tailored to exhibit distinctly anisotropic optical properties, such as birefringence and photoluminescence dichroism, are successfully assembled on fused silica substrates.

Probe based manipulation and assembly of nanowires into organized mesostructures

International Nuclear Information System (INIS)

Reynolds, K; Lovera, P; Iacopino, D; Redmond, G; Komulainen, J; Pudas, M; Vaehaekangas, J; Kivijakola, J; Roening, J

2008-01-01

A convenient approach to patterning inorganic and organic nanowires using a novel probe manipulator is presented. The system utilizes an electrochemically etched tungsten wire probe mounted onto a 3D actuator that is directed by a 3D controller. When it is engaged by the user, the movement of the probe and the forces experienced by the tip are simultaneously reported in real time. Platinum nanowires are manipulated into organized mesostructures on silicon chip substrates. In particular, individual nanowires are systematically removed from aggregates, transferred to a chosen location, and manipulated into complex structures in which selected wires occupy specific positions with defined orientations. Rapid prototyping of complex mesostructures, by pushing, rotating and bending conjugated polymer, i.e., polyfluorene, nanowires into various configurations, is also achieved. By exploiting the strong internal axial alignment of polymer chains within the polyfluorene nanowires, mesostructures tailored to exhibit distinctly anisotropic optical properties, such as birefringence and photoluminescence dichroism, are successfully assembled on fused silica substrates.

Nonlinear refractive index measuring using a double-grating interferometer in pump–probe configuration and Fourier transform analysis

International Nuclear Information System (INIS)

Rasouli, Saifollah; Ghorbani, Mahnaz

2012-01-01

In this paper, we have presented a simple, stable, highly sensitive and timesaving method based on a double-grating interferometer in conjunction with a pump–probe technique for measuring the nonlinear refractive index. A pump laser beam is aligned collinearly with an expanded plane parallel probe beam by a dichroic mirror. These beams pass through the sample, while right behind the sample using a suitable bandpass filter the pump beam is intercepted. The distorted probe beam then passes through a double-grating interferometer. One of the lateral shearing interference patterns is recorded by use of a CCD camera and, after digitization, has been stored in a computer. The interference pattern is analyzed by means of a Fourier transform algorithm. The refractive index changes have been obtained from phase distribution of the recorded fringe patterns. The implementation of the technique is straightforward and the arrangement is very simple and stable yet its sensitivity is comparable with other interferometry methods. It is also not a time consuming method. The method is applied for measuring the thermal nonlinear refractive index n 2 of colloidal gold nanoparticles in water solution. (paper)

FISH with whole chromosome and telomeric probes demonstrates huge karyotypic reorganization with ITS between two species of Oryzomyini (Sigmodontinae, Rodentia): Hylaeamys megacephalus probes on Cerradomys langguthi karyotype.

Science.gov (United States)

Nagamachi, Cleusa Yoshiko; Pieczarka, Julio Cesar; O'Brien, Patricia Caroline Mary; Pinto, Jamilly Amaral; Malcher, Stella Miranda; Pereira, Adenilson Leão; Rissino, Jorge das Dores; Mendes-Oliveira, Ana Cristina; Rossi, Rogério Vieira; Ferguson-Smith, Malcolm Andrew

2013-04-01

Rodentia comprises 42 % of living mammalian species. The taxonomic identification can be difficult, the number of species currently known probably being underestimated, since many species show only slight morphological variations. Few studies surveyed the biodiversity of species, especially in the Amazon region. Cytogenetic studies show great chromosomal variability in rodents, with diploid numbers ranging from 10 to 102, making it difficult to find chromosomal homologies by comparative G banding. Chromosome painting is useful, but only a few species of rodents have been studied by this technique. In this study, we sorted whole chromosome probes by fluorescence-activated cell sorting from two Hylaeamys megacephalus individuals, an adult female (2n = 54) and a fetus (2n = 50). We made reciprocal chromosome painting between these karyotypes and cross-species hybridization on Cerradomys langguthi (2n = 46). Both species belong to the tribe Oryzomyini (Sigmodontinae), which is restricted to South America and were collected in the Amazon region. Twenty-four chromosome-specific probes from the female and 25 from the fetus were sorted. Reciprocal chromosome painting shows that the karyotype of the fetus does not represent a new cytotype, but an unbalanced karyotype with multiple rearrangements. Cross-species hybridization of H. megacephalus probes on metaphases of C. langguthi shows that 11 chromosomes of H. megacephalus revealed conserved synteny, 10 H. megacephalus probes hybridized to two chromosomal regions and three hybridized to three regions. Associations were observed on chromosomes pairs 1-4 and 11. Fluorescence in situ hybridization with a telomeric probe revealed interstitial regions in three pairs (1, 3, and 4) of C. langguthi chromosomes. We discuss the genomic reorganization of the C. langguthi karyotype.

Single molecule fluorescence image patterns linked to dipole orientation and axial position: application to myosin cross-bridges in muscle fibers.

Directory of Open Access Journals (Sweden)

Thomas P Burghardt

2011-02-01

Full Text Available Photoactivatable fluorescent probes developed specifically for single molecule detection extend advantages of single molecule imaging to high probe density regions of cells and tissues. They perform in the native biomolecule environment and have been used to detect both probe position and orientation.Fluorescence emission from a single photoactivated probe captured in an oil immersion, high numerical aperture objective, produces a spatial pattern on the detector that is a linear combination of 6 independent and distinct spatial basis patterns with weighting coefficients specifying emission dipole orientation. Basis patterns are tabulated for single photoactivated probes labeling myosin cross-bridges in a permeabilized muscle fiber undergoing total internal reflection illumination. Emitter proximity to the glass/aqueous interface at the coverslip implies the dipole near-field and dipole power normalization are significant affecters of the basis patterns. Other characteristics of the basis patterns are contributed by field polarization rotation with transmission through the microscope optics and refraction by the filter set. Pattern recognition utilized the generalized linear model, maximum likelihood fitting, for Poisson distributed uncertainties. This fitting method is more appropriate for treating low signal level photon counting data than χ(2 minimization.Results indicate that emission dipole orientation is measurable from the intensity image except for the ambiguity under dipole inversion. The advantage over an alternative method comparing two measured polarized emission intensities using an analyzing polarizer is that information in the intensity spatial distribution provides more constraints on fitted parameters and a single image provides all the information needed. Axial distance dependence in the emission pattern is also exploited to measure relative probe position near focus. Single molecule images from axial scanning fitted

High spatial resolution Kelvin probe force microscopy with coaxial probes

International Nuclear Information System (INIS)

Brown, Keith A; Westervelt, Robert M; Satzinger, Kevin J

2012-01-01

Kelvin probe force microscopy (KPFM) is a widely used technique to measure the local contact potential difference (CPD) between an AFM probe and the sample surface via the electrostatic force. The spatial resolution of KPFM is intrinsically limited by the long range of the electrostatic interaction, which includes contributions from the macroscopic cantilever and the conical tip. Here, we present coaxial AFM probes in which the cantilever and cone are shielded by a conducting shell, confining the tip–sample electrostatic interaction to a small region near the end of the tip. We have developed a technique to measure the true CPD despite the presence of the shell electrode. We find that the behavior of these probes agrees with an electrostatic model of the force, and we observe a factor of five improvement in spatial resolution relative to unshielded probes. Our discussion centers on KPFM, but the field confinement offered by these probes may improve any variant of electrostatic force microscopy. (paper)

A second life for old data: Global patterns in pollution ecology revealed from published observational studies

Energy Technology Data Exchange (ETDEWEB)

Kozlov, Mikhail V., E-mail: mikoz@utu.fi [Section of Ecology, University of Turku, 20014 Turku (Finland); Zvereva, Elena L. [Section of Ecology, University of Turku, 20014 Turku (Finland)

2011-05-15

A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

A second life for old data: Global patterns in pollution ecology revealed from published observational studies

International Nuclear Information System (INIS)

Kozlov, Mikhail V.; Zvereva, Elena L.

2011-01-01

A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

Quantifying relief on alluvial fans using airborne lidar to reveal patterns of sediment accumulation

Science.gov (United States)

Morelan, A. E., III; Oskin, M. E.

2017-12-01

We present a method of quantifying detailed surface relief on alluvial fans from high-resolution topography. Average slope and curvature of the fan are used together to empirically derive an idealized, radially symmetric fan surface, from which we compute residual topography. Maps produced using this technique highlight spatial patterns of fan deposition and avulsion. Regions of high residual topography reveal active and abandoned sediment lobes accumulated from recent depositional events, often with well-defined channels at their apex. Preliminary observations suggest that surface relief is uniform across a collection of fans in a given region and source lithology. Alluvial fans with granitic catchment lithologies in eastern California (n=12), each with varying source catchment size and mean fan slope, all show relief of around 4 meters. A collection of fans from the Carrizo Plain in central California (n=12), with source catchments set within Miocene marine and nonmarine sedimentary rocks, show significantly lower relief values around 2 meters. We hypothesize that particle grain size determines this contrasting relief through its control on the thickness of fan-building debris flows. In both settings we find that sediment lobes tend to extend toward the fan toe. This pattern supports a process, observed in analog experiments, of fan deposition dominated by back-filling and overtopping of distributary channels by debris-flows.

Probing thermomechanics at the nanoscale: impulsively excited pseudosurface acoustic waves in hypersonic phononic crystals.

Science.gov (United States)

Nardi, Damiano; Travagliati, Marco; Siemens, Mark E; Li, Qing; Murnane, Margaret M; Kapteyn, Henry C; Ferrini, Gabriele; Parmigiani, Fulvio; Banfi, Francesco

2011-10-12

High-frequency surface acoustic waves can be generated by ultrafast laser excitation of nanoscale patterned surfaces. Here we study this phenomenon in the hypersonic frequency limit. By modeling the thermomechanics from first-principles, we calculate the system's initial heat-driven impulsive response and follow its time evolution. A scheme is introduced to quantitatively access frequencies and lifetimes of the composite system's excited eigenmodes. A spectral decomposition of the calculated response on the eigemodes of the system reveals asymmetric resonances that result from the coupling between surface and bulk acoustic modes. This finding allows evaluation of impulsively excited pseudosurface acoustic wave frequencies and lifetimes and expands our understanding of the scattering of surface waves in mesoscale metamaterials. The model is successfully benchmarked against time-resolved optical diffraction measurements performed on one-dimensional and two-dimensional surface phononic crystals, probed using light at extreme ultraviolet and near-infrared wavelengths.

Atom probe tomography of a commercial light emitting diode

International Nuclear Information System (INIS)

Larson, D J; Prosa, T J; Olson, D; Lawrence, D; Clifton, P H; Kelly, T F; Lefebvre, W

2013-01-01

The atomic-scale analysis of a commercial light emitting diode device purchased at retail is demonstrated using a local electrode atom probe. Some of the features are correlated with transmission electron microscopy imaging. Subtle details of the structure that are revealed have potential significance for the design and performance of this device

Detection of hepatitis A virus by hybridization with single-stranded RNA probes

International Nuclear Information System (INIS)

Xi, J.; Estes, M.K.; Metcalf, T.G.

1987-01-01

An improved method of dot-blot hybridization to detect hepatitis A virus (HAV) was developed with single-stranded RNA (ssRNA) probes. Radioactive and nonradioactive ssRNA probes were generated by in vitro transcription of HAV templates inserted into the plasmid pGEM-1. 32 P-labeled ssRNA probes were at least eightfold more sensitive than the 32 P-labeled double-stranded cDNA counterparts, whereas biotin-labeled ssRNA probes showed a sensitivity comparable with that of the 32 P-labeled double-stranded cDNA counterparts. Hybridization of HAV with the ssRNA probes at high stringency revealed specific reactions with a high signal-to-noise ratio. The differential hybridization reactions seen with probes of positive and negative sense (compared with HAV genomic RNA) were used to detect HAV in clinical and field samples. A positive/negative ratio was introduced as an indicator that permitted an semiquantitative expression of a positive HAV reaction. Good agreement of this indicator was observed with normal stool samples and with HAV-seeded samples. By using this system, HAV was detected in estuarine and freshwater samples collected from a sewage-polluted bayou in Houston and a saltwater tributary of Galveston Bay

Measurements of monopolar and bipolar current spreads using forward-masking with a fixed probe.

Science.gov (United States)

Bingabr, Mohamed G; Espinoza-Varas, Blas; Sigdel, Saroj

2014-05-01

This research employed a forward-masking paradigm to estimate the current spread of monopolar (MP) and bipolar (BP) maskers, with current amplitudes adjusted to elicit the same loudness. Since the spatial separation between active and return electrodes is smaller in BP than in MP configurations, the BP current spread is more localized and presumably superior in terms of speech intelligibility. Because matching the loudness requires higher current in BP than in MP stimulation, previous forward-masking studies show that BP current spread is not consistently narrower across subjects or electrodes within a subject. The present forward-masking measures of current spread differ from those of previous studies by using the same BP probe electrode configuration for both MP and BP masker configurations, and adjusting the current levels of the MP and BP maskers so as to match them in loudness. With this method, the estimate of masker current spread would not be contaminated by differences in probe current spread. Forward masking was studied in four cochlear implant patients, two females and two males, with speech recognition scores higher than 50%; that is, their auditory-nerve survival status was more than adequate to carry out the experiments. The data showed that MP and BP masker configurations produce equivalent masking patterns (and current spreads) in three participants. A fourth participant displayed asymmetrical patterns with enhancement rather than masking in some cases, especially when the probe and masker were at the same location. This study showed equivalent masking patterns for MP and BP maskers when the BP masker current amplitude was increased to match the loudness of the MP masker, and the same BP probe configuration is used with both maskers. This finding could help to explain why cochlear implant users often fail to accrue higher speech intelligibility benefit from BP stimulation.

Flexible, Penetrating Brain Probes Enabled by Advances in Polymer Microfabrication

Directory of Open Access Journals (Sweden)

Ahuva Weltman

2016-10-01

Full Text Available The acquisition of high-fidelity, long-term neural recordings in vivo is critically important to advance neuroscience and brain–machine interfaces. For decades, rigid materials such as metal microwires and micromachined silicon shanks were used as invasive electrophysiological interfaces to neurons, providing either single or multiple electrode recording sites. Extensive research has revealed that such rigid interfaces suffer from gradual recording quality degradation, in part stemming from tissue damage and the ensuing immune response arising from mechanical mismatch between the probe and brain. The development of “soft” neural probes constructed from polymer shanks has been enabled by advancements in microfabrication; this alternative has the potential to mitigate mismatch-related side effects and thus improve the quality of recordings. This review examines soft neural probe materials and their associated microfabrication techniques, the resulting soft neural probes, and their implementation including custom implantation and electrical packaging strategies. The use of soft materials necessitates careful consideration of surgical placement, often requiring the use of additional surgical shuttles or biodegradable coatings that impart temporary stiffness. Investigation of surgical implantation mechanics and histological evidence to support the use of soft probes will be presented. The review concludes with a critical discussion of the remaining technical challenges and future outlook.

DNA probes

International Nuclear Information System (INIS)

Castelino, J.

1992-01-01

The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

Counting probe

International Nuclear Information System (INIS)

Matsumoto, Haruya; Kaya, Nobuyuki; Yuasa, Kazuhiro; Hayashi, Tomoaki

1976-01-01

Electron counting method has been devised and experimented for the purpose of measuring electron temperature and density, the most fundamental quantities to represent plasma conditions. Electron counting is a method to count the electrons in plasma directly by equipping a probe with the secondary electron multiplier. It has three advantages of adjustable sensitivity, high sensitivity of the secondary electron multiplier, and directional property. Sensitivity adjustment is performed by changing the size of collecting hole (pin hole) on the incident front of the multiplier. The probe is usable as a direct reading thermometer of electron temperature because it requires to collect very small amount of electrons, thus it doesn't disturb the surrounding plasma, and the narrow sweep width of the probe voltage is enough. Therefore it can measure anisotropy more sensitively than a Langmuir probe, and it can be used for very low density plasma. Though many problems remain on anisotropy, computer simulation has been carried out. Also it is planned to provide a Helmholtz coil in the vacuum chamber to eliminate the effect of earth magnetic field. In practical experiments, the measurement with a Langmuir probe and an emission probe mounted to the movable structure, the comparison with the results obtained in reverse magnetic field by using a Helmholtz coil, and the measurement of ionic sound wave are scheduled. (Wakatsuki, Y.)

Correlations between human mobility and social interaction reveal general activity patterns.

Science.gov (United States)

Mollgaard, Anders; Lehmann, Sune; Mathiesen, Joachim

2017-01-01

A day in the life of a person involves a broad range of activities which are common across many people. Going beyond diurnal cycles, a central question is: to what extent do individuals act according to patterns shared across an entire population? Here we investigate the interplay between different activity types, namely communication, motion, and physical proximity by analyzing data collected from smartphones distributed among 638 individuals. We explore two central questions: Which underlying principles govern the formation of the activity patterns? Are the patterns specific to each individual or shared across the entire population? We find that statistics of the entire population allows us to successfully predict 71% of the activity and 85% of the inactivity involved in communication, mobility, and physical proximity. Surprisingly, individual level statistics only result in marginally better predictions, indicating that a majority of activity patterns are shared across our sample population. Finally, we predict short-term activity patterns using a generalized linear model, which suggests that a simple linear description might be sufficient to explain a wide range of actions, whether they be of social or of physical character.

Phenotypical characteristics of leukocyte membranes in Chernobyl clean-up workers from Latvia: use of the fluorescent probe ABM

International Nuclear Information System (INIS)

Kalnina, I.; Meirovics, I.; Garbuseva, N.; Bruvere, R.; Heisele, O.; Zvagule, T.; Volrate, A.; Feldmane, G.

2001-01-01

A fluorescent probe - aminoderivative of benzanthrone, AMB (developed at the Riga Technical University, Riga, Latvia) - has been previously shown to localise within the phospholipid bilayer of the cell membrane, and shown to affect the structural and functional properties of peripheral blood mononuclear cells (PBMC). The probe ABM was used to characterise the PBMC membranes of 97 Chernobyl clean-up workers from Latvia. The study was conducted in the years 1997-1998. After addition of the probe to PBMC, fluorescence intensity of ABM (F) was measured, the depolarisation value P was calculated, and emission spectra were recorded. Screening of all individuals showed 5 different patterns of fluorescence spectra. Four of the patterns had never been previously observed in healthy individuals or patients with tuberculosis, multiple sclerosis, oncologic patients, etc., examined by us. The spectral patterns of ABM suspensions were associated with ability of leukocytes to produce interferons, with the levels of immunoglobulins A, G, and M, the concentration of lead in peripheral blood, and with several neurologic diseases. The use of ABM allowed to show phenotypic differences in PBMC between Chernobyl clean-up workers and individuals who had never had professional contact with radioactivity. (author)

Toward Exposing Timing-Based Probing Attacks in Web Applications

Directory of Open Access Journals (Sweden)

Jian Mao

2017-02-01

Full Text Available Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

Toward Exposing Timing-Based Probing Attacks in Web Applications.

Science.gov (United States)

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-02-25

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users' browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

Mobile probes

DEFF Research Database (Denmark)

Ørngreen, Rikke; Jørgensen, Anna Neustrup; Noesgaard, Signe Schack

2016-01-01

A project investigating the effectiveness of a collection of online resources for teachers' professional development used mobile probes as a data collection method. Teachers received questions and tasks on their mobile in a dialogic manner while in their everyday context as opposed...... to in an interview. This method provided valuable insight into the contextual use, i.e. how did the online resource transfer to the work practice. However, the research team also found that mobile probes may provide the scaffolding necessary for individual and peer learning at a very local (intra-school) community...... level. This paper is an initial investigation of how the mobile probes process proved to engage teachers in their efforts to improve teaching. It also highlights some of the barriers emerging when applying mobile probes as a scaffold for learning....

A flavone-based turn-on fluorescent probe for intracellular cysteine/homocysteine sensing with high selectivity.

Science.gov (United States)

Zhang, Jian; Lv, Yanlin; Zhang, Wei; Ding, Hui; Liu, Rongji; Zhao, Yongsheng; Zhang, Guangjin; Tian, Zhiyuan

2016-01-01

A new type of flavone-based fluorescent probe (DMAF) capable of cysteine (Cys)/homocysteine (Hcy) sensing with high selectivity over other amino acids was developed. Such type of probe undergoes Cys/Hcy-mediated cyclization reaction with the involvement of its aldehyde group, which suppresses of the photoinduced electron transfer (PET) process of the probe molecule and consequently leads to the enhancement of fluorescence emission upon excitation using visible light. The formation of product of the Cys/Hcy-mediated cyclization reaction was confirmed and the preliminary fluorescence imaging experiments revealed the biocompatibility of the as-prepared probe and validated its practicability for intracellular Cys/Hcy sensing. Copyright © 2015 Elsevier B.V. All rights reserved.

Tissue imaging using full field optical coherence microscopy with short multimode fiber probe

Science.gov (United States)

Sato, Manabu; Eto, Kai; Goto, Tetsuhiro; Kurotani, Reiko; Abe, Hiroyuki; Nishidate, Izumi

2018-03-01

In achieving minimally invasive accessibility to deeply located regions the size of the imaging probes is important. We demonstrated full-field optical coherence tomography (FF-OCM) using an ultrathin forward-imaging short multimode fiber (SMMF) probe of 50 μm core diameter, 125 μm diameter, and 7.4 mm length for optical communications. The axial resolution was measured to be 2.14 μm and the lateral resolution was also evaluated to be below 4.38 μm using a test pattern (TP). The spatial mode and polarization characteristics of SMMF were evaluated. Inserting SMMF to in vivo rat brain, 3D images were measured and 2D information of nerve fibers was obtained. The feasibility of an SMMF as an ultrathin forward-imaging probe in FF-OCM has been demonstrated.

Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea.

Science.gov (United States)

Parsons, Rachel J; Breitbart, Mya; Lomas, Michael W; Carlson, Craig A

2012-02-01

There are an estimated 10(30) virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300 m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100 m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochlorococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean.

Experimental facility and void fraction calibration methods for impedance probes

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Fernando L. de; Rocha, Marcelo S., E-mail: floliveira@ipen.br, E-mail: msrocha@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2013-07-01

An experimental facility was designed and constructed with aims of to calibrate a capacitance probe for gas-liquid flow void fraction measurements. The facility is composed of a metallic hack with a vertical 2,300 mm high glass tube with 38 mm ID with stagnant water and compressed air bubbling system simulating the gas phase (vapor). At the lower part, a mixing section with a porous media element releases the air bubbles into the water, and the compressed air flow is measured by two calibrated rotameters. At the upper part a stagnant water tank separates the liquid and gas. Two pressure taps are located near the lower and upper sides of the glass tube for pressure difference measurement. The pressure difference is used for low void fraction values (0-15%) calibration methods, as described in the work. Two electrically controlled quick closing valves are installed between the porous media element and the upward separation tank for high void fraction values measurement (15-50%) used to calibrate the capacitance probe. The experimental facility design, construction, capacitance probe calibration methods and results, as well as flow pattern visualization, are presented. Finally, the capacitance probe will be installed on a natural circulation circuit mounted at the Nuclear Engineering Center (CEN/IPEN/CNEN-SP) for measurement of the instantaneous bulk void. Instantaneous signals generated by the capacitance probe will allow the determination of natural circulation loop global energy balance. (author)

Experimental facility and void fraction calibration methods for impedance probes

International Nuclear Information System (INIS)

Oliveira, Fernando L. de; Rocha, Marcelo S.

2013-01-01

An experimental facility was designed and constructed with aims of to calibrate a capacitance probe for gas-liquid flow void fraction measurements. The facility is composed of a metallic hack with a vertical 2,300 mm high glass tube with 38 mm ID with stagnant water and compressed air bubbling system simulating the gas phase (vapor). At the lower part, a mixing section with a porous media element releases the air bubbles into the water, and the compressed air flow is measured by two calibrated rotameters. At the upper part a stagnant water tank separates the liquid and gas. Two pressure taps are located near the lower and upper sides of the glass tube for pressure difference measurement. The pressure difference is used for low void fraction values (0-15%) calibration methods, as described in the work. Two electrically controlled quick closing valves are installed between the porous media element and the upward separation tank for high void fraction values measurement (15-50%) used to calibrate the capacitance probe. The experimental facility design, construction, capacitance probe calibration methods and results, as well as flow pattern visualization, are presented. Finally, the capacitance probe will be installed on a natural circulation circuit mounted at the Nuclear Engineering Center (CEN/IPEN/CNEN-SP) for measurement of the instantaneous bulk void. Instantaneous signals generated by the capacitance probe will allow the determination of natural circulation loop global energy balance. (author)

CO I barcoding reveals new clades and radiation patterns of Indo-Pacific sponges of the family Irciniidae (Demospongiae: Dictyoceratida.

Directory of Open Access Journals (Sweden)

Judith Pöppe

2010-04-01

Full Text Available DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance.Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates.We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

Directory of Open Access Journals (Sweden)

Jiang Tao

2011-10-01

Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

Science.gov (United States)

Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

2011-10-10

Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

Accuracy of probing attachment levels using a new computerized cemento-enamel junction probe.

Science.gov (United States)

Deepa, R; Prakash, Shobha

2012-01-01

The assessment of clinical attachment level (CAL) represents the gold standard for diagnosing and monitoring periodontal disease. The aim of the present study was to evaluate the performance of the newly introduced cemento-enamel junction (CEJ) probe in detecting CAL, using CEJ as a fixed reference point, and to compare the CEJ probe with the Florida stent probe (FSP) as well as with a standard manual probe, University of North Carolina-15 (UNC-15). Three examiners recorded the probing attachment level in 384 sites in case group (chronic periodontitis), and in 176 sites, in control group (healthy periodontal status), using the three probes. Subjects included both the sexes and ranged from 35 to 45 years. The experimental design was structured to balance the intra- and inter-examiner consistency at the same site during the two visits. CEJ probe showed higher intra-and inter-examiner consistency over both FSP and UNC-15 in both the case and control groups. Frequency distribution of differences of various magnitudes of repeated measurements ≤1 mm was in the higher range of 86.8% to 87.5% for CEJ probe. The FSP was more reproducible than UNC-15 in detecting relative attachment level (RAL). CEJ automated probe was found to have greatest potential for accuracy and consistency in detecting CAL than FSP and UNC-15. The automated probes appeared to be more reproducible than manual probes.

An Experimental Evaluation of the Performance of Two Combination Pitot Pressure Probes

Science.gov (United States)

Arend, David J.; Saunders, John D.

2009-01-01

Experimental tests have been completed which recorded the ability of two combination steady state and high response time varying Pitot probe designs to accurately measure steady stagnation pressure at a single location in a flow field. Tests were conducted of double-barreled and coannular Prati probes in a 3.5 in. diameter free jet probe calibration facility from Mach 0.1 to 0.9. Geometric symmetry and pitch (-40 deg to 40 deg) and yaw (0 deg to 40 deg) angle actuation were used to fully evaluate the probes. These tests revealed that the double-barreled configuration induced error in its steady state measurement at zero incidence that increased consistently with jet Mach number to 1.1 percent at Mach 0.9. For all Mach numbers, the double-barreled probe nulled at a pitch angle of approximately 7.0 deg and provided inconsistent measurements when yawed. The double-barreled probe provided adequate measurements via both its steady state and high response tubes (within +/- 0.15 percent accuracy) over unacceptable ranges of biased pitch and inconsistent yaw angles which varied with Mach number. By comparison, the coannular probe provided accurate measurements (at zero incidence) for all jet Mach numbers as well as over a flow angularity range which varied from +/- 26.0 deg at Mach 0.3 deg to +/- 14.0 deg at Mach 0.9. Based on these results, the Prati probe is established as the preferred design. Further experimental tests are recommended to document the frequency response characteristics of the Prati probe.

Late-replicating X-chromosome: replication patterns in mammalian females

Directory of Open Access Journals (Sweden)

Tunin Karen

2002-01-01

Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

Novel probe for determining the size and position of a relativistic electron beam

International Nuclear Information System (INIS)

Orzechowski, T.J.; Koehler, H.; Edwards, W.; Nelson, M.; Marshall, B.

1984-01-01

In order to determine the size and position of a relativistic electron beam inside the wiggler magnetic field of a Free Electron Laser (FEL), we have developed a new probe which intercepts the electron beam on a high Z target and monitors the resulting bremsstrahlung radiation. The probe is designed to move along the entire three meters of the wiggler. This FEL is designed to operate in the microwave region (2 to 8 mm) and the interaction region is an oversized waveguide with a cross section 3 cm x 9.8 cm. The axial probe moves inside this waveguide. The probe stops the electron beam on a Tantalum target and the resulting x-rays are scattered in the forward direction. A scintillator behind the beam stop reacts to the x-rays and emits visible light in the region where the x-rays strike. An array of fiber optics behind the scintillator transmits the visible light to a Reticon camera system which images the visible pattern from the scintillator. Processing the optical image is done by digitizing and storing the image and/or recording the image on video tape. Resolution and performance of this probe will be discussed

Near-field imaging of interference pattern of counterpropagating evanescent waves

DEFF Research Database (Denmark)

Bozhevolnyi, Sergey I.; Bozhevolnaya, Elena A.

1999-01-01

It is generally accepted that measurement of of the contrast of the intensity interference pattern formed by two counterpropagating evanescent waves can be used to characterize the resolving power of a collection near-field microscope. We argue that, if the light collected by a fiber probe propag...... be equal to the contrast of the interference pattern....

DNA probes

Energy Technology Data Exchange (ETDEWEB)

Castelino, J

1993-12-31

The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

Towards Tamper-Evident Storage on Patterned Media

NARCIS (Netherlands)

Hartel, Pieter H.; Abelmann, Leon; Khatib, Mohammed G.; Baker, M.; Riedel, E.

We propose a tamper-evident storage system based on probe storage with a patterned magnetic medium. This medium supports normal read/write operations by out-of-plane magnetisation of individual magnetic dots. We report on measurements showing that in principle the medium also supports a separate

Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles.

Science.gov (United States)

Fercher, Andreas; Borisov, Sergey M; Zhdanov, Alexander V; Klimant, Ingo; Papkovsky, Dmitri B

2011-07-26

A new intracellular O(2) (icO(2)) sensing probe is presented, which comprises a nanoparticle (NP) formulation of a cationic polymer Eudragit RL-100 and a hydrophobic phosphorescent dye Pt(II)-tetrakis(pentafluorophenyl)porphyrin (PtPFPP). Using the time-resolved fluorescence (TR-F) plate reader set-up, cell loading was investigated in detail, particularly the effects of probe concentration, loading time, serum content in the medium, cell type, density, etc. The use of a fluorescent analogue of the probe in conjunction with confocal microscopy and flow cytometry analysis, revealed that cellular uptake of the NPs is driven by nonspecific energy-dependent endocytosis and that the probe localizes inside the cell close to the nucleus. Probe calibration in biological environment was performed, which allowed conversion of measured phosphorescence lifetime signals into icO(2) concentration (μM). Its analytical performance in icO(2) sensing experiments was demonstrated by monitoring metabolic responses of mouse embryonic fibroblast cells under ambient and hypoxic macroenvironment. The NP probe was seen to generate stable and reproducible signals in different types of mammalian cells and robust responses to their metabolic stimulation, thus allowing accurate quantitative analysis. High brightness and photostability allow its use in screening experiments with cell populations on a commercial TR-F reader, and for single cell analysis on a fluorescent microscope.

Probe Storage

NARCIS (Netherlands)

Gemelli, Marcellino; Abelmann, Leon; Engelen, Johannes Bernardus Charles; Khatib, M.G.; Koelmans, W.W.; Zaboronski, Olog; Campardo, Giovanni; Tiziani, Federico; Laculo, Massimo

2011-01-01

This chapter gives an overview of probe-based data storage research over the last three decades, encompassing all aspects of a probe recording system. Following the division found in all mechanically addressed storage systems, the different subsystems (media, read/write heads, positioning, data

Tandem-pulsed acousto-optics: an analytical framework of modulated high-contrast speckle patterns

NARCIS (Netherlands)

Resink, Steffen; Steenbergen, Wiendelt

2015-01-01

Recently we presented acousto-optic (AO) probing of scattering media using addition or subtraction of speckle patterns due to tandem nanosecond pulses. Here we present a theoretical framework for ideal (polarized, noise-free) speckle patterns with unity contrast that links ultrasound-induced optical

Descriptive parameters for revealing substitution patterns of sugar beet pectins using pectolytic enzymes.

Science.gov (United States)

Remoroza, C; Buchholt, H C; Gruppen, H; Schols, H A

2014-01-30

Enzymatic fingerprinting was applied to sugar beet pectins (SBPs) modified by either plant or fungal pectin methyl esterases and alkali catalyzed de-esterification to reveal the ester distributions over the pectin backbone. A simultaneous pectin lyase (PL) treatment to the commonly used endo-polygalacturonase (endo-PG) degradation showed to be effective in degrading both high and low methylesterified and/or acetylated homogalaturonan regions of SBP simultaneously. Using LC-HILIC-MS/ELSD, we studied in detail all the diagnostic oligomers present, enabling us to discriminate between differently prepared sugar beet pectins having various levels of methylesterification and acetylation. Furthermore, distinction between commercially extracted and de-esterified sugar beet pectin having different patterns of substitution was achieved by using novel descriptive pectin parameters. In addition to DBabs approach for nonmethylesterified sequences degradable by endo-PG, the "degree of hydrolysis" (DHPG) representing all partially saturated methylesterified and/or acetylated galacturonic acid (GalA) moieties was introduced as a new parameter. Consequently, the description DHPL has been introduced to quantify all esterified unsaturated GalA oligomers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Measurement of triboelectric charging of moving micro particles by means of an inductive cylindrical probe

International Nuclear Information System (INIS)

Nesterov, A; Loeffler, F; Koenig, K; Trunk, U; Leibe, K; Felgenhauer, T; Bischoff, F R; Breitling, F; Lindenstruth, V; Stadler, V; Hausmann, M

2007-01-01

We present a method based on induced currents in a cylindrical probe which allows analysis of the micro-particle charging processes in an aerosol. The micro particles were triboelectrically charged by passing through a dielectric tube coaxially mounted into the probe. The cylindrical probe enabled the quantification of particle charging without prior calibration of the probe. An analytic model was developed for the description of the measured induced currents and implemented into a computer simulation program. The combination of model simulations and an appropriate experimental setup revealed comprehensive data for the determination of the particles' electric charge against time of flight through the tube. In methodological proof of principle experiments, the formations of particle clouds with charges of different signs were observed using magnetite micro particles

Colorimetric DNA detection of transgenic plants using gold nanoparticles functionalized with L-shaped DNA probes

Science.gov (United States)

Nourisaeid, Elham; Mousavi, Amir; Arpanaei, Ayyoob

2016-01-01

In this study, a DNA colorimetric detection system based on gold nanoparticles functionalized with L-shaped DNA probes was prepared and evaluated. We investigated the hybridization efficiency of the L-shaped probes and studied the effect of nanoparticle size and the L-shaped DNA probe length on the performance of the as-prepared system. Probes were attached to the surface of gold nanoparticles using an adenine sequence. An optimal sequence of 35S rRNA gene promoter from the cauliflower mosaic virus, which is frequently used in the development of transgenic plants, and the two complementary ends of this gene were employed as model target strands and probe molecules, respectively. The spectrophotometric properties of the as-prepared systems indicated that the large NPs show better changes in the absorption spectrum and consequently present a better performance. The results of this study revealed that the probe/Au-NPs prepared using a vertical spacer containing 5 thymine oligonucleotides exhibited a stronger spectrophotometric response in comparison to that of larger probes. These results in general indicate the suitable performance of the L-shaped DNA probe-functionalized Au-NPs, and in particular emphasize the important role of the gold nanoparticle size and length of the DNA probes in enhancing the performance of such a system.

CO{sub 2} geothermal heat probe - Phase 2; CO{sub 2}-Erdwaermesonde - Phase 2

Energy Technology Data Exchange (ETDEWEB)

Grueniger, A.; Wellig, B.

2009-12-15

In this project the fluid dynamics and thermodynamics inside a CO{sub 2} geothermal heat probe have been investigated. The functionality of such a probe, which works like a thermosyphon, was analyzed by means of a simulation model in MATLAB. The model couples the behaviour inside the heat probe with the heat conduction in the earth. A parameter study revealed that the self-circulation character of such a probe leads to flattening of the vertical earth temperature profile near the probe and, hence, leads to more uniform heat removal along the probe. The circulation of CO{sub 2} even goes on when the heat pump is off. This might be advantageous for the regeneration phase. The heat transfer resistance of the evaporating CO{sub 2} film flowing down the probe wall is very small compared to the conduction resistance of the earth. Therefore, no difference has been found between the performances of a conventional heat pipe and a configuration where the liquid phase injection is distributed on different height stages along the probe. It is estimated that the seasonal performance factor of heat pumps can be improved by 15-25% with a CO{sub 2} geothermal heat probe. The main advantage is that the heat transfer to the evaporator of the heat pump (condensation of CO{sub 2} / evaporation of refrigerant) is much more efficient than in a conventional brine probe without phase change. Furthermore, no circulation pump is needed. (authors)

Novel magnetic heating probe for multimodal cancer treatment.

Science.gov (United States)

Kan-Dapaah, Kwabena; Rahbar, Nima; Soboyejo, Wole

2015-05-01

Multifunctional materials consisting of polymers and magnetic nanoparticles (MNPs) are highly sought after in the field of biomedical engineering. These materials offer new opportunities for the development of novel cancer treatment modalities that can increase the efficacy of cancer therapy. In this paper, a novel probe for multimodal cancer treatment is proposed and analyzed. The probe is essentially a cannula with two main parts: a distal heat generating tip made of a magnetic nanocomposite and a proximal insulated shaft. A description of the concept and functional operations of the probe is presented. In an effort to assess its feasibility, the authors evaluated the ability of probe tip (made of PMMA-Fe3O4 nanocomposite) to generate heat in biological tissue using alternating magnetic field (AMF) parameters (field strength and frequency) that are acceptable for human use. Heat generation by MNPs was determined using the linear response theory. The effects of Fe3O4 volume fraction on heat generation as well as treatment time on the thermal dose were studied. The finite element method model was tested for its validity using an analytical model. Lesions were revealed to have an ellipsoidal shape and their sizes were affected by treatment time. However, their shapes remained unchanged. The comparison with the analytical model showed reasonably a good agreement to within 2%. Furthermore, the authors' numerical predictions also showed reasonable agreement with the experimental results previously reported in the literature. The authors' predictions demonstrate the feasibility of their novel probe to achieve reasonable lesion sizes, during hyperthermic or ablative heating using AMF parameters (field strength and frequency) that are acceptable for human use.

Modular Rake of Pitot Probes

Science.gov (United States)

Dunlap, Timothy A.; Henry, Michael W.; Homyk, Raymond P.

2004-01-01

The figure presents selected views of a modular rake of 17 pitot probes for measuring both transient and steady-state pressures in a supersonic wind tunnel. In addition to pitot tubes visible in the figure, the probe modules contain (1) high-frequency dynamic-pressure transducers connected through wires to remote monitoring circuitry and (2) flow passages that lead to tubes that, in turn, lead to remote steady-state pressure transducers. Prior pitot-probe rakes were fabricated as unitary structures, into which the individual pitot probes were brazed. Repair or replacement of individual probes was difficult, costly, and time-consuming because (1) it was necessary to remove entire rakes in order to unbraze individual malfunctioning probes and (2) the heat of unbrazing a failed probe and of brazing a new probe in place could damage adjacent probes. In contrast, the modules in the present probe are designed to be relatively quickly and easily replaceable with no heating and, in many cases, without need for removal of the entire rake from the wind tunnel. To remove a malfunctioning probe, one first removes a screw-mounted V-cross-section cover that holds the probe and adjacent probes in place. Then one removes a screw-mounted cover plate to gain access to the steady-state pressure tubes and dynamicpressure wires. Next, one disconnects the tube and wires of the affected probe. Finally, one installs a new probe in the reverse of the aforementioned sequence. The wire connections can be made by soldering, but to facilitate removal and installation, they can be made via miniature plugs and sockets. The connections between the probe flow passages and the tubes leading to the remote pressure sensors can be made by use of any of a variety of readily available flexible tubes that can be easily pulled off and slid back on for removal and installation, respectively.

Characterization of coating probe with Ti-DLC for electrical scanning probe microscope

International Nuclear Information System (INIS)

Shia Xiaolei; Guo Liqiu; Bai Yang; Qiao Lijie

2011-01-01

In electrical scanning probe microscope (ESPM) applications, the wear and conductivity of the probe are undoubtedly serious concerns since they affect the integrity of the measurements. This study investigates the characterization of Ti doped diamond-like-carbon (DLC) as coating material on a silicon cantilever for ESPM. We deposited a layer of Ti-DLC thin film on the surface of Si cantilever by magnetron sputtering. The morphology and composition of the Ti-DLC films were characterized by scanning electron microscopy and Raman spectroscopy, respectively. We also compared the wear resistance, electric conductivity and scanning image quality of the Ti-DLC-coated probes with those of commercially available conductive probes. The results showed that the electric conductivity and the scanning image quality of the Ti-DLC-coated probes were the same as the commercial conductive probes, while the wear resistance and service life was significantly better.

Characterization of Direct Current-Electrical Penetration Graph Waveforms and Correlation With the Probing Behavior of Matsumuratettix hiroglyphicus (Hemiptera: Cicadellidae), the Insect Vector of Sugarcane White Leaf Phytoplasma.

Science.gov (United States)

Roddee, J; Kobori, Y; Yorozuya, H; Hanboonsong, Y

2017-06-01

The leafhopper Matsumuratettix hiroglyphicus (Matsumura) (Hemiptera: Cicadellidae) is an important vector of phytoplasma causing white leaf disease in sugarcane. Thus, the aim of our study was to understand and describe the stylet-probing activities of this vector while feeding on sugarcane plants, by using direct current (DC) electrical penetration graph (EPG) monitoring. The EPG signals were classified into six distinct waveforms, according to amplitude, frequency, voltage level, and electrical origin of the observed traces during stylet penetration into the host plant tissues (probing). These six EPG waveforms of probing behavior comprise no stylet penetration (NP); stylet pathway through epidermis, mesophyll, and parenchymal cells (waveform A); contact at the bundle sheath layer (waveform B); salivation into phloem sieve elements (waveform C); phloem sap ingestion (waveform D); and short ingestion time of xylem sap (waveform E). The above waveform patterns were correlated with histological data of salivary sheath termini in plant tissue generated from insect stylet tips. The key findings of this study were that M. hiroglyphicus ingests the phloem sap at a relatively higher rate and for longer duration from any other cell type, suggesting that M. hiroglyphicus is mainly a phloem-feeder. Quantitative comparison of probing behavior revealed that females typically probe more frequently and longer in the phloem than males. Thus, females may acquire and inoculate greater amounts of phytoplasma than males, enhancing the efficiency of phytoplasma transmission and potentially exacerbating disease spreading. Overall, our study provides basic information on the probing behavior and transmission mechanism of M. hiroglyphicus. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Consideration of magnetic field fluctuation measurements in a torus plasma with heavy ion beam probe

International Nuclear Information System (INIS)

Shimizu, A.; Fujisawa, A.; Ohshima, S.; Nakano, H.

2004-03-01

The article discusses feasibility of magnetic fluctuation measurement with a heavy ion beam probe (HIBP) in an axisymmetric torus configuration. In the measurements, path integral fluctuation along the probing beam orbit should be considered as is similar to the density fluctuation measurements with HIBP. A calculation, based on an analytic formula, is performed to estimate the path integral effects for fluctuation patterns that have difference in profile, the correlation length, the radial wavelength, and the poloidal mode number. In addition, the large distance between the plasma and the detector is considered to lessen the path integral effect. As a result, it is found that local fluctuation of magnetic field can be properly detected with a heavy ion beam probe. (author)

Toward Exposing Timing-Based Probing Attacks in Web Applications †

Science.gov (United States)

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-01-01

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach. PMID:28245610

A robust method for processing scanning probe microscopy images and determining nanoobject position and dimensions

NARCIS (Netherlands)

Silly, F.

2009-01-01

P>Processing of scanning probe microscopy (SPM) images is essential to explore nanoscale phenomena. Image processing and pattern recognition techniques are developed to improve the accuracy and consistency of nanoobject and surface characterization. We present a robust and versatile method to

Synthesis of improved upconversion nanoparticles as ultrasensitive fluorescence probe for mycotoxins

Energy Technology Data Exchange (ETDEWEB)

Chen, Quansheng, E-mail: q.s.chen@hotmail.com; Hu, Weiwei; Sun, Cuicui; Li, Huanhuan; Ouyang, Qin

2016-09-28

Rare earth-doped upconversion nanoparticles (UCNPs) have promising potentials in biodetection due to their unique frequency upconverting capability and high detection sensitivity. This paper reports an improved UCNPs-based fluorescence probe for dual-sensing of Aflatoxin B1 (AFB1) and Deoxynivalenol (DON) using a magnetism-induced separation and the specific formation of antibody-targets complex. Herein, the improved UCNPs, which were namely NaYF{sub 4}:Yb/Ho/Gd and NaYF{sub 4}:Yb/Tm/Gd, were systematically studied based on the optimization of reaction time, temperature and the concentration of dopant ions with simultaneous phase and size controlled NaYF{sub 4} nanoparticles; and the targets were detected using the pattern of competitive combination assay. Under an optimized condition, the advanced fluorescent probes revealed stronger fluorescent properties, broader biological applications and better storage stabilities compared to traditional UCNPs-based ones; and ultrasensitive determinations of AFB1 and DON were achieved under a wide sensing range of 0.001–0.1 ng ml{sup −1} with the limit of detection (LOD) of 0.001 ng ml{sup −1}. Additionally, the applicability of the improved nanosensor for the detection of mycotoxins was also confirmed in adulterated oil samples. - Highlights: • Improved rare earth-doped upconversion nanoparticles were prepared with detailed optimizations. • Setup of an upconversion fluorescence spectrometer. • An advanced UCNPs-based immunosensor for dual-sensing mycotoxins was developed with a LOD of 0.001 ng ml{sup −1}. • Application of this biosensor to detect targets in real samples were confirmed with satisfied results.

A tobacco cDNA reveals two different transcription patterns in vegetative and reproductive organs

Directory of Open Access Journals (Sweden)

I. da Silva

2002-08-01

Full Text Available In order to identify genes expressed in the pistil that may have a role in the reproduction process, we have established an expressed sequence tags project to randomly sequence clones from a Nicotiana tabacum stigma/style cDNA library. A cDNA clone (MTL-8 showing high sequence similarity to genes encoding glycine-rich RNA-binding proteins was chosen for further characterization. Based on the extensive identity of MTL-8 to the RGP-1a sequence of N. sylvestris, a primer was defined to extend the 5' sequence of MTL-8 by RT-PCR from stigma/style RNAs. The amplification product was sequenced and it was confirmed that MTL-8 corresponds to an mRNA encoding a glycine-rich RNA-binding protein. Two transcripts of different sizes and expression patterns were identified when the MTL-8 cDNA insert was used as a probe in RNA blots. The largest is 1,100 nucleotides (nt long and markedly predominant in ovaries. The smaller transcript, with 600 nt, is ubiquitous to the vegetative and reproductive organs analyzed (roots, stems, leaves, sepals, petals, stamens, stigmas/styles and ovaries. Plants submitted to stress (wounding, virus infection and ethylene treatment presented an increased level of the 600-nt transcript in leaves, especially after tobacco necrosis virus infection. In contrast, the level of the 1,100-nt transcript seems to be unaffected by the stress conditions tested. Results of Southern blot experiments have suggested that MTL-8 is present in one or two copies in the tobacco genome. Our results suggest that the shorter transcript is related to stress while the larger one is a flower predominant and nonstress-inducible messenger.

Probing the Higgs vacuum with general relativity

Science.gov (United States)

Mannheim, Philip D.; Kazanas, Demosthenes

1991-01-01

It is shown that the structure of the Higgs vacuum can be revealed in gravitational experiments which probe the Schwarzschild geometry to only one order in MG/r beyond that needed for the classical tests of general relativity. The possibility that deviations from the conventional geometry are at least theoretically conceivable is explored. The deviations obtained provide a diagnostic test for searching for the existence of macroscopic scalar fields and open up the possiblity for further exploring the Higgs mechanism.

Proximal Probes Facility

Data.gov (United States)

Federal Laboratory Consortium — The Proximal Probes Facility consists of laboratories for microscopy, spectroscopy, and probing of nanostructured materials and their functional properties. At the...

Preparation and quality test of superparamagnetic iron oxide labeled antisense oligodeoxynucleotide probe: a preliminary study.

Science.gov (United States)

Wen, Ming; Li, Bibo; Ouyang, Yu; Luo, Yi; Li, Shaolin

2009-06-01

Molecular imaging of tumor antisense gene techniques have been applied to the study of magnetic resonance (MR) gene imaging associated with malignant tumors. In this study, we designed, synthesized, and tested a novel molecular probe, in which the antisense oligodeoxynucleotide (ASODN) was labeled with superparamagnetic iron oxide (SPIO), and its efficiency was examined by in vitro MR imaging after SK-Br-3 mammary carcinoma cell lines (oncocytes) transfection. The SPIO-labeled ASODN probe was prepared through SPIO conjugated to ASODN using a chemical cross linking method. Its morphology and size were detected by atomic force microscope, size distribution were detected by laser granulometer, the conjugating rate and biological activity were determined by high performance liquid chromatography, and the stability was determined by polyacrylamide gel electrophoresis. After that, the probes were transfected into the SK-Br-3 oncocytes, cellular iron uptake was analyzed qualitatively at light and electron microscopy and was quantified at atomic absorption spectrometry, and the signal change of the transfected cells was observed and measured using MR imaging. The morphology of the SPIO-labeled ASODN probe was mostly spherical with well-distributed scattering, and the diameters were between 25 and 40 nm (95%) by atomic force microscope and laser granulometer, the conjugating rate of the probe was 99%. Moreover, this probe kept its activity under physiological conditions and could conjugate with antisense oligodeoxynucleotide. In addition, light microscopy revealed an intracellular uptake of iron oxides in the cytosol and electron microscopic studies revealed a lysosomal deposition of iron oxides in the transfected SK-Br-3 oncocytes by antisense probes, some of them gathered stacks, and the iron content of the group of transfected SK-Br-3 oncocytes by antisense probe is significantly higher (18.37 +/- 0.42 pg) than other contrast groups, the MR imaging showed that

Patterns of Storage, Synthesis and Changing Light Levels Revealed by Carbon Isotope Microsampling within Eocene Metasequoia Tree Rings

Science.gov (United States)

Jahren, H.; Sternberg, L.

2005-12-01

Fossil tree rings from Axel Heiberg Island were microanalyzed for δ13C value in order to assess patterns of tree growth and carbon storage within the Middle Eocene (~45 Ma) Arctic paleoenvironment. Wood from four Metasequoia-type individuals was subsampled for analysis: each individual fossil consisted of between 4 and 10 large (~1 cm thick) consecutive tree rings. One of the fossils displayed an obvious concentric pattern, allowing for the determination of the direction of growth with isotopic pattern. Each ring was divided into ~1 mm thick subsamples, resulting in 5-10 δ13C value determinations per period of ring growth (i.e., growing season). All rings revealed a distinct pattern that was characteristic across growing seasons and across individual fossils. Early in the season, δ13C was at its highest value but descended systematically and sharply to its lowest value at the end of the growing season. Total decrease ranged between 3 and 5 ‰ over the course of each growing season. Identical patterns were observed in the δ13C value of alpha-cellulose isolated from each subsample, indicating that the trends observed did not represent changing levels of secondary metabolites, but rather a seasonal adjustment in the bulk source of carbon used during biosynthesis. Our results are consistent with the following annual pattern of wood synthesis 1.) complete dependence on the mobilization of stored carbon compounds early in the growing season; 2.) systematically increasing use of actively-acquired photosynthate during the growing season; 3.) complete reliance on active photosynthate by the end of the growing season. An additional and significant source of 13C discrimination is declining light levels late in the growing season, and likely contributes to the extreme pattern of δ13C decrease seen across each ring. Our results mimic those seen from modern broadleaf deciduous trees (Helle & Schlesser 2004), but differ from those seen in modern conifers (Barbour et al 2002

Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

KAUST Repository

Pearman, John K.

2018-05-18

Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.

Development of conductivity probe and temperature probe for in-situ measurements in hydrological studies

International Nuclear Information System (INIS)

Chandra, U.; Galindo, B.J.; Castagnet, A.C.G.

1981-05-01

A conductivity probe and a temperature probe have been developed for in-situ measurements in various hydrological field studies. The conductivity probe has platinum electrodes and is powered with two 12 volt batteries. The sensing element of the temperature probe consists of a resistor of high coefficient of temperature. Response of the conductivity probe is measured in a milliampere mater while the resistance of the thermistor is read by a digital meter. The values of conductivity and temperature are derived from respective calibration. The probes are prototype and their range of measurement can be improved depending upon the requirement of the field problem. (Author) [pt

A global analysis of bird plumage patterns reveals no association between habitat and camouflage

Directory of Open Access Journals (Sweden)

Marius Somveille

2016-11-01

Full Text Available Evidence suggests that animal patterns (motifs function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular, scales, bars and spots (regular—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

Science.gov (United States)

Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

Laser-heated emissive plasma probe.

Science.gov (United States)

Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K

2008-08-01

Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808 nm wavelength and an output power up to 50 W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge.

Laser-heated emissive plasma probe

International Nuclear Information System (INIS)

Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K.

2008-01-01

Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808 nm wavelength and an output power up to 50 W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge

Laser-heated emissive plasma probe

Science.gov (United States)

Schrittwieser, Roman; Ionita, Codrina; Balan, Petru; Gstrein, Ramona; Grulke, Olaf; Windisch, Thomas; Brandt, Christian; Klinger, Thomas; Madani, Ramin; Amarandei, George; Sarma, Arun K.

2008-08-01

Emissive probes are standard tools in laboratory plasmas for the direct determination of the plasma potential. Usually they consist of a loop of refractory wire heated by an electric current until sufficient electron emission. Recently emissive probes were used also for measuring the radial fluctuation-induced particle flux and other essential parameters of edge turbulence in magnetized toroidal hot plasmas [R. Schrittwieser et al., Plasma Phys. Controlled Fusion 50, 055004 (2008)]. We have developed and investigated various types of emissive probes, which were heated by a focused infrared laser beam. Such a probe has several advantages: higher probe temperature without evaporation or melting and thus higher emissivity and longer lifetime, no deformation of the probe in a magnetic field, no potential drop along the probe wire, and faster time response. The probes are heated by an infrared diode laser with 808nm wavelength and an output power up to 50W. One probe was mounted together with the lens system on a radially movable probe shaft, and radial profiles of the plasma potential and of its oscillations were measured in a linear helicon discharge.

Activity patterns of free-ranging koalas (Phascolarctos cinereus revealed by accelerometry.

Directory of Open Access Journals (Sweden)

Michelle A Ryan

Full Text Available An understanding of koala activity patterns is important for measuring the behavioral response of this species to environmental change, but to date has been limited by the logistical challenges of traditional field methodologies. We addressed this knowledge gap by using tri-axial accelerometer data loggers attached to VHF radio collars to examine activity patterns of adult male and female koalas in a high-density population at Cape Otway, Victoria, Australia. Data were obtained from 27 adult koalas over two 7-d periods during the breeding season: 12 in the early-breeding season in November 2010, and 15 in the late-breeding season in January 2011. Multiple 15 minute observation blocks on each animal were used for validation of activity patterns determined from the accelerometer data loggers. Accelerometry was effective in distinguishing between inactive (sleeping, resting and active (grooming, feeding and moving behaviors. Koalas were more active during the early-breeding season with a higher index of movement (overall dynamic body acceleration [ODBA] for both males and females. Koalas showed a distinct temporal pattern of behavior, with most activity occurring from mid-afternoon to early morning. Accelerometry has potential for examining fine-scale behavior of a wide range of arboreal and terrestrial species.

Activity patterns of free-ranging koalas (Phascolarctos cinereus) revealed by accelerometry.

Science.gov (United States)

Ryan, Michelle A; Whisson, Desley A; Holland, Greg J; Arnould, John P Y

2013-01-01

An understanding of koala activity patterns is important for measuring the behavioral response of this species to environmental change, but to date has been limited by the logistical challenges of traditional field methodologies. We addressed this knowledge gap by using tri-axial accelerometer data loggers attached to VHF radio collars to examine activity patterns of adult male and female koalas in a high-density population at Cape Otway, Victoria, Australia. Data were obtained from 27 adult koalas over two 7-d periods during the breeding season: 12 in the early-breeding season in November 2010, and 15 in the late-breeding season in January 2011. Multiple 15 minute observation blocks on each animal were used for validation of activity patterns determined from the accelerometer data loggers. Accelerometry was effective in distinguishing between inactive (sleeping, resting) and active (grooming, feeding and moving) behaviors. Koalas were more active during the early-breeding season with a higher index of movement (overall dynamic body acceleration [ODBA]) for both males and females. Koalas showed a distinct temporal pattern of behavior, with most activity occurring from mid-afternoon to early morning. Accelerometry has potential for examining fine-scale behavior of a wide range of arboreal and terrestrial species.

Innovative SPM Probes for Energy-Storage Science: MWCNT-Nanopipettes to Nanobattery Probes

Science.gov (United States)

Larson, Jonathan; Talin, Alec; Pearse, Alexander; Kozen, Alexander; Reutt-Robey, Janice

As energy-storage materials and designs continue to advance, new tools are needed to direct and explore ion insertion/de-insertion at well-defined battery materials interfaces. Scanned probe tips, assembled from actual energy-storage materials, permit SPM measures of local cathode-anode (tip-sample) interactions, including ion transfer. We present examples of ``cathode'' MWCNT-terminated STM probe tips interacting with Li(s)/Si(111) anode substrates. The MWCNT tip functions as both SPM probe and Li-nanopipette,[1] for controlled transport and manipulation of Li. Local field conditions for lithium ionization and transfer are determined and compared to electrostatic models. Additional lithium metallic and oxide tips have been prepared by thin film deposition on conventional W tips, the latter of which effectively functions as a nanobattery. We demonstrate use of these novel probe materials in the local lithiation of low-index Si anode interfaces, probing local barriers for lithium insertion. Prospects and limitations of these novel SPM probes will be discussed. U.S. Department of Energy Award Number DESC0001160.

Scanning probe lithography for fabrication of Ti metal nanodot arrays

International Nuclear Information System (INIS)

Jung, B.; Jo, W.; Gwon, M.J.; Lee, E.; Kim, D.-W.

2010-01-01

We report fabrication of Ti metal nanodot arrays by scanning probe microscopic indentation. A thin poly-methylmethacrylate (PMMA) layer was spin-coated on Si substrates with thickness of 70 nm. Nanometer-size pore arrays were formed by indenting the PMMA layer using a cantilever of a scanning probe microscope. Protuberances with irregular boundaries appeared during the indentation process. Control of approach and pulling-out speed during indentation was able to dispose of the protrusions. Ti metal films were deposited on the patterned PMMA layers by a radio-frequency sputtering method and subsequently lifted off to obtain metal nanodot arrays. The fabricated metal nanodot arrays have 200 nm of diameter and 500 nm of interdistance, which corresponds to a density of 4x10 8 /cm 2 . Scanning probe-based measurement of current-voltage (I-V) behaviors for a single Ti metal nanodot showed asymmetric characteristics. Applying external bias is likely to induce oxidation of Ti metal, since the conductance decreased and volume change of the dots was observed. I-V behaviors of Ti metal nanodots by conventional e-beam lithography were also characterized for comparison.

Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology.

Science.gov (United States)

Liu, Liqin; Luo, Qiaoling; Teng, Wan; Li, Bin; Li, Hongwei; Li, Yiwen; Li, Zhensheng; Zheng, Qi

2018-05-01

Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.

Estimating Highway Volumes Using Vehicle Probe Data - Proof of Concept: Preprint

Energy Technology Data Exchange (ETDEWEB)

Hou, Yi [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Young, Stanley E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sadabadi, Kaveh [University of Maryland; SekuBa, PrzemysBaw [University of Maryland; Markow, Denise [I95 Corridor Coalition

2018-03-13

This paper examines the feasibility of using sampled commercial probe data in combination with validated continuous counter data to accurately estimate vehicle volume across the entire roadway network, for any hour during the year. Currently either real time or archived volume data for roadways at specific times are extremely sparse. Most volume data are average annual daily traffic (AADT) measures derived from the Highway Performance Monitoring System (HPMS). Although methods to factor the AADT to hourly averages for typical day of week exist, actual volume data is limited to a sparse collection of locations in which volumes are continuously recorded. This paper explores the use of commercial probe data to generate accurate volume measures that span the highway network providing ubiquitous coverage in space, and specific point-in-time measures for a specific date and time. The paper examines the need for the data, fundamental accuracy limitations based on a basic statistical model that take into account the sampling nature of probe data, and early results from a proof of concept exercise revealing the potential of probe type data calibrated with public continuous count data to meet end user expectations in terms of accuracy of volume estimates.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

Science.gov (United States)

Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

Science.gov (United States)

Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

A nine-electrode probe for simultaneous measurement of all terms in the ideal radial Ohm's law

International Nuclear Information System (INIS)

Si, Jiahe; Wang, Zhehui

2006-01-01

A Nine-Electrode Probe (NEP) has been developed for simultaneous measurement of all terms in the ideal Ohm's law E+UxB=0 in the radial (r) direction in cylindrical geometry, where E is the electric field, U is the plasma flow velocity, and B is the magnetic field. The probe consists of two pairs of directional Langmuir probes ('Mach' probes) to measure the axial (z) and azimuthal (θ) plasma flows, two pairs of floating Langmuir probes at different radial positions to measure the radial electric field, and two B-dot coils to measure the axial and azimuthal magnetic field. The measurement is performed in the Flowing Magnetized Plasma (FMP) experiment. Two flow patterns are identified in the FMP experiment by the NEP. The peak-to-peak values of radial electric field fluctuation is 1.5-4 times of the mean values. Comparisons of UxBvertical bar r and E r show that E r + UxBvertical bar r is not zero within some periods of discharge. This deviation suggests non-ideal effects in Ohm's law can not be neglected

The time resolved measurement of ultrashort terahertz-band electric fields without an ultrashort probe

International Nuclear Information System (INIS)

Walsh, D. A.; Snedden, E. W.; Jamison, S. P.

2015-01-01

The time-resolved detection of ultrashort pulsed THz-band electric field temporal profiles without an ultrashort laser probe is demonstrated. A non-linear interaction between a narrow-bandwidth optical probe and the THz pulse transposes the THz spectral intensity and phase information to the optical region, thereby generating an optical pulse whose temporal electric field envelope replicates the temporal profile of the real THz electric field. This optical envelope is characterised via an autocorrelation based FROG (frequency resolved optical gating) measurement, hence revealing the THz temporal profile. The combination of a narrow-bandwidth, long duration, optical probe, and self-referenced FROG makes the technique inherently immune to timing jitter between the optical probe and THz pulse and may find particular application where the THz field is not initially generated via ultrashort laser methods, such as the measurement of longitudinal electron bunch profiles in particle accelerators

Theory of NMR probe design

International Nuclear Information System (INIS)

Schnall, M.D.

1988-01-01

The NMR probe is the intrinsic part of the NMR system which allows transmission of a stimulus to a sample and the reception of a resulting signal from a sample. NMR probes are used in both imaging and spectroscopy. Optimal probe design is important to the production of adequate signal/moise. It is important for anyone using NMR techniques to understand how NMR probes work and how to optimize probe design

Genomic expression patterns of cardiac tissues from dogs with dilated cardiomyopathy.

Science.gov (United States)

Oyama, Mark A; Chittur, Sridar

2005-07-01

To evaluate global genome expression patterns of left ventricular tissues from dogs with dilated cardiomyopathy (DCM). Tissues obtained from the left ventricle of 2 Doberman Pinschers with end-stage DCM and 5 healthy control dogs. Transcriptional activities of 23,851 canine DNA sequences were determined by use of an oligonucleotide microarray. Genome expression patterns of DCM tissue were evaluated by measuring the relative amount of complementary RNA hybridization to the microarray probes and comparing it with gene expression for tissues from 5 healthy control dogs. 478 transcripts were differentially expressed (> or = 2.5-fold change). In DCM tissue, expression of 173 transcripts was upregulated and expression of 305 transcripts was downregulated, compared with expression for control tissues. Of the 478 transcripts, 167 genes could be specifically identified. These genes were grouped into 1 of 8 categories on the basis of their primary physiologic function. Grouping revealed that pathways involving cellular energy production, signaling and communication, and cell structure were generally downregulated, whereas pathways involving cellular defense and stress responses were upregulated. Many previously unreported genes that may contribute to the pathophysiologic aspects of heart disease were identified. Evaluation of global expression patterns provides a molecular portrait of heart failure, yields insights into the pathophysiologic aspects of DCM, and identifies intriguing genes and pathways for further study.

The Slow:Fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes

Energy Technology Data Exchange (ETDEWEB)

Alm, Eric; Shapiro, B. Jesse

2009-04-15

Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally-relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, while information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally-related sets of genes (e.g., energy production in Pseudomonas fluorescens), while other species apparently evolve mostly by drift (e.g., uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene-trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.

Accurate Extraction of Charge Carrier Mobility in 4-Probe Field-Effect Transistors

KAUST Repository

Choi, Hyun Ho; Rodionov, Yaroslav I.; Paterson, Alexandra F.; Panidi, Julianna; Saranin, Danila; Kharlamov, Nikolai; Didenko, Sergei I.; Anthopoulos, Thomas D.; Cho, Kilwon; Podzorov, Vitaly

2018-01-01

Charge carrier mobility is an important characteristic of organic field-effect transistors (OFETs) and other semiconductor devices. However, accurate mobility determination in FETs is frequently compromised by issues related to Schottky-barrier contact resistance, that can be efficiently addressed by measurements in 4-probe/Hall-bar contact geometry. Here, it is shown that this technique, widely used in materials science, can still lead to significant mobility overestimation due to longitudinal channel shunting caused by voltage probes in 4-probe structures. This effect is investigated numerically and experimentally in specially designed multiterminal OFETs based on optimized novel organic-semiconductor blends and bulk single crystals. Numerical simulations reveal that 4-probe FETs with long but narrow channels and wide voltage probes are especially prone to channel shunting, that can lead to mobilities overestimated by as much as 350%. In addition, the first Hall effect measurements in blended OFETs are reported and how Hall mobility can be affected by channel shunting is shown. As a solution to this problem, a numerical correction factor is introduced that can be used to obtain much more accurate experimental mobilities. This methodology is relevant to characterization of a variety of materials, including organic semiconductors, inorganic oxides, monolayer materials, as well as carbon nanotube and semiconductor nanocrystal arrays.

Accurate Extraction of Charge Carrier Mobility in 4-Probe Field-Effect Transistors

KAUST Repository

Choi, Hyun Ho

2018-04-30

Charge carrier mobility is an important characteristic of organic field-effect transistors (OFETs) and other semiconductor devices. However, accurate mobility determination in FETs is frequently compromised by issues related to Schottky-barrier contact resistance, that can be efficiently addressed by measurements in 4-probe/Hall-bar contact geometry. Here, it is shown that this technique, widely used in materials science, can still lead to significant mobility overestimation due to longitudinal channel shunting caused by voltage probes in 4-probe structures. This effect is investigated numerically and experimentally in specially designed multiterminal OFETs based on optimized novel organic-semiconductor blends and bulk single crystals. Numerical simulations reveal that 4-probe FETs with long but narrow channels and wide voltage probes are especially prone to channel shunting, that can lead to mobilities overestimated by as much as 350%. In addition, the first Hall effect measurements in blended OFETs are reported and how Hall mobility can be affected by channel shunting is shown. As a solution to this problem, a numerical correction factor is introduced that can be used to obtain much more accurate experimental mobilities. This methodology is relevant to characterization of a variety of materials, including organic semiconductors, inorganic oxides, monolayer materials, as well as carbon nanotube and semiconductor nanocrystal arrays.

Selective activation of SHP2 activity by cisplatin revealed by a novel chemical probe-based assay

International Nuclear Information System (INIS)

Kuo, Chun-Chen; Chu, Chi-Yuan; Lin, Jing-Jer; Lo, Lee-Chiang

2010-01-01

Src homology-2 (SH2) domain-containing phosphatase 2 (SHP2) is known to participate in several different signaling pathways to mediate cell growth, survival, migration, and differentiation. However, due to the lack of proper analytical tools, it is unclear whether the phosphatase activity of SHP2 is activated in most studies. We have previously developed an activity-based probe LCL2 that formed covalent linkage with catalytically active protein tyrosine phosphatases (PTPs). Here, by combining LCL2 with a SHP2 specific antibody, we established an assay system that enables the direct monitoring of SHP2 activity upon cisplatin treatment of cancer cells. The protocol is advantageous over conventional colorimetric or in-gel PTP assays as it is specific and does not require the use of radioisotope reagents. Using this assay, we found SHP2 activity was selectively activated by cisplatin. Moreover, the activation of SHP2 appeared to be specific for cisplatin as other DNA damage agents failed to activate the activity. Although the role of SHP2 activation by cisplatin treatments is still unclear to us, our results provide the first direct evidence for the activation of SHP2 during cisplatin treatments. More importantly, the concept of using activity-based probe in conjunction with target-specific antibodies could be extended to other enzyme classes.

Cultural probes

DEFF Research Database (Denmark)

Madsen, Jacob Østergaard

The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation.......The aim of this study was thus to explore cultural probes (Gaver, Boucher et al. 2004), as a possible methodical approach, supporting knowledge production on situated and contextual aspects of occupation....

Abnormal patterns of cerebral lateralisation as revealed by the Universal Chimeric Faces Task in individuals with autistic disorder.

Science.gov (United States)

Taylor, Sandie; Workman, Lance; Yeomans, Heather

2012-01-01

A previous study by Workman, Chilvers, Yeomans, and Taylor (2006), using the "Universal" Chimeric Faces Task (UCFT) for six emotional expressions, demonstrated that an overall left hemispatial/right hemisphere (RH) advantage has begun to develop by the age of 7-8. Moreover, the development of this left hemispatial advantage was observed to correlate positively with the ability to read emotions in the faces of others. Adopting the UCFT, the current study compared autistic children (11-15) with unimpaired children of two age groups (5-6 and 7-8) from this previous study. The autistic children showed a left hemispatial/RH advantage only for the two emotional expressions of "happiness" and "anger". Results for the autistic children revealed a similar overall pattern of lateralisation to the 5-6-year-olds and one that is less lateralised than the pattern for the 7-8-year-olds. Autistic children appear to show a developmental deficit for left hemispatial/RH advantage for emotional expression with the exception of "happiness" and "anger." The findings are discussed in terms of role hemisphericity and an approach-avoidance model.

Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage.

Directory of Open Access Journals (Sweden)

Nicolas Guillemot

Full Text Available The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

Spherical conducting probes in finite Debye length plasmas and E x B fields

International Nuclear Information System (INIS)

Patacchini, Leonardo; Hutchinson, Ian H

2011-01-01

The particle-in-cell code SCEPTIC3D (Patacchini and Hutchinson 2010 Plasma Phys. Control. Fusion 52 035005) is used to calculate the interaction of a transversely flowing magnetized plasma with a negatively charged spherical conductor, in the entire range of magnetization and Debye length. The results allow the first fully self-consistent analysis of probe operation where neither the ion Larmor radius nor the Debye length are approximated by zero or infinity. An important transition in plasma structure occurs when the Debye length exceeds the average ion Larmor radius, as the sphere starts to shield the convective electric field driving the flow. A remarkable result is that in those conditions, the ion current can significantly exceed the unmagnetized orbital motion limit. When both the Debye length and the Larmor radius are small compared with the probe dimensions, however, their ratio does not affect the collection pattern significantly, and Mach-probe calibration methods derived in the context of quasineutral strongly magnetized plasmas (Patacchini and Hutchinson 2009 Phys. Rev. E 80 036403) hold for Debye lengths and ion Larmor radii smaller than about 10% of the probe radius.

Dual-probe decoherence microscopy: probing pockets of coherence in a decohering environment

International Nuclear Information System (INIS)

Jeske, Jan; Cole, Jared H; Müller, Clemens; Marthaler, Michael; Schön, Gerd

2012-01-01

We study the use of a pair of qubits as a decoherence probe of a nontrivial environment. This dual-probe configuration is modelled by three two-level systems (TLSs), which are coupled in a chain in which the middle system represents an environmental TLS. This TLS resides within the environment of the qubits and therefore its coupling to perturbing fluctuations (i.e. its decoherence) is assumed much stronger than the decoherence acting on the probe qubits. We study the evolution of such a tripartite system including the appearance of a decoherence-free state (dark state) and non-Markovian behaviour. We find that all parameters of this TLS can be obtained from measurements of one of the probe qubits. Furthermore, we show the advantages of two qubits in probing environments and the new dynamics imposed by a TLS that couples to two qubits at once. (paper)

Probing Framework-Restricted Metal Axial Ligation and Spin State Patterns in a Post-Synthetically Reduced Iron-Porphyrin-Based Metal–Organic Framework

Energy Technology Data Exchange (ETDEWEB)

Kucheryavy, Pavel; Lahanas, Nicole; Velasco, Ever; Sun, Cheng-Jun; Lockard, Jenny V.

2016-04-07

An iron porphyrin-based metal organic framework, PCN-222(Fe) is investigated upon post-synthetic reduction with piperidine. Fe K-edge X-ray absorption and Kβ mainline emission spectroscopy measurements reveal the local coor-dination geometry, oxidation and spin state changes experi-enced by the Fe sites upon reaction with this axially coordi-nating reducing agent. Analysis and fitting of these data con-firm the binding pattern predicted by a space filling model of the structurally constrained pore environments. These results are further support by UV-vis diffuse reflectance, IR and Raman spectroscopy data.

Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

International Nuclear Information System (INIS)

Collomb, J.; Finance, C.; Alabouch, S.; Laporte, J.

1992-01-01

Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabelling with 32 P and enzymatic labelling through covalent linkage to peroxidase and chemiluminescence detection. The radioactive probe 174 detected as little as 1 to 3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in faecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors)

Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

Energy Technology Data Exchange (ETDEWEB)

Collomb, J; Finance, C; Alabouch, S [Lab. de Microbiologie Moleculaire, Faculte des Sciences Pharmaceutiques et Biologiques, Univ. de Nancy I, Nancy (France); Laporte, J [Station de Virologie et d' Immunologie Moleculaires, INRA, Jouy-en-Josas (France)

1992-01-01

Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabeled with [sup 32]P and enzymatic labeled through covalent linkage to peroxidase for chemiluminescence detection. The radioactive probe 174 detected as little as 1-3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in fecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors).

An interchangeable scanning Hall probe/scanning SQUID microscope

International Nuclear Information System (INIS)

Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin; Chen, Tse-Jun; Wang, M. J.; Ling, D. C.; Chi, C. C.; Chen, Jeng-Chung

2014-01-01

We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (⩽4 μm), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10 −7 T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La 2/3 Ca 1/3 MnO 3 thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K

Model for resonant plasma probe.

Energy Technology Data Exchange (ETDEWEB)

Warne, Larry Kevin; Johnson, William Arthur; Hebner, Gregory Albert; Jorgenson, Roy E.; Coats, Rebecca Sue

2007-04-01

This report constructs simple circuit models for a hairpin shaped resonant plasma probe. Effects of the plasma sheath region surrounding the wires making up the probe are determined. Electromagnetic simulations of the probe are compared to the circuit model results. The perturbing effects of the disc cavity in which the probe operates are also found.

Correlations between human mobility and social interaction reveal general activity patterns

DEFF Research Database (Denmark)

Mollgaard, Anders; Jørgensen, Sune Lehmann; Mathiesen, Joachim

2017-01-01

activity types, namely communication, motion, and physical proximity by analyzing data collected from smartphones distributed among 638 individuals. We explore two central questions: Which underlying principles govern the formation of the activity patterns? Are the patterns specific to each individual...... or shared across the entire population? We find that statistics of the entire population allows us to successfully predict 71% of the activity and 85% of the inactivity involved in communication, mobility, and physical proximity. Surprisingly, individual level statistics only result in marginally better...... they be of social or of physical character....

Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture

International Nuclear Information System (INIS)

Edelstein, P.H.

1986-01-01

A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with 125 I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture

Localized excitation of magnetostatic surface spin waves in yttrium iron garnet by shorted coaxial probe detected via spin pumping and rectification effect

International Nuclear Information System (INIS)

Soh, Wee Tee; Ong, C. K.; Peng, Bin

2015-01-01

We demonstrate the localized excitation and dc electrical detection of magnetostatic surface spin waves (MSSWs) in yttrium iron garnet (YIG) by a shorted coaxial probe. Thin films of NiFe and Pt are patterned at different regions onto a common bulk YIG substrate. A shorted coaxial probe is used to excite spin precession locally near various patterned regions. The dc voltages across the corresponding regions are recorded. For excitation of the Pt regions, the dc voltage spectra are dominated by the spin pumping of MSSWs from YIG, where various modes can be clearly distinguished. For the NiFe region, it is also found that spin pumping from MSSWs generated in YIG dominated the spectra, indicating that the spin pumped currents are dissipated into charge currents via the inverse Spin Hall effect (ISHE) in NiFe. For all regions, dc signals from YIG MSSWs are observed to be much stronger than the ferromagnetic resonance (FMR) uniform mode, likely due to the nature of the microwave excitation. The results indicate the potential of this probe for microwave imaging via dc detection of spin dynamics in continuous and patterned films

Where do pulse oximeter probes break?

Science.gov (United States)

Crede, S; Van der Merwe, G; Hutchinson, J; Woods, D; Karlen, W; Lawn, J

2014-06-01

Pulse oximetry, a non-invasive method for accurate assessment of blood oxygen saturation (SPO2), is an important monitoring tool in health care facilities. However, it is often not available in many low-resource settings, due to expense, overly sophisticated design, a lack of organised procurement systems and inadequate medical device management and maintenance structures. Furthermore medical devices are often fragile and not designed to withstand the conditions of low-resource settings. In order to design a probe, better suited to the needs of health care facilities in low-resource settings this study aimed to document the site and nature of pulse oximeter probe breakages in a range of different probe designs in a low to middle income country. A retrospective review of job cards relating to the assessment and repair of damaged or faulty pulse oximeter probes was conducted at a medical device repair company based in Cape Town, South Africa, specializing in pulse oximeter probe repairs. 1,840 job cards relating to the assessment and repair of pulse oximeter probes were reviewed. 60.2 % of probes sent for assessment were finger-clip probes. For all probes, excluding the neonatal wrap probes, the most common point of failure was the probe wiring (>50 %). The neonatal wrap most commonly failed at the strap (51.5 %). The total cost for quoting on the broken pulse oximeter probes and for the subsequent repair of devices, excluding replacement components, amounted to an estimated ZAR 738,810 (USD $98,508). Improving the probe wiring would increase the life span of pulse oximeter probes. Increasing the life span of probes will make pulse oximetry more affordable and accessible. This is of high priority in low-resource settings where frequent repair or replacement of probes is unaffordable or impossible.

Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

Directory of Open Access Journals (Sweden)

Alicia Lundby

2012-08-01

Full Text Available Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

Multiplexed, high density electrophysiology with nanofabricated neural probes.

Directory of Open Access Journals (Sweden)

Jiangang Du

Full Text Available Extracellular electrode arrays can reveal the neuronal network correlates of behavior with single-cell, single-spike, and sub-millisecond resolution. However, implantable electrodes are inherently invasive, and efforts to scale up the number and density of recording sites must compromise on device size in order to connect the electrodes. Here, we report on silicon-based neural probes employing nanofabricated, high-density electrical leads. Furthermore, we address the challenge of reading out multichannel data with an application-specific integrated circuit (ASIC performing signal amplification, band-pass filtering, and multiplexing functions. We demonstrate high spatial resolution extracellular measurements with a fully integrated, low noise 64-channel system weighing just 330 mg. The on-chip multiplexers make possible recordings with substantially fewer external wires than the number of input channels. By combining nanofabricated probes with ASICs we have implemented a system for performing large-scale, high-density electrophysiology in small, freely behaving animals that is both minimally invasive and highly scalable.

Biological invasion hotspots: a trait-based perspective reveals new sub-continental patterns

Science.gov (United States)

Basil V. Iannone III; Kevin M. Potter; Qinfeng Guo; Andrew M. Liebhold; Bryan C. Pijanowski; Christopher M. Oswalt; Songlin Fei

2015-01-01

Invader traits (including plant growth form) may play an important, and perhaps overlooked, role in determining macroscale patterns of biological invasions and therefore warrant greater consideration in future investigations aimed at understanding these patterns. To assess this need, we used empirical data from a national-level survey of forest in the contiguous 48...

Intraclade heterogeneity in nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP

Directory of Open Access Journals (Sweden)

Michael Morando

2016-12-01

Full Text Available Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP to assess the ability of individual phylotypes to assimilate a particular N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II (MG-II. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e. different levels of N assimilation within clades, likely reflecting niche partitioning by ecotypes. The addition of nitrate utilization to ecosystem and ecosystem models by these globally dominant clades will likely improve the mechanistic accuracy of these models.

How can we probe the atom mass currents induced by synthetic gauge fields?

Science.gov (United States)

Paramekanti, Arun; Killi, Matthew; Trotzky, Stefan

2013-05-01

Ultracold atomic fermions and bosons in an optical lattice can have quantum ground states which support equilibrium currents in the presence of synthetic magnetic fields or spin orbit coupling. As a tool to uncover these mass currents, we propose using an anisotropic quantum quench of the optical lattice which dynamically converts the current patterns into measurable density patterns. Using analytical calculations and numerical simulations, we show that this scheme can probe diverse equilibrium bulk current patterns in Bose superfluids and Fermi fluids induced by synthetic magnetic fields, as well as detect the chiral edge currents in topological states of atomic matter such as quantum Hall and quantum spin Hall insulators. This work is supported by NSERC of Canada and the Canadian Institute for Advanced Research.

Experimental Route to Scanning Probe Hot Electron Nanoscopy (HENs) Applied to 2D Material

KAUST Repository

Giugni, Andrea; Torre, Bruno; Allione, Marco; Das, Gobind; Wang, Zhenwei; He, Xin; Alshareef, Husam N.; Di Fabrizio, Enzo M.

2017-01-01

for applications in electronics: 2D MoS2 single crystal and a p-type SnO layer. Results are supported by complementary scanning Kelvin probe microscopy, traditional conductive AFM, and Raman measurements. New features highlighted by HEN technique reveal details

Machine learning methods reveal the temporal pattern of dengue incidence using meteorological factors in metropolitan Manila, Philippines.

Science.gov (United States)

Carvajal, Thaddeus M; Viacrusis, Katherine M; Hernandez, Lara Fides T; Ho, Howell T; Amalin, Divina M; Watanabe, Kozo

2018-04-17

Several studies have applied ecological factors such as meteorological variables to develop models and accurately predict the temporal pattern of dengue incidence or occurrence. With the vast amount of studies that investigated this premise, the modeling approaches differ from each study and only use a single statistical technique. It raises the question of whether which technique would be robust and reliable. Hence, our study aims to compare the predictive accuracy of the temporal pattern of Dengue incidence in Metropolitan Manila as influenced by meteorological factors from four modeling techniques, (a) General Additive Modeling, (b) Seasonal Autoregressive Integrated Moving Average with exogenous variables (c) Random Forest and (d) Gradient Boosting. Dengue incidence and meteorological data (flood, precipitation, temperature, southern oscillation index, relative humidity, wind speed and direction) of Metropolitan Manila from January 1, 2009 - December 31, 2013 were obtained from respective government agencies. Two types of datasets were used in the analysis; observed meteorological factors (MF) and its corresponding delayed or lagged effect (LG). After which, these datasets were subjected to the four modeling techniques. The predictive accuracy and variable importance of each modeling technique were calculated and evaluated. Among the statistical modeling techniques, Random Forest showed the best predictive accuracy. Moreover, the delayed or lag effects of the meteorological variables was shown to be the best dataset to use for such purpose. Thus, the model of Random Forest with delayed meteorological effects (RF-LG) was deemed the best among all assessed models. Relative humidity was shown to be the top-most important meteorological factor in the best model. The study exhibited that there are indeed different predictive outcomes generated from each statistical modeling technique and it further revealed that the Random forest model with delayed meteorological

Probing thermal evanescent waves with a scattering-type near-field microscope

International Nuclear Information System (INIS)

Kajihara, Y; Kosaka, K; Komiyama, S

2011-01-01

Long wavelength infrared (LWIR) waves contain many important spectra of matters like molecular motions. Thus, probing spontaneous LWIR radiation without external illumination would reveal detailed mesoscopic phenomena that cannot be probed by any other measurement methods. Here we developed a scattering-type scanning near-field optical microscope (s-SNOM) and demonstrated passive near-field microscopy at 14.5 µm wavelength. Our s-SNOM consists of an atomic force microscope and a confocal microscope equipped with a highly sensitive LWIR detector, called a charge-sensitive infrared phototransistor (CSIP). In our s-SNOM, photons scattered by a tungsten probe are collected by an objective of the confocal LWIR microscope and are finally detected by the CSIP. To suppress the far-field background, we vertically modulated the probe and demodulated the signal with a lock-in amplifier. With the s-SNOM, a clear passive image of 3 µm pitch Au/SiC gratings was successfully obtained and the spatial resolution was estimated to be 60 nm (λ/240). The radiation from Au and GaAs was suggested to be due to thermally excited charge/current fluctuations and surface phonons, respectively. This s-SNOM has the potential to observe mesoscopic phenomena such as molecular motions, biomolecular protein interactions and semiconductor conditions in the future

Limitations of turbidity process probes and formazine as their calibration standard.

Science.gov (United States)

Münzberg, Marvin; Hass, Roland; Dinh Duc Khanh, Ninh; Reich, Oliver

2017-01-01

Turbidity measurements are frequently implemented for the monitoring of heterogeneous chemical, physical, or biotechnological processes. However, for quantitative measurements, turbidity probes need calibration, as is requested and regulated by the ISO 7027:1999. Accordingly, a formazine suspension has to be produced. Despite this regulatory demand, no scientific publication on the stability and reproducibility of this polymerization process is available. In addition, no characterization of the optical properties of this calibration material with other optical methods had been achieved so far. Thus, in this contribution, process conditions such as temperature and concentration have been systematically investigated by turbidity probe measurements and Photon Density Wave (PDW) spectroscopy, revealing an influence on the temporal formazine formation onset. In contrast, different reaction temperatures do not lead to different scattering properties for the final formazine suspensions, but give an access to the activation energy for this condensation reaction. Based on PDW spectroscopy data, the synthesis of formazine is reproducible. However, very strong influences of the ambient conditions on the measurements of the turbidity probe have been observed, limiting its applicability. The restrictions of the turbidity probe with respect to scatterer concentration are examined on the basis of formazine and polystyrene suspensions. Compared to PDW spectroscopy data, signal saturation is observed at already low reduced scattering coefficients.

Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D_2O) Stable Isotope Probing

International Nuclear Information System (INIS)

Baran, Richard; Lau, Rebecca; Bowen, Benjamin P.; Diamond, Spencer; Jose, Nick

2017-01-01

In diverse environments on a global scale cyanobacteria are important primary producers of organic matter. Moreover, while mechanisms of CO_2 fixation are well understood, the distribution of the flow of fixed organic carbon within individual cells and complex microbial communities is less well characterized. To obtain a general overview of metabolism, we describe the use of deuterium oxide (D_2O) to measure deuterium incorporation into the intracellular metabolites of two physiologically diverse cyanobacteria: a terrestrial filamentous strain (Microcoleus vaginatus PCC 9802) and a euryhaline unicellular strain (Synechococcus sp. PCC 7002). D_2O was added to the growth medium during different phases of the diel cycle. Incorporation of deuterium into metabolites at nonlabile positions, an indicator of metabolite turnover, was assessed using liquid chromatography mass spectrometry. Expectedly, large differences in turnover among metabolites were observed. Some metabolites, such as fatty acids, did not show significant turnover over 12–24 h time periods but did turn over during longer time periods. Unexpectedly, metabolites commonly regarded to act as compatible solutes, including glutamate, glucosylglycerol, and a dihexose, showed extensive turnover compared to most other metabolites already after 12 h, but only during the light phase in the cycle. We observed extensive turnover and found it surprising considering the conventional view on compatible solutes as biosynthetic end points given the relatively slow growth and constant osmotic conditions. Our suggests the possibility of a metabolic sink for some compatible solutes (e.g., into glycogen) that allows for rapid modulation of intracellular osmolarity. To investigate this, uniformly "1"3C-labeled Synechococcus sp. PCC 7002 were exposed to "1"2C glucosylglycerol. Following metabolite extraction, amylase treatment of methanol-insoluble polymers revealed "1"2C labeling of glycogen. Overall, our work shows that D_2

The use of arc-erosion as a patterning technique for transparent conductive materials

Energy Technology Data Exchange (ETDEWEB)

Jimenez-Trillo, J. [Dpt. Ingenieria de Circuitos y Sistemas, EUIT Telecomunicacion, U. P. M, 28031 Madrid (Spain); Alvarez, A.L., E-mail: angelluis.alvarez@urjc.es [Dpt. Tecnologia Electronica, Univ. Rey Juan Carlos, Mostoles, 28933 Madrid (Spain); Coya, C. [Dpt. Tecnologia Electronica, Univ. Rey Juan Carlos, Mostoles, 28933 Madrid (Spain); Cespedes, E.; Espinosa, A. [Instituto de Ciencia de los Materiales (CSIC), Cantoblanco, 28049 Madrid (Spain)

2011-12-01

Within the framework of cost-effective patterning processes a novel technique that saves photolithographic processing steps, easily scalable to wide area production, is proposed. It consists of a tip-probe, which is biased with respect to a conductive substrate and slides on it, keeping contact with the material. The sliding tip leaves an insulating path (which currently is as narrow as 30 {mu}m) across the material, which enables the drawing of tracks and pads electrically insulated from the surroundings. This ablation method, called arc-erosion, requires an experimental set up that had to be customized for this purpose and is described. Upon instrumental monitoring, a brief proposal of the physics below this process is also presented. As a result an optimal control of the patterning process has been acquired. The system has been used on different substrates, including indium tin oxide either on glass or on polyethylene terephtalate, as well as alloys like Au/Cr, and Al. The influence of conditions such as tip speed and applied voltage is discussed. - Research highlights: Black-Right-Pointing-Pointer An experimental set up has been arranged to use arc erosion as a cost-effective patterning technique of conductive materials (ITO, and thin film metals). Black-Right-Pointing-Pointer Monitoring of the process has revealed that patterning is performed by a sequence of electrical discharges, assisted by the bypass capacitor at the source output. Black-Right-Pointing-Pointer This process has been controlled optimizing the patterning conditions and quality over different materials.

Site-Specific Infrared Probes of Proteins

Science.gov (United States)

Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

2015-01-01

Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

Exploring the resonant vibration of thin plates: Reconstruction of Chladni patterns and determination of resonant wave numbers.

Science.gov (United States)

Tuan, P H; Wen, C P; Chiang, P Y; Yu, Y T; Liang, H C; Huang, K F; Chen, Y F

2015-04-01

The Chladni nodal line patterns and resonant frequencies for a thin plate excited by an electronically controlled mechanical oscillator are experimentally measured. Experimental results reveal that the resonant frequencies can be fairly obtained by means of probing the variation of the effective impedance of the exciter with and without the thin plate. The influence of the extra mass from the central exciter is confirmed to be insignificant in measuring the resonant frequencies of the present system. In the theoretical aspect, the inhomogeneous Helmholtz equation is exploited to derive the response function as a function of the driving wave number for reconstructing experimental Chladni patterns. The resonant wave numbers are theoretically identified with the maximum coupling efficiency as well as the maximum entropy principle. Substituting the theoretical resonant wave numbers into the derived response function, all experimental Chladni patterns can be excellently reconstructed. More importantly, the dispersion relationship for the flexural wave of the vibrating plate can be determined with the experimental resonant frequencies and the theoretical resonant wave numbers. The determined dispersion relationship is confirmed to agree very well with the formula of the Kirchhoff-Love plate theory.

Anomalous diffusion of a probe in a bath of active granular chains

Science.gov (United States)

Jerez, Michael Jade Y.; Confesor, Mark Nolan P.; Carpio-Bernido, M. Victoria; Bernido, Christopher C.

2017-08-01

We investigate the dynamics of a passive probe particle in a bath of active granular chains (AGC). The bath and the probe are enclosed in an experimental compartment with a sinusoidal boundary to prevent AGC congestion along the boundary while connected to an electrodynamic shaker. Single AGC trajectory analysis reveals a persistent type of motion compared to a purely Brownian motion as seen in its mean squared displacement (MSD). It was found that at small concentration, Φ ≤ 0.44, the MSD exhibits two dynamical regimes characterized by two different scaling exponents. For small time scales, the dynamics is superdiffusive (1.32-1.63) with the MSD scaling exponent increasing monotonically with increasing AGC concentration. On the other hand, at long time, we recover the Brownian dynamics regime, MSD = DΔt, where the mobility D ∝ Φ. We quantify the probe dynamics at short time scale by modeling it as a fractional Brownian motion. The analytical form of the MSD agrees with experimental results.

Preventing probe induced topography correlated artifacts in Kelvin Probe Force Microscopy

NARCIS (Netherlands)

Polak, L.; Wijngaarden, Rinke J.

2016-01-01

Kelvin Probe Force Microscopy (KPFM) on samples with rough surface topography can be hindered by topography correlated artifacts. We show that, with the proper experimental configuration and using homogeneously metal coated probes, we are able to obtain amplitude modulation (AM) KPFM results on a

Revealing the surface pattern of medieval pattern welded iron objects - etching tests conducted on reconstructed composites

Czech Academy of Sciences Publication Activity Database

Thiele, Á.; Hošek, Jiří; Haramza, M.; Török, B.

2014-01-01

Roč. 25, č. 1 (2014), s. 18-24 ISSN 1805-7241 R&D Projects: GA ČR GAP405/12/2289 Institutional support: RVO:67985912 Keywords : etching * pattern welding * phosphoric iron * archaeometallurgy Subject RIV: AC - Archeology, Anthropology, Ethnology

Accuracy of micro four-point probe measurements on inhomogeneous samples: A probe spacing dependence study

DEFF Research Database (Denmark)

Wang, Fei; Petersen, Dirch Hjorth; Østerberg, Frederik Westergaard

2009-01-01

In this paper, we discuss a probe spacing dependence study in order to estimate the accuracy of micro four-point probe measurements on inhomogeneous samples. Based on sensitivity calculations, both sheet resistance and Hall effect measurements are studied for samples (e.g. laser annealed samples...... the probe spacing is smaller than 1/40 of the variation wavelength, micro four-point probes can provide an accurate record of local properties with less than 1% measurement error. All the calculations agree well with previous experimental results.......) with periodic variations of sheet resistance, sheet carrier density, and carrier mobility. With a variation wavelength of ¿, probe spacings from 0.0012 to 1002 have been applied to characterize the local variations. The calculations show that the measurement error is highly dependent on the probe spacing. When...

Graphene quantum dots probed by scanning tunneling microscopy

Energy Technology Data Exchange (ETDEWEB)

Morgenstern, Markus; Freitag, Nils; Nent, Alexander; Nemes-Incze, Peter; Liebmann, Marcus [II. Institute of Physics B and JARA-FIT, RWTH Aachen University, Aachen (Germany)

2017-11-15

Scanning tunneling spectroscopy results probing the electronic properties of graphene quantum dots are reviewed. After a short summary of the study of squared wave functions of graphene quantum dots on metal substrates, we firstly present data where the Landau level gaps caused by a perpendicular magnetic field are used to electrostatically confine electrons in monolayer graphene, which are probed by the Coulomb staircase revealing the consecutive charging of a quantum dot. It turns out that these quantum dots exhibit much more regular charging sequences than lithographically confined ones. Namely, the consistent grouping of charging peaks into quadruplets, both, in the electron and hole branch, portrays a regular orbital splitting of about 10meV. At low hole occupation numbers, the charging peaks are, partly, additionally grouped into doublets. The spatially varying energy separation of the doublets indicates a modulation of the valley splitting by the underlying BN substrate. We outline that this property might be used to eventually tune the valley splitting coherently. Afterwards, we describe graphene quantum dots with multiple contacts produced without lithographic resist, namely by local anodic oxidation. Such quantum dots target the goal to probe magnetotransport properties during the imaging of the corresponding wave functions by scanning tunneling spectroscopy. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Eddy-current probe design

International Nuclear Information System (INIS)

Kincaid, T.G.; McCary, R.O.

1983-01-01

This paper describes theoretical and experimental work directed toward finding the optimum probe dimensions and operating frequency for eddy current detection of half-penny surface cracks in nonmagnetic conducting materials. The study applies to probes which excite an approximately uniform spatial field over the length of the crack at the surface of the material. In practical terms, this means that the probe is not smaller than the crack length in any of its critical dimensions. The optimization of a simple coil probe is first analyzed in detail. It is shown that signal-to-noise ratio and lift-off discrimination are maximized by a pancake coil with mean radius not greater than the crack length, operated at a frequency which gives a skin depth equal to the crack depth. The results obtained for the simple coil are then used as a basis for discussion of the design of coils with ferrite cores and shields, and for the design of recording head type probes

Wearable probes for service design

DEFF Research Database (Denmark)

Mullane, Aaron; Laaksolahti, Jarmo Matti; Svanæs, Dag

2014-01-01

Probes are used as a design method in user-centred design to allow end-users to inform design by collecting data from their lives. Probes are potentially useful in service innovation, but current probing methods require users to interrupt their activity and are consequently not ideal for use...... by service employees in reflecting on the delivery of a service. In this paper, we present the ‘wearable probe’, a probe concept that captures sensor data without distracting service employees. Data captured by the probe can be used by the service employees to reflect and co-reflect on the service journey......, helping to identify opportunities for service evolution and innovation....

Aspheric surface measurement using capacitive probes

Science.gov (United States)

Tao, Xin; Yuan, Daocheng; Li, Shaobo

2017-02-01

With the application of aspheres in optical fields, high precision and high efficiency aspheric surface metrology becomes a hot research topic. We describe a novel method of non-contact measurement of aspheric surface with capacitive probe. Taking an eccentric spherical surface as the object of study, the averaging effect of capacitive probe measurement and the influence of tilting the capacitive probe on the measurement results are investigated. By comparing measurement results from simultaneous measurement of the capacitive probe and contact probe of roundness instrument, this paper indicates the feasibility of using capacitive probes to test aspheric surface and proposes the compensation method of measurement error caused by averaging effect and the tilting of the capacitive probe.

Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates.

Science.gov (United States)

Bouts, Mark J R J; Westmoreland, Susan V; de Crespigny, Alex J; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M; Wu, Ona; D'Arceuil, Helen E

2015-12-15

Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by combining quantitative T2 and diffusion MRI indices into MRI 'tissue signatures', (2) to evaluate temporal differences in these signatures between transient (n = 2) and permanent (n = 2) middle cerebral artery occlusion, and (3) to correlate histopathology findings in the chronic stroke period to the acute and subacute MRI derived tissue signatures. An improved iterative self-organizing data analysis algorithm was used to combine T2, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) maps across seven successive timepoints (1, 2, 3, 24, 72, 144, 240 h) which revealed five temporal MRI signatures, that were different from the normal tissue pattern (P MRI signatures associated with specific tissue fates may further aid in assessing and monitoring the efficacy of novel pharmaceutical treatments for stroke in a pre-clinical and clinical setting.

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope

KAUST Repository

Govyadinov, Alexander A.

2017-07-14

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope.

Science.gov (United States)

Govyadinov, Alexander A; Konečná, Andrea; Chuvilin, Andrey; Vélez, Saül; Dolado, Irene; Nikitin, Alexey Y; Lopatin, Sergei; Casanova, Fèlix; Hueso, Luis E; Aizpurua, Javier; Hillenbrand, Rainer

2017-07-21

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Probing low-energy hyperbolic polaritons in van der Waals crystals with an electron microscope

KAUST Repository

Govyadinov, Alexander A.; Konečná , Andrea; Chuvilin, Andrey; Vé lez, Saü l; Dolado, Irene; Nikitin, Alexey Y.; Lopatin, Sergei; Casanova, Fè lix; Hueso, Luis E.; Aizpurua, Javier; Hillenbrand, Rainer

2017-01-01

Van der Waals materials exhibit intriguing structural, electronic, and photonic properties. Electron energy loss spectroscopy within scanning transmission electron microscopy allows for nanoscale mapping of such properties. However, its detection is typically limited to energy losses in the eV range-too large for probing low-energy excitations such as phonons or mid-infrared plasmons. Here, we adapt a conventional instrument to probe energy loss down to 100 meV, and map phononic states in hexagonal boron nitride, a representative van der Waals material. The boron nitride spectra depend on the flake thickness and on the distance of the electron beam to the flake edges. To explain these observations, we developed a classical response theory that describes the interaction of fast electrons with (anisotropic) van der Waals slabs, revealing that the electron energy loss is dominated by excitation of hyperbolic phonon polaritons, and not of bulk phonons as often reported. Thus, our work is of fundamental importance for interpreting future low-energy loss spectra of van der Waals materials.Here the authors adapt a STEM-EELS system to probe energy loss down to 100 meV, and apply it to map phononic states in hexagonal boron nitride, revealing that the electron loss is dominated by hyperbolic phonon polaritons.

Chromosomal Locations of 5S and 45S rDNA in Gossypium Genus and Its Phylogenetic Implications Revealed by FISH.

Science.gov (United States)

Gan, Yimei; Liu, Fang; Chen, Dan; Wu, Qiong; Qin, Qin; Wang, Chunying; Li, Shaohui; Zhang, Xiangdi; Wang, Yuhong; Wang, Kunbo

2013-01-01

We investigated the locations of 5S and 45S rDNA in Gossypium diploid A, B, D, E, F, G genomes and tetraploid genome (AD) using multi-probe fluorescent in situ hybridization (FISH) for evolution analysis in Gossypium genus. The rDNA numbers and sizes, and synteny relationships between 5S and 45S were revealed using 5S and 45S as double-probe for all species, and the rDNA-bearing chromosomes were identified for A, D and AD genomes with one more probe that is single-chromosome-specific BAC clone from G. hirsutum (A1D1). Two to four 45S and one 5S loci were found in diploid-species except two 5S loci in G. incanum (E4), the same as that in tetraploid species. The 45S on the 7th and 9th chromosomes and the 5S on the 9th chromosomes seemed to be conserved in A, D and AD genomes. In the species of B, E, F and G genomes, the rDNA numbers, sizes, and synteny relationships were first reported in this paper. The rDNA pattern agrees with previously reported phylogenetic history with some disagreements. Combined with the whole-genome sequencing data from G. raimondii (D5) and the conserved cotton karyotype, it is suggested that the expansion, decrease and transposition of rDNA other than chromosome rearrangements might occur during the Gossypium evolution.

Microstructural evolution in tungsten and copper probes under hydrogen irradiation at ISTTOK

International Nuclear Information System (INIS)

Nunes, D.; Mateus, R.; Nogueira, I.D.; Carvalho, P.A.; Correia, J.B.; Shohoji, N.; Gomes, R.B.; Fernandes, H.; Silva, C.; Franco, N.; Alves, E.

2009-01-01

Commercially pure tungsten and copper wires acting as Langmuir probes to estimate edge parameters of ISTTOK plasma have been investigated for long term hydrogen migration. The microstructure of both materials revealed recrystallization and strong grain growth at the most severely exposed regions. A low number of large bubbles was observed at the most severely exposed regions, whereas a high density of small intergranular bubbles was found at more moderately exposed regions. Bubble distribution, lattice parameter, grain size, Young's modulus and microhardness were assessed across longitudinal sections of the probes. The results indicate that bubble formation in tungsten and copper first wall components can be expected to occur and strategies for minimization of this retention phenomenon need to be implemented.

Cantilevered probe detector with piezoelectric element

Science.gov (United States)

Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

2013-04-30

A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

The time domain triple probe method

International Nuclear Information System (INIS)

Meier, M.A.; Hallock, G.A.; Tsui, H.Y.W.; Bengtson, R.D.

1994-01-01

A new Langmuir probe technique based on the triple probe method is being developed to provide simultaneous measurement of plasma temperature, potential, and density with the temporal and spatial resolution required to accurately characterize plasma turbulence. When the conventional triple probe method is used in an inhomogeneous plasma, local differences in the plasma measured at each probe introduce significant error in the estimation of turbulence parameters. The Time Domain Triple Probe method (TDTP) uses high speed switching of Langmuir probe potential, rather than spatially separated probes, to gather the triple probe information thus avoiding these errors. Analysis indicates that plasma response times and recent electronics technology meet the requirements to implement the TDTP method. Data reduction techniques of TDTP data are to include linear and higher order correlation analysis to estimate fluctuation induced particle and thermal transport, as well as energy relationships between temperature, density, and potential fluctuations

Transmit-receive eddy current probes

International Nuclear Information System (INIS)

Obrutsky, L.S.; Sullivan, S.P.; Cecco, V.S.

1997-01-01

In the last two decades, due to increased inspection demands, eddy current instrumentation has advanced from single-frequency, single-output instruments to multifrequency, computer-aided systems. This has significantly increased the scope of eddy current testing, but, unfortunately, it has also increased the cost and complexity of inspections. In addition, this approach has not always improved defect detectability or signal-to-noise. Most eddy current testing applications are still performed with impedance probes, which have well known limitations. However, recent research at AECL has led to improved eddy current inspections through the design and development of transmit-receive (T/R) probes. T/R eddy current probes, with laterally displaced transmit and receive coils, present a number of advantages over impedance probes. They have improved signal-to-noise ratio in the presence of variable lift-off compared to impedance probes. They have strong directional properties, permitting probe optimization for circumferential or axial crack detection, and possess good phase discrimination to surface defects. They can significantly increase the scope of eddy current testing permitting reliable detection and sizing of cracks in heat exchanger tubing as well as in welded areas of both ferritic and non-ferromagnetic components. This presentation will describe the operating principles of T/R probes with the help of computer-derived normalized voltage diagrams. We will discuss their directional properties and analyze the advantages of using single and multiple T/R probes over impedance probes for specific inspection cases. Current applications to surface and tube testing and some typical inspection results will be described. (author)

Water cooled static pressure probe

Science.gov (United States)

Lagen, Nicholas T. (Inventor); Eves, John W. (Inventor); Reece, Garland D. (Inventor); Geissinger, Steve L. (Inventor)

1991-01-01

An improved static pressure probe containing a water cooling mechanism is disclosed. This probe has a hollow interior containing a central coolant tube and multiple individual pressure measurement tubes connected to holes placed on the exterior. Coolant from the central tube symmetrically immerses the interior of the probe, allowing it to sustain high temperature (in the region of 2500 F) supersonic jet flow indefinitely, while still recording accurate pressure data. The coolant exits the probe body by way of a reservoir attached to the aft of the probe. The pressure measurement tubes are joined to a single, larger manifold in the reservoir. This manifold is attached to a pressure transducer that records the average static pressure.

Using a short-pulse diffraction-limited laser beam to probe filamentation of a random phase plate smoothed beam

International Nuclear Information System (INIS)

Kline, J. L.; Montgomery, D. S.; Flippo, K. A.; Johnson, R. P.; Rose, H. A.; Shimada, T.; Williams, E. A.

2008-01-01

A short pulse (few picoseconds) laser probe provides high temporal resolution measurements to elucidate details of fast dynamic phenomena not observable with typical longer laser pulse probes and gated diagnostics. Such a short pulse laser probe (SPLP) has been used to measure filamentation of a random phase plate (RPP) smoothed laser beam in a gas-jet plasma. The plasma index of refraction due to driven density and temperature fluctuations by the RPP beam perturbs the phase front of a SPLP propagating at a 90 deg. angle with respect to the RPP interaction beam. The density and temperature fluctuations are quasistatic on the time scale of the SPLP (∼2 ps). The transmitted near-field intensity distribution from the SPLP provides a measure of the phase front perturbation. At low plasma densities, the transmitted intensity pattern is asymmetric with striations across the entire probe beam in the direction of the RPP smoothed beam. As the plasma density increases, the striations break up into smaller sizes along the direction of the RPP beam propagation. The breakup of the intensity pattern is consistent with self-focusing of the RPP smoothed interaction beam. Simulations of the experiment using the wave propagation code, PF3D, are in qualitative agreement demonstrating that the asymmetric striations can be attributed to the RPP driven density fluctuations. Quantification of the beam breakup measured by the transmitted SPLP could lead to a new method for measuring self-focusing of lasers in underdense plasmas.

Using a short-pulse diffraction-limited laser beam to probe filamentation of a random phase plate smoothed beam.

Science.gov (United States)

Kline, J L; Montgomery, D S; Flippo, K A; Johnson, R P; Rose, H A; Shimada, T; Williams, E A

2008-10-01

A short pulse (few picoseconds) laser probe provides high temporal resolution measurements to elucidate details of fast dynamic phenomena not observable with typical longer laser pulse probes and gated diagnostics. Such a short pulse laser probe (SPLP) has been used to measure filamentation of a random phase plate (RPP) smoothed laser beam in a gas-jet plasma. The plasma index of refraction due to driven density and temperature fluctuations by the RPP beam perturbs the phase front of a SPLP propagating at a 90 degree angle with respect to the RPP interaction beam. The density and temperature fluctuations are quasistatic on the time scale of the SPLP (approximately 2 ps). The transmitted near-field intensity distribution from the SPLP provides a measure of the phase front perturbation. At low plasma densities, the transmitted intensity pattern is asymmetric with striations across the entire probe beam in the direction of the RPP smoothed beam. As the plasma density increases, the striations break up into smaller sizes along the direction of the RPP beam propagation. The breakup of the intensity pattern is consistent with self-focusing of the RPP smoothed interaction beam. Simulations of the experiment using the wave propagation code, PF3D, are in qualitative agreement demonstrating that the asymmetric striations can be attributed to the RPP driven density fluctuations. Quantification of the beam breakup measured by the transmitted SPLP could lead to a new method for measuring self-focusing of lasers in underdense plasmas.

Characterization of Antimicrobial Resistance Patterns and Detection of Virulence Genes in Campylobacter Isolates in Italy

Science.gov (United States)

Di Giannatale, Elisabetta; Di Serafino, Gabriella; Zilli, Katiuscia; Alessiani, Alessandra; Sacchini, Lorena; Garofolo, Giuliano; Aprea, Giuseppe; Marotta, Francesca

2014-01-01

Campylobacter has developed resistance to several antimicrobial agents over the years, including macrolides, quinolones and fluoroquinolones, becoming a significant public health hazard. A total of 145 strains derived from raw milk, chicken faeces, chicken carcasses, cattle faeces and human faeces collected from various Italian regions, were screened for antimicrobial susceptibility, molecular characterization (SmaI pulsed-field gel electrophoresis) and detection of virulence genes (sequencing and DNA microarray analysis). The prevalence of C. jejuni and C. coli was 62.75% and 37.24% respectively. Antimicrobial susceptibility revealed a high level of resistance for ciprofloxacin (62.76%), tetracycline (55.86%) and nalidixic acid (55.17%). Genotyping of Campylobacter isolates using PFGE revealed a total of 86 unique SmaI patterns. Virulence gene profiles were determined using a new microbial diagnostic microarray composed of 70-mer oligonucleotide probes targeting genes implicated in Campylobacter pathogenicity. Correspondence between PFGE and microarray clusters was observed. Comparisons of PFGE and virulence profiles reflected the high genetic diversity of the strains examined, leading us to speculate different degrees of pathogenicity inside Campylobacter populations. PMID:24556669

Replicability of time-varying connectivity patterns in large resting state fMRI samples.

Science.gov (United States)

Abrol, Anees; Damaraju, Eswar; Miller, Robyn L; Stephen, Julia M; Claus, Eric D; Mayer, Andrew R; Calhoun, Vince D

2017-12-01

The past few years have seen an emergence of approaches that leverage temporal changes in whole-brain patterns of functional connectivity (the chronnectome). In this chronnectome study, we investigate the replicability of the human brain's inter-regional coupling dynamics during rest by evaluating two different dynamic functional network connectivity (dFNC) analysis frameworks using 7 500 functional magnetic resonance imaging (fMRI) datasets. To quantify the extent to which the emergent functional connectivity (FC) patterns are reproducible, we characterize the temporal dynamics by deriving several summary measures across multiple large, independent age-matched samples. Reproducibility was demonstrated through the existence of basic connectivity patterns (FC states) amidst an ensemble of inter-regional connections. Furthermore, application of the methods to conservatively configured (statistically stationary, linear and Gaussian) surrogate datasets revealed that some of the studied state summary measures were indeed statistically significant and also suggested that this class of null model did not explain the fMRI data fully. This extensive testing of reproducibility of similarity statistics also suggests that the estimated FC states are robust against variation in data quality, analysis, grouping, and decomposition methods. We conclude that future investigations probing the functional and neurophysiological relevance of time-varying connectivity assume critical importance. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The AMEMIYA probe. Theoretical background

International Nuclear Information System (INIS)

Belitz, Hans Joahim; Althausen, Bernhard; Uehara, Kazuya; Amemiya, Hiroshi

2010-01-01

The present probe was developed in order to measure the temperature T i of positive ions in the scrape-off layer (SOL) of tokamak where T i is usually larger than the electron temperature Ti so that the presheath in front of the probe need not be considered and the ions reach the probe with the thermal velocity. The axis of the cylindrical probe is placed parallel to the magnetic field. The important parameter are L/a, the ratio of the length to the radius of the cylindrical probe and κ, the ratio of the probe radius to (π/4) 1/2 , where is the mean ion Larmor radius. The ion current densities to the side and the end surfaces are expressed by the double integral, which can give an analytical formula with respect to the value of κ. If two electrodes with different lengths are placed parallel to the magnetic field, the difference of current densities can be reduced to κ and hence to Ti. Some examples of the application of the probe to tokamaks, JFT-2M and Textor, are demonstrated. (author)

Computer modelling of eddy current probes

International Nuclear Information System (INIS)

Sullivan, S.P.

1992-01-01

Computer programs have been developed for modelling impedance and transmit-receive eddy current probes in two-dimensional axis-symmetric configurations. These programs, which are based on analytic equations, simulate bobbin probes in infinitely long tubes and surface probes on plates. They calculate probe signal due to uniform variations in conductor thickness, resistivity and permeability. These signals depend on probe design and frequency. A finite element numerical program has been procured to calculate magnetic permeability in non-linear ferromagnetic materials. Permeability values from these calculations can be incorporated into the above analytic programs to predict signals from eddy current probes with permanent magnets in ferromagnetic tubes. These programs were used to test various probe designs for new testing applications. Measurements of magnetic permeability in magnetically biased ferromagnetic materials have been performed by superimposing experimental signals, from special laboratory ET probes, on impedance plane diagrams calculated using these programs. (author). 3 refs., 2 figs

Selective imaging of cancer cells with a pH-activatable lysosome-targeting fluorescent probe.

Science.gov (United States)

Shi, Rongguang; Huang, Lu; Duan, Xiaoxue; Sun, Guohao; Yin, Gui; Wang, Ruiyong; Zhu, Jun-Jie

2017-10-02

Fluorescence imaging with tumor-specific fluorescent probe has emerged as a tool to aid surgeons in the identification and removal of tumor tissue. We report here a new lysosome-targeting fluorescent probe (NBOH) with BODIPY fluorephore to distinguish tumor tissue out of normal tissue based on different pH environment. The probe exhibited remarkable pH-dependent fluorescence behavior in a wide pH range from 3.0 to 11.0, especially a sensitive pH-dependent fluorescence change at pH range between 3.5 and 5.5, corresponding well to the acidic microenvironment of tumor cells, in aqueous solution. The response time of NBOH was extremely short and the photostability was proved to be good. Toxicity test and fluorescence cell imaging together with a sub-cellular localization study were carried out revealing its low biotoxicity and good cell membrane permeability. And NBOH was successfully applied to the imaging of tumor tissue in tumor-bearing mice suggesting potential application to surgery as a tumor-specific probe. Copyright © 2017 Elsevier B.V. All rights reserved.

An interchangeable scanning Hall probe/scanning SQUID microscope

Energy Technology Data Exchange (ETDEWEB)

Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Chen, Tse-Jun; Wang, M. J. [Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 10617, Taiwan (China); Ling, D. C. [Department of Physics, Tamkang University, Tamsui Dist., New Taipei City 25137, Taiwan (China); Chi, C. C.; Chen, Jeng-Chung [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

2014-08-15

We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (⩽4 μm), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10{sup −7} T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La{sub 2/3}Ca{sub 1/3}MnO{sub 3} thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K.

Methodology for Calculating Latency of GPS Probe Data

Energy Technology Data Exchange (ETDEWEB)

Young, Stanley E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Wang, Zhongxiang [University of Maryland; Hamedi, Masoud [University of Maryland

2017-10-01

Crowdsourced GPS probe data, such as travel time on changeable-message signs and incident detection, have been gaining popularity in recent years as a source for real-time traffic information to driver operations and transportation systems management and operations. Efforts have been made to evaluate the quality of such data from different perspectives. Although such crowdsourced data are already in widespread use in many states, particularly the high traffic areas on the Eastern seaboard, concerns about latency - the time between traffic being perturbed as a result of an incident and reflection of the disturbance in the outsourced data feed - have escalated in importance. Latency is critical for the accuracy of real-time operations, emergency response, and traveler information systems. This paper offers a methodology for measuring probe data latency regarding a selected reference source. Although Bluetooth reidentification data are used as the reference source, the methodology can be applied to any other ground truth data source of choice. The core of the methodology is an algorithm for maximum pattern matching that works with three fitness objectives. To test the methodology, sample field reference data were collected on multiple freeway segments for a 2-week period by using portable Bluetooth sensors as ground truth. Equivalent GPS probe data were obtained from a private vendor, and their latency was evaluated. Latency at different times of the day, impact of road segmentation scheme on latency, and sensitivity of the latency to both speed-slowdown and recovery-from-slowdown episodes are also discussed.

Contamination-free sounding rocket Langmuir probe

Science.gov (United States)

Amatucci, W. E.; Schuck, P. W.; Walker, D. N.; Kintner, P. M.; Powell, S.; Holback, B.; Leonhardt, D.

2001-04-01

A technique for removing surface contaminants from a sounding rocket spherical Langmuir probe is presented. Contamination layers present on probe surfaces can skew the collected data, resulting in the incorrect determination of plasma parameters. Despite following the usual probe cleaning techniques that are used prior to a launch, the probe surface can become coated with layers of adsorbed neutral gas in less than a second when exposed to atmosphere. The laboratory tests reported here show that by heating the probe from the interior using a small halogen lamp, adsorbed neutral particles can be removed from the probe surface, allowing accurate plasma parameter measurements to be made.

Growth patterns of an intertidal gastropod as revealed by oxygen isotope analysis

Science.gov (United States)

Bean, J. R.; Hill, T. M.; Guerra, C.

2007-12-01

The size and morphology of mollusk shells are affected by environmental conditions. As a result, it is difficult to assess growth rate, population age structure, shell morphologies associated with ontogenetic stages, and to compare life history patterns across various environments. Oxygen isotope analysis is a useful tool for estimating minimum ages and growth rates of calcium carbonate secreting organisms. Calcite shell material from members of two northern California populations of the intertidal muricid gastropod Acanthinucella spirata was sampled for isotopic analysis. Individual shells were sampled from apex to margin, thus providing a sequential record of juvenile and adult growth. A. spirata were collected from a sheltered habitat in Tomales Bay and from an exposed reef in Bolinas. Abiotic factors, such as temperature, wave exposure, and substrate consistency, and biotic composition differ significantly between these sites, possibly resulting in local adaptations and variation in life history and growth patterns. Shell morphology of A. spirata changes with age as internal shell margin thickenings of denticle rows associated with external growth bands are irregularly accreted. It is not known when, either seasonally and/or ontogentically, these thickenings and bands form or whether inter or intra-populational variation exists. Preliminary results demonstrate the seasonal oxygen isotopic variability present at the two coastal sites, indicating 5-6 degC changes from winter to summertime temperatures; these data are consistent with local intertidal temperature records. Analysis of the seasonal patterns indicate that: 1) differences in growth rate and seasonal growth patterns at different ontogenetic stages within populations, and 2) differences in growth patterns and possibly age structure between the two A. spirata populations. These findings indicate that isotopic analyses, in addition to field observations and morphological measurements, are necessary to

Dynamic pressure probe response tests for robust measurements in periodic flows close to probe resonating frequency

Science.gov (United States)

Ceyhun Şahin, Fatma; Schiffmann, Jürg

2018-02-01

A single-hole probe was designed to measure steady and periodic flows with high fluctuation amplitudes and with minimal flow intrusion. Because of its high aspect ratio, estimations showed that the probe resonates at a frequency two orders of magnitude lower than the fast response sensor cut-off frequencies. The high fluctuation amplitudes cause a non-linear behavior of the probe and available models are neither adequate for a quantitative estimation of the resonating frequencies nor for predicting the system damping. Instead, a non-linear data correction procedure based on individual transfer functions defined for each harmonic contribution is introduced for pneumatic probes that allows to extend their operating range beyond the resonating frequencies and linear dynamics. This data correction procedure was assessed on a miniature single-hole probe of 0.35 mm inner diameter which was designed to measure flow speed and direction. For the reliable use of such a probe in periodic flows, its frequency response was reproduced with a siren disk, which allows exciting the probe up to 10 kHz with peak-to-peak amplitudes ranging between 20%-170% of the absolute mean pressure. The effect of the probe interior design on the phase lag and amplitude distortion in periodic flow measurements was investigated on probes with similar inner diameters and different lengths or similar aspect ratios (L/D) and different total interior volumes. The results suggest that while the tube length consistently sets the resonance frequency, the internal total volume affects the non-linear dynamic response in terms of varying gain functions. A detailed analysis of the introduced calibration methodology shows that the goodness of the reconstructed data compared to the reference data is above 75% for fundamental frequencies up to twice the probe resonance frequency. The results clearly suggest that the introduced procedure is adequate to capture non-linear pneumatic probe dynamics and to

Friction behavior of nano-textured polyimide surfaces measured by AFM colloidal probe

Energy Technology Data Exchange (ETDEWEB)

Zhang, Xiaoliang [College of Equipment Manufacturing, Hebei University of Engineering, Handan 056038 (China); State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Wu, Chunxia; Che, Hongwei; Hou, Junxian [College of Equipment Manufacturing, Hebei University of Engineering, Handan 056038 (China); Jia, Junhong, E-mail: jhjia@licp.cas.cn [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

2014-11-30

Highlights: • Flat PI film and nano-textured PI film were prepared by spin-coating process. • The nano-textured PI surface has effectively reduced the adhesion and friction. • Friction increased with the increasing of contact area and adhesion. • The growth rate of friction decreased with the increasing of applied load. - Abstract: Flat polyimide (PI) film and silicon dioxide nanoparticle-textured PI film were prepared by means of the spin-coating technique. The adhesion and friction properties of the flat PI surface and nano-textured PI surface were investigated by a series of Atomic force microscope (AFM) colloidal probes. Experimental results revealed that the nano-textured PI surface can significantly reduce the adhesive force and friction force, compared with the flat PI surface. The main reason is that the nano-textures can reduce the contact area between the sample surface and colloidal probe. The effect of colloidal probe size on the friction behavior of the flat and nano-textured PI surfaces was evaluated. The adhesive force and friction force of nano-textured PI surface were increased with the increasing of the size of interacting pairs (AFM colloidal probe) due to the increased contact area. Moreover, the friction forces of flat and nano-textured PI surfaces were increased with applied load and sliding velocity.

Use of a repetitive DNA probe to type clinical and environmental isolates of Aspergillus flavus from a cluster of cutaneous infections in a neonatal intensive care unit.

Science.gov (United States)

James, M J; Lasker, B A; McNeil, M M; Shelton, M; Warnock, D W; Reiss, E

2000-10-01

Aspergillus flavus is second to A. fumigatus as a cause of invasive aspergillosis, but no standard method exists for molecular typing of strains from human sources. A repetitive DNA sequence cloned from A. flavus and subcloned into a pUC19 vector, pAF28, was used to type 18 isolates from diverse clinical, environmental, and geographic sources. The restriction fragment length polymorphisms generated with EcoRI- or PstI-digested genomic DNA and probed with digoxigenin-labeled pAF28 revealed complete concordance between patterns. Eighteen distinct fingerprints were observed. The probe was used to investigate two cases of cutaneous A. flavus infection in low-birth-weight infants in a neonatal intensive care unit (NICU). Both infants were transported by the same ambulance and crew to the NICU on the same day. A. flavus strains of the same genotype were isolated from both infants, from a roll of tape used to fasten their umbilical catheters, from a canvas bag used to store the tape in the ambulance, and from the tape tray in the ambulance isolette. These cases highlight the need to consider exposures in critically ill neonates that might occur during their transport to the NICU and for stringent infection control practices. The hybridization profiles of strains from a second cluster of invasive A. flavus infections in two pediatric hematology-oncology patients revealed a genotype common to strains from a definite case patient and a health care worker. A probable case patient was infected with a strain with a genotype different from that of the strain from the definite case patient but highly related to that of an environmental isolate. The high degree of discrimination and reproducibility obtained with the pAF28 probe underscores its utility for typing clinical and environmental isolates of A. flavus.

Probe microanalysis of aragonitic structures in marine organisms as a means of measuring population structure and mobility

International Nuclear Information System (INIS)

Thresher, R.E.; Sie, S.H.

1991-01-01

Experiments began in 1987 with a view to using ontogenetic variation in the chemical composition of fish otoliths ('ear bones' - the first calcified tissue to develop in embryonic fishes) as an indicator of movement/migration patterns. Acquiring such data dictated the use of a probe microanalyzer, which could be scanned along the growth axis of an otolith and provide discrete information on otolith composition at different stages in the life of the animal. The suitability of electron and proton probe analyzers is examined and the optimal operating parameters determined for both, when dealing with biogenic aragonite matrices. 1 refs

An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens

Science.gov (United States)

Chater, Caspar C.; Kamisugi, Yasuko

2016-01-01

The patterning of stomata plays a vital role in plant development and has emerged as a paradigm for the role of peptide signals in the spatial control of cellular differentiation. Research in Arabidopsis has identified a series of epidermal patterning factors (EPFs), which interact with an array of membrane-localised receptors and associated proteins (encoded by ERECTA and TMM genes) to control stomatal density and distribution. However, although it is well-established that stomata arose very early in the evolution of land plants, until now it has been unclear whether the established angiosperm stomatal patterning system represented by the EPF/TMM/ERECTA module reflects a conserved, universal mechanism in the plant kingdom. Here, we use molecular genetics to show that the moss Physcomitrella patens has conserved homologues of angiosperm EPF, TMM and at least one ERECTA gene that function together to permit the correct patterning of stomata and that, moreover, elements of the module retain function when transferred to Arabidopsis. Our data characterise the stomatal patterning system in an evolutionarily distinct branch of plants and support the hypothesis that the EPF/TMM/ERECTA module represents an ancient patterning system. PMID:27407102

Multi-point probe for testing electrical properties and a method of producing a multi-point probe

DEFF Research Database (Denmark)

2011-01-01

A multi-point probe for testing electrical properties of a number of specific locations of a test sample comprises a supporting body defining a first surface, a first multitude of conductive probe arms (101-101'''), each of the probe arms defining a proximal end and a distal end. The probe arms...... of contact with the supporting body, and a maximum thickness perpendicular to its perpendicular bisector and its line of contact with the supporting body. Each of the probe arms has a specific area or point of contact (111-111''') at its distal end for contacting a specific location among the number...... of specific locations of the test sample. At least one of the probe arms has an extension defining a pointing distal end providing its specific area or point of contact located offset relative to its perpendicular bisector....

NIR detection of honey adulteration reveals differences in water spectral pattern.

Science.gov (United States)

Bázár, György; Romvári, Róbert; Szabó, András; Somogyi, Tamás; Éles, Viktória; Tsenkova, Roumiana

2016-03-01

High fructose corn syrup (HFCS) was mixed with four artisanal Robinia honeys at various ratios (0-40%) and near infrared (NIR) spectra were recorded with a fiber optic immersion probe. Levels of HFCS adulteration could be detected accurately using leave-one-honey-out cross-validation (RMSECV=1.48; R(2)CV=0.987), partial least squares regression and the 1300-1800nm spectral interval containing absorption bands related to both water and carbohydrates. Aquaphotomics-based evaluations showed that unifloral honeys contained more highly organized water than the industrial sugar syrup, supposedly because of the greater variety of molecules dissolved in the multi-component honeys. Adulteration with HFCS caused a gradual reduction of water molecular structures, especially water trimers, which facilitate interaction with other molecules. Quick, non-destructive NIR spectroscopy combined with aquaphotomics could be used to describe water molecular structures in honey and to detect a rather common form of adulteration. Copyright © 2015 Elsevier Ltd. All rights reserved.

CHARACTERIZATION OF THE ELECTROPHYSICAL PROPERTIES OF SILICON-SILICON DIOXIDE INTERFACE USING PROBE ELECTROMETRY METHODS

Directory of Open Access Journals (Sweden)

V. А. Pilipenko

2017-01-01

Full Text Available Introduction of submicron design standards into microelectronic industry and a decrease of the gate dielectric thickness raise the importance of the analysis of microinhomogeneities in the silicon-silicon dioxide system. However, there is very little to no information on practical implementation of probe electrometry methods, and particularly scanning Kelvin probe method, in the interoperational control of real semiconductor manufacturing process. The purpose of the study was the development of methods for nondestructive testing of semiconductor wafers based on the determination of electrophysical properties of the silicon-silicon dioxide interface and their spatial distribution over wafer’s surface using non-contact probe electrometry methods.Traditional C-V curve analysis and scanning Kelvin probe method were used to characterize silicon- silicon dioxide interface. The samples under testing were silicon wafers of KEF 4.5 and KDB 12 type (orientation <100>, diameter 100 mm.Probe electrometry results revealed uniform spatial distribution of wafer’s surface potential after its preliminary rapid thermal treatment. Silicon-silicon dioxide electric potential values were also higher after treatment than before it. This potential growth correlates with the drop in interface charge density. At the same time local changes in surface potential indicate changes in surface layer structure.Probe electrometry results qualitatively reflect changes of interface charge density in silicon-silicon dioxide structure during its technological treatment. Inhomogeneities of surface potential distribution reflect inhomogeneity of damaged layer thickness and can be used as a means for localization of interface treatment defects.

Structural Probing of Off-Target G Protein-Coupled Receptor Activities within a Series of Adenosine/Adenine Congeners

Science.gov (United States)

Paoletta, Silvia; Tosh, Dilip K.; Salvemini, Daniela; Jacobson, Kenneth A.

2014-01-01

We studied patterns of off-target receptor interactions, mostly at G protein-coupled receptors (GPCRs) in the µM range, of nucleoside derivatives that are highly engineered for nM interaction with adenosine receptors (ARs). Because of the considerable interest of using AR ligands for treating diseases of the CNS, we used the Psychoactive Drug Screening Program (PDSP) for probing promiscuity of these adenosine/adenine congeners at 41 diverse receptors, channels and a transporter. The step-wise truncation of rigidified, trisubstituted (at N6, C2, and 5′ positions) nucleosides revealed unanticipated interactions mainly with biogenic amine receptors, such as adrenergic receptors and serotonergic receptors, with affinities as high as 61 nM. The unmasking of consistent sets of structure activity relationship (SAR) at novel sites suggested similarities between receptor families in molecular recognition. Extensive molecular modeling of the GPCRs affected suggested binding modes of the ligands that supported the patterns of SAR at individual receptors. In some cases, the ligand docking mode closely resembled AR binding and in other cases the ligand assumed different orientations. The recognition patterns for different GPCRs were clustered according to which substituent groups were tolerated and explained in light of the complementarity with the receptor binding site. Thus, some likely off-target interactions, a concern for secondary drug effects, can be predicted for analogues of this set of substructures, aiding the design of additional structural analogues that either eliminate or accentuate certain off-target activities. Moreover, similar analyses could be performed for unrelated structural families for other GPCRs. PMID:24859150

Human MLPA Probe Design (H-MAPD: a probe design tool for both electrophoresis-based and bead-coupled human multiplex ligation-dependent probe amplification assays

Directory of Open Access Journals (Sweden)

Hatchwell Eli

2008-09-01

Full Text Available Abstract Background Multiplex ligation-dependent probe amplification (MLPA is an efficient and reliable technique for gene dosage analysis. Currently MLPA can be conducted on two platforms: traditional electrophoresis-based, and FlexMAP bead-coupled. Since its introduction in 2002, MLPA has been rapidly adopted in both clinical and research situations. However, MLPA probe design is a time consuming process requiring many steps that address multiple criteria. There exist only one or two commercial software packages for traditional electrophoresis-based MLPA probe design. To our knowledge, no software is yet available that performs bead-coupled MLPA probe design. Results We have developed H-MAPD, a web-based tool that automates the generation and selection of probes for human genomic MLPA. The software performs physical-chemical property tests using UNAFold software, and uniqueness tests using the UCSC genome browser. H-MAPD supports both traditional electrophoresis-based assays, as well as FlexMAP bead-coupled MLPA. Conclusion H-MAPD greatly reduces the efforts for human genomic MLPA probe design. The software is written in Perl-CGI, hosted on a Linux server, and is freely available to non-commercial users.

Mobile Probes in Mobile Learning

DEFF Research Database (Denmark)

Ørngreen, Rikke; Blomhøj, Ulla; Duvaa, Uffe

In this paper experiences from using mobile probes in educational design of a mobile learning application is presented. The probing process stems from the cultural probe method, and was influenced by qualitative interview and inquiry approaches. In the project, the mobile phone was not only acting...... as an agent for acquiring empirical data (as the situation in hitherto mobile probe settings) but was also the technological medium for which data should say something about (mobile learning). Consequently, not only the content of the data but also the ways in which data was delivered and handled, provided...... a valuable dimension for investigating mobile use. The data was collected at the same time as design activities took place and the collective data was analysed based on user experience goals and cognitive processes from interaction design and mobile learning. The mobile probe increased the knowledge base...

Neutron-based portable drug probe

International Nuclear Information System (INIS)

Womble, P. C.; Vourvopoulos, G.; Ball Howard, J.; Paschal, J.

1999-01-01

Based on previous measurements, a probe prototype for contraband detection utilizing the neutron technique of Pulsed Fast-Thermal Neutron Analysis (PFTNA) is being constructed. The prototype weighs less than 45 kg and is composed of a probe (5 cm diameter), a power pack and a data acquisition and display system. The probe is designed to be inserted in confined spaces such as the boiler of a ship or a tanker truck filled with liquid. The probe provides information on a) the elemental content, and b) the density variations of the interrogated object. By measuring elemental content, the probe can differentiate between innocuous materials and drugs. Density variations can be found through fast neutron transmission. In all cases, hidden drugs are identified through the measurement of the elemental content of the object, and the comparison of expected and measured elemental ratios

Adjustable Pitot Probe

Science.gov (United States)

Ashby, George C., Jr.; Robbins, W. Eugene; Horsley, Lewis A.

1991-01-01

Probe readily positionable in core of uniform flow in hypersonic wind tunnel. Formed of pair of mating cylindrical housings: transducer housing and pitot-tube housing. Pitot tube supported by adjustable wedge fairing attached to top of pitot-tube housing with semicircular foot. Probe adjusted both radially and circumferentially. In addition, pressure-sensing transducer cooled internally by water or other cooling fluid passing through annulus of cooling system.

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

Science.gov (United States)

Mayali, Xavier; Weber, Peter K

2018-05-01

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

Positron annihilation probing for the hydratation rate of cement paste

International Nuclear Information System (INIS)

Myllylae, R.; Karras, M.

1975-01-01

Positron annihilation has been found to be a possible probe for the exponential hydratation of cement paste. Both lifetime and Doppler line broadening measurements revealed the hydratation rate. With the aid of increased stability in the lifetime spectrometer it has been possible to extend the measuring sensitivity over a period of several weeks. Two main lifetimes, tau 1 = 480 +- 20 psec and tau 2 = 2.1 +- 0.1 nsec, were observed to be constant during the hydratation. The intensity of the 2.1 nsec component changed from 4 to 8% after 47 days, and simultaneously the annihilation line narrowed from 2.6 to 2.4 keV. This behaviour has been interpreted as an increase in positronium formation. The possible practical applications of positron annihilation radiation as a hydratation probe has been evaluated for use in a concrete laboratory and even for regular construction work. (orig.) [de

The Antartic Ice Borehole Probe

Science.gov (United States)

Behar, A.; Carsey, F.; Lane, A.; Engelhardt, H.

2000-01-01

The Antartic Ice Borehole Probe mission is a glaciological investigation, scheduled for November 2000-2001, that will place a probe in a hot-water drilled hole in the West Antartic ice sheet. The objectives of the probe are to observe ice-bed interactions with a downward looking camera, and ice inclusions and structure, including hypothesized ice accretion, with a side-looking camera.

Can a Soft Robotic Probe Use Stiffness Control Like a Human Finger to Improve Efficacy of Haptic Perception?

Science.gov (United States)

Sornkarn, Nantachai; Nanayakkara, Thrishantha

2017-01-01

When humans are asked to palpate a soft tissue to locate a hard nodule, they regulate the stiffness, speed, and force of the finger during examination. If we understand the relationship between these behavioral variables and haptic information gain (transfer entropy) during manual probing, we can improve the efficacy of soft robotic probes for soft tissue palpation, such as in tumor localization in minimally invasive surgery. Here, we recorded the muscle co-contraction activity of the finger using EMG sensors to address the question as to whether joint stiffness control during manual palpation plays an important role in the haptic information gain. To address this question, we used a soft robotic probe with a controllable stiffness joint and a force sensor mounted at the base to represent the function of the tendon in a biological finger. Then, we trained a Markov chain using muscle co-contraction patterns of human subjects, and used it to control the stiffness of the soft robotic probe in the same soft tissue palpation task. The soft robotic experiments showed that haptic information gain about the depth of the hard nodule can be maximized by varying the internal stiffness of the soft probe.

Detecting order and lateral pressure at biomimetic interfaces using a mechanosensitive second-harmonic-generation probe.

Science.gov (United States)

Licari, Giuseppe; Beckwith, Joseph S; Soleimanpour, Saeideh; Matile, Stefan; Vauthey, Eric

2018-04-04

A planarizable push-pull molecular probe with mechanosensitive properties was investigated at several biomimetic interfaces, consisting of different phospholipid monolayers located between dodecane and an aqueous buffer solution, using the interface-specific surface-second-harmonic-generation (SSHG) technique. Whereas the SSHG spectra recorded at liquid-disordered interfaces were similar to the absorption spectra in bulk solutions, those measured at liquid-ordered phases exhibited a remarkable shift towards lower energies to an extent depending on the surface pressure of the phospholipid monolayer. On the basis of quantum-chemical calculations, this effect was accounted for by the planarization of the mechanosensitive probe. Polarization-resolved SSHG measurements revealed that the average orientation of the probe at the interface is an even more sensitive reporter of lateral pressure and order than the spectral shape. Additionally, time-resolved SSHG measurements pointed to slower dynamics upon intercalation inside the phospholipid monolayer, most likely due to the more constrained environment. This study demonstrates that the concept of mechanosensitive optical probes can be further exploited when combined with a surface-selective nonlinear optical technique.

Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis.

Science.gov (United States)

Hammond, Stephanie; Wagenknecht-Wiesner, Alice; Veatch, Sarah L; Holowka, David; Baird, Barbara

2009-10-01

In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

Generalised power graph compression reveals dominant relationship patterns in complex networks.

Science.gov (United States)

Ahnert, Sebastian E

2014-03-25

We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

Neutrons as a probe

International Nuclear Information System (INIS)

Iizumi, Masashi

1993-01-01

As an introduction to the symposium a brief overview will be given about the features of neutrons as a probe. First it will be pointed out that the utilization of neutrons as a probe for investigating the structural and dynamical properties of condensed matters is a benign gift eventuated from the release of atomic energy initiated by Enrico Fermi exactly half century ago. Features of neutrons as a probe are discussed in accordance with the four basic physical properties of neutrons as an elementary particle; (1) no electric charge (the interaction with matter is nuclear), (2) the mass of neutron is 1 amu, (3) spin is 1/2 and (4) neutrons have magnetic dipole moment. Overview will be given on the uniqueness of neutrons as a probe and on the variety in the way they are used in the wide research area from the pure science to the industrial applications. (author)

Costochondral ossification pattern. Analysis by 3-dimensional CT image

International Nuclear Information System (INIS)

Ma, Hailong; Nakatani, Kimiko

2005-01-01

We reviewed about an ossification pattern of costal cartilage with using three dimensional images made from computed tomography. We analyzed ossification of 16 costal cartilages in each case. We classified ossification pattern into eight groups by its configuration in one hundred cases. The sexual specificity of ossification pattern was revealed, and we can determinate sex in 82%. It was also revealed that ossification grows with increasing age. Finally, the knowledge of costochondral ossification pattern must help in case of reading chest radiographs. (author)

Charge-exchange giant resonances as probes of nuclear structure

International Nuclear Information System (INIS)

Blomgren, J.

2001-09-01

Giant resonances populated in charge-exchange reactions can reveal detailed information about nuclear structure properties, in spite of their apparent featurelessness. The (p,n) and (n,p) reactions - as well as their analog reactions - proceed via the same nuclear matrix element as beta decay. Thereby, they are useful for probing electroweak properties in nuclei, especially for those not accessible to beta decay. The nuclear physics aspects of double beta decay might be investigated in double charge-exchange reactions. detailed nuclear structure information, such as the presence of ground-state correlations, can be revealed via identification of 'first-forbidden' transitions. In addition, astrophysics aspects and halo properties of nuclei have been investigated in charge exchange. Finally, these experiments have questioned our knowledge of the absolute strength of the strong interaction

Probe tests microweld strength

Science.gov (United States)

1965-01-01

Probe is developed to test strength of soldered, brazed or microwelded joints. It consists of a spring which may be adjusted to the desired test pressure by means of a threaded probe head, and an indicator lamp. Device may be used for electronic equipment testing.

Non-inductive current probe

DEFF Research Database (Denmark)

Bak, Christen Kjeldahl

1977-01-01

The current probe described is a low-cost, shunt resistor for monitoring current pulses in e.g., pulsed lasers. Rise time is......The current probe described is a low-cost, shunt resistor for monitoring current pulses in e.g., pulsed lasers. Rise time is...

Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry.

Directory of Open Access Journals (Sweden)

Yukihiro Yoshimura

Full Text Available Black rice (Oryza sativa L. Japonica contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS.

EDITORIAL: Probing the nanoworld Probing the nanoworld

Science.gov (United States)

Miles, Mervyn

2009-10-01

In nanotechnology, it is the unique properties arising from nanometre-scale structures that lead not only to their technological importance but also to a better understanding of the underlying science. Over the last twenty years, material properties at the nanoscale have been dominated by the properties of carbon in the form of the C60 molecule, single- and multi-wall carbon nanotubes, nanodiamonds, and recently graphene. During this period, research published in the journal Nanotechnology has revealed the amazing mechanical properties of such materials as well as their remarkable electronic properties with the promise of new devices. Furthermore, nanoparticles, nanotubes, nanorods, and nanowires from metals and dielectrics have been characterized for their electronic, mechanical, optical, chemical and catalytic properties. Scanning probe microscopy (SPM) has become the main characterization technique and atomic force microscopy (AFM) the most frequently used SPM. Over the past twenty years, SPM techniques that were previously experimental in nature have become routine. At the same time, investigations using AFM continue to yield impressive results that demonstrate the great potential of this powerful imaging tool, particularly in close to physiological conditions. In this special issue a collaboration of researchers in Europe report the use of AFM to provide high-resolution topographical images of individual carbon nanotubes immobilized on various biological membranes, including a nuclear membrane for the first time (Lamprecht C et al 2009 Nanotechnology 20 434001). Other SPM developments such as high-speed AFM appear to be making a transition from specialist laboratories to the mainstream, and perhaps the same may be said for non-contact AFM. Looking to the future, characterisation techniques involving SPM and spectroscopy, such as tip-enhanced Raman spectroscopy, could emerge as everyday methods. In all these advanced techniques, routinely available probes will

NASA SMART Probe: Breast Cancer Application

Science.gov (United States)

Mah, Robert W.; Norvig, Peter (Technical Monitor)

2000-01-01

There is evidence in breast cancer and other malignancies that the physiologic environment within a tumor correlates with clinical outcome. We are developing a unique percutaneous Smart Probe to be used at the time of needle biopsy of the breast. The Smart Probe will simultaneously measure multiple physiologic parameters within a breast tumor. Direct and indirect measurements of tissue oxygen levels, blood flow, pH, and tissue fluid pressure will be analyzed in real-time. These parameters will be interpreted individually and collectively by innovative neural network techniques using advanced intelligent software. The goals are 1) develop a pecutaneous Smart Probe with multiple sensor modalities and applying advanced Information Technologies to provide real time diagnostic information of the tissue at tip of the probe, 2) test the percutaneous Smart Probe in women with benign and malignant breast masses who will be undergoing surgical biopsy, 3) correlate probe sensor data with benign and malignant status of breast masses, 4) determine whether the probe can detect physiologic differences within a breast tumor, and its margins, and in adjacent normal breast tissue, 5) correlate probe sensor data with known prognostic factors for breast caner, including tumor size, tumor grade, axillary lymph node metastases, estrogen receptor and progesterone receptor status.

Detection of Dysplastic Intestinal Adenomas Using a Fluorescent Folate Imaging Probe

Directory of Open Access Journals (Sweden)

Wei-Tsung Chen

2005-01-01

Full Text Available Macrophages have long been recognized as a prominent component of tumors. Activated macrophages overexpress folate receptors and we used this phenomenon to image inflammatory reactions in colon dysplasia using a fluorescent folate probe (FFP. APCΔ468 mice injected with FFP showed fluorescent adenomas (target-to-background ratio, adenoma vs. adjacent normal mucosa, of 2.46 ± 0.41, significantly higher (p < .001 than adenomas in animals injected with a non-folate-containing control probe. Fluorescence-activated cell-sorting analysis revealed a 3-fold higher content of Mac1-positive cells in colonic adenomas compared with normal adjacent mucosa (6.8% vs. 2.2%, and confirmed the source of FFP-positive cells to be primarily an F4/80-positive macrophage subpopulation. Taken together, these results indicate that FFP potentially can be used to image dysplastic intestinal adenomas in vivo.

Probing the recreational home –The cultural probe as a communicative tool for researcher and user

OpenAIRE

Kristav, Per

2005-01-01

How can qualitative, ethnographic and emotional aspects from probe users be mapped at the same time as they get something meaningful in return? The emphasis is here on intellectual rewards during probe work rather than future good designs that in a long term perspective can be beneficial for the probe user. This case study has elaborated the traditional use of cultural probes [1] with a selection of ten families with small children in the Öresund region. The idea was to evoke thoughts abou...

Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes.

Directory of Open Access Journals (Sweden)

Maria Grazia Doro

Full Text Available We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.

Nanometal Skin of Plasmonic Heterostructures for Highly Efficient Near-Field Scattering Probes

Science.gov (United States)

Zito, Gianluigi; Rusciano, Giulia; Vecchione, Antonio; Pesce, Giuseppe; di Girolamo, Rocco; Malafronte, Anna; Sasso, Antonio

2016-08-01

In this work, atomic force microscopy probes are functionalized by virtue of self-assembling monolayers of block copolymer (BCP) micelles loaded either with clusters of silver nanoparticles or bimetallic heterostructures consisting of mixed species of silver and gold nanoparticles. The resulting self-organized patterns allow coating the tips with a sort of nanometal skin made of geometrically confined nanoislands. This approach favors the reproducible engineering and tuning of the plasmonic properties of the resulting structured tip by varying the nanometal loading of the micelles. The newly conceived tips are applied for experiments of tip-enhanced Raman scattering (TERS) spectroscopy and scattering-type scanning near-field optical microscopy (s-SNOM). TERS and s-SNOM probe characterizations on several standard Raman analytes and patterned nanostructures demonstrate excellent enhancement factor with the possibility of fast scanning and spatial resolution <12 nm. In fact, each metal nanoisland consists of a multiscale heterostructure that favors large scattering and near-field amplification. Then, we verify the tips to allow challenging nongap-TER spectroscopy on thick biosamples. Our approach introduces a synergistic chemical functionalization of the tips for versatile inclusion and delivery of plasmonic nanoparticles at the tip apex, which may promote the tuning of the plasmonic properties, a large enhancement, and the possibility of adding new degrees of freedom for tip functionalization.

Dynamics of exciton relaxation in LH2 antenna probed by multipulse nonlinear spectroscopy.

Science.gov (United States)

Novoderezhkin, Vladimir I; Cohen Stuart, Thomas A; van Grondelle, Rienk

2011-04-28

We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump-dump-probe spectroscopy (Th. A. Cohen Stuart, M. Vengris, V. I. Novoderezhkin, R. J. Cogdell, C. N. Hunter, R. van Grondelle, submitted). The theory of pump-dump-probe response is evaluated using the doorway-window approach in combination with the modified Redfield theory. We demonstrate that a simultaneous fit of linear spectra, pump-probe, and pump-dump-probe kinetics can be obtained at a quantitative level using the disordered exciton model, which is essentially the same as used to model the spectral fluctuations in single LH2 complexes (Novoderezhkin, V.; Rutkauskas, D.; van Grondelle, R. Biophys. J. 2006, 90, 2890). The present studies suggest that the observed relaxation rates are strongly dependent on the realization of the disorder. A big spread of the rates (exceeding 3 orders of magnitude) is correlated with the disorder-induced changes in delocalization length and overlap of the exciton wave functions. We conclude that the bulk kinetics reflect a superposition of many pathways corresponding to different physical limits of energy transfer, varying from sub-20 fs relaxation between delocalized and highly spatially overlapping exciton states to >20 ps jumps between states localized at the opposite sides of the ring.

Nanopatterning reconfigurable magnetic landscapes via thermally assisted scanning probe lithography

Science.gov (United States)

Albisetti, E.; Petti, D.; Pancaldi, M.; Madami, M.; Tacchi, S.; Curtis, J.; King, W. P.; Papp, A.; Csaba, G.; Porod, W.; Vavassori, P.; Riedo, E.; Bertacco, R.

2016-06-01

The search for novel tools to control magnetism at the nanoscale is crucial for the development of new paradigms in optics, electronics and spintronics. So far, the fabrication of magnetic nanostructures has been achieved mainly through irreversible structural or chemical modifications. Here, we propose a new concept for creating reconfigurable magnetic nanopatterns by crafting, at the nanoscale, the magnetic anisotropy landscape of a ferromagnetic layer exchange-coupled to an antiferromagnetic layer. By performing localized field cooling with the hot tip of a scanning probe microscope, magnetic structures, with arbitrarily oriented magnetization and tunable unidirectional anisotropy, are reversibly patterned without modifying the film chemistry and topography. This opens unforeseen possibilities for the development of novel metamaterials with finely tuned magnetic properties, such as reconfigurable magneto-plasmonic and magnonic crystals. In this context, we experimentally demonstrate spatially controlled spin wave excitation and propagation in magnetic structures patterned with the proposed method.

Inexpensive Ultrasound Demonstrations as Analogs of Radio Diffraction in the field : Huygens Probe Bistatic experiment on Titan and the Sea Interferometer (Invited)

Science.gov (United States)

Lorenz, R. D.

2013-12-01

The wave nature of electromagnetic radiation can be exploited in a number of astronomical and remote sensing methods, but is often challenging to visualize in the classroom. One approach with conveniently-inexpensive components is to use sound as an analog. Readily-available ultrasonic transducers at 40 kHz can be driven with a 555 oscillator and received intensity detected with an op-amp and visualized with a digital voltmeter, a lightbulb, or even acoustically. The wavelength of 9mm is convenient for tabletop experiments, with a relevant example being Lloyds Mirror, the interference of a direct wave from a source just above a surface with the reflected wave. As a distant receiver moves in angle through this interference pattern, a series of peaks and nulls in recorded intensity can be interpreted as the height of the transmitter and the reflectivity (i.e. with some assumptions, the roughness) of the reflecting surface. This $10 experiment will be demonstrated at the poster. Such an observation was (serendipitously) made in 2005 after the landing of the Huygens probe on the surface of Titan, where the radio signal measured by Cassini as it set on the horizon as seen from the probe underwent sharp dips in strength that were inverted into a precise measurement of the post-impact probe height. A similar technique in reverse was applied a half century earlier in early Australian radio astronomy to measure the position and width of astrophysical sources from a single clifftop antenna. Ultrasound can be convenient to emulate other radio work, exploiting Doppler effects and (for pulsed sources, like those used in rangers for amateur robotics) propagation time rather than diffraction. Some experiments on tracking Frisbees as an analog for measuring planetary winds by tracking descent probes, and on bistatic delay/Doppler scatterometry as in the CYGNSS GPS-based experiment to measure hurricane winds via sea state, will also be discussed. Huygens probe on the surface of

Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

International Nuclear Information System (INIS)

Escalante, Maryana; Maury, Pascale; Bruinink, Christiaan M; Werf, Kees van der; Olsen, John D; Timney, John A; Huskens, Jurriaan; Hunter, C Neil; Subramaniam, Vinod; Otto, Cees

2008-01-01

We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures

Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

Energy Technology Data Exchange (ETDEWEB)

Escalante, Maryana [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Maury, Pascale [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Bruinink, Christiaan M [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Werf, Kees van der [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Olsen, John D [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Timney, John A [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Huskens, Jurriaan [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Hunter, C Neil [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Subramaniam, Vinod [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Otto, Cees [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands)

2008-01-16

We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures.

Application of synthetic DNA probes to the analysis of DNA sequence variants in man

International Nuclear Information System (INIS)

Wallace, R.B.; Petz, L.D.; Yam, P.Y.

1986-01-01

Oligonucleotide probes provide a tool to discriminate between any two alleles on the basis of hybridization. Random sampling of the genome with different oligonucleotide probes should reveal polymorphism in a certain percentage of the cases. In the hope of identifying polymorphic regions more efficiently, we chose to take advantage of the proposed hypermutability of repeated DNA sequences and the specificity of oligonucleotide hybridization. Since, under appropriate conditions, oligonucleotide probes require complete base pairing for hybridization to occur, they will only hybridize to a subset of the members of a repeat family when all members of the family are not identical. The results presented here suggest that oligonucleotide hybridization can be used to extend the genomic sequences that can be tested for the presence of RFLPs. This expands the tools available to human genetics. In addition, the results suggest that repeated DNA sequences are indeed more polymorphic than single-copy sequences. 28 references, 2 figures

Conductivity Probe

Science.gov (United States)

2008-01-01

The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air. The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air. The needles on the probe are 15 millimeters (0.6 inch) long. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

Plasma density measurement with ring-type cutoff probe

International Nuclear Information System (INIS)

Kim, D.W.; You, S.J.; Na, B.K.; Kim, J.H.; Shin, Y.H.; Chang, H.Y.; Oh, W.Y.

2013-01-01

We proposed a cutoff probe with a ring-type detection tip enclosing a bar-type radiation tip. A comparative study between a proposed ring-type cutoff (RTC) probe and a conventional bar-type cutoff (BTC) probe showed that the RTC probe solved the problem of the BTC probe, the large measurement uncertainty of the electron density in a capacitively coupled plasma source. This improved characteristics of the RTC probe might have originated from the geometrical structure of the RTC probe concerning the monopole antennae radiation. This proposed cutoff probe can be expected to expand the applicable diagnostic range and to enhance the sensitivity of the cutoff probe. - Highlights: ► A cutoff probe with a ring type detection tip is proposed. ► Comparative experiment and simulation were conducted. ► The proposed probe showed a small uncertainty of measured plasma density. ► Improved characteristics might be originated from the geometrical structure

Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy.

Science.gov (United States)

Fang, Peng; An, Jie; Zeng, Ling-Li; Shen, Hui; Chen, Fanglin; Wang, Wensheng; Qiu, Shijun; Hu, Dewen

2015-01-01

Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE), but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right) mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

Science.gov (United States)

Janssen, Ralf

2012-09-01

Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

Nuclear borehole probes - theory and experiments

International Nuclear Information System (INIS)

Joergensen, J.L.; Korsbech, U.; Gynther Nielsen, K.; Oelgaard, P.L.

1985-06-01

The report gives a summary of the theoretical and expeimental work on borehole probes that has been performed since 1971 at The Department of Electrophysics, The Technical University of Denmark. The first part of the report concerns the use of a spectral natural gamma-ray probe (SNG-probe), which is used for measurements of the spectral distribution of the gamma-rays of the geological strata around a borehole. In general the spectrum is divided into three parts - the gamma-rays from potassium-40, from thorium-232 and daughters, and from uranium-238 and daughters. A set of curves showing the intensities of the gamm-radiation from K, Th, and U versus depth is called a SNG-log. If proper calibrated, the SNG-log gives the concentration of Th, U, and K in the formation surrounding the borehole. Initially the basis for an interpretation of SNG-logs is discussed. Then follows a description og some SNG-problems designed and built by The Department of Electrophysics, and a discussion of the calibration of SNG-probes. Some examples of SNG-logs are presented, and some general comments on the use of SNG-logs are given. The second part of the report concerns mainly the development of theoretical models for neutron-neutron probes, gamma-gamma probes, and pulsed-neutron probes. The purpose of this work has been to examine how well the models correlate with measured results and - where reasonable agreement is found - to use the models in studies of the factors that affect the probe responses in interpretation of experimental results and in probe design. (author)

Measurement of left ventricular ejection fraction with ionic sup(113m)In and a cardiac probe

Energy Technology Data Exchange (ETDEWEB)

Liu, X.; Harrison, K.S.; Wagner, H.N. Jr.

1982-09-01

Left ventricular ejection fraction (LVEF) was measured with a cardiac probe (Nuclear Stethoscope. Bios Inc., Valhalla, New York) and sup(113m)In in 28 normal subjects and 86 patients with coronary artery disease (CAD). In 20 normal subjects sup(99m)TC-RBCs were compared with sup(113m)In, which binds to transferrin after IV injection. With sup(99m)Tc-RBCs average LVEF was 57+-7% (1 SD); with sup(113m)In, average LEVF was 55+-8% (N.S.). Sequential measurements at different times over 60 min revealed good reproducibility. Comparison of LVEF's obtained using sup(99m)Tc-RBCs with a gamma camera and cardiac probe revealed a good correlation. The correlation coefficients were 0.92 in 25 patients with CAD and 0.95 in 10 patients with LV wall motion abnormalities. The LVEF obtained using a cardiac probe and sup(113m)In increased in 28 normals from 57+-9% to 64+-13% (P<0.001) during handgrip exercise, while the LVEF decreased from 45+-9% to 41+-10% (P<0.01) in patients with acute myocardial infarction 4-7 weeks after episode, from 48+-11 to 40+-12% (P<0.001) in patients with old myocardial infarction, and from 52+-9 to 42+-9% (P<0.001) in patients with angina pectoris. The cardiac probe and sup(113m)In provide a useful alternate means of determining left ventricular dysfunction in facilities where sup(99m)Tc and a gamma camera computer system are not readily available.

Measurement of left ventricular ejection fraction with ionic sup(113m)In and a cardiac probe

International Nuclear Information System (INIS)

Liu, X.; Harrison, K.S.; Wagner, H.N. Jr.

1982-01-01

Left ventricular ejection fraction (LVEF) was measured with a cardiac probe (Nuclear Stethoscope. Bios Inc., Valhalla, New York) and sup(113m)In in 28 normal subjects and 86 patients with coronary artery disease (CAD). In 20 normal subjects sup(99m)TC-RBCs were compared with sup(113m)In, which binds to transferrin after IV injection. With sup(99m)Tc-RBCs average LVEF was 57+-7% (1 SD); with sup(113m)In, average LEVF was 55+-8% (N.S.). Sequential measurements at different times over 60 min revealed good reproducibility. Comparison of LVEF's obtained using sup(99m)Tc-RBCs with a gamma camera and cardiac probe revealed a good correlation. The correlation coefficients were 0.92 in 25 patients with CAD and 0.95 in 10 patients with LV wall motion abnormalities. The LVEF obtained using a cardiac probe and sup(113m)In increased in 28 normals from 57+-9% to 64+-13% (P<0.001) during handgrip exercise, while the LVEF decreased from 45+-9% to 41+-10% (P<0.01) in patients with acute myocardial infarction 4-7 weeks after episode, from 48+-11 to 40+-12% (P<0.001) in patients with old myocardial infarction, and from 52+-9 to 42+-9% (P<0.001) in patients with angina pectoris. The cardiac probe and sup(113m)In provide a useful alternate means of determining left ventricular dysfunction in facilities where sup(99m)Tc and a gamma camera computer system are not readily available. (orig.)

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site.

Science.gov (United States)

Jayamani, Indumathy; Cupples, Alison M

2015-07-01

This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

A monolithic microsphere-fiber probe for spatially resolved Raman spectroscopy: Application to head and neck squamous cell carcinomas

Science.gov (United States)

Holler, S.; Haig, B.; Donovan, M. J.; Sobrero, M.; Miles, B. A.

2018-03-01

The ability to identify precise cancer margins in vivo during a surgical excision is critical to the well-being of the patient. Decreased operative time has been linked to shorter patient recovery time, and there are risks associated with removing either too much or too little tissue from the surgical site. The more rapidly and accurately a surgeon can identify and excise diseased tissue, the better the prognosis for the patient. To this end, we investigate both malignant and healthy oral cavity tissue using the Raman spectroscopy, with a monolithic microsphere-fiber probe. Our results indicate that this probe has decreased the size of the analyzed area by more than an order of magnitude, as compared to a conventional fiber reflection probe. Scanning the probe across the tissues reveals variations in the Raman spectra that enable us to differentiate between malignant and healthy tissues. Consequently, we anticipate that the high spatial resolution afforded by the probe will permit us to identify tumor margins in detail, thereby optimizing tissue removal and improving patient outcomes.

Differential thermodynamic signature of carbon nanomaterials using amphiphilic micellar probe

Science.gov (United States)

Bhattacharyya, Tamoghna; Dasgupta, Anjan Kr

2018-04-01

The thermodynamic signature of single-wall carbon nanotubes (SWCNTs), multi-walled carbon nanotubes (MWCNTs) and reduced graphene oxide (rG-O) using amphiphilic micellar probe has been explored. The study reveals an intricate correlation between nano-surface topology and calorimetric profile of SWCNTs, MWCNTs and rG-O. The critical micelle concentration (CMC) is found to be sensitive to the topological diversity of nanomaterials. The study explores a thermodynamic approach to characterize the nano-surface topology of SWCNTs, MWCNTs and graphene surface.

TORE SUPRA fast reciprocating radio frequency probe

International Nuclear Information System (INIS)

Thomas, C.E. Jr.; Harris, J.H.; Haste, G.R.; Kwon, M.; Goulding, R.H.; Hoffman, D.J.; Saoutic, B.; Becoulet, A.; Fraboulet, D.; Beaumont, B.; Kuus, H.; Ladurelle, L.; Pascal, J.Y.

1995-01-01

A fast reciprocating ion cyclotron range of frequencies (ICRF) probe was installed and operated on TORE SUPRA during 1992/1993. The body of the probe was originally used on the ATF experiment at Oak Ridge National Laboratory. The probe was adapted for use on TORE SUPRA, and mounted on one of the two fast reciprocating probe mounts. The probe consists of two orthogonal single-turn wire loops, mounted so that one loop senses toroidal rf magnetic fields and the other senses poloidal rf magnetic fields. The probe began operation in June, 1993. The probe active area is approximately 5 cm long by 2 cm, and the reciprocating mount has a slow stroke (5 cm/s) of 30 cm and a fast stroke (1.5 m/s) of about 10 cm. The probe was operated at distances from the plasma edge ranging from 30 to -5 cm (i.e., inside the last closed flux surface). The probe design, electronics, calibration, data acquisition, and data processing are discussed. First data from the probe are presented as a function of ICRF power, distance from the plasma, loop orientation, and other plasma parameters. Initial data show parametric instabilities do not play an important role for ICRF in the TORE SUPRA edge and scrape-off-layer (SOL) plasmas. Additionally it is observed that the probe signal has little or no dependence on position in the SOL/plasma edge

Hyperpolarized NMR Probes for Biological Assays

Directory of Open Access Journals (Sweden)

Sebastian Meier

2014-01-01

Full Text Available During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.

Chronic malaria revealed by a new fluorescence pattern on the antinuclear autoantibodies test.

Directory of Open Access Journals (Sweden)

Benjamin Hommel

Full Text Available BACKGROUND: Several clinical forms of malaria such as chronic carriage, gestational malaria or hyper-reactive malarial splenomegaly may follow a cryptic evolution with afebrile chronic fatigue sometimes accompanied by anemia and/or splenomegaly. Conventional parasitological tests are often negative or not performed, and severe complications may occur. Extensive explorations of these conditions often include the search for antinuclear autoantibodies (ANA. METHODS: We analysed fluorescence patterns in the ANA test in patients with either chronic cryptic or acute symptomatic malaria, then conducted a one-year prospective study at a single hospital on all available sera drawn for ANA detections. We then identified autoantibodies differentially expressed in malaria patients and in controls using human protein microarray. RESULTS: We uncovered and defined a new, malaria-related, nucleo-cytoplasmic ANA pattern displaying the specific association of a nuclear speckled pattern with diffuse cytoplasmic perinuclearly-enhanced fluorescence. In the one-year prospective analysis, 79% of sera displaying this new nucleo-cytoplasmic fluorescence were from patients with malaria. This specific pattern, not seen in other parasitic diseases, allowed a timely reorientation of the diagnosis toward malaria. To assess if the autoantibody immune response was due to autoreactivity or molecular mimicry we isolated 42 autoantigens, targets of malarial autoantibodies. BLAST analysis indicated that 23 of recognized autoantigens were homologous to plasmodial proteins suggesting autoimmune responses directly driven by the plasmodial infection. CONCLUSION: In patients with malaria in whom parasitological tests have not been performed recognition of this new, malaria-related fluorescence pattern on the ANA test is highly suggestive of the diagnosis and triggers immediate, easy confirmation and adapted therapy.

Probing for heavy element impurities in the shell of the Pacific oyster, Crassostrea gigas, with nuclear microscopy

International Nuclear Information System (INIS)

Markwitz, A.; Barry, B.; Gauldie, R.W.; Roberts, R.D.

2003-01-01

Nuclear microscopy was performed on shells of the Pacific oyster, Crassostrea gigas, to probe for heavy element impurities. For the studies 14 shells from the Auckland and the Marlborough Sounds region were chosen. In sections, the shells appear as opaque with white and grey zones, which are related to alternating layers of calcite and aragonite. Raster scans with 2.5 MeV protons over the sections (scan area 5 x 5 mm) were used in the experiment to measure trace elements in the ppm region using proton induced X-ray spectroscopy. Two dimensional maps and line scans revealed the presence of bromine in all shells investigated. Bromine was found to be related with the pattern of calcium. Hot spots of iron proved to be a common feature in the shells as well. In some shells, copper and zinc were also measured in hot spots of a few micrometers in diameter. Spatially resolved results on the micrometer level indicate the usefulness of nuclear microscopy for the detection of heavy elements in shells of the Pacific oyster

Convective heat flow probe

Science.gov (United States)

Dunn, James C.; Hardee, Harry C.; Striker, Richard P.

1985-01-01

A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packer-type seals are provided along the probe above and below the heater pads.

Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope

Directory of Open Access Journals (Sweden)

Matthew F. B. Green

2014-10-01

Full Text Available One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM, which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s is largely unknown.

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

Directory of Open Access Journals (Sweden)

De Marzo Angelo M

2011-06-01

Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure.

Directory of Open Access Journals (Sweden)

Amira Amrani

Full Text Available RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.

Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure

Science.gov (United States)

Amrani, Amira; Bergon, Aurélie; Holota, Hélène; Tamburini, Christian; Garel, Marc; Ollivier, Bernard; Imbert, Jean; Dolla, Alain; Pradel, Nathalie

2014-01-01

RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria. PMID:25215865

Solar Probe Plus: A NASA Mission to Touch the SunMission Status Update

Science.gov (United States)

Fox, N. J.

2016-12-01

Solar Probe Plus (SPP), currently in Phase D, will be the first mission to fly into the low solar corona, revealing how the corona is heated and the solar wind and energetic particles are accelerated, solving fundamental mysteries that have been top priority science goals since such a mission was first proposed in 1958. The scale and concept of such a mission has been revised at intervals since that time, yet the core has always been a close encounter with the Sun. The primary science goal of the Solar Probe Plus mission is to determine the structure and dynamics of the Sun's coronal magnetic field, understand how the solar corona and wind are heated and accelerated, and determine what mechanisms accelerate and transport energetic particles. SPP uses an innovative mission design, significant technology development and a risk-reducing engineering development to meet the SPP science objectives. In this presentation, we provide an update on the progress of the Solar Probe Plus mission as we prepare for the July 2018 launch.

Parker Solar Probe: A NASA Mission to Touch the Sun: Mission Status Update

Science.gov (United States)

Fox, N. J.

2017-12-01

The newly renamed, Parker Solar Probe (PSP) mission will be the first mission to fly into the low solar corona, revealing how the corona is heated and the solar wind and energetic particles are accelerated, solving fundamental mysteries that have been top priority science goals since such a mission was first proposed in 1958. The scale and concept of such a mission has been revised at intervals since that time, yet the core has always been a close encounter with the Sun. The primary science goal of the Parker Solar Probe mission is to determine the structure and dynamics of the Sun's coronal magnetic field, understand how the solar corona and wind are heated and accelerated, and determine what mechanisms accelerate and transport energetic particles. PSP uses an innovative mission design, significant technology development and a risk-reducing engineering development to meet the science objectives. In this presentation, we provide an update on the progress of the Parker Solar Probe mission as we prepare for the July 2018 launch.

Novel Acoustic Feedback Cancellation Approaches In Hearing Aid Applications Using Probe Noise and Probe Noise Enhancement

DEFF Research Database (Denmark)

Guo, Meng; Jensen, Søren Holdt; Jensen, Jesper

2012-01-01

. In many cases, this bias problem causes the cancellation system to fail. The traditional probe noise approach, where a noise signal is added to the loudspeaker signal can, in theory, prevent the bias. However, in practice, the probe noise level must often be so high that the noise is clearly audible...... and annoying; this makes the traditional probe noise approach less useful in practical applications. In this work, we explain theoretically the decreased convergence rate when using low-level probe noise in the traditional approach, before we propose and study analytically two new probe noise approaches...... the proposed approaches much more attractive in practical applications. We demonstrate this through a simulation experiment with audio signals in a hearing aid acoustic feedback cancellation system, where the convergence rate is improved by as much as a factor of 10....

The TORE SUPRA fast reciprocating RF probe

International Nuclear Information System (INIS)

Thomas, C.E. Jr.; Harris, J.H.; Haste, G.R.

1994-01-01

A fast reciprocating ICRF (Ion Cyclotron Range of Frequencies) probe was installed and operated on TORE SUPRA during 1992/1993. The body of the probe was originally used on the ATF experiment at ORNL. The probe was adapted for use on TORE SUPRA, and mounted on one of the two fast reciprocating probe mounts. The probe consists of two orthogonal single-turn wire loops, mounted so that one loop senses toroidal RF magnetic fields and the other senses poloidal RF magnetic fields. The probe began operation in June, 1993. The probe active area is approximately 5 cm long by 2 cm, and the reciprocating mount has a slow stroke (5 cm/sec) of 30 cm by 2 cm, and the reciprocating mount has a slow stroke (5 cm/sec) of 30 cm and a fast stroke (1.5 m/sec) of about 10 cm. The probe was operated at distances from the plasma edge ranging from 30 cm to -5 cm (i.e., inside the last closed flux surface). The probe design, electronics, calibration, data acquisition and data processing are discussed. First data from the probe are presented as a function of ICRF power, distance from the plasma, loop orientation, and other plasma parameters. Initial data shows parametric instabilities do not play an important role for ICRF in the TORE SUPRA edge and scrape-off-layer (SOL) plasmas. Additionally it is observed that the probe signal has little or no dependence on position in the SOL/plasma edge

Probing anisotropies of gravitational-wave backgrounds with a space-based interferometer: Geometric properties of antenna patterns and their angular power

International Nuclear Information System (INIS)

Kudoh, Hideaki; Taruya, Atsushi

2005-01-01

We discuss the sensitivity to anisotropies of stochastic gravitational-wave backgrounds (GWBs) observed via space-based interferometer. In addition to the unresolved galactic binaries as the most promising GWB source of the planned Laser Interferometer Space Antenna (LISA), the extragalactic sources for GWBs might be detected in the future space missions. The anisotropies of the GWBs thus play a crucial role to discriminate various components of the GWBs. We study general features of antenna pattern sensitivity to the anisotropies of GWBs beyond the low-frequency approximation. We show that the sensitivity of space-based interferometer to GWBs is severely restricted by the data combinations and the symmetries of the detector configuration. The spherical harmonic analysis of the antenna pattern functions reveals that the angular power of the detector response increases with frequency and the detectable multipole moments with effective sensitivity h eff ∼10 -20 Hz -1/2 may reach l∼8-10 at f∼f * =10 mHz in the case of the single LISA detector. However, the cross correlation of optimal interferometric variables is blind to the monopole (l=0) intensity anisotropy, and also to the dipole (l=1) in some case, irrespective of the frequency band. Besides, all the self-correlated signals are shown to be blind to the odd multipole moments (l=odd), independently of the frequency band

Evapotranspiration patterns in complex upland forests reveal contrasting topographic thresholds of non-linearity

Science.gov (United States)

Metzen, D.; Sheridan, G. J.; Benyon, R. G.; Bolstad, P. V.; Nyman, P.; Lane, P. N. J.

2017-12-01

Large areas of forest are often treated as being homogeneous just because they fall in a single climate category. However, we observe strong vegetation patterns in relation to topography in SE Australian forests and thus hypothesise that ET will vary spatially as well. Spatial heterogeneity evolves over different temporal scales in response to climatic forcing with increasing time lag from soil moisture (sub-yearly), to vegetation (10s -100s of years) to soil properties and topography (>100s of years). Most importantly, these processes and time scales are not independent, creating feedbacks that result in "co-evolved stable states" which yield the current spatial terrain, vegetation and ET patterns. We used up-scaled sap flux and understory ET measurements from water-balance plots, as well as LiDAR derived terrain and vegetation information, to infer links between spatio-temporal energy and water fluxes, topography and vegetation patterns at small catchment scale. Topography caused variations in aridity index between polar and equatorial-facing slopes (1.3 vs 1.8), which in turn manifested in significant differences in sapwood area index (6.9 vs 5.8), overstory LAI (3.0 vs 2.3), understory LAI (0.5 vs 0.4), sub-canopy radiation load (4.6 vs 6.8 MJ m-2 d-1), overstory transpiration (501 vs 347 mm a-1) and understory ET (79 vs 155 mm a-1). Large spatial variation in overstory transpiration (195 to 891 mm a-1) was observed over very short distances (100s m); a range representative of diverse forests such as arid open woodlands and wet mountain ash forests. Contrasting, non-linear overstory and understory ET patterns were unveiled between aspects, and topographic thresholds were lower for overstory than understory ET. While ET partitioning remained stable on polar-facing slopes regardless of slope position, overstory contribution gradually decreased with increasing slope inclination on equatorial aspects. Further, we show that ET patterns and controls underlie strong

Chromosome-specific DNA Repeat Probes

Energy Technology Data Exchange (ETDEWEB)

Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

2006-03-16

In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

Fabrication of nano-sized magnetic tunnel junctions using lift-off process assisted by atomic force probe tip.

Science.gov (United States)

Jung, Ku Youl; Min, Byoung-Chul; Ahn, Chiyui; Choi, Gyung-Min; Shin, Il-Jae; Park, Seung-Young; Rhie, Kungwon; Shin, Kyung-Ho

2013-09-01

We present a fabrication method for nano-scale magnetic tunnel junctions (MTJs), employing e-beam lithography and lift-off process assisted by the probe tip of atomic force microscope (AFM). It is challenging to fabricate nano-sized MTJs on small substrates because it is difficult to use chemical mechanical planarization (CMP) process. The AFM-assisted lift-off process enables us to fabricate nano-sized MTJs on small substrates (12.5 mm x 12.5 mm) without CMP process. The e-beam patterning has been done using bi-layer resist, the poly methyl methacrylate (PMMA)/ hydrogen silsesquioxane (HSQ). The PMMA/HSQ resist patterns are used for both the etch mask for ion milling and the self-aligned mask for top contact formation after passivation. The self-aligned mask buried inside a passivation oxide layer, is readily lifted-off by the force exerted by the probe tip. The nano-MTJs (160 nm x 90 nm) fabricated by this method show clear current-induced magnetization switching with a reasonable TMR and critical switching current density.

Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns

Directory of Open Access Journals (Sweden)

Ojurongbe Olusola

2012-05-01

Full Text Available Abstract Background Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility. Methods We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET method to genotype four functional SNPs including -986 G > A (#rs3124952, -602 G > A (#rs3124953, -4A > G (#rs17514136 and +6424 G > T (#rs7851696 in the ficolin-2 (FCN2 gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176, Nigerian (n = 180, Vietnamese (n = 172 and European Caucasian ethnicity (n = 165. Results We observed that the genotype distribution of three functional SNP variants (−986 G > A, -602 G > A and -4A > G differ significantly between the populations investigated (p p  Conclusions The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.

Inspecting Friction Stir Welding using Electromagnetic Probes

Science.gov (United States)

Kinchen, David G.

2004-01-01

A report describes the use of advanced electromagnetic probes to measure the dimensions, the spatial distribution of electrical conductivity, and related other properties of friction stir welds (FSWs) between parts made of the same or different aluminum alloy(s). The probes are of the type described in in another Tech Brief. To recapitulate: A probe of this type is essentially an eddy-current probe that includes a primary (driver) winding that meanders and multiple secondary (sensing) windings that meander along the primary winding. Electrical conductivity is commonly used as a measure of heat treatment and tempering of aluminum alloys, but prior to the development of these probes, the inadequate sensitivity and limited accuracy of electrical-conductivity probes precluded such use on FSWs between different aluminum alloys, and the resolution of those probes was inadequate for measurement of FSW dimensions with positions and metallurgical properties. In contrast, the present probes afford adequate accuracy and spatial resolution for the purposes of measuring the dimensions of FSW welds and correlating spatially varying electrical conductivities with metallurgical properties, including surface defects.

Suite of Activity-Based Probes for Cellulose-Degrading Enzymes

Energy Technology Data Exchange (ETDEWEB)

Chauvigne-Hines, Lacie M.; Anderson, Lindsey N.; Weaver, Holly M.; Brown, Joseph N.; Koech, Phillip K.; Nicora, Carrie D.; Hofstad, Beth A.; Smith, Richard D.; Wilkins, Michael J.; Callister, Stephen J.; Wright, Aaron T.

2012-12-19

Microbial glycoside hydrolases play a dominant role in the biochemical conversion of cellulosic biomass to high-value biofuels. Anaerobic cellulolytic bacteria are capable of producing multicomplex catalytic subunits containing cell-adherent cellulases, hemicellulases, xylanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and other related plant cell wall polysaccharides. Clostridium thermocellum is a cellulosome producing bacterium that couples rapid reproduction rates to highly efficient degradation of crystalline cellulose. Herein, we have developed and applied a suite of difluoromethylphenyl aglycone, N-halogenated glycosylamine, and 2-deoxy-2-fluoroglycoside activity-based protein profiling (ABPP) probes to the direct labeling of the C. thermocellum cellulosomal secretome. These activity-based probes (ABPs) were synthesized with alkynes to harness the utility and multimodal possibilities of click chemistry, and to increase enzyme active site inclusion for LC-MS analysis. We directly analyzed ABP-labeled and unlabeled global MS data, revealing ABP selectivity for glycoside hydrolase (GH) enzymes in addition to a large collection of integral cellulosome-containing proteins. By identifying reactivity and selectivity profiles for each ABP, we demonstrate our ability to widely profile the functional cellulose degrading machinery of the bacterium. Derivatization of the ABPs, including reactive groups, acetylation of the glycoside binding groups, and mono- and disaccharide binding groups, resulted in considerable variability in protein labeling. Our probe suite is applicable to aerobic and anaerobic cellulose degrading systems, and facilitates a greater understanding of the organismal role associated within biofuel development.

Probe suppression in conformal phased array

CERN Document Server

Singh, Hema; Neethu, P S

2017-01-01

This book considers a cylindrical phased array with microstrip patch antenna elements and half-wavelength dipole antenna elements. The effect of platform and mutual coupling effect is included in the analysis. The non-planar geometry is tackled by using Euler's transformation towards the calculation of array manifold. Results are presented for both conducting and dielectric cylinder. The optimal weights obtained are used to generate adapted pattern according to a given signal scenario. It is shown that array along with adaptive algorithm is able to cater to an arbitrary signal environment even when the platform effect and mutual coupling is taken into account. This book provides a step-by-step approach for analyzing the probe suppression in non-planar geometry. Its detailed illustrations and analysis will be a useful text for graduate and research students, scientists and engineers working in the area of phased arrays, low-observables and stealth technology.

Gamma-ray imaging probes

International Nuclear Information System (INIS)

Wild, W.J.

1988-01-01

External nuclear medicine diagnostic imaging of early primary and metastatic lung cancer tumors is difficult due to the poor sensitivity and resolution of existing gamma cameras. Nonimaging counting detectors used for internal tumor detection give ambiguous results because distant background variations are difficult to discriminate from neighboring tumor sites. This suggests that an internal imaging nuclear medicine probe, particularly an esophageal probe, may be advantageously used to detect small tumors because of the ability to discriminate against background variations and the capability to get close to sites neighboring the esophagus. The design, theory of operation, preliminary bench tests, characterization of noise behavior and optimization of such an imaging probe is the central theme of this work

Evaluation of diel patterns of relative changes in cell turgor of tomato plants using leaf patch clamp pressure probes

NARCIS (Netherlands)

Lee, K.M.; Driever, S.M.; Heuvelink, E.; Rüger, S.; Zimmermann, U.; Gelder, de A.; Marcelis, L.F.M.

2012-01-01

Relative changes in cell turgor of leaves of well-watered tomato plants were evaluated using the leaf patch clamp pressure probe (LPCP) under dynamic greenhouse climate conditions. Leaf patch clamp pressure changes, a measure for relative changes in cell turgor, were monitored at three different

Photon-assisted Beam Probes for Low Temperature Plasmas and Installation of Neutral Beam Probe in Helimak

Science.gov (United States)

Garcia de Gorordo, Alvaro; Hallock, Gary A.; Kandadai, Nirmala

2008-11-01

The Heavy Ion Beam Probe (HIBP) diagnostic has successfully measured the electric potential in a number of major plasma devices in the fusion community. In contrast to a Langmuir probe, the HIBP measures the exact electric potential rather than the floating potential. It is also has the advantage of being a very nonperturbing diagnostic. We propose a new photon-assisted beam probe technique that would extend the HIBP type of diagnostics into the low temperature plasma regime. We expect this method to probe plasmas colder than 10 eV. The novelty of the proposed diagnostic is a VUV laser that ionizes the probing particle. Excimer lasers produce the pulsed VUV radiation needed. The lasers on the market don't have a short enough wavelength too ionize any ion directly and so we calculate the population density of excited states in a NLTE plasma. These new photo-ionization techniques can take an instantaneous one-dimensional potential measurement of a plasma and are ideal for nonmagnitized plasmas where continuous time resolution is not required. Also the status of the Neutral Beam Probe installation on the Helimak experiment will be presented.

Cell patterning on poly(sodium 4-styrenesulfonate)-patterned fluoropolymer substrate

Energy Technology Data Exchange (ETDEWEB)

Kim, Wan-Joong [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 580-185 (Korea, Republic of); Department of Polymer Science and Engineering, Chungnam National University, Yuseong-gu, Daejeon 305-764 (Korea, Republic of); Jung, Chang-Hee; Hwang, In-Tae [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 580-185 (Korea, Republic of); Jung, Chan-Hee, E-mail: jch@kaeri.re.kr [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 580-185 (Korea, Republic of); Choi, Jae-Hak, E-mail: jaehakchoi@cnu.ac.kr [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do 580-185 (Korea, Republic of); Department of Polymer Science and Engineering, Chungnam National University, Yuseong-gu, Daejeon 305-764 (Korea, Republic of); Hong, Sung-Kwon [Department of Polymer Science and Engineering, Chungnam National University, Yuseong-gu, Daejeon 305-764 (Korea, Republic of)

2013-10-15

Highlights: •PFA films were functionalized by ion-beam induced surface graft polymerization. •Poly(sodium 4-styrenesulfonate) (PSS)-patterned PFA films were prepared. •Well-organized cell patterns were obtained on PSS-patterned PFA films. •This method is useful to fabricate bio-platforms for cell-based biodevices. -- Abstract: The surface functionalization of bio-inert fluoropolymer films through ion beam-induced surface graft polymerization was investigated to control the cellular behavior. The surface of poly(tetrafluoroethylene-co-perfluoropropl vinyl ether) (PFA) films was selectively activated by 150 keV H{sup +} ion implantation in the presence of a pattern mask and sodium 4-styrenesulfonate (SS) was then graft polymerized onto the implanted PFA films to form hydrophilic poly(sodium 4-styrenesulfonate) (PSS)-patterned PFA films. The surface of the resulting PSS-patterned PFA films was investigated in terms of the degree of graft polymerization, chemical structure, chemical composition, wettability, and morphology. The analytical results revealed that PSS was selectively grafted onto the implanted regions of the PFA films. Furthermore, in vitro cell culture on the PSS-patterned PFA films exhibited a preferential adhesion and growth of cells onto the PSS-grafted regions, resulting in well-organized 100 μm cell patterns.

Cell patterning on poly(sodium 4-styrenesulfonate)-patterned fluoropolymer substrate

International Nuclear Information System (INIS)

Kim, Wan-Joong; Jung, Chang-Hee; Hwang, In-Tae; Jung, Chan-Hee; Choi, Jae-Hak; Hong, Sung-Kwon

2013-01-01

Highlights: •PFA films were functionalized by ion-beam induced surface graft polymerization. •Poly(sodium 4-styrenesulfonate) (PSS)-patterned PFA films were prepared. •Well-organized cell patterns were obtained on PSS-patterned PFA films. •This method is useful to fabricate bio-platforms for cell-based biodevices. -- Abstract: The surface functionalization of bio-inert fluoropolymer films through ion beam-induced surface graft polymerization was investigated to control the cellular behavior. The surface of poly(tetrafluoroethylene-co-perfluoropropl vinyl ether) (PFA) films was selectively activated by 150 keV H + ion implantation in the presence of a pattern mask and sodium 4-styrenesulfonate (SS) was then graft polymerized onto the implanted PFA films to form hydrophilic poly(sodium 4-styrenesulfonate) (PSS)-patterned PFA films. The surface of the resulting PSS-patterned PFA films was investigated in terms of the degree of graft polymerization, chemical structure, chemical composition, wettability, and morphology. The analytical results revealed that PSS was selectively grafted onto the implanted regions of the PFA films. Furthermore, in vitro cell culture on the PSS-patterned PFA films exhibited a preferential adhesion and growth of cells onto the PSS-grafted regions, resulting in well-organized 100 μm cell patterns

Key electronic states in lithium battery materials probed by soft X-ray spectroscopy

International Nuclear Information System (INIS)

Yang, Wanli; Liu, Xiaosong; Qiao, Ruimin; Olalde-Velasco, Paul; Spear, Jonathan D.; Roseguo, Louis; Pepper, John X.; Chuang, Yi-de; Denlinger, Jonathan D.; Hussain, Zahid

2013-01-01

Highlights: •Key electronic states in battery materials revealed by soft X-ray spectroscopy. •Soft X-ray absorption consistently probes Mn oxidation states in different systems. •Soft X-ray absorption and emission fingerprint battery operations in LiFePO 4 . •Spectroscopic guidelines for selecting/optimizing polymer materials for batteries. •Distinct SEI formation on same electrode material with different crystal orientations. -- Abstract: The formidable challenges for developing a safe, low-cost, high-capacity, and high-power battery necessitate employing advanced tools that are capable of directly probing the key electronic states relevant to battery performance. Synchrotron based soft X-ray spectroscopy directly measures both the occupied and unoccupied states in the vicinity of the Fermi level, including transition-metal-3d and anion-p states. This article presents the basic concepts on how fundamental physics in electronic structure could provide valuable information for lithium-ion battery applications. We then discuss some of our recent studies on transition-metal oxide based cathodes, silicon based anode, and solid-electrolyte-interphase through soft X-ray absorption and emission spectroscopy. We argue that spectroscopic results reveal the evolution of electronic states for fingerprinting, understanding, and optimizing lithium-ion battery operations

Pneumatic probe with laser interferometer

International Nuclear Information System (INIS)

Wilkens, P.H.

1978-01-01

Improvements to upgrade the accuracy of Rotacon probes by a complete redesign of probe to include a Michelson interferometer to replace the existing long-range capacity transducer are described. This has resulted in a compact and interchangeable probe cartridge with a 3 μin. resolution and accuracy; the cartridge can be installed and replaced in the Rotacon gauge with the minimum of realignment, which should reduce our dependence on operator skill. In addition, the stylus contact force can be reduced to 750 mg for the contacting types, but an alternative feature, which we are still developing, will use a gas jet cushion in place of the stylus to provide a noncontacting version of the same basic probe cartridge. This device is very sensitive to external vibration effects because it is virtually frictionless

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

Science.gov (United States)

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Zero voltage mass spectrometry probes and systems

Science.gov (United States)

Cooks, Robert Graham; Wleklinski, Michael Stanley; Bag, Soumabha; Li, Yafeng

2017-10-10

The invention generally relates to zero volt mass spectrometry probes and systems. In certain embodiments, the invention provides a system including a mass spectrometry probe including a porous material, and a mass spectrometer (bench-top or miniature mass spectrometer). The system operates without an application of voltage to the probe. In certain embodiments, the probe is oriented such that a distal end faces an inlet of the mass spectrometer. In other embodiments, the distal end of the probe is 5 mm or less from an inlet of the mass spectrometer.

Ultrafast optical pump terahertz-probe spectroscopy of strongly correlated electron materials

International Nuclear Information System (INIS)

Averitt, R.D.; Taylor, Antoinette J.; Thorsmolle, V.K.; Jia, Quanxi; Lobad, A.I.; Trugman, S.A.

2001-01-01

We have used optical-pump far-infrared probe spectroscopy to probe the low energy electron dynamics of high temperature superconductors and colossal magnetoresistance manganites. For the superconductor YBa2Cu3O7, picosecond conductivity measurements probe the interplay between Cooper-pairs and quasiparticles. In optimally doped films, the recovery time for long-range phase-coherent pairing increases from ∼1.5 ps at 4K to ∼3.5 ps near Tc, consistent with the closing of the superconducting gap. For underdoped films, the measured recovery time is temperature independent (3.5 ps) in accordance with the presence of a pseudogap. Ultrafast picosecond measurements of optically induced changes in the absolute conductivity of La0:7M0:3MnO3 thin films (M = Ca, Sr) from 10K to ∼0.9Tc reveal a two-component relaxation. A fast, ∼2 ps, conductivity decrease arises from optically induced modification of the effective phonon temperature. The slower component, related to spin-lattice relaxation, has a lifetime that increases upon approaching Tc from below in accordance with an increasing spin specific heat. Our results indicate that for T<< Tc, the conductivity is determined by incoherent phonons while spin fluctuations dominate near Tc.

Interaction of a ballistic probe with gaseous media

International Nuclear Information System (INIS)

Kucerovsky, Zden; Greason, William D

2008-01-01

Free-flying metal probes are used to determine charge densities in gaseous media containing free charge or low density plasma. The trajectory of the probe is ensured either by gravity or by propelling the probe to a certain velocity at the launch site. While travelling, the probe charge changes from its launch-site magnitude to that related to the space charge density existing along the trajectory. The degree to which the probe's arrival-site charge magnitude matches the space charge density in the area of interest depends on the probe shape and on the charge exchange processes between the probe body and the medium. The paper studies a probe acting as a free-flying charge carrier in air, and discusses the problems that may lead to an imbalance between the charge collected by the probe in the area of interest and the charge measured at the arrival site. The analysis and the described experiments are of the ballistic type: a small, triboelectrically pre-charged metal probe was propelled on a horizontal path, and the charge carried by the probe was measured at several points along the trajectory by means of contact-free induction rings; the initial and final charges were determined by static Faraday cups. A charge disparity was found under certain conditions, and its degree explained by the effects of the charge carrier potential. The studied probe charges ranged from 10 to 50 nF, and the fly-times needed to cross a one-meter path ranged from 20 to 40 ms. The probe to gas charge exchange experiments and their analysis yielded conditions under which the probe lost approximately 10 % of its charge. The results of our study may be of interest to those who intend to use the free-flying probe technique for the determination of space charge density.

Position of probe determines prognostic information of brain tissue PO2 in severe traumatic brain injury.

Science.gov (United States)

Ponce, Lucido L; Pillai, Shibu; Cruz, Jovany; Li, Xiaoqi; Julia, H; Gopinath, Shankar; Robertson, Claudia S

2012-06-01

Monitoring brain tissue PO2 (PbtO2) is part of multimodality monitoring of patients with traumatic brain injury (TBI). However, PbtO2 measurement is a sampling of only a small area of tissue surrounding the sensor tip. To examine the effect of catheter location on the relationship between PbtO2 and neurological outcome. A total of 405 patients who had PbtO2 monitoring as part of standard management of severe traumatic brain injury were studied. The relationships between probe location and resulting PbtO2 and outcome were examined. When the probe was located in normal brain, PbtO2 averaged 30.8 ± 18.2 compared with 25.6 ± 14.8 mm Hg when placed in abnormal brain (P < .001). Factors related to neurological outcome in the best-fit logistic regression model were age, PbtO2 probe position, postresuscitation motor Glasgow Coma Scale score, and PbtO2 trend pattern. Although average PbtO2 was significantly related to outcome in univariate analyses, it was not significant in the final logistic model. However, the interaction between PbtO2 and probe position was statistically significant. When the PbtO2 probe was placed in abnormal brain, the average PbtO2 was higher in those with a favorable outcome, 28.8 ± 12.0 mm Hg, compared with those with an unfavorable outcome, 19.5 ± 13.7 mm Hg (P = .01). PbtO2 and outcome were not related when the probe was placed in normal-appearing brain. These results suggest that the location of the PbtO2 probe determines the PbtO2 values and the relationship of PbtO2 to neurological outcome.

Design and operation of a high-heat flux, flush-mounted ‘rail’ Langmuir probe array on Alcator C-Mod

Directory of Open Access Journals (Sweden)

A.Q. Kuang

2017-08-01

Full Text Available A poloidal array of toroidally-extended, flush-mounted ‘rail’ Langmuir probes was recently installed on Alcator C-Mod's vertical target plate divertor. The aim was to investigate if a Langmuir probe array could be designed to survive reactor-level heat fluxes and have the ability to make measurements that could be reliably interpreted under reactor-level plasma densities, neutral densities and magnetic fields. Langmuir probes are typically built to have incident field-line angles >10° to avoid interpretation issues associated with sheath expansion. However, at the high parallel heat fluxes experienced in reactor-relevant conditions such a probe would quickly overheat and melt. To mitigate both the issues of extreme heat flux and sheath expansion, each probe was designed to be flush with the divertor surface, toroidally-extended and field-aligned, giving it a ‘rail’ geometry. The flush mounted probes have proven to be exceptionally robust surviving the 2015–2016 campaign – a first for a C-Mod probe system. Examination of the probe current-voltage (I-V characteristics reveals that they are immune to sheath expansion at incident field angles down to ∼0.5°. Comparison of the flush probes to traditional proud probes shows that both measure the same electron pressure across the divertor plate. However, there are significant and systematic differences in the density, temperature and floating potential. This suggests that there is important physics, perhaps unique to conditions in a vertical-target plate divertor with small field-line attack angles, that affects the I-V characteristics and is not currently included in probe data analyses. Finally, the probe response is examined in the ‘death-ray’ regime, just near detachment. Previous work using proud probes has suggested that the ‘death-ray’ is an artefact of the probe bias. However, on flush mounted probes the ‘death-ray’ manifests itself under different conditions, which

Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy

Directory of Open Access Journals (Sweden)

Peng Fang

2015-01-01

Full Text Available Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE, but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

Primitive chain network simulations of probe rheology.

Science.gov (United States)

Masubuchi, Yuichi; Amamoto, Yoshifumi; Pandey, Ankita; Liu, Cheng-Yang

2017-09-27

Probe rheology experiments, in which the dynamics of a small amount of probe chains dissolved in immobile matrix chains is discussed, have been performed for the development of molecular theories for entangled polymer dynamics. Although probe chain dynamics in probe rheology is considered hypothetically as single chain dynamics in fixed tube-shaped confinement, it has not been fully elucidated. For instance, the end-to-end relaxation of probe chains is slower than that for monodisperse melts, unlike the conventional molecular theories. In this study, the viscoelastic and dielectric relaxations of probe chains were calculated by primitive chain network simulations. The simulations semi-quantitatively reproduced the dielectric relaxation, which reflects the effect of constraint release on the end-to-end relaxation. Fair agreement was also obtained for the viscoelastic relaxation time. However, the viscoelastic relaxation intensity was underestimated, possibly due to some flaws in the model for the inter-chain cross-correlations between probe and matrix chains.

Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe.

Science.gov (United States)

Richard, B; Groisillier, A; Badet, C; Dorignac, G; Lonvaud-Funel, A

2001-03-01

The Lactobacillus genus has been shown to be associated with the dental carious process, but little is known about the species related to the decay, although Lactobacillus rhamnosus is suspected to be the most implicated species. Conventional identification methods based on biochemical criteria lead to ambiguous results, since the Lactobacillus species found in saliva are phenotypically close. To clarify the role of this genus in the evolution of carious disease, this work aimed to find a rapid and reliable method for identifying the L. rhamnosus species. Methods based on hybridization with DNA probes and DNA amplification by PCR were used. The dominant salivary Lactobacillus species (reference strains from the ATCC) were selected for this purpose as well as some wild strains isolated from children's saliva. DNA profiling using semirandom polymorphic DNA amplification (semi-RAPD) generated specific patterns for L. rhamnosus ATCC 7469. The profiles of all L. rhamnosus strains tested were similar and could be grouped; these strains shared four common fragments. Wild strains first identified with classic methods shared common patterns with the L. rhamnosus species and could be reclassified. One fragment of the profile was purified, cloned, used as a probe and found to be specific to the L. rhamnosus species. These results may help to localize this species within its ecological niche and to elucidate the progression of the carious process.

Determination of gene expression patterns using high-throughput RNA in situ hybridizaion to whole-mount Drosophila embryos

Energy Technology Data Exchange (ETDEWEB)

Weiszmann, R.; Hammonds, A.S.; Celniker, S.E.

2009-04-09

We describe a high-throughput protocol for RNA in situ hybridization (ISH) to Drosophila embryos in a 96-well format. cDNA or genomic DNA templates are amplified by PCR and then digoxigenin-labeled ribonucleotides are incorporated into antisense RNA probes by in vitro transcription. The quality of each probe is evaluated before ISH using a RNA probe quantification (dot blot) assay. RNA probes are hybridized to fixed, mixed-staged Drosophila embryos in 96-well plates. The resulting stained embryos can be examined and photographed immediately or stored at 4oC for later analysis. Starting with fixed, staged embryos, the protocol takes 6 d from probe template production through hybridization. Preparation of fixed embryos requires a minimum of 2 weeks to collect embryos representing all stages. The method has been used to determine the expression patterns of over 6,000 genes throughout embryogenesis.

Designs of Langmuir probes for W7-X

International Nuclear Information System (INIS)

Laube, Ralph; Laux, Michael; Ye, Min You; Greuner, Henri; Lindig, Stefan

2011-01-01

Several designs of Langmuir probes for the stellarator Wendelstein 7-X (W7-X) are described. Different types of probes are proposed for the different divertors to be used during different operational phases of W7-X. Comb-like arrays of stiff probes, arrays of flexible probes, and fixed inlay probes are reviewed. For the initial phase of W7-X it was decided to install arrays of fixed inlay probes. Two mockups were manufactured and one of them was tested with success in the high heat flux test facility GLADIS. For long-pulse operation of W7-X different conceptual designs are proposed and are still developed further. This paper summarizes the different design constrains for the Langmuir probes in the different divertor surroundings, describes the design of the array of inlay probes for the initial phase and the result of the GLADIS test, and gives a preview of the conceptual designs of probes for the long-pulse operational phase of W7-X.

Correlations between human mobility and social interaction reveal general activity patterns

DEFF Research Database (Denmark)

Mollgaard, Anders; Jørgensen, Sune Lehmann; Mathiesen, Joachim

2017-01-01

A day in the life of a person involves a broad range of activities which are common across many people. Going beyond diurnal cycles, a central question is: to what extent do individuals act according to patterns shared across an entire population? Here we investigate the interplay between differe...... they be of social or of physical character....

Reciprocity theory of apertureless scanning near-field optical microscopy with point-dipole probes.

Science.gov (United States)

Esslinger, Moritz; Vogelgesang, Ralf

2012-09-25

Near-field microscopy offers the opportunity to reveal optical contrast at deep subwavelength scales. In scanning near-field optical microscopy (SNOM), the diffraction limit is overcome by a nanoscopic probe in close proximity to the sample. The interaction of the probe with the sample fields necessarily perturbs the bare sample response, and a critical issue is the interpretation of recorded signals. For a few specific SNOM configurations, individual descriptions have been modeled, but a general and intuitive framework is still lacking. Here, we give an exact formulation of the measurable signals in SNOM which is easily applicable to experimental configurations. Our results are in close analogy with the description Tersoff and Hamann have derived for the tunneling currents in scanning tunneling microscopy. For point-like scattering probe tips, such as used in apertureless SNOM, the theory simplifies dramatically to a single scalar relation. We find that the measured signal is directly proportional to the field of the coupled tip-sample system at the position of the tip. For weakly interacting probes, the model thus verifies the empirical findings that the recorded signal is proportional to the unperturbed field of the bare sample. In the more general case, it provides guidance to an intuitive and faithful interpretation of recorded images, facilitating the characterization of tip-related distortions and the evaluation of novel SNOM configurations, both for aperture-based and apertureless SNOM.

Accounting for Laser Extinction, Signal Attenuation, and Secondary Emission While Performing Optical Patternation in a Single Plane

National Research Council Canada - National Science Library

Brown, C

2002-01-01

An optical patternation method is described where the effects of laser extinction and signal attenuation can be corrected for, and where secondary scattering effects are reduced by probing the spray...

IVVS probe mechanical concept design

Energy Technology Data Exchange (ETDEWEB)

Rossi, Paolo, E-mail: paolo.rossi@enea.it; Neri, Carlo; De Collibus, Mario Ferri; Mugnaini, Giampiero; Pollastrone, Fabio; Crescenzi, Fabio

2015-10-15

Highlights: • ENEA designed, developed and tested a laser based In Vessel Viewing System (IVVS). • IVVS mechanical design has been revised from 2011 to 2013 to meet ITER requirements. • Main improvements are piezoceramic actuators and a step focus system. • Successful qualification activities validated the concept design for ITER environment. - Abstract: ENEA has been deeply involved in the design, development and testing of a laser based In Vessel Viewing System (IVVS) required for the inspection of ITER plasma-facing components. The IVVS probe shall be deployed into the vacuum vessel, providing high resolution images and metrology measurements to detect damages and possible erosion. ENEA already designed and manufactured an IVVS probe prototype based on a rad-hard concept and driven by commercial micro-step motors, which demonstrated satisfying viewing and metrology performances at room conditions. The probe sends a laser beam through a reflective rotating prism. By rotating the axes of the prism, the probe can scan all the environment points except those present in a shadow cone and the backscattered light signal is then processed to measure the intensity level (viewing) and the distance from the probe (metrology). During the last years, in order to meet all the ITER environmental conditions, such as high vacuum, gamma radiation lifetime dose up to 5 MGy, cumulative neutron fluence of about 2.3 × 10{sup 17} n/cm{sup 2}, temperature of 120 °C and magnetic field of 8 T, the probe mechanical design was significantly revised introducing a new actuating system based on piezo-ceramic actuators and improved with a new step focus system. The optical and mechanical schemes have been then modified and refined to meet also the geometrical constraints. The paper describes the mechanical concept design solutions adopted in order to fulfill IVVS probe functional performance requirements considering ITER working environment and geometrical constraints.

Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

Directory of Open Access Journals (Sweden)

Zhou Sun

2012-05-01

or filtered by AFST. Conclusions cDNA terminal pattern analysis, as implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.

Probing intracellular motor protein activity using an inducible cargo trafficking assay.

Science.gov (United States)

Kapitein, Lukas C; Schlager, Max A; van der Zwan, Wouter A; Wulf, Phebe S; Keijzer, Nanda; Hoogenraad, Casper C

2010-10-06

Although purified cytoskeletal motor proteins have been studied extensively with the use of in vitro approaches, a generic approach to selectively probe actin and microtubule-based motor protein activity inside living cells is lacking. To examine specific motor activity inside living cells, we utilized the FKBP-rapalog-FRB heterodimerization system to develop an in vivo peroxisomal trafficking assay that allows inducible recruitment of exogenous and endogenous kinesin, dynein, and myosin motors to drive specific cargo transport. We demonstrate that cargo rapidly redistributes with distinct dynamics for each respective motor, and that combined (antagonistic) actions of more complex motor combinations can also be probed. Of importance, robust cargo redistribution is readily achieved by one type of motor protein and does not require the presence of opposite-polarity motors. Simultaneous live-cell imaging of microtubules and kinesin or dynein-propelled peroxisomes, combined with high-resolution particle tracking, revealed that peroxisomes frequently pause at microtubule intersections. Titration and washout experiments furthermore revealed that motor recruitment by rapalog-induced heterodimerization is dose-dependent but irreversible. Our assay directly demonstrates that robust cargo motility does not require the presence of opposite-polarity motors, and can therefore be used to characterize the motile properties of specific types of motor proteins. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei

Energy Technology Data Exchange (ETDEWEB)

Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta [University of Heidelberg, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, D-69120 Heidelberg (Germany); Schmitt, Eberhard, E-mail: eschmitt@kip.uni-heidelberg.de [University of Heidelberg, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, D-69120 Heidelberg (Germany); University of Göttingen, Institute for Numerical and Applied Mathematics, Lotzestraße 16-18, D-37083 Göttingen (Germany); Hausmann, Michael, E-mail: hausmann@kip.uni-heidelberg.de [University of Heidelberg, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, D-69120 Heidelberg (Germany)

2016-07-01

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes). Gene targets can be specifically labelled with at least about 20 PNA-probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3D-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. - Highlights: • Denaturation free protocols preserve 3D architecture of chromosomes and nuclei. • Labelling sets are determined in silico for duplex and triplex binding. • Probes are produced chemically with freely chosen backbones and base variants. • Peptide nucleic acid backbones reduce hindering charge interactions. • Intercalating side chains stabilize binding of short oligonucleotides.

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei

International Nuclear Information System (INIS)

Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta; Schmitt, Eberhard; Hausmann, Michael

2016-01-01

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes). Gene targets can be specifically labelled with at least about 20 PNA-probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3D-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. - Highlights: • Denaturation free protocols preserve 3D architecture of chromosomes and nuclei. • Labelling sets are determined in silico for duplex and triplex binding. • Probes are produced chemically with freely chosen backbones and base variants. • Peptide nucleic acid backbones reduce hindering charge interactions. • Intercalating side chains stabilize binding of short oligonucleotides.

Ultrafast probing of core hole localization in N2.

Science.gov (United States)

Schöffler, M S; Titze, J; Petridis, N; Jahnke, T; Cole, K; Schmidt, L Ph H; Czasch, A; Akoury, D; Jagutzki, O; Williams, J B; Cherepkov, N A; Semenov, S K; McCurdy, C W; Rescigno, T N; Cocke, C L; Osipov, T; Lee, S; Prior, M H; Belkacem, A; Landers, A L; Schmidt-Böcking, H; Weber, Th; Dörner, R

2008-05-16

Although valence electrons are clearly delocalized in molecular bonding frameworks, chemists and physicists have long debated the question of whether the core vacancy created in a homonuclear diatomic molecule by absorption of a single x-ray photon is localized on one atom or delocalized over both. We have been able to clarify this question with an experiment that uses Auger electron angular emission patterns from molecular nitrogen after inner-shell ionization as an ultrafast probe of hole localization. The experiment, along with the accompanying theory, shows that observation of symmetry breaking (localization) or preservation (delocalization) depends on how the quantum entangled Bell state created by Auger decay is detected by the measurement.

Objective, Quantitative, Data-Driven Assessment of Chemical Probes.

Science.gov (United States)

Antolin, Albert A; Tym, Joseph E; Komianou, Angeliki; Collins, Ian; Workman, Paul; Al-Lazikani, Bissan

2018-02-15

Chemical probes are essential tools for understanding biological systems and for target validation, yet selecting probes for biomedical research is rarely based on objective assessment of all potential compounds. Here, we describe the Probe Miner: Chemical Probes Objective Assessment resource, capitalizing on the plethora of public medicinal chemistry data to empower quantitative, objective, data-driven evaluation of chemical probes. We assess >1.8 million compounds for their suitability as chemical tools against 2,220 human targets and dissect the biases and limitations encountered. Probe Miner represents a valuable resource to aid the identification of potential chemical probes, particularly when used alongside expert curation. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain.

Science.gov (United States)

Tan, Powell Patrick Cheng; French, Leon; Pavlidis, Paul

2013-01-01

An important goal in neuroscience is to understand gene expression patterns in the brain. The recent availability of comprehensive and detailed expression atlases for mouse and human creates opportunities to discover global patterns and perform cross-species comparisons. Recently we reported that the major source of variation in gene transcript expression in the adult normal mouse brain can be parsimoniously explained as reflecting regional variation in glia to neuron ratios, and is correlated with degree of connectivity and location in the brain along the anterior-posterior axis. Here we extend this investigation to two gene expression assays of adult normal human brains that consisted of over 300 brain region samples, and perform comparative analyses of brain-wide expression patterns to the mouse. We performed principal components analysis (PCA) on the regional gene expression of the adult human brain to identify the expression pattern that has the largest variance. As in the mouse, we observed that the first principal component is composed of two anti-correlated patterns enriched in oligodendrocyte and neuron markers respectively. However, we also observed interesting discordant patterns between the two species. For example, a few mouse neuron markers show expression patterns that are more correlated with the human oligodendrocyte-enriched pattern and vice-versa. In conclusion, our work provides insights into human brain function and evolution by probing global relationships between regional cell type marker expression patterns in the human and mouse brain.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

Science.gov (United States)

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Handheld magnetic probe with permanent magnet and Hall sensor for identifying sentinel lymph nodes in breast cancer patients.

Science.gov (United States)

Sekino, Masaki; Kuwahata, Akihiro; Ookubo, Tetsu; Shiozawa, Mikio; Ohashi, Kaichi; Kaneko, Miki; Saito, Itsuro; Inoue, Yusuke; Ohsaki, Hiroyuki; Takei, Hiroyuki; Kusakabe, Moriaki

2018-01-19

The newly developed radioisotope-free technique based on magnetic nanoparticle detection using a magnetic probe is a promising method for sentinel lymph node biopsy. In this study, a novel handheld magnetic probe with a permanent magnet and magnetic sensor is developed to detect the sentinel lymph nodes in breast cancer patients. An outstanding feature of the probe is the precise positioning of the sensor at the magnetic null point of the magnet, leading to highly sensitive measurements unaffected by the strong ambient magnetic fields of the magnet. Numerical and experimental results show that the longitudinal detection length is approximately 10 mm, for 140 μg of iron. Clinical tests were performed, for the first time, using magnetic and blue dye tracers-without radioisotopes-in breast cancer patients to demonstrate the performance of the probe. The nodes were identified through transcutaneous and ex-vivo measurements, and the iron accumulation in the nodes was quantitatively revealed. These results show that the handheld magnetic probe is useful in sentinel lymph node biopsy and that magnetic techniques are widely being accepted as future standard methods in medical institutions lacking nuclear medicine facilities.

β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes.

Science.gov (United States)

Maj, Michał; Ahn, Changwoo; Kossowska, Dorota; Park, Kwanghee; Kwak, Kyungwon; Han, Hogyu; Cho, Minhaeng

2015-05-07

An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump-probe spectroscopy. It is found that the NC stretching mode is very sensitive to the hydrogen-bonding ability of solvent molecules. Moreover, its transition dipole strength is larger than that of nitrile (CN) in nitrile-derivatized IR probe 2. The vibrational lifetime of the NC stretching mode is found to be 5.5 ± 0.2 ps in both D2O and DMF solvents, which is several times longer than that of the azido (N3) stretching mode in azido-derivatized IR probe 3. Altogether these properties suggest that the NC group can be a very promising sensing moiety of IR probes for studying the solvation structure and dynamics of biomolecules.

Conception, synthesis and evaluation of fluorescent probes and PET radioligands for the oxytocin and vasopressin receptors

International Nuclear Information System (INIS)

Karpenko, Iuliia

2014-01-01

In order to better understand the role of OTR and AVPR in ASD, to reveal new features in its pharmacology and signaling and to establish high-throughput screening method on wild-type G protein-coupled receptors, we developed imaging probes for the oxytocin-vasopressin receptors family, namely radiotracers for positron emission tomography and optical probes for fluorescence detection and imaging. The fluorescent ligands have been used to establish TR-FRET binding assay for OTR and to initiate the development the screening assay for the wild-type oxytocin receptor. The PET radiotracers will be shortly tested in mice and monkeys to evaluate their potency in detecting the central oxytocin receptors. (author)

A scanning Hall probe microscope for high resolution magnetic imaging down to 300 mK

International Nuclear Information System (INIS)

Khotkevych, V. V.; Bending, S. J.; Milosevic, M. V.

2008-01-01

We present the design, construction, and performance of a low-temperature scanning Hall probe microscope with submicron lateral resolution and a large scanning range. The detachable microscope head is mounted on the cold flange of a commercial 3 He-refrigerator (Oxford Instruments, Heliox VT-50) and operates between room temperature and 300 mK. It is fitted with a three-axis slip-stick nanopositioner that enables precise in situ adjustment of the probe location within a 6x6x7 mm 3 space. The local magnetic induction at the sample surface is mapped with an easily changeable microfabricated Hall probe [typically GsAs/AlGaAs or AlGaAs/InGaAs/GaAs Hall sensors with integrated scanning tunnel microscopy (STM) tunneling tips] and can achieve minimum detectable fields ≥10 mG/Hz 1/2 . The Hall probe is brought into very close proximity to the sample surface by sensing and controlling tunnel currents at the integrated STM tip. The instrument is capable of simultaneous tunneling and Hall signal acquisition in surface-tracking mode. We illustrate the potential of the system with images of superconducting vortices at the surface of a Nb thin film down to 372 mK, and also of labyrinth magnetic-domain patterns of an yttrium iron garnet film captured at room temperature.

Probing the structure of heterogeneous diluted materials by diffraction tomography.

Science.gov (United States)

Bleuet, Pierre; Welcomme, Eléonore; Dooryhée, Eric; Susini, Jean; Hodeau, Jean-Louis; Walter, Philippe

2008-06-01

The advent of nanosciences calls for the development of local structural probes, in particular to characterize ill-ordered or heterogeneous materials. Furthermore, because materials properties are often related to their heterogeneity and the hierarchical arrangement of their structure, different structural probes covering a wide range of scales are required. X-ray diffraction is one of the prime structural methods but suffers from a relatively poor detection limit, whereas transmission electron analysis involves destructive sample preparation. Here we show the potential of coupling pencil-beam tomography with X-ray diffraction to examine unidentified phases in nanomaterials and polycrystalline materials. The demonstration is carried out on a high-pressure pellet containing several carbon phases and on a heterogeneous powder containing chalcedony and iron pigments. The present method enables a non-invasive structural refinement with a weight sensitivity of one part per thousand. It enables the extraction of the scattering patterns of amorphous and crystalline compounds with similar atomic densities and compositions. Furthermore, such a diffraction-tomography experiment can be carried out simultaneously with X-ray fluorescence, Compton and absorption tomographies, enabling a multimodal analysis of prime importance in materials science, chemistry, geology, environmental science, medical science, palaeontology and cultural heritage.

Probing the binding of coumarins and cyclothialidines to DNA gyrase

DEFF Research Database (Denmark)

Kampranis, S C; Gormley, N A; Tranter, R

1999-01-01

B and coumarin and cyclothialidine drugs and made mutations by site-directed mutagenesis. We used proteolysis as a probe of drug binding to wild-type and mutant proteins. Limited proteolysis of gyrase revealed that binding of these antibiotics is associated with a characteristic proteolytic fingerprint......, suggesting a drug-induced conformational change. The ability of the mutants to bind the drugs was studied by testing their ability to induce the coumarin-associated proteolytic signature and to bind to a novobiocin-affinity column. To analyze further the interaction of the drugs with gyrase, we studied...

Theory of Langmuir probes in anisotropic plasmas

International Nuclear Information System (INIS)

Sudit, I.D.; Woods, R.C.

1994-01-01

A theory has been developed for electron retardation by Langmuir probes of several geometries in a general anisotropic plasma with arbitrary probe orientation and valid for any sheath thickness. Electron densities and electron velocity distribution functions (EVDFs) are obtained from the second derivative of probe I-V curves, as in Druyvesteyn's original method, which was developed for isotropic plasmas. Fedorov had extended the latter method in the context of a thin sheath approximation, to axisymmetric plasmas, in which the EVDF is expanded in a series of Legendary polynomials. In the present work an expansion in a series of spherical harmonics is employed, and the coordinate transformations are handled using the irreducible representation of the three dimensional rotation group. It is shown that the Volterra integral equations that must be solved to obtain the expansion coefficients of the EVDF from the second derivative data are no more complicated in the general case that hose for the axisymmetric plasma. Furthermore in the latter case the results can be shown to be equivalent to Fedrov's thin sheath expression. For the case of planar probes a formulation based on first derivatives of the I-V curves has been obtained. If data is obtained at enough different probe orientation of a one sided planar disc probe, any number of spherical harmonic coefficient functions may be obtained by inverting a set of linear equations and the complete EVDF deduced. For a cylindrical probe or a two-sided planar disc probe the integration of the second derivative of the probe current gives the exact electron density with any arbitrary probe orientation and any degree of plasma anisotropy

Molecular Imaging Probe Development using Microfluidics

Science.gov (United States)

Liu, Kan; Wang, Ming-Wei; Lin, Wei-Yu; Phung, Duy Linh; Girgis, Mark D.; Wu, Anna M.; Tomlinson, James S.; Shen, Clifton K.-F.

2012-01-01

In this manuscript, we review the latest advancement of microfluidics in molecular imaging probe development. Due to increasing needs for medical imaging, high demand for many types of molecular imaging probes will have to be met by exploiting novel chemistry/radiochemistry and engineering technologies to improve the production and development of suitable probes. The microfluidic-based probe synthesis is currently attracting a great deal of interest because of their potential to deliver many advantages over conventional systems. Numerous chemical reactions have been successfully performed in micro-reactors and the results convincingly demonstrate with great benefits to aid synthetic procedures, such as purer products, higher yields, shorter reaction times compared to the corresponding batch/macroscale reactions, and more benign reaction conditions. Several ‘proof-of-principle’ examples of molecular imaging probe syntheses using microfluidics, along with basics of device architecture and operation, and their potential limitations are discussed here. PMID:22977436

Contamination effects on fixed-bias Langmuir probes

Energy Technology Data Exchange (ETDEWEB)

Steigies, C. T. [Institut fuer Experimentelle und Angewandte Physik, Christian-Albrechts-Universitaet zu Kiel, 24098 Kiel (Germany); Barjatya, A. [Department of Physical Sciences, Embry-Riddle Aeronautical University, Daytona Beach, Florida 32114 (United States)

2012-11-15

Langmuir probes are standard instruments for plasma density measurements on many sounding rockets. These probes can be operated in swept-bias as well as in fixed-bias modes. In swept-bias Langmuir probes, contamination effects are frequently visible as a hysteresis between consecutive up and down voltage ramps. This hysteresis, if not corrected, leads to poorly determined plasma densities and temperatures. With a properly chosen sweep function, the contamination parameters can be determined from the measurements and correct plasma parameters can then be determined. In this paper, we study the contamination effects on fixed-bias Langmuir probes, where no hysteresis type effect is seen in the data. Even though the contamination is not evident from the measurements, it does affect the plasma density fluctuation spectrum as measured by the fixed-bias Langmuir probe. We model the contamination as a simple resistor-capacitor circuit between the probe surface and the plasma. We find that measurements of small scale plasma fluctuations (meter to sub-meter scale) along a rocket trajectory are not affected, but the measured amplitude of large scale plasma density variation (tens of meters or larger) is attenuated. From the model calculations, we determine amplitude and cross-over frequency of the contamination effect on fixed-bias probes for different contamination parameters. The model results also show that a fixed bias probe operating in the ion-saturation region is affected less by contamination as compared to a fixed bias probe operating in the electron saturation region.

Developpement of a photoaffinity probe for the sensitive detection of matrix metallo-protease active forms from complex biological systems

International Nuclear Information System (INIS)

Nury, Catherine

2012-01-01

A new activity-based probe able to covalently modify the active site of proteases belonging to the matrix metallo-protease family (MMPs) has been developed in this thesis project. The probe was shown to behave as potent inhibitor of several MMPs, with nanomolar Ki values. This probe was also able to modify specifically only the free active site of MMPs, with particular high yields of cross-linking varying from 50 % to 11 %, depending of the MMPs tested. Using radioactivity as means of detection, this probe was able to detect active form of MMPs with a threshold of 1 femto-mole. Applied to the study of bronchoalveolar fluids (BAL) from mice exposed to nanoparticles by a lung aspiration protocol, this probe revealed the presence of the catalytic domain of MMP-12 under its active form, but not in control animals. When used to detect active form of MMPs from extracts obtained from human arteries of patient suffering from atherosclerosis, the probe was not able to detect such MMP active forms. Despite this negative result, the detection of active form of MMP in pathological fluid like BAL has never been reported before this work. Having validated this novel MMP activity-based probe, it will be possible to use it now for detecting MMPs from other pathological fluids or tissues extracts in which MMPs can be good markers of the pathology. (author) [fr

Intrauterine photoacoustic and ultrasound imaging probe

Science.gov (United States)

Miranda, Christopher; Barkley, Joel; Smith, Barbara S.

2018-04-01

Intrauterine photoacoustic and ultrasound imaging are probe-based imaging modalities with translational potential for use in detecting endometrial diseases. This deep-tissue imaging probe design allows for the retrofitting of commercially available endometrial sampling curettes. The imaging probe presented here has a 2.92-mm diameter and approximate length of 26 cm, which allows for entry into the human endometrial cavity, making it possible to use photoacoustic imaging and high-resolution ultrasound to characterize the uterus. We demonstrate the imaging probes' ability to provide structural information of an excised pig uterus using ultrasound imaging and detect photoacoustic signals at a radial depth of 1 cm.

Probing convex polygons with X-rays

International Nuclear Information System (INIS)

Edelsbrunner, H.; Skiena, S.S.

1988-01-01

An X-ray probe through a polygon measures the length of intersection between a line and the polygon. This paper considers the properties of various classes of X-ray probes, and shows how they interact to give finite strategies for completely describing convex n-gons. It is shown that (3n/2)+6 probes are sufficient to verify a specified n-gon, while for determining convex polygons (3n-1)/2 X-ray probes are necessary and 5n+O(1) sufficient, with 3n+O(1) sufficient given that a lower bound on the size of the smallest edge of P is known

Free radical scavenging properties of some wine probes

International Nuclear Information System (INIS)

Stasko, A.; Liptakova, M.; Malik, F.

1999-01-01

There are preliminary results of investigation of scavenging properties of 8 probes of Slovak wines (consisting of one reference, 3 probes of white wine and 4 probes of red wine). According to the literature so far, wine probes contain paramagnetic species (Mn 2+ , characterised with sextet spectrum, and a singlet line around g=2,00). In our probes we observed Mn 2+ signals, but no significant evidence for a single line of free radical was found. We can conclude that Mn 2+ content in the red wines is generally higher than in the white ones. Further, we investigated the scavenging activities of the probes adding solution of dinitropicryl hydrazyl (DPPH-stable radical) to them. Their ability to terminate free radicals resulted in the decrease of the final DPPH concentrations in the probes. The red wines have significantly higher capability to scavenge free radicals than the probes of white wines. (authors)

The Interstellar Ethics of Self-Replicating Probes

Science.gov (United States)

Cooper, K.

Robotic spacecraft have been our primary means of exploring the Universe for over 50 years. Should interstellar travel become reality it seems unlikely that humankind will stop using robotic probes. These probes will be able to replicate themselves ad infinitum by extracting raw materials from the space resources around them and reconfiguring them into replicas of themselves, using technology such as 3D printing. This will create a colonising wave of probes across the Galaxy. However, such probes could have negative as well as positive consequences and it is incumbent upon us to factor self-replicating probes into our interstellar philosophies and to take responsibility for their actions.

Concordant patterns of mtDNA and nuclear phylogeographic structure reveal Pleistocene vicariant event in the green crab Carcinus aestuarii across the Siculo-Tunisian Strait

Directory of Open Access Journals (Sweden)

T. DELI

2016-07-01

Full Text Available This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr to 0.69 Myr (95% HPD: 0.44–0.98 Myr. This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously

Rhythmic Patterns in Ragtime and Jazz

NARCIS (Netherlands)

Odekerken, Daphne; Volk, A.; Koops, Hendrik Vincent

2017-01-01

This paper presents a corpus-based study on rhythmic patterns in ragtime and jazz. Ragtime and jazz are related genres, but there are open questions on what specifies the two genres. Earlier studies revealed that variations of a particular syncopation pattern, referred to as 121, are among the most

Application of the iterative probe correction technique for a high-order probe in spherical near-field antenna measurements

DEFF Research Database (Denmark)

Laitinen, Tommi; Pivnenko, Sergey; Breinbjerg, Olav

2006-01-01

An iterative probe-correction technique for spherical near-field antenna measurements is examined. This technique has previously been shown to be well-suited for non-ideal first-order probes. In this paper, its performance in the case of a high-order probe (a dual-ridged horn) is examined....

Probing of flowing electron plasmas

International Nuclear Information System (INIS)

Himura, H.; Nakashima, C.; Saito, H.; Yoshida, Z.

2001-01-01

Probing of streaming electron plasmas with finite temperature is studied. For the first time, a current-voltage characteristic of an electric probe is measured in electron plasmas. Due to the fast flow of the electron plasmas, the characteristic curve spreads out significantly and exhibits a long tail. This feature can be explained calculating the currents collected to the probe. In flowing electron plasmas, the distribution function observed in the laboratory frame is non-Maxwellian even if the plasmas come to a state of thermal equilibrium. Another significant feature of the characteristic is that it determines a floating potential where the current equals zero, despite there being very few ions in the electron plasma. A high impedance probe, which is popularly used to determine the space potential of electron plasmas, outputs the potential. The method is available only for plasmas with density much smaller than the Brillouin limit

Migration history of air-breathing fishes reveals Neogene atmospheric circulation patterns

Science.gov (United States)

Böhme, M.

2004-05-01

The migration history of an air-breathing fish group (Channidae; snakehead fishes) is used for reconstructing Neogene Eurasian precipitation and atmospheric circulation patterns. The study shows that snakeheads are sensitive indicators of summer precipitation maxima in subtropical and temperate regions, and are present regularly if the wettest month exceeds 150 mm precipitation and 20 °C mean temperature. The analysis of 515 fossil freshwater fish deposits of the past 50 m.y. from Africa and Eurasia shows two continental-scale migration events from the snakeheads' center of origin in the south Himalayan region, events that can be related to changes in the Northern Hemisphere circulation pattern. The first migration, ca. 17.5 Ma, into western and central Eurasia may have been caused by a northward shift of the Intertropical Convergence Zone that brought western Eurasia under the influence of trade winds that produced a zonal and meridional precipitation gradient in Europe. During the second migration, between 8 and 4 Ma, into Africa and East Asia, snakeheads reached their present-day distribution. This migration could have been related to the intensification of the Asian monsoon that brought summer precipitation to their migratory pathways in East Africa Arabia and East Asia.

Development and use of fluorescent 16S rRNA-targeted probes for the specific detection of Methylophaga species by in situ hybridization in marine sediments.

Science.gov (United States)

Janvier, Monique; Regnault, Béatrice; Grimont, Patrick

2003-09-01

Methylotrophic bacteria are widespread in nature. They may play an important role in the cycling of carbon and in the metabolism of dimethylsulfide in a marine environment. Bacteria belonging to the genus Methylophaga are a unique group of aerobic, halophilic, non-methane-utilizing methylotrophs. Two 16S rRNA-targeted oligonucleotide probes were developed for the specific detection of Methylophaga species, marine methylobacteria, by fluorescence in situ hybridization. Probe MPH-730 was highly specific for all members of the genus Methylophaga while probe MPHm-994 targeted exclusively M. marina. The application of these probes were demonstrated by the detection of Methylophaga species in enrichment cultures from various marine sediments. All isolates recovered were visualized by using the genus specific probe MPH-730. The results were confirmed by 16S rDNA sequencing which demonstrated that all selected isolates belong to Methylophaga. Five isolates could be detected by the M. marina-specific probe MPHm-994 and were confirmed by rRNA gene restriction pattern (ribotyping). With the development of these specific probes, fluorescence in situ hybridization shows that the genus Methylophaga is widespread in marine samples.

"Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

Science.gov (United States)

Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

2008-02-01

The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

Short recovery time NMR probe

International Nuclear Information System (INIS)

Ramia, M.E.; Martin, C.A.; Jeandrevin, S.

2011-01-01

A NMR probe for low frequency and short recovery time is presented in this work. The probe contains the tuning circuit, diode expanders and quarter wavelength networks to protect the receiver from both the amplifier noise and the coil ringing following the transmitter power pulse. It also possesses a coil damper which is activated by of non active components. The probe performance shows a recovery time of about of 15μs a sensitive Q factor reduction and an increase of the signal to noise ratio of about 68% during the reception at a work frequency of 2 MHz. (author)

Study of probe-sample distance for biomedical spectra measurement

Directory of Open Access Journals (Sweden)

Li Lei

2011-11-01

Full Text Available Abstract Background Fiber-based optical spectroscopy has been widely used for biomedical applications. However, the effect of probe-sample distance on the collection efficiency has not been well investigated. Method In this paper, we presented a theoretical model to maximize the illumination and collection efficiency in designing fiber optic probes for biomedical spectra measurement. This model was in general applicable to probes with single or multiple fibers at an arbitrary incident angle. In order to demonstrate the theory, a fluorescence spectrometer was used to measure the fluorescence of human finger skin at various probe-sample distances. The fluorescence spectrum and the total fluorescence intensity were recorded. Results The theoretical results show that for single fiber probes, contact measurement always provides the best results. While for multi-fiber probes, there is an optimal probe distance. When a 400- μm excitation fiber is used to deliver the light to the skin and another six 400- μm fibers surrounding the excitation fiber are used to collect the fluorescence signal, the experimental results show that human finger skin has very strong fluorescence between 475 nm and 700 nm under 450 nm excitation. The fluorescence intensity is heavily dependent on the probe-sample distance and there is an optimal probe distance. Conclusions We investigated a number of probe-sample configurations and found that contact measurement could be the primary choice for single-fiber probes, but was very inefficient for multi-fiber probes. There was an optimal probe-sample distance for multi-fiber probes. By carefully choosing the probe-sample distance, the collection efficiency could be enhanced by 5-10 times. Our experiments demonstrated that the experimental results of the probe-sample distance dependence of collection efficiency in multi-fiber probes were in general agreement with our theory.

Why nano-oxidation with carbon nanotube probes is so stable: II. Bending behaviour of CNT probes during nano-oxidation

International Nuclear Information System (INIS)

Kuramochi, H; Tokizaki, T; Ando, K; Yokoyama, H; Dagata, J A

2007-01-01

Part I demonstrated that nano-oxidation in the dynamic-force mode was enhanced by the use of conductive carbon nanotube (CNT) probes. Fabrication of oxide nanostructures using CNT probes benefited not only from the smaller tip apex compared to conventional probes but from improved operational stability over a wide range of exposure conditions primarily due to the hydrophobic nature of the CNT. Here we investigate the bending response of CNT probes to electrostatic and meniscus forces during nano-oxidation. We conclude that bending of the CNT introduces an additional cushion in the combined cantilever-probe deflection system, thus improving overall stability of the tip-sample junction during nano-oxidation

TORE SUPRA fast reciprocating radio frequency probe (abstract)

International Nuclear Information System (INIS)

Thomas, C.E. Jr.; Harris, J.H.; Haste, G.R.; Kwon, M.; Goulding, R.H.; Hoffman, D.J.; Saoutic, B.; Becoulet, A.; Fraboulet, D.; Beaumont, B.; Kuus, H.; Ladurelle, L.; Pascal, J.Y.

1995-01-01

A fast reciprocating ion cyclotron range of frequencies (ICRF) probe was installed and operated on TORE SUPRA during 1992/1993. The body of the probe was originally used on the ATF experiment at Oak Ridge National Laboratory. The probe was adapted for use on TORE SUPRA, and mounted on one of the two fast reciprocating probe mounts. The probe consists of two orthogonal single-turn wire loops, mounted so that one loop senses toroidal rf magnetic fields and the other senses poloidal rf magnetic fields. The probe began operation in June, 1993. The probe active area is approximately 5 cm long by 2 cm, and the reciprocating mount has a slow stroke (5 cm/s) of 30 cm and a fast stroke (1.5 m/s) of about 10 cm. The probe was operated at distances from the plasma edge ranging from 30 to -5 cm (i.e., inside the last closed flux surface). The probe design, electronics, calibration, data acquisition, and data processing are discussed. First data from the probe are presented as a function of ICRF power, distance from the plasma, loop orientation, and other plasma parameters. Initial data show parametric instabilities do not play an important role for ICRF in the TORE SUPRA edge and scrape-off-layer (SOL) plasmas. Additionally it is observed that the probe signal has little or no dependence on position in the SOL/plasma edge

Single-cell resolution imaging of retinal ganglion cell apoptosis in vivo using a cell-penetrating caspase-activatable peptide probe.

Directory of Open Access Journals (Sweden)

Xudong Qiu

Full Text Available Peptide probes for imaging retinal ganglion cell (RGC apoptosis consist of a cell-penetrating peptide targeting moiety and a fluorophore-quencher pair flanking an effector caspase consensus sequence. Using ex vivo fluorescence imaging, we previously validated the capacity of these probes to identify apoptotic RGCs in cell culture and in an in vivo rat model of N-methyl- D-aspartate (NMDA-induced neurotoxicity. Herein, using TcapQ488, a new probe designed and synthesized for compatibility with clinically-relevant imaging instruments, and real time imaging of a live rat RGC degeneration model, we fully characterized time- and dose-dependent probe activation, signal-to-noise ratios, and probe safety profiles in vivo. Adult rats received intravitreal injections of four NMDA concentrations followed by varying TcapQ488 doses. Fluorescence fundus imaging was performed sequentially in vivo using a confocal scanning laser ophthalmoscope and individual RGCs displaying activated probe were counted and analyzed. Rats also underwent electroretinography following intravitreal injection of probe. In vivo fluorescence fundus imaging revealed distinct single-cell probe activation as an indicator of RGC apoptosis induced by intravitreal NMDA injection that corresponded to the identical cells observed in retinal flat mounts of the same eye. Peak activation of probe in vivo was detected 12 hours post probe injection. Detectable fluorescent RGCs increased with increasing NMDA concentration; sensitivity of detection generally increased with increasing TcapQ488 dose until saturating at 0.387 nmol. Electroretinography following intravitreal injections of TcapQ488 showed no significant difference compared with control injections. We optimized the signal-to-noise ratio of a caspase-activatable cell penetrating peptide probe for quantitative non-invasive detection of RGC apoptosis in vivo. Full characterization of probe performance in this setting creates an important in

Donated chemical probes for open science.

Science.gov (United States)

Müller, Susanne; Ackloo, Suzanne; Arrowsmith, Cheryl H; Bauser, Marcus; Baryza, Jeremy L; Blagg, Julian; Böttcher, Jark; Bountra, Chas; Brown, Peter J; Bunnage, Mark E; Carter, Adrian J; Damerell, David; Dötsch, Volker; Drewry, David H; Edwards, Aled M; Edwards, James; Elkins, Jon M; Fischer, Christian; Frye, Stephen V; Gollner, Andreas; Grimshaw, Charles E; IJzerman, Adriaan; Hanke, Thomas; Hartung, Ingo V; Hitchcock, Steve; Howe, Trevor; Hughes, Terry V; Laufer, Stefan; Li, Volkhart Mj; Liras, Spiros; Marsden, Brian D; Matsui, Hisanori; Mathias, John; O'Hagan, Ronan C; Owen, Dafydd R; Pande, Vineet; Rauh, Daniel; Rosenberg, Saul H; Roth, Bryan L; Schneider, Natalie S; Scholten, Cora; Singh Saikatendu, Kumar; Simeonov, Anton; Takizawa, Masayuki; Tse, Chris; Thompson, Paul R; Treiber, Daniel K; Viana, Amélia Yi; Wells, Carrow I; Willson, Timothy M; Zuercher, William J; Knapp, Stefan; Mueller-Fahrnow, Anke

2018-04-20

Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de">https://openscienceprobes.sgc-frankfurt.dehttps://openscienceprobes.sgc-frankfurt.de/">/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project. © 2018, Müller et al.

Application of FRET probes in the analysis of neuronal plasticity

Directory of Open Access Journals (Sweden)

Yoshibumi eUeda

2013-10-01

Full Text Available Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since GFP was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET, which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo.

Atomic quantum superposition state generation via optical probing

DEFF Research Database (Denmark)

Nielsen, Anne E. B.; Poulsen, Uffe Vestergaard; Negretti, Antonio

2009-01-01

investigate cavity enhanced probing with continuous beams of both coherent and squeezed light. The stochastic master equations used in the analysis are expressed in terms of the Hamiltonian of the probed system and the interaction between the probed system and the probe field and are thus quite generally...

Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

Directory of Open Access Journals (Sweden)

Zhu Tong

2009-10-01

Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

Imaging optical probe for pressurized steam-water environment

International Nuclear Information System (INIS)

Donaldson, M.R.; Pulfrey, R.E.

1979-01-01

An air-cooled imaging optical probe, with an outside diameter of 25.4 mm, has been developed to provide high resolution viewing of flow regimes in a steam-water environment at 343 0 C and 15.2 MPa. The design study considered a 3-m length probe. A 0.3-m length probe prototype was fabricated and tested. The optical probe consists of a 3.5-mm diameter optics train surrounded by two coaxial coolant flow channels and two coaxial insulating dead air spaces. With air flowing through the probe at 5.7 g/s, thermal analysis shows that no part of the optics train will exceed 93 0 C when a 3-m length probe is immersed in a 343 0 C environment. Computer stress analysis plus actual tests show that the probe can operate successfully with conservative safety factors. The imaging optical probe was tested five times in the design environment at the semiscale facility at the INEL. Two-phase flow regimes in the high temperature, high pressure, steam-water blowdown and reflood experiments were recorded on video tape for the first time with the imaging optical probe

New rather than old? For working memory tasks with abstract patterns the P3 and the single-trial delta response are larger for modified than identical probe stimuli.

Science.gov (United States)

Mathes, B; Schmiedt, J; Schmiedt-Fehr, C; Pantelis, C; Basar-Eroglu, C

2012-07-01

Memory-guided decision making is dynamic and context-dependent, even though many studies describe an enhancement of the P3 for recognized items in memory tasks ("old-new effect"). This study utilized a delay-dependent working memory task during which decision making could be optimized by focusing attention on detected changes instead of recognized similarities. Mean P3 amplitude and delta activity were analyzed from participants who classified probe stimuli as identical or modified. The P3 amplitudes were larger for modified than for identical probes, even when the probe occurred 4,000 ms after the primary stimulus. Enhanced single-trial amplitude, trial-by-trial consistency, and frontoparietal phase coherence of delta activity contributed to the larger P3 for the modified probe. Thus, context-dependent attentional resource allocation supporting memory-guided decisions might explain the enhancement of the P3 for specific probe types. Copyright © 2012 Society for Psychophysiological Research.

Intrauterine photoacoustic and ultrasound imaging probe.

Science.gov (United States)

Miranda, Christopher; Barkley, Joel; Smith, Barbara

2018-04-01

Intrauterine photoacoustic and ultrasound imaging are probe-based imaging modalities with translational potential for use in detecting endometrial diseases. This deep-tissue imaging probe design allows for the retrofitting of commercially available endometrial sampling curettes. The imaging probe presented here has a 2.92-mm diameter and approximate length of 26 cm, which allows for entry into the human endometrial cavity, making it possible to use photoacoustic imaging and high-resolution ultrasound to characterize the uterus. We demonstrate the imaging probes' ability to provide structural information of an excised pig uterus using ultrasound imaging and detect photoacoustic signals at a radial depth of 1 cm. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Categorical speech processing in Broca's area: an fMRI study using multivariate pattern-based analysis.

Science.gov (United States)

Lee, Yune-Sang; Turkeltaub, Peter; Granger, Richard; Raizada, Rajeev D S

2012-03-14

Although much effort has been directed toward understanding the neural basis of speech processing, the neural processes involved in the categorical perception of speech have been relatively less studied, and many questions remain open. In this functional magnetic resonance imaging (fMRI) study, we probed the cortical regions mediating categorical speech perception using an advanced brain-mapping technique, whole-brain multivariate pattern-based analysis (MVPA). Normal healthy human subjects (native English speakers) were scanned while they listened to 10 consonant-vowel syllables along the /ba/-/da/ continuum. Outside of the scanner, individuals' own category boundaries were measured to divide the fMRI data into /ba/ and /da/ conditions per subject. The whole-brain MVPA revealed that Broca's area and the left pre-supplementary motor area evoked distinct neural activity patterns between the two perceptual categories (/ba/ vs /da/). Broca's area was also found when the same analysis was applied to another dataset (Raizada and Poldrack, 2007), which previously yielded the supramarginal gyrus using a univariate adaptation-fMRI paradigm. The consistent MVPA findings from two independent datasets strongly indicate that Broca's area participates in categorical speech perception, with a possible role of translating speech signals into articulatory codes. The difference in results between univariate and multivariate pattern-based analyses of the same data suggest that processes in different cortical areas along the dorsal speech perception stream are distributed on different spatial scales.

Monitoring probe for groundwater flow

Science.gov (United States)

Looney, B.B.; Ballard, S.

1994-08-23

A monitoring probe for detecting groundwater migration is disclosed. The monitor features a cylinder made of a permeable membrane carrying an array of electrical conductivity sensors on its outer surface. The cylinder is filled with a fluid that has a conductivity different than the groundwater. The probe is placed in the ground at an area of interest to be monitored. The fluid, typically saltwater, diffuses through the permeable membrane into the groundwater. The flow of groundwater passing around the permeable membrane walls of the cylinder carries the conductive fluid in the same general direction and distorts the conductivity field measured by the sensors. The degree of distortion from top to bottom and around the probe is precisely related to the vertical and horizontal flow rates, respectively. The electrical conductivities measured by the sensors about the outer surface of the probe are analyzed to determine the rate and direction of the groundwater flow. 4 figs.

Characterization of WRKY transcription factors in Solanum lycopersicum reveals collinearity and their expression patterns under cold treatment.

Science.gov (United States)

Chen, Lin; Yang, Yang; Liu, Can; Zheng, Yanyan; Xu, Mingshuang; Wu, Na; Sheng, Jiping; Shen, Lin

2015-08-28

WRKY transcription factors play an important role in cold defense of plants. However, little information is available about the cold-responsive WRKYs in tomato (Solanum lycopersicum). In the present study, a complete characterization of this gene family was described. Eighty WRKY genes in the tomato genome were identified. Almost all WRKY genes contain putative stress-responsive cis-elements in their promoter regions. Segmental duplications contributed significantly to the expansion of the SlWRKY gene family. Transcriptional analysis revealed notable differential expression in tomato tissues and expression patterns under cold stress, which indicated wide functional divergence in this family. Ten WRKYs in tomato were strongly induced more than 2-fold during cold stress. These genes represented candidate genes for future functional analysis of WRKYs involved in the cold-related signal pathways. Our data provide valuable information about tomato WRKY proteins and form a foundation for future studies of these proteins, especially for those that play an important role in response to cold stress. Copyright © 2015 Elsevier Inc. All rights reserved.

Transverse Electromagnetic Mode Conversion for High-Harmonic Self-Probing Spectroscopy

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Antoine Camper

2015-02-01

Full Text Available We report on high-order harmonic (HHG two-source interferometry (TSI in molecular gases. We used a 0-\\(\\pi\\ phase plate to create two bright spots at the focus of a lens by converting a Gaussian laser beam into a TEM please define \\(_{01}\\ Transverse Electromagnetic Mode. The two bright foci produce two synchronized HHG sources. One of them is used to probe on-going dynamics in the generating medium, while the other serves to heterodyne the signal. The interference of the emissions in the far–field gives access to the phase difference between the two sources. In self–probing HHG phase spectroscopy, one of the two sources is used as a reference while the other one probes some on goin dynamics in the generating medium. We first compute overlap integrals to investigate the mode conversion efficiency. We then establish a clear relation between the laser phase-front curvature and the far-field overlap of the two HHG beams. Both Fresnel diffraction calculations and an experimental lens position scan are used to reveal variations of the phase front inclination in each source. We show that this arrangement offers \\(\\frac{\\lambda_{XUV}}{100}\\ precision, enabling extremely sensitive phase measurements. Finally, we use this compact setup for TSI and measure phase variations across the molecular alignment revival of nitrogen and in vibrating sulfur hexafluoride. In both gases, the phase variations change sign around the ionization threshold of the investigated molecule.

Solar Probe Plus: A NASA Mission to Touch the Sun

Science.gov (United States)

Fox, N. J.; Velli, M. M. C.; Kasper, J. C.; McComas, D. J.; Howard, R.; Bale, S. D.; Decker, R. B.

2014-12-01

Solar Probe Plus (SPP), currently in Phase C, will be the first mission to fly into the low solar corona, revealing how the corona is heated and the solar wind and energetic particles are accelerated, solving fundamental mysteries that have been top priority science goals since such a mission was first proposed in 1958. The scale and concept of such a mission has been revised at intervals since that time, yet the core has always been a close encounter with the Sun. The primary science goal of the Solar Probe Plus mission is to determine the structure and dynamics of the Sun's coronal magnetic field, understand how the solar corona and wind are heated and accelerated, and determine what mechanisms accelerate and transport energetic particles. The SPP mission will achieve this by identifying and quantifying the basic plasma physical processes at the heart of the Heliosphere. SPP uses an innovative mission design, significant technology development and a risk-reducing engineering development to meet the SPP science objectives: 1) Trace the flow of energy that heats and accelerates the solar corona and solar wind; 2) Determine the structure and dynamics of the plasma and magnetic fields at the sources of the solar wind; and 3) Explore mechanisms that accelerate and transport energetic particles. In this presentation, we present Solar Probe Plus and examine how the mission will address the science questions that have remained unanswered for over 5 decades.

21 CFR 882.4725 - Radiofrequency lesion probe.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Radiofrequency lesion probe. 882.4725 Section 882...) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Surgical Devices § 882.4725 Radiofrequency lesion probe. (a) Identification. A radiofrequency lesion probe is a device connected to a radiofrequency (RF...

In-vitro accuracy and reproducibility evaluation of probing depth measurements of selected periodontal probes

Directory of Open Access Journals (Sweden)

K.N. Al Shayeb

2014-01-01

Conclusion: Depth measurements with the Chapple UB-CF-15 probe were more accurate and reproducible compared to measurements with the Vivacare TPS and Williams 14 W probes. This in vitro model may be useful for intra-examiner calibration or clinician training prior to the clinical evaluation of patients or in longitudinal studies involving periodontal evaluation.

Revealing patterns of cultural transmission from frequency data: equilibrium and non-equilibrium assumptions

Science.gov (United States)

Crema, Enrico R.; Kandler, Anne; Shennan, Stephen

2016-12-01

A long tradition of cultural evolutionary studies has developed a rich repertoire of mathematical models of social learning. Early studies have laid the foundation of more recent endeavours to infer patterns of cultural transmission from observed frequencies of a variety of cultural data, from decorative motifs on potsherds to baby names and musical preferences. While this wide range of applications provides an opportunity for the development of generalisable analytical workflows, archaeological data present new questions and challenges that require further methodological and theoretical discussion. Here we examine the decorative motifs of Neolithic pottery from an archaeological assemblage in Western Germany, and argue that the widely used (and relatively undiscussed) assumption that observed frequencies are the result of a system in equilibrium conditions is unwarranted, and can lead to incorrect conclusions. We analyse our data with a simulation-based inferential framework that can overcome some of the intrinsic limitations in archaeological data, as well as handle both equilibrium conditions and instances where the mode of cultural transmission is time-variant. Results suggest that none of the models examined can produce the observed pattern under equilibrium conditions, and suggest. instead temporal shifts in the patterns of cultural transmission.

RESULTS OF THE EXAMINATION OF ELECTROCHEMICAL NOISE PROBE SPECIMENS REMOVED FROM TANK 241-AN-107, JUNE, 2010

International Nuclear Information System (INIS)

Cooke, G.A.; Wyrwas, R.B.; Duncan, J.B.

2010-01-01

An Integrated Multi-function Corrosion Probe (IMCP) was installed in Tank 241-AN-107 on September 20, 2006. A portion of the probe was retrieved on June 8, 2010 and the sections holding the detectors were delivered to the 222-S Laboratory for analysis. The examination and disassembly of the probe sections encountered a number of challenges. However, disassembly and relevant analyses were successfully completed. The following summarizes our observations. Brittle failure of the fiberglass probe in the middle of detector 2 resulted in the recovery of only three vapor space C-rings and six supernatant bullet specimens. The design of the bullets and how they were attached to the probe made the recovery of the components more difficult. The use of glue/epoxy on the bullets and the attachment of the flat bottom of the bullets to the curved surface of the fiberglass probe body meant that weight loss on cleaning and surface area of the specimens could not be determined with acceptable accuracy. Macrophotography of all specimens reveals that corrosion was slight in the vapor space and extremely slight in the supernatant. The one pre-cracked C-ring recovered from the vapor space still had the stress bulge visible on the polished surface, indicating that crack propagation had not occurred in the tank. No photographs were taken of the C-ring before deployment. No further analysis was conducted on this specimen. A detailed discussion and photographic documentation are provided in this report.

SNAP: Small Next-generation Atmospheric Probe Concept

Science.gov (United States)

Sayanagi, K. M.; Dillman, R. A.; Atkinson, D. H.; Li, J.; Saikia, S.; Simon, A. A.; Spilker, T. R.; Wong, M. H.; Hope, D.

2017-12-01

We present a concept for a small, atmospheric probe that could be flexibly added to future missions that orbit or fly-by a giant planet as a secondary payload, which we call the Small Next-generation Atmospheric Probe (SNAP). SNAP's main scientific objectives are to determine the vertical distribution of clouds and cloud-forming chemical species, thermal stratification, and wind speed as a function of depth. As a case study, we present the advantages, cost and risk of adding SNAP to the future Uranus Orbiter and Probe flagship mission; in combination with the mission's main probe, SNAP would perform atmospheric in-situ measurements at a second location, and thus enable and enhance the scientific objectives recommended by the 2013 Planetary Science Decadal Survey and the 2014 NASA Science Plan to determine atmospheric spatial variabilities. We envision that the science objectives can be achieved with a 30-kg entry probe 0.5m in diameter (less than half the size of the Galileo probe) that reaches 5-bar pressure-altitude and returns data to Earth via the carrier spacecraft. As the baseline instruments, the probe will carry an Atmospheric Structure Instrument (ASI) that measures the temperature, pressure and acceleration, a carbon nanotube-based NanoChem atmospheric composition sensor, and an Ultra-Stable Oscillator (USO) to conduct a Doppler Wind Experiment (DWE). We also catalog promising technologies currently under development that will strengthen small atmospheric entry probe missions in the future. While SNAP is applicable to multiple planets, we examine the feasibility, benefits and impacts of adding SNAP to the Uranus Orbiter and Probe flagship mission. Our project is supported by NASA PSDS3 grant NNX17AK31G.

Poster — Thur Eve — 77: Implanted Brachythearpy Seed Movement due to Transrectal Ultrasound Probe-Induced Prostate Deformation

International Nuclear Information System (INIS)

Liu, D; Usmani, N; Sloboda, R; Meyer, T; Husain, S; Angyalfi, S; Kay, I

2014-01-01

The study investigated the movement of implanted brachytherapy seeds upon transrectal US probe removal, providing insight into the underlying prostate deformation and an estimate of the impact on prostate dosimetry. Implanted seed distributions, one obtained with the prostate under probe compression and another with the probe removed, were reconstructed using C-arm fluoroscopy imaging. The prostate, delineated on ultrasound images, was registered to the fluoroscopy images using seeds and needle tracks identified on ultrasound. A deformation tensor and shearing model was developed to correlate probe-induced seed movement with position. Changes in prostate TG-43 dosimetry were calculated. The model was used to infer the underlying prostate deformation and to estimate the location of the prostate surface in the absence of probe compression. Seed movement patterns upon probe removal reflected elastic decompression, lateral shearing, and rectal bending. Elastic decompression was characterized by expansion in the anterior-posterior direction and contraction in the superior-inferior and lateral directions. Lateral shearing resulted in large anterior movement for extra-prostatic seeds in the lateral peripheral region. Whole prostate D90 increased up to 8 Gy, mainly due to the small but systematic seed movement associated with elastic decompression. For selected patients, lateral shearing movement increased prostate D90 by 4 Gy, due to increased dose coverage in the anterior-lateral region at the expense of the posterior-lateral region. The effect of shearing movement on whole prostate D90 was small compared to elastic decompression due to the subset of peripheral seeds involved, but is expected to have greater consequences for local dose coverage

Study, design and manufacture eddy current probes for industry applications

International Nuclear Information System (INIS)

Nguyen Phuc; Nguyen Van Thuy; Vuong Binh Duong; Do Minh Duc; Trinh Dinh Truong; Tran Trong Duc; Do Tung Khanh; Dang Quang Trung

2016-01-01

This study is based on the studying, designing and manufacturing of eddy current probes for industry applications. The main tasks of this study include: i) Describes the overview and classification of eddy current probes (which can be classified into three categories based on the mode of operation: absolute eddy current probe, differential eddy current probe and reflect eddy current probe); ii) Describes the three methods of probe designing and manufacturing (including experimental, analytical and numerical designs); iii) Describes the designing and manufacturing of eddy current probes for industry applications, which based on experimental and analytical methods. Based on this study, we have successfully manufactured some current probes (including absolute eddy current probe, differential eddy current probe and reflect eddy current probe) for surface and tube inspections. (author)

Irradiation-induced patterning in dilute Cu–Fe alloys

International Nuclear Information System (INIS)

Stumphy, B.; Chee, S.W.; Vo, N.Q.; Averback, R.S.; Bellon, P.; Ghafari, M.

2014-01-01

Compositional patterning in dilute Cu 1−x Fe x (x ≈ 12%) induced by 1.8 MeV Kr + irradiation was studied as a function of temperature using atom probe tomography. Irradiation near room temperature led to homogenization of the sample, whereas irradiation at 300 °C and above led to precipitation and macroscopic coarsening. Between these two temperatures the irradiated alloys formed steady state patterns of composition where precipitates grew to a fixed size. The size in this regime increased somewhat with temperature. It was also observed that the steady state concentrations of Fe in Cu matrix and Cu in the Fe precipitates both greatly exceeded their equilibrium solubilities, with the degree of supersaturation in each phase decreasing with increasing temperature. In the macroscopic coarsening regime, the Fe-rich precipitates showed indications of a “cherry-pit” structure, with Cu precipitates forming within the Fe precipitates. In the patterning regime, interfaces between Fe-rich precipitates and the Cu-rich matrix were irregular and diffuse

Probing the Gaps: A Synthesis of Well-known and Lesser-known Hydrological Feedbacks Influencing Vegetation Patterning and Long-term Geomorphic Change in Low-gradient Fluvial Landscapes

Science.gov (United States)

Larsen, L.; Christensen, A.; Harvey, J. W.; Ma, H.; Newman, S.; Saunders, C.; Twilley, R.

2017-12-01

Emergence of vegetation patterning in fluvial landscapes is a classic example of how autogenic processes can drive long term fluvial and geomorphic adjustments in aquatic ecosystems. Studies elucidating the physics of flow through vegetation patches have produced understanding of how patterning in topography and vegetation commonly emerges and what effect it has on long term geomorphic change. However, with regard to mechanisms underlying pattern existence and resilience, several knowledge gaps remain, including the role of landscape-scale flow-vegetation feedbacks, feedbacks that invoke additional biogeochemical or biological agents, and determination of the relative importance of autogenic processes relative to external drivers. Here we provide a synthesis of the processes over a range of scales known to drive vegetation patterning and sedimentation in low gradient fluvial landscapes, emphasizing recent field and modeling studies in the Everglades, FL and Wax Lake Delta, LA that address these gaps. In the Everglades, while flow routing and sediment redistribution at the patch scale is known to be a primary driver of vegetation pattern emergence, landscape-scale routing of flow, as driven by the landscape's connectivity, can set up positive feedbacks that influence the rate of pattern degradation. Recent flow release experiments reveal that an additional feedback, involving phosphorus concentrations, flow, and floating vegetation communities that are abundant under low phosphorus, low flow conditions further stabilizes the alternative landscape states established through local scale sediment redistribution. Biogeochemistry-vegetation-sediment feedbacks may also be important for geomorphic development of newly emerging landscapes such as the Wax Lake Delta. There, fine sediment deposition shapes hydrogeomorphic zones with vegetation patterns that stimulate the growth of biofilm, while biofilm characteristics override the physical characteristics of vegetation

A bio-inspired spatial patterning circuit.

Science.gov (United States)

Chen, Kai-Yuan; Joe, Danial J; Shealy, James B; Land, Bruce R; Shen, Xiling

2014-01-01

Lateral Inhibition (LI) is a widely conserved patterning mechanism in biological systems across species. Distinct from better-known Turing patterns, LI depend on cell-cell contact rather than diffusion. We built an in silico genetic circuit model to analyze the dynamic properties of LI. The model revealed that LI amplifies differences between neighboring cells to push them into opposite states, hence forming stable 2-D patterns. Inspired by this insight, we designed and implemented an electronic circuit that recapitulates LI patterning dynamics. This biomimetic system serve as a physical model to elucidate the design principle of generating robust patterning through spatial feedback, regardless of the underlying devices being biological or electrical.

Plasma probe characteristics in low density hydrogen pulsed plasmas

International Nuclear Information System (INIS)

Astakhov, D I; Lee, C J; Bijkerk, F; Goedheer, W J; Ivanov, V V; Krivtsun, V M; Zotovich, A I; Zyryanov, S M; Lopaev, D V

2015-01-01

Probe theories are only applicable in the regime where the probe’s perturbation of the plasma can be neglected. However, it is not always possible to know, a priori, that a particular probe theory can be successfully applied, especially in low density plasmas. This is especially difficult in the case of transient, low density plasmas. Here, we applied probe diagnostics in combination with a 2D particle-in-cell model, to an experiment with a pulsed low density hydrogen plasma. The calculations took into account the full chamber geometry, including the plasma probe as an electrode in the chamber. It was found that the simulations reproduce the time evolution of the probe IV characteristics with good accuracy. The disagreement between the simulated and probe measured plasma density is attributed to the limited applicability of probe theory to measurements of low density pulsed plasmas on a similarly short time scale as investigated here. Indeed, in the case studied here, probe measurements would lead to, either a large overestimate, or underestimate of the plasma density, depending on the chosen probe theory. In contrast, the simulations of the plasma evolution and the probe characteristics do not suffer from such strict applicability limits. These studies show that probe theory cannot be justified through probe measurements. However, limiting cases of probe theories can be used to estimate upper and lower bounds on plasma densities. These theories include and neglect orbital motion, respectively, with different collisional terms leading to intermediate estimates. (paper)

Nanomaterials and MRI molecular probe

International Nuclear Information System (INIS)

Inubushi, Toshiro

2008-01-01

This paper presents the current state and future prospect of enhancing probes in MRI which enable to image specific cells and molecules mainly from the aspect of cell trafficking. Although MRI requires such probes for specific imaging, it has an advantage that anatomical images are simultaneously available even during surgical operation without radiation exposure, differing from X-CT, -transillumination and positron emission tomography (PET). In the development of novel MRI molecular probes, the recent topic concerns the cell trafficking biology where cells related with transplantation and immunological therapy can be traced. Although superparamagnetic iron oxide (SPIO) has been used as a commercially available enhancer, this nanoparticle has problems like a difficulty to penetrate cell, cytotoxicity and others. For these, authors have developed the nanoparticle SPIO covered with silica shell, which can be chemically modified, e.g., by binding fluorescent pigments to possibly allow MR bimodal molecular imaging. For penetration of particles in cells, envelop of Sendai virus is used. PET-CT has been more popular these days; however, MRI is superior to CT for imaging soft tissues, and development of PET-MRI is actively under progress aiming the multi-modal imaging. At present, molecular probes for MRI are certainly not so many as those for PET and cooperative efforts to develop the probes are required in medical, technological and pharmaceutical fields. (R.T.)

Interpretation of plasma impurity deposition probes. Analytic approximation

Science.gov (United States)

Stangeby, P. C.

1987-10-01

Insertion of a probe into the plasma induces a high speed flow of the hydrogenic plasma to the probe which, by friction, accelerates the impurity ions to velocities approaching the hydrogenic ion acoustic speed, i.e., higher than the impurity ion thermal speed. A simple analytic theory based on this effect provides a relation between impurity fluxes to the probe Γimp and the undisturbed impurity ion density nimp, with the hydrogenic temperature and density as input parameters. Probe size also influences the collection process and large probes are found to attract a higher flux density than small probes in the same plasma. The quantity actually measured, cimp, the impurity atom surface density (m-2) net-deposited on the probe, is related to Γimp and thus to nimp by taking into account the partial removal of deposited material caused by sputtering and the redeposition process.

Full information acquisition in scanning probe microscopy and spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Jesse, Stephen; Belianinov, Alex; Kalinin, Sergei V.; Somnath, Suhas

2017-04-04

Apparatus and methods are described for scanning probe microscopy and spectroscopy based on acquisition of full probe response. The full probe response contains valuable information about the probe-sample interaction that is lost in traditional scanning probe microscopy and spectroscopy methods. The full probe response is analyzed post data acquisition using fast Fourier transform and adaptive filtering, as well as multivariate analysis. The full response data is further compressed to retain only statistically significant components before being permanently stored.

Automated design of genomic Southern blot probes

Directory of Open Access Journals (Sweden)

Komiyama Noboru H

2010-01-01

Full Text Available Abstract Background Sothern blotting is a DNA analysis technique that has found widespread application in molecular biology. It has been used for gene discovery and mapping and has diagnostic and forensic applications, including mutation detection in patient samples and DNA fingerprinting in criminal investigations. Southern blotting has been employed as the definitive method for detecting transgene integration, and successful homologous recombination in gene targeting experiments. The technique employs a labeled DNA probe to detect a specific DNA sequence in a complex DNA sample that has been separated by restriction-digest and gel electrophoresis. Critically for the technique to succeed the probe must be unique to the target locus so as not to cross-hybridize to other endogenous DNA within the sample. Investigators routinely employ a manual approach to probe design. A genome browser is used to extract DNA sequence from the locus of interest, which is searched against the target genome using a BLAST-like tool. Ideally a single perfect match is obtained to the target, with little cross-reactivity caused by homologous DNA sequence present in the genome and/or repetitive and low-complexity elements in the candidate probe. This is a labor intensive process often requiring several attempts to find a suitable probe for laboratory testing. Results We have written an informatic pipeline to automatically design genomic Sothern blot probes that specifically attempts to optimize the resultant probe, employing a brute-force strategy of generating many candidate probes of acceptable length in the user-specified design window, searching all against the target genome, then scoring and ranking the candidates by uniqueness and repetitive DNA element content. Using these in silico measures we can automatically design probes that we predict to perform as well, or better, than our previous manual designs, while considerably reducing design time. We went on to

Magnetic nanostructures: radioactive probes and recent developments

International Nuclear Information System (INIS)

Prandolini, M J

2006-01-01

The miniaturization of magnetic sensors and storage devices down to the nano-scale leads to drastic changes in magnetic phenomena compared with the same devices with a larger size. Excited-nuclear-probe (radioactive probe) techniques are ideal for investigating these new magnetic nanostructures. By observing the magnetic hyperfine fields (and in some cases the electric-field-gradients (EFGs)) at the nuclei of radioactive probes, microscopic information about the magnetic environment of the probes is acquired. The magnetic hyperfine field is particularly sensitive to the s-spin polarization of the conduction electrons and to the orbital magnetic moment of the probe atom. Three methods of inserting radioactive probes into magnetic nanostructures are presented; neutron activation, recoil implantation and 'soft-landing', followed by descriptions of their application to selected examples. In some cases, these methods offer the simultaneous creation and observation of new magnetic materials at the atomic scale. This review focuses firstly on the induced magnetism in noble-metal spacer layers between either ferromagnetic (FM) or FM/antiferromagnetic (AFM) layers in a trilayer structure. Using the method of low-temperature nuclear orientation, the s-spin polarization of noble-metal probes was measured and was found to be very sensitive to the magnetic properties at both the FM and AFM interfaces. Secondly, the recoil implantation of radioactive Fe probes into rare-earth hosts and d-band alloys and subsequent measurement using time-differential perturbed angular distribution offer the possibility of controlling the chemical composition and number of nearest-neighbours. This method was used to prepare local 3d-magnetic clusters in a non-magnetic matrix and to observe their magnetic behaviour. Finally, non-magnetic radioactive probes were 'soft-landed' onto Ni surfaces and extremely lattice-expanded ultrathin Ni films. By measuring the magnetic hyperfine fields and EFGs at